@article {70246, title = {High performance sorting of motor unit action potentials with EMUsort}, journal = {bioRxiv}, year = {2026}, month = {2026 Jan 07}, abstract = {

Understanding how neural signals control muscle activity during behavior is a key challenge in motor neuroscience. To this end, recent advances in intramuscular multielectrode arrays have enabled high-quality multichannel recordings of many motor unit action potentials (MUAPs) in freely moving subjects. However, identifying individual MUAP events within multichannel recordings is a significant challenge for existing spike sorting methods, which are typically optimized for identifying action potentials from neurons in the brain. To overcome this challenge, we developed the Enhanced Motor Unit sorter (EMUsort), an extension of Kilosort4 (KS4) that achieves high-performance MUAP spike sorting. We applied EMUsort to high-resolution intramuscular recordings from rat forelimb during locomotion and monkey forelimb during a reaching task. EMUsort improves upon prior methods by addressing key challenges encountered with MUAP datasets, including: 1) long time delays across electrodes due to propagation along muscle fibers, 2) more complex waveform shapes compared to neuronal action potentials, and 3) a high degree of MUAP overlap due to cumulative motor unit recruitment. We compared EMUsort to existing spike sorting methods quantitatively using simulated datasets that closely emulated the rat and monkey datasets we recorded. EMUsort provided median error rate reductions of 67.5\% and 49.9\% during periods of high motor unit activation for the rat and monkey datasets, respectively. In sum, EMUsort provides a substantial improvement to MUAP spike sorter accuracy, especially during regions of high MUAP overlap, in an easy-to-use software package.

}, doi = {10.64898/2026.01.06.697952}, url = {https://www.biorxiv.org/content/early/2026/01/07/2026.01.06.697952}, author = {O{\textquoteright}Connell, Sean and Michaels, Jonathan A. and Wang, Runming and Mamidipaka, Sahit and Venkatesh, Manikandan and Aresh, Nevin and Pachitariu, Marius and Pruszynski, J. Andrew and Sober, Samuel J. and Pandarinath, Chethan} } @article {70321, title = {High performance sorting of motor unit action potentials with EMUsort}, journal = {eLife}, year = {2026}, month = {2026 Mar 16}, abstract = {

Understanding how neural signals control muscle activity during behavior is a key challenge in motor neuroscience. To this end, recent advances in intramuscular multielectrode arrays have enabled high-quality multichannel recordings of many motor unit action potentials (MUAPs) in freely moving subjects. However, identifying individual MUAP events within multichannel recordings is a significant challenge for existing spike sorting methods, which are typically optimized for identifying action potentials from neurons in the brain. To overcome this challenge, we developed the Enhanced Motor Unit sorter (EMUsort), an extension of Kilosort4 (KS4) that achieves high-performance MUAP spike sorting. We applied EMUsort to high-resolution intramuscular recordings from rat forelimb during locomotion and monkey forelimb during a reaching task. EMUsort improves upon prior methods by addressing key challenges encountered with MUAP datasets, including: 1) long time delays across electrodes due to propagation along muscle fibers, 2) more complex waveform shapes compared to neuronal action potentials, and 3) a high degree of MUAP overlap due to cumulative motor unit recruitment. We compared EMUsort to existing spike sorting methods quantitatively using simulated datasets that closely emulated the rat and monkey datasets we recorded. EMUsort provided median error rate reductions of 67.5\% and 49.9\% during periods of high motor unit activation for the rat and monkey datasets, respectively. In sum, EMUsort provides a substantial improvement to MUAP spike sorter accuracy, especially during regions of high MUAP overlap, in an easy-to-use software package.

}, doi = {10.7554/elife.110417.1}, url = {http://dx.doi.org/10.7554/eLife.110417.1}, author = {O{\textquoteright}Connell, Sean and Michaels, Jonathan A and Wang, Runming and Mamidipaka, Sahit and Venkatesh, Manikandan and Aresh, Nevin and Pachitariu, Marius and Pruszynski, J Andrew and Sober, Samuel J and Pandarinath, Chethan} } @article {69720, title = {HD2Net: A deep learning framework for simultaneous denoising and deaberration in fluorescence microscopy}, journal = {bioRxiv}, year = {2025}, month = {01/2025}, abstract = {

Fluorescence microscopy is essential for biological research, offering high-contrast imaging of microscopic structures. However, the quality of these images is often compromised by optical aberrations and noise, particularly in low signal-to-noise ratio (SNR) conditions. While adaptive optics (AO) can correct aberrations, it requires costly hardware and slows down imaging; whereas current denoising approaches boost the SNR but leave out the aberration compensation. To address these limitations, we introduce HD2Net, a deep learning framework that enhances image quality by simultaneously denoising and suppressing the effect of aberrations without the need for additional hardware. Building on our previous work, HD2Net incorporates noise estimation and aberration removal modules, effectively restoring images degraded by noise and aberrations. Through comprehensive evaluation of synthetic phantoms and biological data, we demonstrate that HD2Net outperforms existing methods, significantly improving image resolution and contrast. This framework offers a promising solution for enhancing biological imaging, particularly in challenging aberrating and low-light conditions.

}, doi = {10.1101/2025.01.06.631475}, url = {https://www.biorxiv.org/content/early/2025/01/08/2025.01.06.631475}, author = {Hou, Xuekai and Li, Yue and Hobson, Chad M. and Shroff, Hari and Guo, Min and Liu, Huafeng} } @article {69734, title = {HD2Net: A Deep Learning Framework for Simultaneous Denoising and Deaberration in Fluorescence Microscopy}, journal = {bioRxiv}, year = {2025}, month = {2025 Jan 8}, abstract = {

Fluorescence microscopy is essential for biological research, offering high-contrast imaging of microscopic structures. However, the quality of these images is often compromised by optical aberrations and noise, particularly in low signal-to-noise ratio (SNR) conditions. While adaptive optics (AO) can correct aberrations, it requires costly hardware and slows down imaging; whereas current denoising approaches boost the SNR but leave out the aberration compensation. To address these limitations, we introduce HD2Net, a deep learning framework that enhances image quality by simultaneously denoising and suppressing the effect of aberrations without the need for additional hardware. Building on our previous work, HD2Net incorporates noise estimation and aberration removal modules, effectively restoring images degraded by noise and aberrations. Through comprehensive evaluation of synthetic phantoms and biological data, we demonstrate that HD2Net outperforms existing methods, significantly improving image resolution and contrast. This framework offers a promising solution for enhancing biological imaging, particularly in challenging aberrating and low-light conditions.

}, doi = {10.1101/2025.01.06.631475}, url = {https://www.biorxiv.org/content/early/2025/01/08/2025.01.06.631475}, author = {Hou, Xuekai and Li, Yue and Hobson, Chad M. and Shroff, Hari and Guo, Min and Liu, Huafeng} } @article {69842, title = {Hedonic eating is controlled by dopamine neurons that oppose GLP-1R satiety.}, journal = {Science}, volume = {387}, year = {2025}, month = {2025 Mar 28}, pages = {eadt0773}, abstract = {

Hedonic eating is defined as food consumption driven by palatability without physiological need. However, neural control of palatable food intake is poorly understood. We discovered that hedonic eating is controlled by a neural pathway from the peri-locus ceruleus to the ventral tegmental area (VTA). Using photometry-calibrated optogenetics, we found that VTA dopamine (VTA) neurons encode palatability to bidirectionally regulate hedonic food consumption. VTA neuron responsiveness was suppressed during food consumption by semaglutide, a glucagon-like peptide receptor 1 (GLP-1R) agonist used as an antiobesity drug. Mice recovered palatable food appetite and VTA neuron activity during repeated semaglutide treatment, which was reversed by consumption-triggered VTA neuron inhibition. Thus, hedonic food intake activates VTA neurons, which sustain further consumption, a mechanism that opposes appetite reduction by semaglutide.

}, keywords = {Animals, Anti-Obesity Agents, Appetite, Dopaminergic Neurons, Eating, Glucagon-Like Peptide 1, Glucagon-Like Peptide-1 Receptor, Glucagon-Like Peptides, Male, Mice, Mice, Inbred C57BL, Neural Pathways, Optogenetics, Satiation, Satiety Response, Ventral Tegmental Area}, issn = {1095-9203}, doi = {10.1126/science.adt0773}, url = {https://doi.org/10.1126/science.adt0773}, author = {Zhu, Zhenggang and Gong, Rong and Rodriguez, Vicente and Quach, Kathleen T and Chen, Xinyu and Sternson, Scott M} } @article {69954, title = {High-resolution imaging of RNA and proteins in thick tissues using cycleHCR.}, journal = {Nat Rev Genet}, year = {2025}, month = {2025 May 28}, issn = {1471-0064}, doi = {10.1038/s41576-025-00860-z}, url = {https://doi.org/10.1038/s41576-025-00860-z}, author = {Kim, Jun and Liu, Zhe J} } @article {69905, title = {History of hypoxia exposure aids future cell invasion according to cell type and collagen density.}, journal = {Mol Biol Cell}, year = {2025}, month = {2025 May 06}, pages = {mbcE24120580}, abstract = {

In cancer progression, tumor microenvironments progressively become denser and hypoxic, and cell migrate toward higher oxygen levels as they invade across the tumor-stromal boundary. While cell invasion dependence on optimal collagen density is well appreciated, it remains unclear whether past oxygen conditions alter future invasion phenotype of cells. Here, we show that normal human mammary epithelial cells (MCF10A) and leader-like human breast tumor cells (BT549) undergo higher rates of invasion and collagen deformation after past exposure to hypoxia, compared to normoxia controls. Upon increasing collagen density by \~{}50\%, cell invasion under normoxia reduced, as expected due to the increased matrix crowding. However, surprisingly, past hypoxia increased cell invasion in future normoxic dense collagen, with more pronounced invasion of cancer cells. This culmination of cancer-related conditions of hypoxia history, tumor cell, and denser collagen led to more aggressive invasion phenotypes. We found that hypoxia-primed cancer cells produce laminin332, a basement membrane protein required for cell-matrix adhesions, which could explain the additional adhesion feedback from the matrix that led to invasion after hypoxia priming. Depletion of Cdh3 disrupts the hypoxia-dependent laminin production and thus disables the rise in rates of cancer cell invasion and collagen deformation caused by hypoxia memory. These findings highlight the importance of considering past oxygen conditions in combination with current mechanical composition of tissues to better understand tumor invasion in physically evolving tumor microenvironments.

}, issn = {1939-4586}, doi = {10.1091/mbc.E24-12-0580}, url = {https://doi.org/10.1091/mbc.e24-12-0580}, author = {Almeida, Jos{\'e} A and Avila, Diego B and Longmore, Gregory D and Pathak, Amit} } @article {69825, title = {HortaCloud: An open and collaborative platform for whole brain neuronal reconstructions}, journal = {bioRxiv}, year = {2025}, month = {2025 Mar 13}, abstract = {

HortaCloud is a cloud-based, open-source platform designed to facilitate the collaborative reconstruction of long-range projection neurons from whole-brain light microscopy data. By providing virtual environments directly within the cloud, it eliminates the need for costly and time-consuming data downloads, allowing researchers to work efficiently with terabyte- scale volumetric datasets. Standardization of computational resources in the cloud make deployment easier and more predictable. The pay-as-you-go cloud model reduces adoption barriers by eliminating upfront investments in expensive hardware. Finally, HortaCloud{\textquoteright}s decentralized architecture enables global collaboration between researchers and between institutions.

}, doi = {10.1101/2025.03.13.642887}, url = {https://www.biorxiv.org/content/early/2025/03/14/2025.03.13.642887}, author = {Rokicki, Konrad and Schauder, David and Olbris, Donald J. and Goina, Cristian and Clements, Jody and Edson, Patrick and Kawase, Takashi and Svirskas, Robert and Arshadi, Cameron and Feng, David and Chandrashekar, Jayaram and Ferreira, Tiago A. and MouseLight Project Team} } @article {70016, title = {How short peptides disassemble tau fibrils in Alzheimer{\textquoteright}s disease}, journal = {Nature}, year = {2025}, month = {2025 Jul 09}, abstract = {

Reducing fibrous aggregates of the protein tau is a possible strategy for halting the progression of Alzheimer{\textquoteright}s disease (AD). Previously, we found that in vitro, the D-enantiomeric peptide (D-peptide) D-TLKIVWC disassembles ultra-stable tau fibrils extracted from the autopsied brains of individuals with AD (hereafter, these tau fibrils are referred to as AD-tau) into benign segments, with no energy source other than ambient thermal agitation. To consider D-peptide-mediated disassembly as a potential route to therapeutics for AD, it is essential to understand the mechanism and energy source of the disassembly action. Here, we show that the assembly of D-peptides into amyloid-like ({\textquoteright}mock-amyloid{\textquoteright}) fibrils is essential for AD-tau disassembly. These mock-amyloid fibrils have a right-handed twist but are constrained to adopt a left-handed twist when templated in complex with AD-tau. The release of strain that accompanies the conversion of left-twisted to right-twisted, relaxed mock-amyloid produces a torque that is sufficient to break the local hydrogen bonding between tau molecules, and leads to the fragmentation of AD-tau. This strain-relief mechanism seems to operate in other examples of amyloid fibril disassembly, and could inform the development of first-in-class therapeutics for amyloid diseases.

Preprint:\ https://doi.org/10.1101/2024.03.25.586668

}, issn = {1476-4687}, doi = {10.1038/s41586-025-09244-z}, url = {https://doi.org/10.1038/s41586-025-09244-z}, author = {Hou, Ke and Ge, Peng and Sawaya, Michael R and Lutter, Liisa and Dolinsky, Joshua L and Yang, Yuan and Jiang, Yi Xiao and Boyer, David R and Cheng, Xinyi and Pi, Justin and Zhang, Jeffrey and Lu, Jiahui and Abskharon, Romany and Yang, Shixin and Yu, Zhiheng and Feigon, Juli and Eisenberg, David S} } @article {69254, title = {Haploidy-linked cell proliferation defects limit larval growth in Zebrafish}, journal = {Open Biol.}, volume = {14}, year = {2024}, month = {2024 Oct 09}, pages = {240126}, abstract = {

Haploid larvae in non-mammalian vertebrates are lethal, with characteristic organ growth retardation collectively called {\textquoteright}haploid syndrome{\textquoteright}. In contrast to mammals, whose haploid intolerance is attributed to imprinting misregulation, the cellular principle of haploidy-linked defects in non-mammalian vertebrates remains unknown. Here, we investigated cellular defects that disrupt the ontogeny of gynogenetic haploid zebrafish larvae. Unlike diploid control larvae, haploid larvae manifested unscheduled cell death at the organogenesis stage, attributed to haploidy-linked p53 upregulation. Moreover, we found that haploid larvae specifically suffered the gradual aggravation of mitotic spindle monopolarization during 1-3 days post-fertilization, causing spindle assembly checkpoint-mediated mitotic arrest throughout the entire body. High-resolution imaging revealed that this mitotic defect accompanied the haploidy-linked centrosome loss occurring concomitantly with the gradual decrease in larval cell size. Either resolution of mitotic arrest or depletion of p53 partially improved organ growth in haploid larvae. Based on these results, we propose that haploidy-linked mitotic defects and cell death are parts of critical cellular causes shared among vertebrates that limit the larval growth in the haploid state, contributing to an evolutionary constraint on allowable ploidy status in the vertebrate life cycle.

}, doi = {10.1098/rsob.240126}, url = {https://doi.org/10.1098/rsob.240126}, author = {Kan Yaguchi and Daiki Saito and Triveni Menon and Akira Matsura and Takeomi Mizutani and Tomoya Kotani and Sreelaja Nair and Ryota Uehara} } @article {69250, title = {High-Performance Genetically Encoded Green Fluorescent Biosensors for Intracellular l-Lactate.}, journal = {ACS Central Science}, volume = {10}, year = {2024}, month = {2024 Feb 28}, pages = {402-416}, abstract = {

l-Lactate is a monocarboxylate produced during the process of cellular glycolysis and has long generally been considered a waste product. However, studies in recent decades have provided new perspectives on the physiological roles of l-lactate as a major energy substrate and a signaling molecule. To enable further investigations of the physiological roles of l-lactate, we have developed a series of high-performance (Δ/ = 15 to 30 ), intensiometric, genetically encoded green fluorescent protein (GFP)-based intracellular l-lactate biosensors with a range of affinities. We evaluated these biosensors in cultured cells and demonstrated their application in an preparation of brain tissue. Using these biosensors, we were able to detect glycolytic oscillations, which we analyzed and mathematically modeled.

}, issn = {2374-7943}, doi = {10.1021/acscentsci.3c01250}, author = {Hario, Saaya and Le, Giang N T and Sugimoto, Hikaru and Takahashi-Yamashiro, Kei and Nishinami, Suguru and Toda, Hirofumi and Li, Selene and Marvin, Jonathan S and Kuroda, Shinya and Drobizhev, Mikhail and Terai, Takuya and Nasu, Yusuke and Campbell, Robert E} } @article {69578, title = {A high-throughput microfabricated platform for rapid quantification of metastatic potential.}, journal = {Sci Adv}, volume = {10}, year = {2024}, month = {2024 Aug 16}, pages = {eadk0015}, abstract = {

Assays that measure morphology, proliferation, motility, deformability, and migration are used to study the invasiveness of cancer cells. However, native invasive potential of cells may be hidden from these contextual metrics because they depend on culture conditions. We created a micropatterned chip that mimics the native environmental conditions, quantifies the invasive potential of tumor cells, and improves our understanding of the malignancy signatures. Unlike conventional assays, which rely on indirect measurements of metastatic potential, our method uses three-dimensional microchannels to measure the basal native invasiveness without chemoattractants or microfluidics. No change in cell death or proliferation is observed on our chips. Using six cancer cell lines, we show that our system is more sensitive than other motility-based assays, measures of nuclear deformability, or cell morphometrics. In addition to quantifying metastatic potential, our platform can distinguish between motility and invasiveness, help study molecular mechanisms of invasion, and screen for targeted therapeutics.

}, keywords = {Cell Line, Tumor, Cell Movement, Cell Proliferation, High-Throughput Screening Assays, Humans, Lab-On-A-Chip Devices, Microtechnology, Neoplasm Invasiveness, Neoplasm Metastasis, Neoplasms}, issn = {2375-2548}, doi = {10.1126/sciadv.adk0015}, url = {https://doi.org/10.1126/sciadv.adk0015}, author = {Bhattacharya, Smiti and Ettela, Abora and Haydak, Jonathan and Hobson, Chad M and Stern, Alan and Yoo, Miran and Chew, Teng-Leong and Gusella, G Luca and Gallagher, Emily J and Hone, James C and Azeloglu, Evren U} } @article {69383, title = {Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning}, journal = {Neuron}, year = {2024}, month = {2024 Apr 17}, abstract = {

Cholecystokinin-expressing interneurons (CCKIs) are hypothesized to shape pyramidal cell-firing patterns and regulate network oscillations and related network state transitions. To directly probe their role in the CA1 region, we silenced their activity using optogenetic and chemogenetic tools in mice. Opto-tagged CCKIs revealed a heterogeneous population, and their optogenetic silencing triggered wide disinhibitory network changes affecting both pyramidal cells and other interneurons. CCKI silencing enhanced pyramidal cell burst firing and altered the temporal coding of place cells: theta phase precession was disrupted, whereas sequence reactivation was enhanced. Chemogenetic CCKI silencing did not alter the acquisition of spatial reference memories on the Morris water maze but enhanced the recall of contextual fear memories and enabled selective recall when similar environments were tested. This work suggests the key involvement of CCKIs in the control of place-cell temporal coding and the formation of contextual memories.

}, issn = {08966273}, doi = {10.1016/j.neuron.2024.03.019}, url = {https://doi.org/10.1016/j.neuron.2024.03.019}, author = {Rangel Guerrero, D{\'a}maris K. and Balueva, Kira and Barayeu, Uladzislau and Baracskay, Peter and Gridchyn, Igor and Nardin, Michele and Roth, Chiara Nina and Wulff, Peer and Csicsvari, Jozsef} } @article {69040, title = {hkb is required for DIP-α expression and target recognition in the Drosophila neuromuscular circuit}, journal = {Communications Biology}, volume = {7}, year = {2024}, month = {2024 Apr 27}, abstract = {

Our nervous system contains billions of neurons that form precise connections with each other through interactions between cell surface proteins (CSPs). In Drosophila, the Dpr and DIP immunoglobulin protein subfamilies form homophilic or heterophilic interactions to instruct synaptic connectivity, synaptic growth and cell survival. However, the upstream regulation and downstream signaling mechanisms of Dprs and DIPs are not clear. In the Drosophila larval neuromuscular system,\ DIP-α\ is expressed in the dorsal and ventral type-Is motor neurons (MNs). We conducted an F1 dominant modifier genetic screen to identify regulators of Dprs and DIPs. We found that the transcription factor,\ huckebein\ (hkb), genetically interacts with\ DIP-α\ and is important for target recognition specifically in the dorsal Is MN, but not the ventral Is MN. Loss of\ hkb\ led to complete removal of\ DIP-α\ expression. We then confirmed that this specificity is through the dorsal Is MN specific transcription factor,\ even-skipped\ (eve), which acts downstream of\ hkb. Genetic interaction between\ hkb\ and\ eve\ revealed that they act in the same pathway to regulate dorsal Is MN connectivity. Our study provides insight into the transcriptional regulation of\ DIP-α\ and suggests that distinct regulatory mechanisms exist for the same CSP in different neurons.

}, doi = {10.1038/s42003-024-06184-8}, url = {https://doi.org/10.1038/s42003-024-06184-8}, author = {Robert A Carrillo and Yupu Wang and Rio Salazar and Luciano Simonetta and Violet Sorrentino and Terrence J Gatton and Bill Wu and Christopher G Vecsey} } @article {68279, title = {Homeodomain proteins hierarchically specify neuronal diversity and synaptic connectivity}, journal = {eLife}, year = {2024}, month = {2024 Jan 05}, abstract = {

The brain generates diverse neuron types which express unique homeodomain transcription factors (TFs) and assemble into precise neural circuits. Yet a mechanistic framework is lacking for how homeodomain TFs specify both neuronal fate and synaptic connectivity. We use\ Drosophila\ lamina neurons (L1-L5) to show the homeodomain TF Brain-specific homeobox (Bsh) is initiated in lamina precursor cells (LPCs) where it specifies L4/L5 fate and suppresses homeodomain TF Zfh1 to prevent L1/L3 fate. Subsequently, Bsh activates the homeodomain TF Apterous (Ap) in L4 in a feedforward loop to express the synapse recognition molecule DIP-β, in part by Bsh direct binding a\ DIP-β\ intron. Thus, homeodomain TFs function hierarchically: primary homeodomain TF (Bsh) first specifies neuronal fate, and subsequently acts with secondary homeodomain TF (Ap) to activate DIP-β, thereby generating precise synaptic connectivity. We speculate that hierarchical homeodomain TF function may represent a general principle for coordinating neuronal fate specification and circuit assembly.

}, doi = {10.7554/eLife.90133}, url = {https://doi.org/10.7554/eLife.90133}, author = {Chundi Xu and Tyler B. Ramos and Ed M. Rogers and Michael B. Reiser and Chris Q. Doe} } @article {68831, title = {Host ZCCHC3 blocks HIV-1 infection and production by a dual mechanism}, journal = {iScience}, year = {2024}, month = {05/2024}, abstract = {

Most mammalian cells prevent viral infection and proliferation by expressing various restriction factors and sensors that activate the immune system. While anti-human immunodeficiency virus type 1 (HIV-1) host restriction factors have been identified, most of them are antagonized by viral proteins. This has severely hindered their development in anti-HIV-1 therapy. Here, we describe CCHC-type zinc-finger-containing protein 3 (ZCCHC3) as a novel anti-HIV-1 factor that is not antagonized by viral proteins. ZCCHC3 suppresses production of HIV-1 and other retroviruses. We show that ZCCHC3 acts by binding to Gag nucleocapsid protein via zinc-finger motifs. This prevents interaction between the Gag nucleocapsid protein and viral genome and results in production of genome-deficient virions. ZCCHC3 also binds to the long terminal repeat on the viral genome via the middle-folded domain, sequestering the viral genome to P-bodies, which leads to decreased viral replication and production. Such a dual antiviral mechanism is distinct from that of any other known host restriction factors. Therefore, ZCCHC3 is a novel potential target in anti-HIV-1 therapy.

}, doi = {10.1101/2023.06.14.544911}, url = {https://doi.org/10.1101/2023.06.14.544911}, author = {Binbin Yi and Yuri L Tanaka and Hidetaka Kosako and Erika P Butlertanaka and Prabuddha Sengupta and Jennifer Lippincott-Schwartz and Akatsuki Saito and Shige H. Yoshimura} } @article {69518, title = {Hot-Distance: Combining One-Hot and Signed Distance Embeddings for Segmentation}, journal = {arXiv}, year = {2024}, month = {2024 Jun 25}, pages = {2406.17936}, abstract = {

Machine learning models are only as good as the data to which they are fit. As such, it is always preferable to use as much data as possible in training models. What data can be used for fitting a model depends a lot on the formulation of the task. We introduce Hot-Distance, a novel segmentation target that incorporates the strength of signed boundary distance prediction with the flexibility of one-hot encoding, to increase the amount of usable training data for segmentation of subcellular structures in focused ion beam scanning electron microscopy (FIB-SEM).

}, doi = {10.48550/arXiv.2406.17936}, url = {https://doi.org/10.48550/arXiv.2406.17936}, author = {Marwan Zouinkhi and Jeff L Rhoades and Aubrey V. Weigel} } @article {68589, title = {How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution}, journal = {eLife}, year = {2024}, month = {2024 Feb 20}, abstract = {

The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population{\textquoteright}s mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of an evolving population subject to a standard serial dilution protocol. We find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but has a negligible effect when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape.

}, doi = {10.7554/eLife.87895}, url = {https://doi.org/10.7554/eLife.87895}, author = {Nicholas M. Boffi and Yipei Guo and Chris H. Rycroft and Ariel Amir} } @article {69730, title = {How short peptides can disassemble ultra-stable tau fibrils extracted from Alzheimer{\textquoteright}s disease brain by a strain-relief mechanism}, journal = {Alzheimer{\textquoteright}s \& Dementia}, volume = {20}, year = {2024}, month = {01/2025}, abstract = {

Background

Reducing fibrous aggregates of protein tau is a possible strategy for halting progression of Alzheimer{\textquoteright}s disease (AD). Previously we found that in vitro the D-peptide D-TLKIVWC fragments tau fibrils from AD brains (AD-tau) into benign segments, whereas its six-residue analog D-TLKIVW cannot. However, the underlying fragmentation mechanism remains unknown, preventing the further development of this type of drug candidate for AD.

Method

To understand the necessity of the cysteine residue of D-TLKIVWC in fragmenting AD-tau, we designed a series of peptides of sequence D-TLKIVWX varying only at the seventh residue, X. To better understand the fragmentation process of AD-tau, we conducted a time-course dot blot and EM experiment. We determined the structures of D-TLKIVWX amyloid-like fibrils by atomic force microscopy and cryo-electron microscopy. We studied the complexes of D-TLKIVWX (X = I, S, R) with AD-tau by cryo-electron microscopy and confirmed the binding site between D-TLKIVWX and Tau through NMR.

Result

These D-TLKIVWX candidates showed various efficacies in fragmenting AD-tau in vitro, in which X = Ile was the best performer. From electron microscopy, we discovered that D-TLKIVWX peptides form amyloid-like fibrils themselves, and from atomic force microscopy we learned that these fibrils have a right-handed helical twist, in contrast to the left-handed helical twist of AD-tau. From cryo-EM we learned that D-TLKIVWX protofilaments bind to tau fibrils of opposing twist.

Conclusion

We find that the amyloid-like, fibril-forming property of D-TLKIVWX contributes to the fragmentation of AD-tau fibrils. We propose the strain-relief mechanism of fragmentation and believe the fragmentation of AD-tau fibrils is driven by the release of torsion in D-TLKIVWX protofilaments.

}, issn = {1552-5260}, doi = {10.1002/alz.085001}, url = {https://alz-journals.onlinelibrary.wiley.com/toc/15525279/20/S6}, author = {Hou, Ke and Ge, Peng and Sawaya, Michael R and Dolinsky, Joshua L. and Yang, Yuan and Jiang, Yi Xiao and Lutter, Liisa and Boyer, David and Cheng, Xinyi and Pi, Justin and Zhang, Jeffrey and Lu, Jiahui and Yang, Shixin and Yu, Zhiheng and Feigon, Juli and Eisenberg, David S.} } @article {69456, title = {Hue selectivity from recurrent circuitry in Drosophila}, journal = {Nat Neurosci}, year = {2024}, month = {2024 May 16}, abstract = {

In the perception of color, wavelengths of light reflected off objects are transformed into the derived quantities of brightness, saturation and hue. Neurons responding selectively to hue have been reported in primate cortex, but it is unknown how their narrow tuning in color space is produced by upstream circuit mechanisms. We report the discovery of neurons in the Drosophila optic lobe with hue-selective properties, which enables circuit-level analysis of color processing. From our analysis of an electron microscopy volume of a whole Drosophila brain, we construct a connectomics-constrained circuit model that accounts for this hue selectivity. Our model predicts that recurrent connections in the circuit are critical for generating hue selectivity. Experiments using genetic manipulations to perturb recurrence in adult flies confirm this prediction. Our findings reveal a circuit basis for hue selectivity in color vision.

}, issn = {1546-1726}, doi = {10.1038/s41593-024-01640-4}, author = {Christenson, Matthias P and Sanz Diez, Alvaro and Heath, Sarah L and Saavedra-Weisenhaus, Maia and Adachi, Atsuko and Nern, Aljoscha and Abbott, L F and Behnia, Rudy} } @article {68595, title = {Hacking brain development to test models of sensory coding}, journal = {bioRxiv}, year = {2023}, month = {2023 Jan 26}, abstract = {

Animals can discriminate myriad sensory stimuli but can also generalize from learned experience. You can probably distinguish the favorite teas of your colleagues while still recognizing that all tea pales in comparison to coffee. Tradeoffs between detection, discrimination, and generalization are inherent at every layer of sensory processing. During development, specific quantitative parameters are wired into perceptual circuits and set the playing field on which plasticity mechanisms play out. A primary goal of systems neuroscience is to understand how material properties of a circuit define the logical operations{\textemdash} computations--that it makes, and what good these computations are for survival. A cardinal method in biology{\textemdash}and the mechanism of evolution--is to change a unit or variable within a system and ask how this affects organismal function. Here, we make use of our knowledge of developmental wiring mechanisms to modify hard-wired circuit parameters in the\ Drosophila melanogaster\ mushroom body and assess the functional and behavioral consequences. By altering the number of expansion layer neurons (Kenyon cells) and their dendritic complexity, we find that input number, but not cell number, tunes odor selectivity. Simple odor discrimination performance is maintained when Kenyon cell number is reduced and augmented by Kenyon cell expansion.

}, doi = {10.1101/2023.01.25.525425}, url = {https://doi.org/10.1101/2023.01.25.525425}, author = {Maria Ahmed and Adithya E. Rajagopalan and Yijie Pan and Ye Li and Donnell L. Williams and Erik A. Pedersen and Manav Thakral and Angelica Previero and Kari C. Close and Christina P. Christoforou and Dawen Cai and Glenn C. Turner and Josephine Clowney} } @article {68008, title = {Hierarchical architecture of dopaminergic circuits enables second-order conditioning in Drosophila}, journal = {eLife}, year = {2023}, month = {2023 Jan 24}, abstract = {

Dopaminergic neurons with distinct projection patterns and physiological properties compose memory subsystems in a brain. However, it is poorly understood whether or how they interact during complex learning. Here, we identify a feedforward circuit formed between dopamine subsystems and show that it is essential for second-order conditioning, an ethologically important form of higher-order associative learning. The\ Drosophila\ mushroom body comprises a series of dopaminergic compartments, each of which exhibits distinct memory dynamics. We find that a slow and stable memory compartment can serve as an effective {\textquotedblleft}teacher{\textquotedblright} by instructing other faster and transient memory compartments via a single key interneuron, which we identify by connectome analysis and neurotransmitter prediction. This excitatory interneuron acquires enhanced response to reward-predicting odor after first-order conditioning and, upon activation, evokes dopamine release in the {\textquotedblleft}student{\textquotedblright} compartments. These hierarchical connections between dopamine subsystems explain distinct properties of first- and second-order memory long known by behavioral psychologists.

}, doi = {10.7554/eLife.79042}, url = {https://doi.org/10.7554/eLife.79042}, author = {Daichi Yamada and Daniel Bushey and Li Feng and Karen Hibbard and Megan Sammons and Jan Funke and Ashok Litwin-Kumar and Toshihide Hige and Yoshinori Aso} } @article {69076, title = {High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation.}, journal = {Nature Methods}, year = {2023}, month = {2023 Nov 13}, abstract = {

Live-cell super-resolution microscopy enables the imaging of biological structure dynamics below the diffraction limit. Here we present enhanced super-resolution radial fluctuations (eSRRF), substantially improving image fidelity and resolution compared to the original SRRF method. eSRRF incorporates automated parameter optimization based on the data itself, giving insight into the trade-off between resolution and fidelity. We demonstrate eSRRF across a range of imaging modalities and biological systems. Notably, we extend eSRRF to three dimensions by combining it with multifocus microscopy. This realizes live-cell volumetric super-resolution imaging with an acquisition speed of ~1 volume per second. eSRRF provides an accessible super-resolution approach, maximizing information extraction across varied experimental conditions while minimizing artifacts. Its optimal parameter prediction strategy is generalizable, moving toward unbiased and optimized analyses in super-resolution microscopy.

}, issn = {1548-7105}, doi = {10.1038/s41592-023-02057-w}, author = {Laine, Romain F and Heil, Hannah S and Coelho, Simao and Nixon-Abell, Jonathon and Jimenez, Ang{\'e}lique and Wiesner, Theresa and Mart{\'\i}nez, Dami{\'a}n and Galgani, Tommaso and R{\'e}gnier, Louise and Stubb, Aki and Follain, Gautier and Webster, Samantha and Goyette, Jesse and Dauphin, Aurelien and Salles, Audrey and Culley, Si{\^a}n and Jacquemet, Guillaume and Hajj, Bassam and Leterrier, Christophe and Henriques, Ricardo} } @article {68560, title = {Hippocampal spatial representations exhibit a hyperbolic geometry that expands with experience.}, journal = {Nature Neuroscience}, volume = {26}, year = {2023}, month = {2023 Jan 01}, pages = {131-139}, abstract = {

Daily experience suggests that we perceive distances near us linearly. However, the actual geometry of spatial representation in the brain is unknown. Here we report that neurons in the CA1 region of rat hippocampus that mediate spatial perception represent space according to a non-linear hyperbolic geometry. This geometry uses an exponential scale and yields greater positional information than a linear scale. We found that the size of the representation matches the optimal predictions for the number of CA1 neurons. The representations also dynamically expanded proportional to the logarithm of time that the animal spent exploring the environment, in correspondence with the maximal mutual information that can be received. The dynamic changes tracked even small variations due to changes in the running speed of the animal. These results demonstrate how neural circuits achieve efficient representations using dynamic hyperbolic geometry.

}, keywords = {Animals, Brain, CA1 Region, Hippocampal, Hippocampus, Neurons, Rats, Space Perception}, issn = {1546-1726}, doi = {10.1038/s41593-022-01212-4}, author = {Zhang, Huanqiu and Rich, P Dylan and Lee, Albert K and Sharpee, Tatyana O} } @article {68957, title = {Hydrophobic interactions dominate the recognition of a KRAS G12V neoantigen.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Aug 21}, pages = {5063}, abstract = {

Specificity remains a major challenge to current therapeutic strategies for cancer. Mutation associated neoantigens (MANAs) are products of genetic alterations, making them highly specific therapeutic targets. MANAs are HLA-presented (pHLA) peptides derived from intracellular mutant proteins that are otherwise inaccessible to antibody-based therapeutics. Here, we describe the cryo-EM structure of an antibody-MANA pHLA complex. Specifically, we determine a TCR mimic (TCRm) antibody bound to its MANA target, the KRAS peptide presented by HLA-A*03:01. Hydrophobic residues appear to account for the specificity of the mutant G12V residue. We also determine the structure of the wild-type G12 peptide bound to HLA-A*03:01, using X-ray crystallography. Based on these structures, we perform screens to validate the key residues required for peptide specificity. These experiments led us to a model for discrimination between the mutant and the wild-type peptides presented on HLA-A*03:01 based exclusively on hydrophobic interactions.

}, keywords = {Antibodies, HLA-A Antigens, Hydrophobic and Hydrophilic Interactions, Proto-Oncogene Proteins p21(ras), Recognition, Psychology}, issn = {2041-1723}, doi = {10.1038/s41467-023-40821-w}, author = {Wright, Katharine M and DiNapoli, Sarah R and Miller, Michelle S and Aitana Azurmendi, P and Zhao, Xiaowei and Yu, Zhiheng and Chakrabarti, Mayukh and Shi, WuXian and Douglass, Jacqueline and Hwang, Michael S and Hsiue, Emily Han-Chung and Mog, Brian J and Pearlman, Alexander H and Paul, Suman and Konig, Maximilian F and Pardoll, Drew M and Bettegowda, Chetan and Papadopoulos, Nickolas and Kinzler, Kenneth W and Vogelstein, Bert and Zhou, Shibin and Gabelli, Sandra B} } @article {68414, title = {High-throughput automated methods for classical and operant conditioning of larvae.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Oct 28}, abstract = {

Learning which stimuli (classical conditioning) or which actions (operant conditioning) predict rewards or punishments can improve chances of survival. However, the circuit mechanisms that underlie distinct types of associative learning are still not fully understood. Automated, high-throughput paradigms for studying different types of associative learning, combined with manipulation of specific neurons in freely behaving animals, can help advance this field. The Drosophila melanogaster larva is a tractable model system for studying the circuit basis of behaviour, but many forms of associative learning have not yet been demonstrated in this animal. Here, we developed a high-throughput (i. e. multi-larva) training system that combines real-time behaviour detection of freely moving larvae with targeted opto- and thermogenetic stimulation of tracked animals. Both stimuli are controlled in either open- or closed-loop, and delivered with high temporal and spatial precision. Using this tracker, we show for the first time that Drosophila larvae can perform classical conditioning with no overlap between sensory stimuli (i. e. trace conditioning). We also demonstrate that larvae are capable of operant conditioning by inducing a bend direction preference through optogenetic activation of reward-encoding serotonergic neurons. Our results extend the known associative learning capacities of Drosophila larvae. Our automated training rig will facilitate the study of many different forms of associative learning and the identification of the neural circuits that underpin them.

}, issn = {2050-084X}, doi = {10.7554/eLife.70015}, author = {Croteau-Chonka, Elise C and Clayton, Michael S and Venkatasubramanian, Lalanti and Harris, Samuel N and Jones, Benjamin M W and Narayan, Lakshmi and Winding, Michael and Masson, Jean-Baptiste and Zlatic, Marta and Klein, Kristina T} } @article {68516, title = {Hippocampal representations of foraging trajectories depend upon spatial context.}, journal = {Nature Neuroscience}, volume = {25}, year = {2022}, month = {2022 Dec 02}, pages = {1693-1705}, abstract = {

Animals learn trajectories to rewards in both spatial, navigational contexts and relational, non-navigational contexts. Synchronous reactivation of hippocampal activity is thought to be critical for recall and evaluation of trajectories for learning. Do hippocampal representations differentially contribute to experience-dependent learning of trajectories across spatial and relational contexts? In this study, we trained mice to navigate to a hidden target in a physical arena or manipulate a joystick to a virtual target to collect delayed rewards. In a navigational context, calcium imaging in freely moving mice revealed that synchronous CA1 reactivation was retrospective and important for evaluation of prior navigational trajectories. In a non-navigational context, reactivation was prospective and important for initiation of joystick trajectories, even in the same animals trained in both contexts. Adaptation of trajectories to a new target was well-explained by a common learning algorithm in which hippocampal activity makes dissociable contributions to reinforcement learning computations depending upon spatial context.

}, keywords = {Animals, Hippocampus, Mental Recall, Mice, Prospective Studies, Retrospective Studies, Spatial Navigation}, issn = {1546-1726}, doi = {10.1038/s41593-022-01201-7}, author = {Jiang, Wan-Chen and Xu, Shengjin and Dudman, Joshua T} } @article {68067, title = {Hormone-controlled changes in the differentiation state of post-mitotic neurons.}, journal = {Current Biology}, volume = {32}, year = {2022}, month = {2022 May 23}, pages = {2341-2348}, abstract = {

While we think of neurons as having a fixed identity, many show spectacular plasticity. Metamorphosis drives massive changes in the fly brain; neurons that persist into adulthood often change in response to the steroid hormone ecdysone. Besides driving remodeling, ecdysone signaling can also alter the differentiation status of neurons. The three sequentially born subtypes of mushroom body (MB) Kenyon cells (γ, followed by α{\textquoteright}/β{\textquoteright}, and finally α/β) serve as a model of temporal fating. γ neurons are also used as a model of remodeling during metamorphosis. As γ neurons are the only functional Kenyon cells in the larval brain, they serve the function of all three adult subtypes. Correspondingly, larval γ neurons have a similar morphology to α{\textquoteright}/β{\textquoteright} and α/β neurons-their axons project dorsally and medially. During metamorphosis, γ neurons remodel to form a single medial projection. Both temporal fate changes and defects in remodeling therefore alter γ-neuron morphology in similar ways. Mamo, a broad-complex, tramtrack, and bric-{\`a}-brac/poxvirus and zinc finger (BTB/POZ)\ transcription factor critical for temporal specification of α{\textquoteright}/β{\textquoteright} neurons, was recently described as essential for γ remodeling. In a previous study, we noticed a change in the number of adult Kenyon cells expressing γ-specific markers when mamo was manipulated. These data implied a role for Mamo in γ-neuron fate specification, yet mamo is not expressed in γ neurons until pupariation, well past γ specification. This indicates that mamo has a later role in ensuring that γ neurons express the correct Kenyon cell subtype-specific genes in the adult brain.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2022.04.027}, author = {Lai, Yen-Wei and Miyares, Rosa L and Liu, Ling-Yu and Chu, Sao-Yu and Lee, Tzumin and Yu, Hung-Hsiang} } @article {68985, title = {Human primed and na{\"\i}ve PSCs are both able to differentiate into trophoblast stem cells.}, journal = {Stem Cell Reports}, volume = {17}, year = {2022}, month = {11/2022}, pages = {2484-2500}, abstract = {

The recent derivation of human trophoblast stem cells (TSCs) from placental cytotrophoblasts and blastocysts opened opportunities for studying the development and function of the human placenta. Recent reports have suggested that human na{\"\i}ve, but not primed, pluripotent stem cells (PSCs) retain an exclusive potential to generate TSCs. Here we report that, in the absence of WNT stimulation, transforming growth factor β (TGF-β) pathway inhibition leads to direct and robust conversion of primed human PSCs into TSCs. The resulting primed PSC-derived TSC lines exhibit self-renewal, can differentiate into the main trophoblast lineages, and present RNA and epigenetic profiles that are indistinguishable from recently established TSC lines derived from human placenta, blastocysts, or isogenic human na{\"\i}ve PSCs expanded under human enhanced na{\"\i}ve stem cell medium (HENSM) conditions. Activation of nuclear Yes-associated protein (YAP) signaling is sufficient for this conversion and necessary for human TSC maintenance. Our findings underscore a residual plasticity in primed human PSCs that allows their in\ vitro conversion into extra-embryonic trophoblast lineages.

}, keywords = {Blastocyst, Cell Differentiation, Female, Humans, Placenta, Pluripotent Stem Cells, Pregnancy, Trophoblasts}, issn = {2213-6711}, doi = {10.1016/j.stemcr.2022.09.008}, author = {Viukov, Sergey and Shani, Tom and Bayerl, Jonathan and Aguilera-Castrejon, Alejandro and Oldak, Bernardo and Sheban, Daoud and Tarazi, Shadi and Stelzer, Yonatan and Hanna, Jacob H and Novershtern, Noa} } @article {67197, title = {The HaloTag as a general scaffold for far-red tunable chemigenetic indicators.}, journal = {Nature Chemical Biology}, year = {2021}, month = {2021 Apr 01}, abstract = {

Functional imaging using fluorescent indicators has revolutionized biology, but additional sensor scaffolds are needed to access properties such as bright, far-red emission. Here, we introduce a new platform for {\textquoteright}chemigenetic{\textquoteright} fluorescent indicators, utilizing the self-labeling HaloTag protein conjugated to environmentally sensitive synthetic fluorophores. We solve a crystal structure of HaloTag bound to a rhodamine dye ligand to guide engineering efforts to modulate the dye environment. We show that fusion of HaloTag with protein sensor domains that undergo conformational changes near the bound dye results in large and rapid changes in fluorescence output. This generalizable approach affords bright, far-red calcium and voltage sensors with highly tunable photophysical and chemical properties, which can reliably detect single action potentials in cultured neurons.

}, issn = {1552-4469}, doi = {10.1038/s41589-021-00775-w}, author = {Deo, Claire and Abdelfattah, Ahmed S and Bhargava, Hersh K and Berro, Adam J and Falco, Natalie and Farrants, Helen and Moeyaert, Benjamien and Chupanova, Mariam and Lavis, Luke D and Schreiter, Eric R} } @article {67211, title = {High-fidelity estimates of spikes and subthreshold waveforms from 1-photon voltage imaging in~vivo.}, journal = {Cell Reports}, volume = {35}, year = {2021}, month = {2021 Apr 06}, pages = {108954}, abstract = {

The ability to probe the membrane potential of multiple genetically defined neurons simultaneously would have a profound impact on neuroscience research. Genetically encoded voltage indicators are a promising tool for this purpose, and recent developments have achieved a high signal-to-noise ratio in\ vivo with 1-photon fluorescence imaging. However, these recordings exhibit several sources of noise and signal extraction remains a challenge. We present an improved signal extraction pipeline, spike-guided penalized matrix decomposition-nonnegative matrix factorization (SGPMD-NMF), which resolves supra- and subthreshold voltages in\ vivo. The method incorporates biophysical and optical constraints. We validate the pipeline with simultaneous patch-clamp and optical recordings from mouse layer 1 in\ vivo and with simulated and composite datasets with realistic noise. We demonstrate applications to mouse hippocampus expressing paQuasAr3-s or SomArchon1, mouse cortex expressing SomArchon1 or Voltron, and zebrafish spines expressing zArchon1.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2021.108954}, author = {Xie, Michael E and Adam, Yoav and Fan, Linlin Z and B{\"o}hm, Urs L and Kinsella, Ian and Zhou, Ding and Rozsa, Marton and Singh, Amrita and Svoboda, Karel and Paninski, Liam and Cohen, Adam E} } @article {67234, title = {High-precision coding in visual cortex.}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 May 13}, pages = {2767-78}, abstract = {

Individual neurons in visual cortex provide the brain with unreliable estimates of visual features. It is not known whether the single-neuron variability is correlated across large neural populations, thus impairing the global encoding of stimuli. We recorded simultaneously from up to 50,000 neurons in mouse primary visual cortex (V1) and in higher order visual areas and measured stimulus discrimination thresholds of 0.35{\textdegree} and 0.37{\textdegree}, respectively, in an orientation decoding task. These neural thresholds were almost 100 times smaller than the behavioral discrimination thresholds reported in mice. This discrepancy could not be explained by stimulus properties or arousal states. Furthermore, behavioral variability during a sensory discrimination task could not be explained by neural variability in V1. Instead, behavior-related neural activity arose dynamically across a network of non-sensory brain areas. These results imply that perceptual discrimination in mice is limited by downstream decoders, not by neural noise in sensory representations.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.03.042}, author = {Stringer, Carsen and Michaelos, Michalis and Tsyboulski, Dmitri and Lindo, Sarah E and Pachitariu, Marius} } @article {65999, title = {A high-throughput predictive method for sequence-similar fold switchers.}, journal = {Biopolymers}, volume = {112}, year = {2021}, month = {2021 Oct 01}, pages = {e23416}, abstract = {

Although most experimentally characterized proteins with similar sequences assume the same folds and perform similar functions, an increasing number of exceptions is emerging. One class of exceptions comprises sequence-similar fold switchers, whose secondary structures shift from α-helix \<-\> β-sheet through a small number of mutations, a sequence insertion, or a deletion. Predictive methods for identifying sequence-similar fold switchers are desirable because some are associated with disease and/or can perform different functions in cells. Here, we use homology-based secondary structure predictions to identify sequence-similar fold switchers from their amino acid sequences alone. To do this, we predicted the secondary structures of sequence-similar fold switchers using three different homology-based secondary structure predictors: PSIPRED, JPred4, and SPIDER3. We found that α-helix \<-\> β-strand prediction discrepancies from JPred4 discriminated between the different conformations of sequence-similar fold switchers with high statistical significance (P \< 1.8*10 ). Thus, we used these discrepancies as a classifier and found that they can often robustly discriminate between sequence-similar fold switchers and sequence-similar proteins that maintain the same folds (Matthews Correlation Coefficient of 0.82). We found that JPred4 is a more robust predictor of sequence-similar fold switchers because of (a) the curated sequence database it uses to produce multiple sequence alignments and (b) its use of sequence profiles based on Hidden Markov Models. Our results indicate that inconsistencies between JPred4 secondary structure predictions can be used to identify some sequence-similar fold switchers from their sequences alone. Thus, the negative information from inconsistent secondary structure predictions can potentially be leveraged to identify sequence-similar fold switchers from the broad base of genomic sequences.

}, issn = {1097-0282}, doi = {10.1002/bip.23416}, author = {Kim, Allen K and Looger, Loren L and Porter, Lauren L} } @article {67186, title = {Hippocampal and thalamic afferents form distinct synaptic microcircuits in the mouse frontal cortex.}, journal = {Cell Reports}, volume = {37}, year = {2021}, month = {2021 October 19}, pages = {109837}, abstract = {

Neural circuits within the frontal cortex support the flexible selection of goal-directed behaviors by integrating input from brain regions associated with sensory, emotional, episodic, and semantic memory functions. From a connectomics perspective, determining how these disparate afferent inputs target their synapses to specific cell types in the frontal cortex may prove crucial in understanding circuit-level information processing. Here, we used monosynaptic retrograde rabies mapping to examine the distribution of afferent neurons targeting four distinct classes of local inhibitory interneurons and four distinct classes of excitatory projection neurons in mouse infralimbic cortex. Interneurons expressing parvalbumin, somatostatin, or vasoactive intestinal peptide received a large proportion of inputs from hippocampal regions, while interneurons expressing neuron-derived neurotrophic factor received a large proportion of inputs from thalamic regions. A more moderate hippocampal-thalamic dichotomy was found among the inputs targeting excitatory neurons that project to the basolateral amygdala, lateral entorhinal cortex, nucleus reuniens of the thalamus, and the periaqueductal gray. Together, these results show a prominent bias among hippocampal and thalamic afferent systems in their targeting to genetically or anatomically defined sets of frontal cortical neurons. Moreover, they suggest the presence of two distinct local microcircuits that control how different inputs govern frontal cortical information processing.

}, author = {Kourtney Graham and Nelson Spruston and Erik Bloss} } @article {67263, title = {Hunger or thirst state uncertainty is resolved by outcome evaluation in medial prefrontal cortex to guide decision-making.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 Jul 01}, pages = {907-912}, abstract = {

Physiological need states direct decision-making toward re-establishing homeostasis. Using a two-alternative forced choice task for mice that models elements of human decisions, we found that varying hunger and thirst states caused need-inappropriate choices, such as food seeking when thirsty. These results show limits on interoceptive knowledge of hunger and thirst states to guide decision-making. Instead, need states were identified after food and water consumption by outcome evaluation, which depended on the medial prefrontal cortex.

}, issn = {1546-1726}, doi = {10.1038/s41593-021-00850-4}, author = {Eiselt, Anne-Kathrin and Chen, Susu and Chen, Jim and Arnold, Jon and Kim, Tahnbee and Pachitariu, Marius and Sternson, Scott M} } @article {65972, title = {High throughput instrument to screen fluorescent proteins under two-photon excitation.}, journal = {Biomedical Optics Express}, volume = {11}, year = {2020}, month = {2020 Dec 01}, pages = {7192-7203}, abstract = {

Two-photon microscopy together with fluorescent proteins and fluorescent protein-based biosensors are commonly used tools in neuroscience. To enhance their experimental scope, it is important to optimize fluorescent proteins for two-photon excitation. Directed evolution of fluorescent proteins under one-photon excitation is common, but many one-photon properties do not correlate with two-photon properties. A simple system for expressing fluorescent protein mutants is colonies on an agar plate. The small focal volume of two-photon excitation makes creating a high throughput screen in this system a challenge for a conventional point-scanning approach. We present an instrument and accompanying software that solves this challenge by selectively scanning each colony based on a colony map captured under one-photon excitation. This instrument, called the GIZMO, can measure the two-photon excited fluorescence of 10,000 colonies in 7 hours. We show that the GIZMO can be used to evolve a fluorescent protein under two-photon excitation.

}, issn = {2156-7085}, doi = {10.1364/BOE.409353}, author = {Molina, Rosana S and King, Jonathan and Franklin, Jacob and Clack, Nathan and McRaven, Christopher and Goncharov, Vasily and Flickinger, Daniel and Svoboda, Karel and Drobizhev, Mikhail and Hughes, Thomas E} } @article {65377, title = {High-throughput cellular-resolution synaptic connectivity mapping in vivo with concurrent two-photon optogenetics and volumetric Ca2+ imaging}, journal = {bioRxiv}, year = {2020}, month = {2020 Feb 25}, abstract = {

The ability to measure synaptic connectivity and properties is essential for understanding neuronal circuits. However, existing methods that allow such measurements at cellular resolution are laborious and technically demanding. Here, we describe a system that allows such measurements in a high-throughput way by combining two-photon optogenetics and volumetric Ca2+\ imaging with whole-cell recording. We reveal a circuit motif for generating fast undulatory locomotion in zebrafish.

}, doi = {https://doi.org/10.1101/2020.02.21.959650}, author = {McRaven, Christopher and Tanese, Dimitrii and Zhang, Lixia and Yang, Chao-Tsung and Ahrens, Misha B and Emiliani, Valentina and Koyama, Minoru} } @article {65696, title = {Hindbrain double-negative feedback mediates palatability-guided food and water consumption.}, journal = {Cell}, volume = {182}, year = {2020}, month = {2020 Sep 17}, pages = {1589-1605}, abstract = {

Hunger and thirst have distinct goals but control similar ingestive behaviors, and little is known about neural processes that are shared between these behavioral states. We identify glutamatergic neurons in the peri-locus coeruleus (periLC neurons) as a polysynaptic convergence node from separate energy-sensitive and hydration-sensitive cell populations. We develop methods for stable hindbrain calcium imaging in free-moving mice, which show that periLC neurons are tuned to ingestive behaviors and respond similarly to food or water consumption. PeriLC neurons are scalably inhibited by palatability and homeostatic need during consumption. Inhibition of periLC neurons is rewarding and increases consumption by enhancing palatability and prolonging ingestion duration. These properties comprise a double-negative feedback relationship that sustains food or water consumption without affecting food- or water-seeking. PeriLC neurons are a hub between hunger and thirst that specifically controls motivation for food and water ingestion, which is a factor that contributes to hedonic overeating and obesity.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.07.031}, author = {Gong, Rong and Xu, Shengjin and Hermundstad, Ann and Yu, Yang and Sternson, Scott M} } @article {65825, title = {Hypothesis-driven quantitative fluorescence microscopy - the importance of reverse-thinking in experimental design.}, journal = {Journal of Cell Science}, volume = {133}, year = {2020}, month = {2020 Nov 05}, abstract = {

One of the challenges in modern fluorescence microscopy is to reconcile the conventional utilization of microscopes as exploratory instruments with their emerging and rapidly expanding role as a quantitative tools. The contribution of microscopy to observational biology will remain enormous owing to the improvements in acquisition speed, imaging depth, resolution and biocompatibility of modern imaging instruments. However, the use of fluorescence microscopy to facilitate the quantitative measurements necessary to challenge hypotheses is a relatively recent concept, made possible by advanced optics, functional imaging probes and rapidly increasing computational power. We argue here that to fully leverage the rapidly evolving application of microscopes in hypothesis-driven biology, we not only need to ensure that images are acquired quantitatively but must also re-evaluate how microscopy-based experiments are designed. In this Opinion, we present a reverse logic that guides the design of quantitative fluorescence microscopy experiments. This unique approach starts from identifying the results that would quantitatively inform the hypothesis and map the process backward to microscope selection. This ensures that the quantitative aspects of testing the hypothesis remain the central focus of the entire experimental design.

}, issn = {1477-9137}, doi = {10.1242/jcs.250027}, author = {Wait, Eric C and Reiche, Michael A and Chew, Teng-Leong} } @article {64824, title = {Heterogeneity within classical cell types is the rule: lessons from hippocampal pyramidal neurons.}, journal = {Nature Reviews. Neuroscience}, volume = {20}, year = {2019}, month = {2019 Feb 18}, pages = {193-204}, abstract = {

The mechanistic operation of brain regions is often interpreted by partitioning constituent neurons into {\textquoteright}cell types{\textquoteright}. Historically, such cell types were broadly defined by their correspondence to gross features of the nervous system (such as cytoarchitecture). Modern-day neuroscientific techniques, enabling a more nuanced examination of neuronal properties, have illustrated a wealth of heterogeneity within these classical cell types. Here, we review the extent of this within-cell-type heterogeneity in one of the simplest cortical regions of the mammalian brain, the rodent hippocampus. We focus on the mounting evidence\ that the classical CA3, CA1 and subiculum pyramidal cell types all exhibit prominent\ and spatially patterned within-cell-type heterogeneity, and suggest these cell\ types\ provide a model system for exploring the organization and function of such heterogeneity. Given that the hippocampus is structurally simple and evolutionarily ancient,\ within-cell-type heterogeneity is likely to be a general and crucial feature of the\ mammalian brain.

}, issn = {1471-0048}, doi = {10.1038/s41583-019-0125-5}, author = {Cembrowski, Mark S and Spruston, Nelson} } @article {65752, title = {High precision coding in visual cortex}, journal = {BioRxiv}, year = {2019}, month = {06/2019}, pages = {679324}, abstract = {

Single neurons in visual cortex provide unreliable measurements of visual features due to their high trial-to-trial variability. It is not known if this {\textquotedblleft}noise{\textquotedblright} extends its effects over large neural populations to impair the global encoding of sensory stimuli. We recorded simultaneously from \~{}20,000 neurons in mouse visual cortex and found that the neural population had discrimination thresholds of 0.3{\textdegree} in an orientation decoding task. These thresholds are \~{}100 times smaller than those reported behaviorally in mice. The discrepancy between neural and behavioral discrimination could not be explained by the types of stimuli we used, by behavioral states or by the sequential nature of trial-by-trial perceptual learning tasks. These results imply that the limits of sensory perception in mice are not set by neural noise in sensory cortex, but by the limitations of downstream decoders.

}, doi = {https://doi.org/10.1101/679324}, author = {Stringer, Carsen and Michaelos, Michalis and Pachitariu, Marius} } @article {68757, title = {A high-content imaging approach to profile C. elegans embryonic development}, journal = {Development}, volume = {146}, year = {2019}, month = {04-2019}, abstract = {

The Caenorhabditis elegans embryo is an important model for analyzing mechanisms of cell fate specification and tissue morphogenesis. Sophisticated lineage-tracing approaches for analyzing embryogenesis have been developed but are labor intensive and do not naturally integrate morphogenetic readouts. To enable the rapid classification of developmental phenotypes, we developed a high-content method that employs two custom strains: a Germ Layer strain that expresses nuclear markers in the ectoderm, mesoderm and endoderm/pharynx; and a Morphogenesis strain that expresses markers labeling epidermal cell junctions and the neuronal cell surface. We describe a procedure that allows simultaneous live imaging of development in 80-100 embryos and provide a custom program that generates cropped, oriented image stacks of individual embryos to facilitate analysis. We demonstrate the utility of our method by perturbing 40 previously characterized developmental genes in variants of the two strains containing RNAi-sensitizing mutations. The resulting datasets yielded distinct, reproducible signature phenotypes for a broad spectrum of genes that are involved in cell fate specification and morphogenesis. In addition, our analysis provides new in vivo evidence for MBK-2 function in mesoderm fate specification and LET-381 function in elongation.

}, issn = {0950-1991}, doi = {10.1242/dev.174029}, url = {https://doi.org/10.1242/dev.174029}, author = {Wang, Shaohe and Ochoa, Stacy D. and Khaliullin, Renat N. and Gerson-Gurwitz, Adina and Hendel, Jeffrey M. and Zhao, Zhiling and Biggs, Ronald and Chisholm, Andrew D. and Desai, Arshad and Oegema, Karen and Green, Rebecca A.} } @article {49534, title = {High-dimensional geometry of population responses in visual cortex.}, journal = {Nature}, volume = {571}, year = {2019}, month = {2019 Jun 26}, pages = {361-65}, abstract = {

A neuronal population encodes information most efficiently when its activity is uncorrelated and high-dimensional, and most robustly when its activity is correlated and lower-dimensional. Here, we analyzed the correlation structure of natural image coding, in large visual cortical populations recorded from awake mice. Evoked population activity was high dimensional, with correlations obeying an unexpected power-law: the n-th principal component variance scaled as 1/n. This was not inherited from the 1/f spectrum of natural images, because it persisted after stimulus whitening. We proved mathematically that the variance spectrum must decay at least this fast if a population code is smooth, i.e. if small changes in input cannot dominate population activity. The theory also predicts larger power-law exponents for lower-dimensional stimulus ensembles, which we validated experimentally. These results suggest that coding smoothness represents a fundamental constraint governing correlations in neural population codes.

}, doi = {10.1038/s41586-019-1346-5}, author = {Stringer, Carsen and Pachitariu, Marius and Steinmetz, Nicholas A and Carandini, Matteo and Harris, Kenneth D} } @article {64986, title = {High-performance calcium sensors for imaging activity in neuronal populations and microcompartments.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Jun 17}, pages = {649-57}, abstract = {

Calcium imaging with genetically encoded calcium indicators (GECIs) is routinely used to measure neural activity in intact nervous systems. GECIs are frequently used in one of two different modes: to track activity in large populations of neuronal cell bodies, or to follow dynamics in subcellular compartments such as axons, dendrites and individual synaptic compartments. Despite major advances, calcium imaging is still limited by the biophysical properties of existing GECIs, including affinity, signal-to-noise ratio, rise and decay kinetics and dynamic range. Using structure-guided mutagenesis and neuron-based screening, we optimized the green fluorescent protein-based GECI GCaMP6 for different modes of in vivo imaging. The resulting jGCaMP7 sensors provide improved detection of individual spikes (jGCaMP7s,f), imaging in neurites and neuropil (jGCaMP7b), and may allow tracking larger populations of neurons using two-photon (jGCaMP7s,f) or wide-field (jGCaMP7c) imaging.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0435-6}, author = {Dana, Hod and Sun, Yi and Mohar, Boaz and Hulse, Brad K and Kerlin, Aaron M and Hasseman, Jeremy P and Tsegaye, Getahun and Tsang, Arthur and Wong, Allan and Patel, Ronak and Macklin, John J and Chen, Yang and Konnerth, Arthur and Jayaraman, Vivek and Looger, Loren L and Schreiter, Eric R and Svoboda, Karel and Kim, Douglas S} } @article {64971, title = {High-resolution cryo-EM structures of outbreak strain human norovirus shells reveal size variations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, year = {2019}, month = {2019 Jun 25}, pages = {12828-32}, abstract = {

Noroviruses are a leading cause of foodborne illnesses worldwide. Although GII.4 strains have been responsible for most norovirus outbreaks, the assembled virus shell structures have been available in detail for only a single strain (GI.1). We present high-resolution (2.6- to 4.1-{\r A}) cryoelectron microscopy (cryo-EM) structures of GII.4, GII.2, GI.7, and GI.1 human norovirus outbreak strain virus-like particles (VLPs). Although norovirus VLPs have been thought to exist in a single-sized assembly, our structures reveal polymorphism between and within genogroups, with small, medium, and large particle sizes observed. Using asymmetric reconstruction, we were able to resolve a Zn2+\ metal ion adjacent to the coreceptor binding site, which affected the structural stability of the shell. Our structures serve as valuable templates for facilitating vaccine formulations.

}, doi = {10.1073/pnas.1903562116}, author = {Jung, James and Grant, Timothy and Thomas, Dennis R. and Diehnelt, Chris W. and Grigorieff, Nikolaus and Leemor, Joshua-Tor} } @article {65041, title = {High-resolution imaging reveals how the spindle midzone impacts chromosome movement.}, journal = {The Journal of Cell Biology}, volume = {218}, year = {2019}, month = {27 Jun 2019}, pages = {2529-44}, abstract = {

In the spindle midzone, microtubules from opposite half-spindles form bundles between segregating chromosomes. Microtubule bundles can either push or restrict chromosome movement during anaphase in different cellular contexts, but how these activities are achieved remains poorly understood. Here, we use high-resolution live-cell imaging to analyze individual microtubule bundles, growing filaments, and chromosome movement in dividing human cells. Within bundles, filament overlap length marked by the cross-linking protein PRC1 decreases during anaphase as chromosome segregation slows. Filament ends within microtubule bundles appear capped despite dynamic PRC1 turnover and submicrometer proximity to growing microtubules. Chromosome segregation distance and rate are increased in two human cell lines when microtubule bundle assembly is prevented via PRC1 knockdown. Upon expressing a mutant PRC1 with reduced microtubule affinity, bundles assemble but chromosome hypersegregation is still observed. We propose that microtubule overlap length reduction, typically linked to pushing forces generated within filament bundles, is needed to properly restrict spindle elongation and position chromosomes within daughter cells.

}, issn = {0021-9525}, doi = {10.1083/jcb.201904169}, url = {http://www.jcb.org/lookup/doi/10.1083/jcb.201904169https://syndication.highwire.org/content/doi/10.1083/jcb.201904169}, author = {Pamula, Melissa C. and Carlini, Lina and Forth, Scott and Verma, Priyanka and Suresh, Subbulakshmi and Legant, Wesley R. and Khodjakov, Alexey and Betzig, Eric and Kapoor, Tarun M.} } @article {65244, title = {High-throughput dense reconstruction of cell lineages.}, journal = {Open Biology}, volume = {9}, year = {2019}, month = {2019 Dec 01}, pages = {190229}, abstract = {

The first meeting exclusively dedicated to the {\textquoteright}High-throughput dense reconstruction of cell lineages{\textquoteright} took place at Janelia Research Campus (Howard Hughes Medical Institute) from 14 to 18 April 2019. Organized by Tzumin Lee, Connie Cepko, Jorge Garcia-Marques and Isabel Espinosa-Medina, this meeting echoed the recent eruption of new tools that allow the reconstruction of lineages based on the phylogenetic analysis of DNA mutations induced during development. Combined with single-cell RNA sequencing, these tools promise to solve the lineage of complex model organisms at single-cell resolution. Here, we compile the conference consensus on the technological and computational challenges emerging from the use of the new strategies, as well as potential solutions.

}, issn = {2046-2441}, doi = {10.1098/rsob.190229}, author = {Isabel Espinosa Medina and Garcia-Marques, Jorge and Cepko, Connie and Lee, Tzumin} } @article {49597, title = {High-throughput synapse-resolving two-photon fluorescence microendoscopy for deep-brain volumetric imaging .}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Jan 03}, abstract = {

Optical imaging has become a powerful tool for studying brains . The opacity of adult brains makes microendoscopy, with an optical probe such as a gradient index (GRIN) lens embedded into brain tissue to provide optical relay, the method of choice for imaging neurons and neural activity in deeply buried brain structures. Incorporating a Bessel focus scanning module into two-photon fluorescence microendoscopy, we extended the excitation focus axially and improved its lateral resolution. Scanning the Bessel focus in 2D, we imaged volumes of neurons at high-throughput while resolving fine structures such as synaptic terminals. We applied this approach to the volumetric anatomical imaging of dendritic spines and axonal boutons in the mouse hippocampus, and functional imaging of GABAergic neurons in the mouse lateral hypothalamus .

}, issn = {2050-084X}, doi = {10.7554/eLife.40805}, author = {Meng, Guanghan and Liang, Yajie and Sarsfield, Sarah and Jiang, Wan-Chen and Lu, Rongwen and Dudman, Joshua Tate and Aponte, Yeka and Ji, Na} } @article {65204, title = {High-yield, automated intracellular electrophysiology in retinal pigment epithelia.}, journal = {Journal of Neuroscience Methods}, volume = {328}, year = {2019}, month = {2019 Dec 01}, pages = {108442}, abstract = {

BACKGROUND: Recent advancements with induced pluripotent stem cell-derived (iPSC) retinal pigment epithelium (RPE) have made disease modeling and cell therapy for macular degeneration feasible. However, current techniques for intracellular electrophysiology - used to validate epithelial function - are painstaking and require manual skill; limiting experimental throughput.

NEW METHOD: A five-stage algorithm, leveraging advances in automated patch clamping, systematically derived and optimized, improves yield and reduces skill when compared to conventional, manual techniques.

RESULTS: The automated algorithm improves yield per attempt from 17\% (manually, n = 23) to 22\% (automated, n = 120) (chi-squared, p = 0.004). Specifically for RPE, depressing the local cell membrane by 6 μm and electroporating (buzzing) just prior to this depth (5 μm) maximized yield.

COMPARISON WITH EXISTING METHOD: Conventionally, intracellular epithelial electrophysiology is performed by manually lowering a pipette with a micromanipulator, blindly, towards a monolayer of cells and spontaneously stopping when the magnitude of the instantaneous measured membrane potential decreased below a predetermined threshold. The new method automatically measures the pipette tip resistance during the descent, detects the cell surface, indents the cell membrane, and briefly buzzes to electroporate the membrane while descending, overall achieving a higher yield than conventional methods.

CONCLUSIONS: This paper presents an algorithm for high-yield, automated intracellular electrophysiology in epithelia; optimized for human RPE. Automation reduces required user skill and training while, simultaneously, improving yield. This algorithm could enable large-scale exploration of drug toxicity and physiological function verification for numerous kinds of epithelia.

}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2019.108442}, author = {Lewallen, Colby F and Wan, Qin and Maminishkis, Arvydas and Stoy, William and Kolb, Ilya and Hotaling, Nathan and Bharti, Kapil and Forest, Craig R} } @article {65175, title = {Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis.}, journal = {Development}, volume = {146}, year = {2019}, month = {2019 Sep 30}, abstract = {

Histone post-translational modifications are key gene expression regulators, but their rapid dynamics during development remain difficult to capture. We applied a Fab-based live endogenous modification labeling technique to monitor the changes in histone modification levels during zygotic genome activation (ZGA) in living zebrafish embryos. Among various histone modifications, H3 Lys27 acetylation (H3K27ac) exhibited most drastic changes, accumulating in two nuclear foci in the 64- to 1k-cell-stage embryos. The elongating form of RNA polymerase II, which is phosphorylated at Ser2 in heptad repeats within the C-terminal domain (RNAP2 Ser2ph), and miR-430 transcripts were also concentrated in foci closely associated with H3K27ac. When treated with α-amanitin to inhibit transcription or JQ-1 to inhibit binding of acetyl-reader proteins, H3K27ac foci still appeared but RNAP2 Ser2ph and miR-430 morpholino were not concentrated in foci, suggesting that H3K27ac precedes active transcription during ZGA. We anticipate that the method presented here could be applied to a variety of developmental processes in any model and non-model organisms.

}, issn = {1477-9129}, doi = {10.1242/dev.179127}, author = {Sato, Yuko and Hilbert, Lennart and Oda, Haruka and Wan, Yinan and Heddleston, John M and Chew, Teng-Leong and Zaburdaev, Vasily and Keller, Philipp and Lionnet, Timoth{\'e}e and Vastenhouw, Nadine and Kimura, Hiroshi} } @article {64985, title = {How to design a chalk talk-the million dollar sales pitch}, journal = {Molecular Biology of the Cell}, volume = {30}, year = {2019}, month = {2019 Jun 15}, pages = {1575-1577}, abstract = {

Each faculty recruiting season, many postdocs ask, "What is a chalk talk?" The chalk talk is many things-a sales pitch, a teaching demonstration, a barrage of questions, and a description of a future research program. The chalk talk is arguably the most important component of a faculty search interview. Yet few postdocs or grad students receive training or practice in giving a chalk talk. In the following essay, I{\textquoteright}ll cover the basics of chalk talk design and preparation.

}, issn = {1939-4586}, doi = {10.1091/mbc.E19-01-0007}, author = {Snapp, Erik Lee} } @article {49813, title = {High-performance GFP-based calcium indicators for imaging activity in neuronal populations and microcompartments.}, journal = {bioRxiv}, year = {2018}, month = {2018 Oct 3}, abstract = {

Calcium imaging with genetically encoded calcium indicators (GECIs) is routinely used to measure neural activity in intact nervous systems. GECIs are frequently used in one of two different modes: to track activity in large populations of neuronal cell bodies, or to follow dynamics in subcellular compartments such as axons, dendrites and individual synaptic compartments. Despite major advances, calcium imaging is still limited by the biophysical properties of existing GECIs, including affinity, signal-to-noise ratio, rise and decay kinetics, and dynamic range. Using structure-guided mutagenesis and neuron-based screening, we optimized the green fluorescent protein-based GECI GCaMP6 for different modes of in vivo imaging. The jGCaMP7 sensors provide improved detection of individual spikes (jGCaMP7s,f), imaging in neurites and neuropil (jGCaMP7b), and tracking large populations of neurons using 2-photon (jGCaMP7s,f) or wide-field (jGCaMP7c) imaging.

}, doi = {10.1101/434589}, author = {Dana, Hod and Sun, Yi and Mohar, Boaz and Hulse, Brad and Hasseman, Jeremy P and Tsegaye, Getahun and Tsang, Arthur and Wong, Allan and Patel, Ronak and Macklin, John J and Chen, Yang and Konnerth, Arthur and Jayaraman, Vivek and Looger, Loren L and Schreiter, Eric R and Svoboda, Karel and Kim, Douglas S} } @article {51794, title = {High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a co-reprogramming factor.}, journal = {PLoS Genetics}, volume = {14}, year = {2018}, month = {2018 07}, pages = {e1007552}, abstract = {

In vivo direct conversion of differentiated cells holds promise for regenerative medicine; however, improving the conversion efficiency and producing functional target cells remain challenging. Ectopic Atoh1 expression in non-sensory supporting cells (SCs) in mouse cochleae induces their partial conversion to hair cells (HCs) at low efficiency. Here, we performed single-cell RNA sequencing of whole mouse sensory epithelia harvested at multiple time points after conditional overexpression of Atoh1. Pseudotemporal ordering revealed that converted HCs (cHCs) are present along a conversion continuum that correlates with both endogenous and exogenous Atoh1 expression. Bulk sequencing of isolated cell populations and single-cell qPCR confirmed 51 transcription factors, including Isl1, are differentially expressed among cHCs, SCs and HCs. In transgenic mice, co-overexpression of Atoh1 and Isl1 enhanced the HC conversion efficiency. Together, our study shows how high-resolution transcriptional profiling of direct cell conversion can identify co-reprogramming factors required for efficient conversion.

}, keywords = {Animals, Animals, Newborn, Basic Helix-Loop-Helix Transcription Factors, Cellular Reprogramming, Gene Expression Profiling, Hair Cells, Auditory, LIM-Homeodomain Proteins, Mice, Mice, Inbred C57BL, Mice, Transgenic, Regeneration, Sequence Analysis, RNA, Single-Cell Analysis, Transcription Factors}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1007552}, author = {Yamashita, Tetsuji and Zheng, Fei and Finkelstein, David and Kellard, Zoe and Carter, Robert and Rosencrance, Celeste D and Sugino, Ken and Easton, John and Gawad, Charles and Zuo, Jian} } @conference {49317, title = {Honeybee detection and pose estimation using convolutional neural networks.}, booktitle = {RFIAP 2018}, year = {2018}, month = {2018 Jun 26}, abstract = {

The ability to automatize the analysis of video for monitoring animals and insects is of great interest for behavior science and ecology [1]. In particular, honeybees play a crucial role in agriculture as natural pollinators. However, recent studies has shown that phenomena such as colony collapse disorder are causing the loss of many colonies [2]. Due to the high number of interacting factors to explain these events, a multi-faceted analysis of the bees in their environment is required. We focus in our work in developing tools to help model and understand their behavior as individuals, in relation with the health and performance of the colony.

In this paper, we report the development of a new system for the detection, locali- zation and tracking of honeybee body parts from video on the entrance ramp of the colony. The proposed system builds on the recent advances in Convolutional Neu- ral Networks (CNN) for Human pose estimation and evaluates the suitability for the detection of honeybee pose as shown in Figure 1. This opens the door for novel animal behavior analysis systems that take advantage of the precise detection and tracking of the insect pose.\ 

}, url = {https://rfiap2018.ign.fr/sites/default/files/ARTICLES/RFIAP_2018/RFIAP_2018_Felipe_Honeybee.pdf}, author = {Rodriguez, Ivan F and Branson, Kristin M and Acuna, Edgar and Agosto-Rivera, Jose and Giray, Tugrul and Megret, Remi} } @article {48374, title = {Heuristic rules underlying dragonfly prey selection and interception.}, journal = {Current Biology : CB}, volume = {27}, year = {2017}, month = {2017 Mar 28}, pages = {1124-37}, abstract = {

Animals use rules to initiate behaviors. Such rules are\ often described as triggers that determine when behavior begins. However, although less explored, these selection rules are also an opportunity to establish sensorimotor constraints that influence how the behavior ends. These constraints may be particularly significant in influencing success in prey capture. Here we explore this in dragonfly prey interception. We found that in the moments leading up to takeoff, perched dragonflies employ a series of sensorimotor rules that determine the time of takeoff and increase the probability of successful capture. First, the dragonfly makes a head saccade followed by smooth pursuit movements to orient its\ direction-of-gaze at potential prey. Second, the dragonfly assesses whether the prey{\textquoteright}s angular size and speed co-vary within a privileged range. Finally, the dragonfly times the moment of its takeoff to a prediction of when the prey will cross the zenith. Each of these processes serves a purpose. The angular size-speed criteria biases interception flights to catchable prey, while the head movements and the predictive takeoff ensure flights begin with the prey visually fixated and directly overhead-the key parameters that underlie interception steering. Prey that do not elicit takeoff generally fail at least one of the criterion, and the loss of prey fixation or overhead positioning during flight is strongly correlated with terminated flights. Thus from an abundance of potential targets, the dragonfly selects a stereotyped set of takeoff conditions based on the prey and body states most likely to end in successful capture.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2017.03.010}, author = {Lin, Huai-Ti and Leonardo, Anthony} } @article {65886, title = {Homeostatic plasticity shapes the visual system{\textquoteright}s first synapse}, journal = {Nature Communications}, volume = {8}, year = {2017}, month = {10/2017}, abstract = {

Vision in dim light depends on synapses between rods and rod bipolar cells (RBCs). Here, we find that these synapses exist in multiple configurations, in which single release sites of rods are apposed by one to three postsynaptic densities (PSDs). Single RBCs often form multiple PSDs with one rod; and neighboring RBCs share ~13\% of their inputs. Rod-RBC synapses develop while ~7\% of RBCs undergo programmed cell death (PCD). Although PCD is common throughout the nervous system, its influences on circuit development and function are not well understood. We generate mice in which ~53 and ~93\% of RBCs, respectively, are removed during development. In these mice, dendrites of the remaining RBCs expand in graded fashion independent of light-evoked input. As RBC dendrites expand, they form fewer multi-PSD contacts with rods. Electrophysiological recordings indicate that this homeostatic co-regulation of neurite and synapse development preserves retinal function in dim light.

}, doi = {10.1038/s41467-017-01332-7}, url = {http://www.nature.com/articles/s41467-017-01332-7http://www.nature.com/articles/s41467-017-01332-7.pdfhttp://www.nature.com/articles/s41467-017-01332-7.pdfhttp://www.nature.com/articles/s41467-017-01332-7}, author = {Johnson, Robert E. and Tien, Nai-Wen and Shen, Ning and Pearson, James T. and Soto, Florentina and Kerschensteiner, Daniel} } @article {48669, title = {How to make a worm twitch.}, journal = {Biophysical Journal}, volume = {112}, year = {2017}, month = {2017 May 09}, pages = {1737-1738}, issn = {1542-0086}, doi = {10.1016/j.bpj.2017.03.035}, author = {Keller, Philipp J} } @article {47348, title = {High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry.}, journal = {Nature Genetics}, volume = {48}, year = {2016}, month = {2016 Mar}, pages = {323-30}, abstract = {

Systemic lupus erythematosus (SLE) has a strong but incompletely understood genetic architecture. We conducted an association study with replication in 4,478 SLE cases and 12,656 controls from six East Asian cohorts to identify new SLE susceptibility loci and better localize known loci. We identified ten new loci and confirmed 20 known loci with genome-wide significance. Among the new loci, the most significant locus was GTF2IRD1-GTF2I at 7q11.23 (rs73366469, Pmeta = 3.75 {\texttimes} 10(-117), odds ratio (OR) = 2.38), followed by DEF6, IL12B, TCF7, TERT, CD226, PCNXL3, RASGRP1, SYNGR1 and SIGLEC6. We identified the most likely functional variants at each locus by analyzing epigenetic marks and gene expression data. Ten candidate variants are known to alter gene expression in cis or in trans. Enrichment analysis highlights the importance of these loci in B cell and T cell biology. The new loci, together with previously known loci, increase the explained heritability of SLE to 24\%. The new loci share functional and ontological characteristics with previously reported loci and are possible drug targets for SLE therapeutics.

}, issn = {1546-1718}, doi = {10.1038/ng.3496}, author = {Sun, Celi and Molineros, Julio E and Looger, Loren L and Zhou, Xu-Jie and Kim, Kwangwoo and Okada, Yukinori and Ma, Jianyang and Qi, Yuan-Yuan and Kim-Howard, Xana and Motghare, Prasenjeet and Bhattarai, Krishna and Adler, Adam and Bang, So-Young and Lee, Hye-Soon and Kim, Tae-Hwan and Kang, Young Mo and Suh, Chang-Hee and Chung, Won Tae and Park, Yong-Beom and Choe, Jung-Yoon and Shim, Seung Cheol and Kochi, Yuta and Suzuki, Akari and Kubo, Michiaki and Sumida, Takayuki and Yamamoto, Kazuhiko and Lee, Shin-Seok and Kim, Young Jin and Han, Bok-Ghee and Dozmorov, Mikhail and Kaufman, Kenneth M and Wren, Jonathan D and Harley, John B and Shen, Nan and Chua, Kek Heng and Zhang, Hong and Bae, Sang-Cheol and Nath, Swapan K} } @article {47374, title = {High-density three-dimensional localization microscopy across large volumes.}, journal = {Nature Methods}, year = {2016}, month = {2016 Mar 7}, abstract = {

Extending three-dimensional (3D) single-molecule localization microscopy away from the coverslip and into thicker specimens will greatly broaden its biological utility. However, because of the limitations of both conventional imaging modalities and conventional labeling techniques, it is a challenge to localize molecules in three dimensions with high precision in such samples while simultaneously achieving the labeling densities required for high resolution of densely crowded structures. Here we combined lattice light-sheet microscopy with newly developed, freely diffusing, cell-permeable chemical probes with targeted affinity for DNA, intracellular membranes or the plasma membrane. We used this combination to perform high-localization precision, ultrahigh-labeling density, multicolor localization microscopy in samples up to 20 μm thick, including dividing cells and the neuromast organ of a zebrafish embryo. We also demonstrate super-resolution correlative imaging with protein-specific photoactivable fluorophores, providing a mutually compatible, single-platform alternative to correlative light-electron microscopy over large volumes.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3797}, author = {Legant, Wesley R and Shao, Lin and Grimm, Jonathan B and Brown, Timothy A and Milkie, Daniel E and Avants, Brian B and Lavis, Luke D and Betzig, Eric} } @article {47811, title = {Highly photostable, reversibly photoswitchable fluorescent protein with high contrast ratio for live-cell superresolution microscopy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, year = {2016}, month = {2016 Aug 25}, pages = {10364-9}, abstract = {

Two long-standing problems for superresolution (SR) fluorescence microscopy are high illumination intensity and long acquisition time, which significantly hamper its application for live-cell imaging. Reversibly photoswitchable fluorescent proteins (RSFPs) have made it possible to dramatically lower the illumination intensities in saturated depletion-based SR techniques, such as saturated depletion nonlinear structured illumination microscopy (NL-SIM) and reversible saturable optical fluorescence transition microscopy. The characteristics of RSFPs most critical for SR live-cell imaging include, first, the integrated fluorescence signal across each switching cycle, which depends upon the absorption cross-section, effective quantum yield, and characteristic switching time from the fluorescent "on" to "off" state; second, the fluorescence contrast ratio of on/off states; and third, the photostability under excitation and depletion. Up to now, the RSFPs of the Dronpa and rsEGFP (reversibly switchable EGFP) families have been exploited for SR imaging. However, their limited number of switching cycles, relatively low fluorescence signal, and poor contrast ratio under physiological conditions ultimately restrict their utility in time-lapse live-cell imaging and their ability to reach the desired resolution at a reasonable signal-to-noise ratio. Here, we present a truly monomeric RSFP, Skylan-NS, whose properties are optimized for the recently developed patterned activation NL-SIM, which enables low-intensity (\~{}100 W/cm(2)) live-cell SR imaging at \~{}60-nm resolution at subsecond acquisition times for tens of time points over broad field of view.

}, issn = {1091-6490}, doi = {10.1073/pnas.1611038113}, author = {Zhang, Xi and Zhang, Mingshu and Li, Dong and He, Wenting and Peng, Jianxin and Betzig, Eric and Xu, Pingyong} } @article {47558, title = {High-resolution macromolecular structure determination by MicroED, a cryo-EM method.}, journal = {Methods in Enzymology}, year = {2016}, month = {2016 Jun 16}, abstract = {

Microelectron diffraction (MicroED) is a new cryo-electron microscopy (cryo-EM) method capable of determining macromolecular structures at atomic resolution from vanishingly small 3D crystals. MicroED promises to solve atomic resolution structures from even the tiniest of crystals, less than a few hundred nanometers thick. MicroED complements frontier advances in crystallography and represents part of the rebirth of cryo-EM that is making macromolecular structure determination more accessible for all. Here we review the concept and practice of MicroED, for both the electron microscopist and crystallographer. Where other reviews have addressed specific details of the technique (Hattne et al., 2015,\ Shi et al., 2016\ and\ Shi et al., 2013), we aim to provide context and highlight important features that should be considered when performing a MicroED experiment.

}, keywords = {Electron; Diffraction; MicroED; Crystal; Protein; Crystallography; cryo-EM}, doi = {10.1016/bs.mie.2016.04.017}, author = {Rodriguez, J A and Gonen, Tamir} } @article {47526, title = {Hippocampal global remapping for different sensory modalities in flying bats.}, journal = {Nature Neuroscience}, volume = {19}, year = {2016}, month = {2016 May 30}, pages = {952-8}, abstract = {

Hippocampal place cells encode the animal{\textquoteright}s spatial position. However, it is unknown how different long-range sensory systems affect spatial representations. Here we alternated usage of vision and echolocation in Egyptian fruit bats while recording from single neurons in hippocampal areas CA1 and subiculum. Bats flew back and forth along a linear flight track, employing echolocation in darkness or vision in light. Hippocampal representations remapped between vision and echolocation via two kinds of remapping: subiculum neurons turned on or off, while CA1 neurons shifted their place fields. Interneurons also exhibited strong remapping. Finally, hippocampal place fields were sharper under vision than echolocation, matching the superior sensory resolution of vision over echolocation. Simulating several theoretical models of place-cells suggested that combining sensory information and path integration best explains the experimental sharpening data. In summary, here we show sensory-based global remapping in a mammal, suggesting that the hippocampus does not contain an abstract spatial map but rather a {\textquoteright}cognitive atlas{\textquoteright}, with multiple maps for different sensory modalities.

}, issn = {1546-1726}, doi = {10.1038/nn.4310}, author = {Geva-Sagiv, Maya and Romani, Sandro and Las, Liora and Ulanovsky, Nachum} } @article {47442, title = {Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016}, abstract = {

Clarifying gene expression in narrowly defined neuronal populations can provide insight into cellular identity, computation, and functionality. Here, we used next-generation RNA sequencing (RNA-seq) to produce a quantitative, whole genome characterization of gene expression for the major excitatory neuronal classes of the hippocampus; namely, granule cells and mossy cells of the dentate gyrus, and pyramidal cells of areas CA3, CA2, and CA1. Moreover, for the canonical cell classes of the trisynaptic loop, we profiled transcriptomes at both dorsal and ventral poles, producing a cell-class- and region-specific transcriptional description for these populations. This dataset clarifies the transcriptional properties and identities of lesser-known cell classes, and moreover reveals unexpected variation in the trisynaptic loop across the dorsal-ventral axis. We have created a public resource, Hipposeq (http://hipposeq.janelia.org), which provides analysis and visualization of these data and will act as a roadmap relating molecules to cells, circuits, and computation in the hippocampus.

}, issn = {2050-084X}, doi = {10.7554/eLife.14997}, author = {Cembrowski, Mark S and Wang, Lihua and Sugino, Ken and Shields, Brenda C and Spruston, Nelson} } @article {47883, title = {Hunger: The carrot and the stick.}, journal = {Molecular Metabolism}, volume = {5}, year = {2016}, month = {2016 Jan}, pages = {1-2}, issn = {2212-8778}, doi = {10.1016/j.molmet.2015.10.002}, author = {Sternson, Scott M} } @article {46973, title = {H2A histone-fold and DNA elements in nucleosome activate SWR1-mediated H2A.Z replacement in budding yeast.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Jun 27}, abstract = {

The histone variant H2A.Z is a universal mark of gene promoters, enhancers, and regulatory elements in eukaryotic chromatin. The chromatin remodeler SWR1 mediates site-specific incorporation of H2A.Z by a multi-step histone replacement reaction, evicting histone H2A-H2B from the canonical nucleosome and depositing the H2A.Z-H2B dimer. Binding of both substrates, the canonical nucleosome and the H2A.Z-H2B dimer, is essential for activation of SWR1. We found that SWR1 primarily recognizes key residues within the α2 helix in the histone-fold of nucleosomal histone H2A, a region not previously known to influence remodeler activity. Moreover, SWR1 interacts preferentially with nucleosomal DNA at superhelix location 2 on the nucleosome face distal to its linker-binding site. Our findings provide new molecular insights on recognition of the canonical nucleosome by a chromatin remodeler and have implications for ATP-driven mechanisms of histone eviction and deposition.

}, issn = {2050-084X}, doi = {10.7554/eLife.06845}, author = {Ranjan, Anand and Wang, Feng and Mizuguchi, Gaku and Wei, Debbie and Huang, Yingzi and Wu, Carl} } @article {47180, title = {Heterosynaptic plasticity underlies aversive olfactory learning in Drosophila}, journal = {Neuron}, volume = {88}, year = {2015}, month = {2015 Dec 2}, pages = {985-98}, abstract = {

Although associative learning has been localized to specific brain areas in many animals, identifying the underlying synaptic processes in vivo has been difficult. Here, we provide the first demonstration of long-term synaptic plasticity at the output site of the Drosophila mushroom body. Pairing an odor with activation of specific dopamine neurons induces both learning and odor-specific synaptic depression. The plasticity induction strictly depends on the temporal order of the two stimuli, replicating the logical requirement for associative learning. Furthermore, we reveal that dopamine action is confined to and distinct across different anatomical compartments of the mushroom body lobes. Finally, we find that overlap between sparse representations of different odors defines both stimulus specificity of the plasticity and generalizability of associative memories across odors. Thus, the plasticity we find here not only manifests important features of associative learning but also provides general insights into how a sparse sensory code is read out.

}, doi = {10.1016/j.neuron.2015.11.003}, author = {Hige, Toshihide and Aso, Yoshinori and Modi, Mehrab and Rubin, Gerald M and Turner, Glenn C} } @article {46895, title = {A high throughput (>90\%), large compensation range, single-prism femtosecond pulse compressor.}, journal = {arXiv}, year = {2015}, month = {2015 Jun 20}, pages = {arXiv:1306.5011 }, abstract = {

We demonstrate a high throughput, large compensation range, single-prism femtosecond pulse compressor, using a single prism and two roof mirrors. The compressor has zero angular dispersion, zero spatial dispersion, zero pulse-front tilt, and unity magnification. The high efficiency is achieved by adopting two roof mirrors as the retroreflectors. We experimentally achieved ~ -14500 fs2 group delay dispersion (GDD) with 30 cm of prism tip-roof mirror prism separation, and ~90.7\% system throughput with the current implementation. With better components, the throughput can be even higher.

}, url = {http://arxiv.org/abs/1306.5011}, author = {Kong, Lingjie and Cui, Meng} } @article {47128, title = {A higher order visual neuron tuned to the spatial amplitude spectra of natural scenes.}, journal = {Nature Communications}, volume = {6}, year = {2015}, month = {2015 Oct 06}, pages = {8522}, abstract = {

Animal sensory systems are optimally adapted to those features typically encountered in natural surrounds, thus allowing neurons with limited bandwidth to encode challengingly large input ranges. Natural scenes are not random, and peripheral visual systems in vertebrates and insects have evolved to respond efficiently to their typical spatial statistics. The mammalian visual cortex is also tuned to natural spatial statistics, but less is known about coding in higher order neurons in insects. To redress this we here record intracellularly from a higher order visual neuron in the hoverfly. We show that the cSIFE neuron, which is inhibited by stationary images, is maximally inhibited when the slope constant of the amplitude spectrum is close to the mean in natural scenes. The behavioural optomotor response is also strongest to images with naturalistic image statistics. Our results thus reveal a close coupling between the inherent statistics of natural scenes and higher order visual processing in insects.

}, issn = {2041-1723}, doi = {10.1038/ncomms9522}, author = {Dyakova, Olga and Lee, Yu-Jen and Longden, Kit D and Kiselev, Valerij G and Nordstr{\"o}m, Karin} } @article {46576, title = {High-performance probes for light and electron microscopy.}, journal = {Nature Methods}, volume = {12}, year = {2015}, month = {2015 Apr 27}, pages = {568-76}, abstract = {

We describe an engineered family of highly antigenic molecules based on GFP-like fluorescent proteins. These molecules contain numerous copies of peptide epitopes and simultaneously bind IgG antibodies at each location. These {\textquoteright}spaghetti monster{\textquoteright} fluorescent proteins (smFPs) distributed well in neurons, notably into small dendrites, spines and axons. smFP immunolabeling localized weakly expressed proteins not well resolved with traditional epitope tags. By varying epitope and scaffold, we generated a diverse family of mutually orthogonal antigens. In cultured neurons and mouse and fly brains, smFP probes allowed robust, orthogonal multicolor visualization of proteins, cell populations and neuropil. smFP variants complement existing tracers and greatly increase the number of simultaneous imaging channels, and they performed well in advanced preparations such as array tomography, super-resolution fluorescence imaging and electron microscopy. In living cells, the probes improved single-molecule image tracking and increased yield for RNA-seq. These probes facilitate new experiments in connectomics, transcriptomics and protein localization.

}, issn = {1548-7105}, doi = {10.1038/nmeth.3365}, author = {Viswanathan, Sarada and Williams, Megan E. and Bloss, Erik B. and Stasevich, Timothy J. and Speer, Colenso M. and Nern, Aljoscha and Pfeiffer, Barret D. and Hooks, Bryan M. and Li, Wei-Ping and English, Brian P. and Tian, Teresa and Henry, Gilbert L. and Macklin, John J. and Patel, Ronak and Gerfen, Charles R and Zhuang, Xiaowei and Wang, Yalin and Rubin, Gerald M and Looger, Loren L} } @article {46891, title = {High-resolution in vivo imaging of mouse brain through the intact skull.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, year = {2015}, month = {2015-Jul 13}, pages = {9236-41}, abstract = {

Multiphoton microscopy is the current method of choice for in vivo deep-tissue imaging. The long laser wavelength suffers less scattering, and the 3D-confined excitation permits the use of scattered signal light. However, the imaging depth is still limited because of the complex refractive index distribution of biological tissue, which scrambles the incident light and destroys the optical focus needed for high resolution imaging. Here, we demonstrate a wavefront-shaping scheme that allows clear imaging through extremely turbid biological tissue, such as the skull, over an extended corrected field of view (FOV). The complex wavefront correction is obtained and directly conjugated to the turbid layer in a noninvasive manner. Using this technique, we demonstrate in vivo submicron-resolution imaging of neural dendrites and microglia dynamics through the intact skulls of adult mice. This is the first observation, to our knowledge, of dynamic morphological changes of microglia through the intact skull, allowing truly noninvasive studies of microglial immune activities free from external perturbations.

}, keywords = {neuroimaging nonlinear microscopy wavefront shaping immunology adaptive optics}, doi = {10.1073/pnas.1505939112 }, url = {https://www.pnas.org/content/112/30/9236}, author = {Park, Jung-Hoon and Sun, Wei and Cui, Meng} } @article {46819, title = {High-resolution live imaging reveals axon-glia interactions during peripheral nerve injury and repair in zebrafish.}, journal = {Disease Models \& Mechanisms}, volume = {8}, year = {2015}, month = {2015 Jun 1}, pages = {553-64}, abstract = {

Neural damage is a devastating outcome of physical trauma. The glia are one of the main effectors of neuronal repair in the nervous system, but the dynamic interactions between peripheral neurons and Schwann cells during injury and regeneration remain incompletely characterized. Here, we combine laser microsurgery, genetic analysis, high-resolution intravital imaging and lattice light-sheet microscopy to study the interaction between Schwann cells and sensory neurons in a zebrafish model of neurotrauma. We found that chronic denervation by neuronal ablation leads to Schwann-cell death, whereas acute denervation by axonal severing does not affect the overall complexity and architecture of the glia. Neuronal-circuit regeneration begins when Schwann cells extend bridging processes to close the injury gap. Regenerating axons grow faster and directionally after the physiological clearing of distal debris by the Schwann cells. This might facilitate circuit repair by ensuring that axons are guided through unoccupied spaces within bands of B{\"u}ngner towards their original peripheral target. Accordingly, in the absence of Schwann cells, regenerating axons are misrouted, impairing the re-innervation of sensory organs. Our results indicate that regenerating axons use haptotaxis as a directional cue during the reconstitution of a neural circuit. These findings have implications for therapies aimed at neurorepair, which will benefit from preserving the architecture of the peripheral glia during periods of denervation.

}, issn = {1754-8411}, doi = {10.1242/dmm.018184}, author = {Xiao, Yan and Faucherre, Ad{\`e}le and Pola-Morell, Laura and Heddleston, John M and Liu, Tsung-Li and Chew, Teng-Leong and Sato, Fuminori and Sehara-Fujisawa, Atsuko and Kawakami, Koichi and L{\'o}pez-Schier, Hern{\'a}n} } @article {47145, title = {Histone H3 threonine phosphorylation regulates asymmetric histone inheritance in the Drosophila male germline.}, journal = {Cell}, volume = {163}, year = {2015}, month = {2015 Nov 5}, pages = {920-33}, abstract = {

A long-standing question concerns how stem cells maintain their identity through multiple divisions. Previously, we reported that pre-existing and newly synthesized histone H3 are asymmetrically distributed during Drosophila male germline stem cell (GSC) asymmetric division. Here, we show that phosphorylation at threonine 3 of H3 (H3T3P) distinguishes pre-existing versus newly synthesized H3. Converting T3 to the unphosphorylatable residue alanine (H3T3A) or to the phosphomimetic aspartate (H3T3D) disrupts asymmetric H3 inheritance. Expression of H3T3A or H3T3D specifically in early-stage germline also leads to cellular defects, including GSC loss and germline tumors. Finally, compromising the activity of the H3T3 kinase Haspin enhances the H3T3A but suppresses the H3T3D phenotypes. These studies demonstrate that H3T3P distinguishes sister chromatids enriched with distinct pools of H3 in order to coordinate asymmetric segregation of "old" H3 into GSCs and that tight regulation of H3T3 phosphorylation is required for male germline activity.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2015.10.002}, author = {Xie, Jing and Wooten, Matthew and Tran, Vuong and Chen, Bi-Chang and Pozmanter, Caitlin and Simbolon, Christine and Betzig, Eric and Chen, Xin} } @article {46742, title = {HMMER web server: 2015 update.}, journal = {Nucleic Acids Research}, year = {2015}, month = {2015 May 5}, abstract = {

The HMMER website, available at http://www.ebi.ac.uk/Tools/hmmer/, provides access to the protein homology search algorithms found in the HMMER software suite. Since the first release of the website in 2011, the search repertoire has been expanded to include the iterative search algorithm, jackhmmer. The continued growth of the target sequence databases means that traditional tabular representations of significant sequence hits can be overwhelming to the user. Consequently, additional ways of presenting homology search results have been developed, allowing them to be summarised according to taxonomic distribution or domain architecture. The taxonomy and domain architecture representations can be used in combination to filter the results according to the needs of a user. Searches can also be restricted prior to submission using a new taxonomic filter, which not only ensures that the results are specific to the requested taxonomic group, but also improves search performance. The repertoire of profile hidden Markov model libraries, which are used for annotation of query sequences with protein families and domains, has been expanded to include the libraries from CATH-Gene3D, PIRSF, Superfamily and TIGRFAMs. Finally, we discuss the relocation of the HMMER webserver to the European Bioinformatics Institute and the potential impact that this will have.

}, issn = {1362-4962}, doi = {10.1093/nar/gkv397}, author = {Finn, Robert D and Clements, Jody and Arndt, William and Miller, Benjamin L and Wheeler, Travis J and Schreiber, Fabian and Bateman, Alex and Eddy, Sean R} } @article {46480, title = {Homology searches for structural RNAs: from proof of principle to practical use.}, journal = {RNA}, volume = {21}, year = {2015}, month = {2015 Apr}, pages = {605-7}, issn = {1469-9001}, doi = {10.1261/rna.050484.115}, author = {Eddy, Sean R} } @conference {65046, title = {A Hebbian/Anti-Hebbian network derived from online non-negative matrix factorization can cluster and discover sparse features.}, booktitle = {2014 48th Asilomar Conference on Signals, Systems and Computers2014 48th Asilomar Conference on Signals, Systems and Computers}, year = {2014}, month = {2015 Mar 02}, publisher = {IEEE}, organization = {IEEE}, address = {Pacific Grove, CA, USA}, abstract = {

Olshausen and Field (OF) proposed that neural computations in the primary visual cortex (V1) can be partially modelled by sparse dictionary learning. By minimizing the regularized representation error they derived an online algorithm, which learns Gabor-filter receptive fields from a natural image ensemble in agreement with physiological experiments. Whereas the OF algorithm can be mapped onto the dynamics and synaptic plasticity in a single-layer neural network, the derived learning rule is nonlocal - the synaptic weight update depends on the activity of neurons other than just pre- and postsynaptic ones {\textendash} and hence biologically implausible. Here, to overcome this problem, we derive sparse dictionary learning from a novel cost-function - a regularized error of the symmetric factorization of the input{\textquoteright}s similarity matrix. Our algorithm maps onto a neural network of the same architecture as OF but using only biologically plausible local learning rules. When trained on natural images our network learns Gabor-filter receptive fields and reproduces the correlation among synaptic weights hard-wired in the OF network. Therefore, online symmetric matrix factorization may serve as an algorithmic theory of neural computation.\ 

}, doi = {10.1109/ACSSC.2014.7094553}, url = {http://ieeexplore.ieee.org/document/7094553/http://xplorestaging.ieee.org/ielx7/7066991/7094373/07094553.pdf?arnumber=7094553}, author = {Pehlevan, Cengiz and Chklovskii, Dmitri B.} } @article {46704, title = {Heterogeneity in periodontitis prevalence in the Hispanic Community Health Study/Study of Latinos.}, journal = {Annals of Epidemiology}, volume = {24}, year = {2014}, month = {2014 Jun}, pages = {455-62}, abstract = {

PURPOSE: The aim of the study was to examine acculturation and established risk factors in explaining variation in periodontitis prevalence among Hispanic/Latino subgroups.

METHODS: Participants were 12,730 dentate adults aged 18-74 years recruited into the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) from four U.S. field centers between 2008 and 2011. A standardized periodontal assessment measured probing pocket depth and gingival recession at six sites per tooth for up to 28 teeth. Periodontitis was defined according to the Centers for Disease Control and Prevention and American Academy of Periodontology case classifications developed for population surveillance. Covariates included acculturation indicators and established periodontitis risk factors. Survey estimation procedures took account of the complex sampling design. Adjusted multivariate binomial regression estimated prevalence ratios and 95\% confidence limits (CLs).

RESULTS: Unadjusted prevalence of moderate and severe periodontitis was 38.5\% and ranged from 24.7\% among Dominicans to 52.1\% among Cubans. Adjusted prevalence ratios for subgroups relative to Dominicans were as follows: (1) 1.34 (95\% CL, 1.13-1.58) among South Americans; (2) 1.37 (95\% CL, 1.17-1.61) among Puerto Ricans; (3) 1.43 (95\% CL, 1.25-1.64) among Mexicans; (4) 1.53 (95\% CL, 1.32-1.76) among Cubans; and (5) 1.55 (95\% CL, 1.35-1.78) among Central Americans.

CONCLUSIONS: Heterogeneity in prevalence of moderate/severe periodontitis among Hispanic/Latino subpopulations was not explained by acculturation or periodontitis risk factors.

}, keywords = {Adult, Aged, Attitude to Health, Dental Health Surveys, Female, Hispanic Americans, Humans, Male, Middle Aged, Oral Hygiene, Periodontitis, Population Surveillance, Prevalence, Risk Assessment, Risk Factors, United States, Young Adult}, issn = {1873-2585}, doi = {10.1016/j.annepidem.2014.02.018}, author = {Sanders, Anne E and Campbell, Steven M and Mauriello, Sally M and Beck, James D and Jimenez, Monik C and Kaste, Linda M and Singer, Richard H and Beaver, Shirley M and Finlayson, Tracy L and Badner, Victor M} } @article {45637, title = {High thermodynamic stability of parametrically designed helical bundles.}, journal = {Science}, volume = {346}, year = {2014}, month = {2014 Oct 24}, pages = {481-5}, abstract = {

We describe a procedure for designing proteins with backbones produced by varying the parameters in the Crick coiled coil-generating equations. Combinatorial design calculations identify low-energy sequences for alternative helix supercoil arrangements, and the helices in the lowest-energy arrangements are connected by loop building. We design an antiparallel monomeric untwisted three-helix bundle with 80-residue helices, an antiparallel monomeric right-handed four-helix bundle, and a pentameric parallel left-handed five-helix bundle. The designed proteins are extremely stable (extrapolated ΔGfold \> 60 kilocalories per mole), and their crystal structures are close to those of the design models with nearly identical core packing between the helices. The approach enables the custom design of hyperstable proteins with fine-tuned geometries for a wide range of applications.

}, issn = {1095-9203}, doi = {10.1126/science.1257481}, author = {Huang, Po-Ssu and Oberdorfer, Gustav and Xu, Chunfu and Pei, Xue Y and Nannenga, Brent L and Rogers, Joseph M and DiMaio, Frank and Gonen, Tamir and Luisi, Ben and Baker, David} } @article {47897, title = {A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain.}, journal = {Neuron}, volume = {83}, year = {2014}, month = {2014 Jul 16}, pages = {309-23}, abstract = {

To provide a temporal framework for the genoarchitecture of brain development, we generated in situ hybridization data for embryonic and postnatal mouse brain at seven developmental stages for \~{}2,100 genes, which were processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, seven reference atlases, an ontogenetic ontology, and tools to explore coexpression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org).

}, keywords = {Animals, Brain, Brain Mapping, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Developmental, Mice}, issn = {1097-4199}, doi = {10.1016/j.neuron.2014.05.033}, author = {Thompson, Carol L and Ng, Lydia and Menon, Vilas and Martinez, Salvador and Lee, Chang-Kyu and Glattfelder, Katie and Sunkin, Susan M and Henry, Alex and Lau, Christopher and Dang, Chinh and Garcia-Lopez, Raquel and Martinez-Ferre, Almudena and Pombero, Ana and Rubenstein, John L R and Wakeman, Wayne B and Hohmann, John and Dee, Nick and Sodt, Andrew J and Young, Rob and Smith, Kimberly and Nguyen, Thuc-Nghi and Kidney, Jolene and Kuan, Leonard and Jeromin, Andreas and Kaykas, Ajamete and Miller, Jeremy and Page, Damon and Orta, Geri and Bernard, Amy and Riley, Zackery and Smith, Simon and Wohnoutka, Paul and Hawrylycz, Michael J and Puelles, Luis and Jones, Allan R} } @article {45860, title = {High-resolution structure determination by continuous-rotation data collection in MicroED.}, journal = {Nature Methods}, volume = {11}, year = {2014}, month = {2014 Sep}, pages = {927-30}, abstract = {

MicroED uses very small three-dimensional protein crystals and electron diffraction for structure determination. We present an improved data collection protocol for MicroED called {\textquoteright}continuous rotation{\textquoteright}. Microcrystals are continuously rotated during data collection, yielding more accurate data. The method enables data processing with the crystallographic software tool MOSFLM, which resulted in improved resolution for the model protein lysozyme. These improvements are paving the way for the broad implementation and application of MicroED in structural biology.

}, keywords = {Algorithms, Databases, Protein, Electrons, Imaging, Three-Dimensional, Information Storage and Retrieval, Lasers, Microscopy, Video, Protein Conformation, Proteins, Rotation, Scattering, Small Angle, X-Ray Diffraction}, issn = {1548-7105}, doi = {10.1038/nmeth.3043}, author = {Nannenga, Brent L and Shi, Dan and Leslie, Andrew G W and Gonen, Tamir} } @article {6414, title = {Haemolysin coregulated protein is an exported receptor and chaperone of type VI secretion substrates.}, journal = {Molecular Cell}, volume = {51}, year = {2013}, month = {2013 Sep 12}, pages = {584-93}, abstract = {

Secretion systems require high-fidelity mechanisms to discriminate substrates among the vast cytoplasmic pool of proteins. Factors mediating substrate recognition by the type VI secretion system (T6SS) of Gram-negative bacteria, a widespread pathway that translocates effector proteins into target bacterial cells, have not been defined. We report that haemolysin coregulated protein (Hcp), a ring-shaped hexamer secreted by all characterized T6SSs, binds specifically to cognate effector molecules. Electron microscopy analysis of an Hcp-effector complex from Pseudomonas aeruginosa revealed the effector bound to the inner surface of Hcp. Further studies demonstrated that interaction with the Hcp pore is a general requirement for secretion of diverse effectors encompassing several enzymatic classes. Though previous models depict Hcp as a static conduit, our data indicate it is a chaperone and receptor of substrates. These unique functions of a secreted protein highlight fundamental differences between the export mechanism of T6 and other characterized secretory pathways.

}, issn = {1097-4164}, doi = {10.1016/j.molcel.2013.07.025}, author = {Silverman, Julie M and Agnello, Danielle M and Zheng, Hongjin and Andrews, Benjamin T and Li, Mo and Catalano, Carlos E and Gonen, Tamir and Mougous, Joseph D} } @article {5803, title = {HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation.}, journal = {Nature Structural \& Molecular Biology}, volume = {20}, year = {2013}, month = {2013 Feb}, pages = {150-8}, abstract = {

The internal ribosome entry site (IRES) of the hepatitis C virus (HCV) drives noncanonical initiation of protein synthesis necessary for viral replication. Functional studies of the HCV IRES have focused on 80S ribosome formation but have not explored its role after the 80S ribosome is poised at the start codon. Here, we report that mutations of an IRES domain that docks in the 40S subunit{\textquoteright}s decoding groove cause only a local perturbation in IRES structure and result in conformational changes in the IRES-rabbit 40S subunit complex. Functionally, the mutations decrease IRES activity by inhibiting the first ribosomal translocation event, and modeling results suggest that this effect occurs through an interaction with a single ribosomal protein. The ability of the HCV IRES to manipulate the ribosome provides insight into how the ribosome{\textquoteright}s structure and function can be altered by bound RNAs, including those derived from cellular invaders.

}, issn = {1545-9985}, doi = {10.1038/nsmb.2465}, author = {Filbin, Megan E and Vollmar, Breanna S and Shi, Dan and Gonen, Tamir and Kieft, Jeffrey S} } @article {6279, title = {High speed phase distortion measurement and compensation for focusing in space and time.}, journal = {Proceedings of SPIE}, volume = {8589}, year = {2013}, month = {2013}, pages = {85890V}, abstract = {

Random scattering and aberrations severely limit the imaging depth in optical microscopy. We introduce a rapid, parallel wavefront compensation technique that efficiently compensates even highly complex phase distortions. Using coherence gated backscattered light as a feedback signal, we focus light deep inside highly scattering brain tissue. We demonstrate that the same wavefront optimization technique can also be used to compensate spectral phase distortions in ultrashort laser pulses using nonlinear iterative feedback. We can restore transform limited pulse durations at any selected target location and compensate for dispersion that has occurred in the optical train and within the sample.

}, doi = {10.1117/12.2001121}, author = {Fiolka, Reto and Cui, Meng} } @article {4056, title = {High throughput methods for electron crystallography.}, journal = {Methods in Molecular Biology}, volume = {955}, year = {2013}, month = {2013}, pages = {273-96}, abstract = {

Membrane proteins play a tremendously important role in cell physiology and serve as a target for an increasing number of drugs. Structural information is key to understanding their function and for developing new strategies for combating disease. However, the complex physical chemistry associated with membrane proteins has made them more difficult to study than their soluble cousins. Electron crystallography has historically been a successful method for solving membrane protein structures and has the advantage of providing a native lipid environment for these proteins. Specifically, when membrane proteins form two-dimensional arrays within a lipid bilayer, electron microscopy can be used to collect images and diffraction and the corresponding data can be combined to produce a three-dimensional reconstruction, which under favorable conditions can extend to atomic resolution. Like X-ray crystallography, the quality of the structures are very much dependent on the order and size of the crystals. However, unlike X-ray crystallography, high-throughput methods for screening crystallization trials for electron crystallography are not in general use. In this chapter, we describe two alternative methods for high-throughput screening of membrane protein crystallization within the lipid bilayer. The first method relies on the conventional use of dialysis for removing detergent and thus reconstituting the bilayer; an array of dialysis wells in the standard 96-well format allows the use of a liquid-handling robot and greatly increases throughput. The second method relies on titration of cyclodextrin as a chelating agent for detergent; a specialized pipetting robot has been designed not only to add cyclodextrin in a systematic way, but to use light scattering to monitor the reconstitution process. In addition, the use of liquid-handling robots for making negatively stained grids and methods for automatically imaging samples in the electron microscope are described.

}, doi = {10.1007/978-1-62703-176-9_15}, author = {Stoke, DL and Ubarretxena-Belandia, I and Gonen, T and Engel, A} } @article {6262, title = {High-throughput analysis of stimulus-evoked behaviors in Drosophila larva reveals multiple modality-specific escape strategies.}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013 Aug 20}, pages = {e71706}, abstract = {

All organisms react to noxious and mechanical stimuli but we still lack a complete understanding of cellular and molecular mechanisms by which somatosensory information is transformed into appropriate motor outputs. The small number of neurons and excellent genetic tools make Drosophila larva an especially tractable model system in which to address this problem. We developed high throughput assays with which we can simultaneously expose more than 1,000 larvae per man-hour to precisely timed noxious heat, vibration, air current, or optogenetic stimuli. Using this hardware in combination with custom software we characterized larval reactions to somatosensory stimuli in far greater detail than possible previously. Each stimulus evoked a distinctive escape strategy that consisted of multiple actions. The escape strategy was context-dependent. Using our system we confirmed that the nociceptive class IV multidendritic neurons were involved in the reactions to noxious heat. Chordotonal (ch) neurons were necessary for normal modulation of head casting, crawling and hunching, in response to mechanical stimuli. Consistent with this we observed increases in calcium transients in response to vibration in ch neurons. Optogenetic activation of ch neurons was sufficient to evoke head casting and crawling. These studies significantly increase our understanding of the functional roles of larval ch neurons. More generally, our system and the detailed description of wild type reactions to somatosensory stimuli provide a basis for systematic identification of neurons and genes underlying these behaviors.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0071706}, author = {Ohyama, Tomoko and Jovanic, Tihana and Denisov, Gennady and Dang, Tam C and Hoffmann, Dominik and Kerr, Rex A and Zlatic, Marta} } @article {68819, title = {Hindbrain V2a Neurons in the Excitation of Spinal Locomotor Circuits during Zebrafish Swimming}, journal = {Current Biology}, volume = {23}, year = {2013}, month = {05/2013}, pages = {843-849}, abstract = {

During locomotion in vertebrates, reticulospinal neurons in the hindbrain play critical roles in providing descending excitation to the spinal cord locomotor systems. However, despite the fact that many genes that are used to classify the neuronal identities of neurons in the hindbrain have been identified, the molecular identity of the reticulospinal neurons that are critically involved in locomotor drive is not well understood. Chx10-expressing neurons (V2a neurons) are ipsilaterally projecting glutamatergic neurons in the spinal cord and the hindbrain. Many of the V2a neurons in the hindbrain are known to project to the spinal cord in zebrafish, making hindbrain V2a neurons a prime candidate in descending locomotor drive. Results We investigated the roles of hindbrain V2a neurons using optogenetic and electrophysiological approaches. The forced activation of hindbrain V2a neurons using channelrhodopsin efficiently evoked swimming, whereas the forced inactivation of them using Archearhodopsin3 or Halorhodpsin reliably stopped ongoing swimming. Electrophysiological recordings of two populations of hindbrain reticulospinal V2a neurons showed that they were active during swimming. One population of neurons, small V2a neurons in the caudal hindbrain, fired with low rhythmicity, whereas the other population of neurons, large reticulospinal V2a neurons, called MiV1 neurons, fired more rhythmically. Conclusions These results indicated that hindbrain reticulospinal V2a neurons play critical roles in providing excitation to the spinal locomotor circuits during swimming by providing both tonic and phasic inputs to the circuits.

}, issn = {0960-9822}, doi = {https://doi.org/10.1016/j.cub.2013.03.066}, url = {https://www.sciencedirect.com/science/article/pii/S0960982213003680}, author = {Yukiko Kimura and Chie Satou and Shunji Fujioka and Wataru Shoji and Keiko Umeda and Toru Ishizuka and Hiromu Yawo and Shin-ichi Higashijima} } @article {5889, title = {Hypothalamic survival circuits: blueprints for purposive behaviors.}, journal = {Neuron}, volume = {77}, year = {2013}, month = {2013 Mar 6}, pages = {810-24}, abstract = {

Neural processes that direct an animal{\textquoteright}s actions toward environmental goals are critical elements for understanding behavior. The hypothalamus is closely associated with motivated behaviors required for survival and reproduction. Intense feeding, drinking, aggressive, and sexual behaviors can be produced by a simple neuronal stimulus applied to discrete hypothalamic regions. What can these "evoked behaviors" teach us about the neural processes that determine behavioral intent and intensity? Small populations of neurons sufficient to evoke a complex motivated behavior may be used as entry points to identify circuits that energize and direct behavior to specific goals. Here, I review recent applications of molecular genetic, optogenetic, and pharmacogenetic approaches that overcome previous limitations for analyzing anatomically complex hypothalamic circuits and their interactions with the rest of the brain. These new tools have the potential to bridge the gaps between neurobiological and psychological thinking about the mechanisms of complex motivated behavior.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.02.018}, author = {Sternson, Scott M} } @article {4590, title = {Hierarchical deployment of factors regulating temporal fate in a diverse neuronal lineage of the Drosophila central brain.}, journal = {Neuron}, volume = {73}, year = {2012}, month = {2012 Feb 23}, pages = {677-84}, abstract = {

The anterodorsal projection neuron lineage of Drosophila melanogaster produces 40 neuronal types in a stereotypic order. Here we take advantage of this complete lineage sequence to examine the role of known temporal fating factors, including Chinmo and the Hb/Kr/Pdm/Cas transcriptional cascade, within this diverse central brain lineage. Kr mutation affects the temporal fate of the neuroblast (NB) itself, causing a single fate to be skipped, whereas Chinmo null only elicits fate transformation of NB progeny without altering cell counts. Notably, Chinmo operates in two separate windows to prevent fate transformation (into the subsequent Chinmo-indenpendent fate) within each window. By contrast, Hb/Pdm/Cas play no detectable role, indicating that Kr either acts outside of the cascade identified in the ventral nerve cord or that redundancy exists at the level of fating factors. Therefore, hierarchical fating mechanisms operate within the lineage to generate neuronal diversity in an unprecedented fashion.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.12.018}, author = {Kao, Chih-Fei and Yu, Hung-Hsiang and He, Yisheng and Kao, Jui-Chun and Lee, Tzumin} } @article {5659, title = {A hierarchical structure of cortical interneuron electrical diversity revealed by automated statistical analysis.}, journal = {Cerebral Cortex}, volume = {23}, year = {2012}, month = {2012 Sep 17}, pages = {2994-3006}, abstract = {

Although the diversity of cortical interneuron electrical properties is well recognized, the number of distinct electrical types (e-types) is still a matter of debate. Recently, descriptions of interneuron variability were standardized by multiple laboratories on the basis of a subjective classification scheme as set out by the Petilla convention (Petilla Interneuron Nomenclature Group, PING). Here, we present a quantitative, statistical analysis of a database of nearly five hundred neurons manually annotated according to the PING nomenclature. For each cell, 38 features were extracted from responses to suprathreshold current stimuli and statistically analyzed to examine whether cortical interneurons subdivide into e-types. We showed that the partitioning into different e-types is indeed the major component of data variability. The analysis suggests refining the PING e-type classification to be hierarchical, whereby most variability is first captured within a coarse subpartition, and then subsequently divided into finer subpartitions. The coarse partition matches the well-known partitioning of interneurons into fast spiking and adapting cells. Finer subpartitions match the burst, continuous, and delayed subtypes. Additionally, our analysis enabled the ranking of features according to their ability to differentiate among e-types. We showed that our quantitative e-type assignment is more than 90\% accurate and manages to catch several human errors.

}, issn = {1460-2199}, doi = {10.1093/cercor/bhs290}, author = {Druckmann, S and Hill, Sean and Sch{\"u}rmann, Felix and Markram, Henry and Segev, Idan} } @article {6493, title = {Hippocampal phase precession from dual input components.}, journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience}, volume = {32}, year = {2012}, month = {2012 Nov 21}, pages = {16693-703a}, abstract = {

Phase precession is a well known phenomenon in which a hippocampal place cell will fire action potentials at successively earlier phases (relative to the theta-band oscillations recorded in the local field potential) as an animal moves through the cell{\textquoteright}s receptive field (also known as a place field). We present a model in which CA1 pyramidal cell spiking is driven by dual input components arising from CA3 and EC3. The receptive fields of these two input components overlap but are offset in space from each other such that as the animal moves through the model place field, action potentials are driven first by the CA3 input component and then the EC3 input component. As CA3 synaptic input is known to arrive in CA1 at a later theta phase than EC3 input (Mizuseki et al., 2009; Montgomery et al., 2009), CA1 spiking advances in phase as the model transitions from CA3-driven spiking to EC3-driven spiking. Here spike phase is a function of animal location, placing our results in agreement with many experimental observations characterizing CA1 phase precession (O{\textquoteright}Keefe and Recce, 1993; Huxter et al., 2003; Geisler et al., 2007). We predict that experimental manipulations that dramatically enhance or disrupt activity in either of these areas should have a significant effect on phase precession observed in CA1.

}, keywords = {Action Potentials, Algorithms, Animals, CA1 Region, CA3 Region, Computer Simulation, Electric Stimulation, Electroencephalography, Electrophysiological Phenomena, Entorhinal Cortex, Environment, Hippocampal, Hippocampus, Membrane Potentials, Mice, Models, Neurological, Pyramidal Cells, Rats, Synapses, Theta Rhythm}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2786-12.2012}, author = {Chance, Frances S} } @article {5103, title = {Hippocampal place fields emerge upon single-cell manipulation of excitability during behavior.}, journal = {Science}, volume = {337}, year = {2012}, month = {2012 Aug 17}, pages = {849-53}, abstract = {

The origin of the spatial receptive fields of hippocampal place cells has not been established. A hippocampal CA1 pyramidal cell receives thousands of synaptic inputs, mostly from other spatially tuned neurons; however, how the postsynaptic neuron{\textquoteright}s cellular properties determine the response to these inputs during behavior is unknown. We discovered that, contrary to expectations from basic models of place cells and neuronal integration, a small, spatially uniform depolarization of the spatially untuned somatic membrane potential of a silent cell leads to the sudden and reversible emergence of a spatially tuned subthreshold response and place-field spiking. Such gating of inputs by postsynaptic neuronal excitability reveals a cellular mechanism for receptive field origin and may be critical for the formation of hippocampal memory representations.

}, issn = {1095-9203}, doi = {10.1126/science.1221489}, author = {Lee, Doyun and Lin, Bei-Jung and Lee, Albert K} } @article {6720, title = {Hippocampal pyramidal neurons comprise two distinct cell types that are countermodulated by metabotropic receptors.}, journal = {Neuron}, volume = {76}, year = {2012}, month = {2012 Nov 21}, pages = {776-89}, abstract = {

Relating the function of neuronal cell types to information processing and behavior is a central goal of neuroscience. In the hippocampus, pyramidal cells in CA1 and the subiculum process sensory and motor cues to form a cognitive map encoding spatial, contextual, and emotional information, which they transmit throughout the brain. Do these cells constitute a single class or are there multiple cell types with specialized functions? Using unbiased cluster analysis, we show that there are two morphologically and electrophysiologically distinct principal cell types that carry hippocampal output. We show further that these two cell types are inversely modulated by the synergistic action of glutamate and acetylcholine acting on metabotropic receptors that are central to hippocampal function. Combined with prior connectivity studies, our results support a model of hippocampal processing in which the two pyramidal cell types are predominantly segregated into two parallel pathways that process distinct modalities of information.

}, keywords = {3-dione, 6-Cyano-7-nitroquinoxaline-2, Analysis of Variance, Animals, Benzylamines, Biophysics, CA1 Region, Electric Stimulation, Excitatory Amino Acid Antagonists, Excitatory Amino Acid Transporter 3, GABA Antagonists, Glutamate Decarboxylase, Hippocampal, Lysine, Male, Membrane Potentials, Metabotropic Glutamate, Neurons, Newborn, Patch-Clamp Techniques, Phosphinic Acids, Pyridazines, Rats, Receptors, Time Factors}, issn = {1097-4199}, doi = {10.1016/j.neuron.2012.09.036}, author = {Graves, Austin R and Moore, Shannon J and Bloss, Erik B and Mensh, Brett D and Kath, William L and Spruston, Nelson} } @article {5626, title = {How does juvenile hormone control insect metamorphosis and reproduction?}, journal = {General and Comparative Endocrinology}, volume = {179}, year = {2012}, month = {2012 Dec 1}, pages = {477-84}, abstract = {

In insects juvenile hormone (JH) regulates both metamorphosis and reproduction. This lecture focuses on our current understanding of JH action at the molecular level in both of these processes based primarily on studies in the tobacco hornworm Manduca sexta, the flour beetle Tribolium castaneum, the mosquito Aedes aegypti, and the fruit fly Drosophila melanogaster. The roles of the JH receptor complex and the transcription factors that it regulates during larval molting and metamorphosis are summarized. Also highlighted are the intriguing interactions of the JH and insulin signaling pathways in both imaginal disc development and vitellogenesis. Critical actions of JH and its receptor in the timing of maturation of the adult optic lobe and of female receptivity in Drosophila are also discussed.

}, issn = {1095-6840}, doi = {10.1016/j.ygcen.2012.06.001}, author = {Riddiford, Lynn M} } @article {47905, title = {Hallmarks of molecular action of microtubule stabilizing agents: effects of epothilone B, ixabepilone, peloruside A, and laulimalide on microtubule conformation.}, journal = {The Journal of biological chemistry}, volume = {286}, year = {2011}, month = {2011 Apr 1}, pages = {11765-78}, abstract = {

Microtubule stabilizing agents (MSAs) comprise a class of drugs that bind to microtubule (MT) polymers and stabilize them against disassembly. Several of these agents are currently in clinical use as anticancer drugs, whereas others are in various stages of development. Nonetheless, there is insufficient knowledge about the molecular modes of their action. Recent studies from our laboratory utilizing hydrogen-deuterium exchange in combination with mass spectrometry (MS) provide new information on the conformational effects of Taxol and discodermolide on microtubules isolated from chicken erythrocytes (CET). We report here a comprehensive analysis of the effects of epothilone B, ixabepilone (IXEMPRA(TM)), laulimalide, and peloruside A on CET conformation. The results of our comparative hydrogen-deuterium exchange MS studies indicate that all MSAs have significant conformational effects on the C-terminal H12 helix of α-tubulin, which is a likely molecular mechanism for the previously observed modulations of MT interactions with microtubule-associated and motor proteins. More importantly, the major mode of MT stabilization by MSAs is the tightening of the longitudinal interactions between two adjacent αβ-tubulin heterodimers at the interdimer interface. In contrast to previous observations reported with bovine brain tubulin, the lateral interactions between the adjacent protofilaments in CET are particularly strongly stabilized by peloruside A and laulimalide, drugs that bind outside the taxane site. This not only highlights the significance of tubulin isotype composition in modulating drug effects on MT conformation and stability but also provides a potential explanation for the synergy observed when combinations of taxane and alternative site binding drugs are used.

}, keywords = {Animals, Bicyclo Compounds, Heterocyclic, Binding Sites, Brain, Brain Chemistry, Cattle, Epothilones, Lactones, Macrolides, Mass Spectrometry, Microtubules, Nerve Tissue Proteins, Protein Structure, Secondary, Tubulin, Tubulin Modulators}, issn = {1083-351X}, doi = {10.1074/jbc.M110.162214}, author = {Khrapunovich-Baine, Marina and Menon, Vilas and Yang, Chia-Ping Huang and Northcote, Peter T and Miller, John H and Angeletti, Ruth Hogue and Fiser, Andras and Horwitz, Susan Band and Xiao, Hui} } @article {47222, title = {Heterotypic gap junctions between two neurons in the drosophila brain are critical for memory.}, journal = {Current Biology : CB}, volume = {21}, year = {2011}, month = {2011 May 24}, pages = {848-54}, abstract = {

Gap junctions play an important role in the regulation of neuronal metabolism and homeostasis by serving as connections that enable small molecules to pass between cells and synchronize activity between cells. Although recent studies have linked gap junctions to memory formation, it remains unclear how they contribute to this process. Gap junctions are hexameric hemichannels formed from the connexin and pannexin gene families in chordates and the innexin (inx) gene family in invertebrates. Here we show that two modulatory neurons, the anterior paired lateral (APL) neuron and the dorsal paired medial (DPM) neuron, form heterotypic gap junctions within the mushroom body (MB), a learning and memory center in the Drosophila brain. Using RNA interference-mediated knockdowns of inx7 and inx6 in the APL and DPM neurons, respectively, we found that flies showed normal olfactory associative learning and intact anesthesia-resistant memory (ARM) but failed to form anesthesia-sensitive memory (ASM). Our results reveal that the heterotypic gap junctions between the APL and DPM neurons are an essential part of the MB circuitry for memory formation, potentially constituting a recurrent neural network to stabilize ASM.

}, keywords = {Anesthesia, Animals, Animals, Genetically Modified, Connexins, Drosophila, Drosophila Proteins, Gap Junctions, Memory, Mushroom Bodies, Neurons, RNA Interference, Smell}, issn = {1879-0445}, doi = {10.1016/j.cub.2011.02.041}, author = {Wu, Chia-Lin and Shih, Meng-Fu Maxwell and Lai, Jason Sih-Yu and Yang, Hsun-Ti and Turner, Glenn C and Chen, Linyi and Chiang, Ann-Shyn} } @article {4325, title = {High resolution segmentation of neuronal tissues from low depth-resolution EM imagery.}, journal = {8th International Conference of Energy Minimization Methods in Computer Vision and Pattern Recognition Energy Minimization Methods in Computer Vision and Pattern Recognition}, volume = {6819}, year = {2011}, month = {2011}, pages = {261-72}, abstract = {

The challenge of recovering the topology of massive neuronal circuits can potentially be met by high throughput Electron Microscopy (EM) imagery. Segmenting a 3-dimensional stack of EM images into the individual neurons is difficult, due to the low depth-resolution in existing high-throughput EM technology, such as serial section Transmission EM (ssTEM). In this paper we propose methods for detecting the high resolution locations of membranes from low depth-resolution images. We approach this problem using both a method that learns a discriminative, over-complete dictionary and a kernel SVM. We test this approach on tomographic sections produced in simulations from high resolution Focused Ion Beam (FIB) images and on low depth-resolution images acquired with ssTEM and evaluate our results by comparing it to manual labeling of this data.

}, issn = {978-3-642-23093-6}, author = {Glasner, Daniel and Hu, Tao and Nunez-Iglesias, Juan and Scheffer, Lou and Xu, CS and Hess, Harald and Fetter, Richard and Chklovskii, Dmitri and Basri, Ronen} } @article {2474, title = {A high speed wavefront determination method based on spatial frequency modulations for focusing light through random scattering media.}, journal = {Optics Express}, volume = {19}, year = {2011}, month = {2011 Feb 14}, pages = {2989-95}, abstract = {

A large number of degrees of freedom are required to produce a high quality focus through random scattering media. Previous demonstrations based on spatial phase modulations suffer from either a slow speed or a small number of degrees of freedom. In this work, a high speed wavefront determination technique based on spatial frequency domain wavefront modulations is proposed and experimentally demonstrated, which is capable of providing both a high operation speed and a large number of degrees of freedom. The technique was employed to focus light through a strongly scattering medium and the entire wavefront was determined in 400 milliseconds, \ three orders of magnitude faster than the previous report.

}, issn = {1094-4087}, doi = {10.1364/OE.19.002989}, author = {Cui, Meng} } @article {6135, title = {High-throughput behavioral analysis in C. elegans.}, journal = {Nature Methods}, volume = {8}, year = {2011}, month = {2011 Jun 5}, pages = {592-8}, abstract = {

We designed a real-time computer vision system, the Multi-Worm Tracker (MWT), which can simultaneously quantify the behavior of dozens of Caenorhabditis elegans on a Petri plate at video rates. We examined three traditional behavioral paradigms using this system: spontaneous movement on food, where the behavior changes over tens of minutes; chemotaxis, where turning events must be detected accurately to determine strategy; and habituation of response to tap, where the response is stochastic and changes over time. In each case, manual analysis or automated single-worm tracking would be tedious and time-consuming, but the MWT system allowed rapid quantification of behavior with minimal human effort. Thus, this system will enable large-scale forward and reverse genetic screens for complex behaviors.

}, keywords = {Animal, Animals, Behavior, Caenorhabditis elegans, Chemotaxis, Computer-Assisted, Image Processing, Movement, Software, Stochastic Processes, Time Factors}, issn = {1548-7105}, doi = {10.1038/nmeth.1625}, author = {Swierczek, Nicholas A and Giles, Andrew C and Rankin, Catharine H and Kerr, Rex A} } @article {68486, title = {A high-throughput method for generating uniform microislands for autaptic neuronal cultures.}, journal = {J Neurosci Methods}, volume = {198}, year = {2011}, month = {06/2011}, pages = {230-5}, abstract = {

Generating microislands of culture substrate on coverslips by spray application of poly-d lysine is a commonly used method for culturing isolated neurons that form self (autaptic) synapses. This preparation has multiple advantages for studying synaptic transmission in isolation; however, generating microislands by spraying produces islands of non-uniform size and thus cultures vary widely in the number of islands containing single neurons. To address these problems, we developed a high-throughput method for reliably generating uniformly shaped microislands of culture substrate. Stamp molds formed of poly(dimethylsiloxane) (PDMS) were fabricated with arrays of circles and used to generate stamps made of 9.2\% agarose. The agarose stamps were capable of loading sufficient poly D-lysine and collagen dissolved in acetic acid to rapidly generate coverslips containing at least 64 microislands per coverslip. When hippocampal neurons were cultured on these coverslips, there were significantly more single-neuron islands per coverslip. We noted that single neurons tended to form one of three distinct neurite-arbor morphologies, which varied with island size and the location of the cell body on the island. To our surprise, the number of synapses per autaptic neuron did not correlate with arbor shape or island size, suggesting that other factors regulate the number of synapses formed by isolated neurons. The stamping method we report can be used to increase the number of single-neuron islands per culture and aid in the rapid visualization of microislands.

}, keywords = {Animals, Cell Communication, Cell Culture Techniques, Cells, Cultured, Dendrites, Hippocampus, Mice, Neurons, Synapses, Synaptic Transmission}, issn = {1872-678X}, doi = {10.1016/j.jneumeth.2011.04.012}, author = {Sgro, Allyson E and Nowak, Amy L and Austin, Naola S and Custer, Kenneth L and Allen, Peter B and Chiu, Daniel T and Bajjalieh, Sandra M} } @article {1093, title = {Histochemistry: live and in color.}, journal = {The Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society}, volume = {59}, year = {2011}, month = {2011 Feb}, pages = {139-45}, abstract = {

Histochemistry (chemistry in the context of biological tissue) is an invaluable set of techniques used to visualize biological structures. This field lies at the interface of organic chemistry, biochemistry, and biology. Integration of these disciplines over the past century has permitted the imaging of cells and tissues using microscopy. Today, by exploiting the unique chemical environments within cells, heterologous expression techniques, and enzymatic activity, histochemical methods can be used to visualize structures in living matter. This review focuses on the labeling techniques and organic fluorophores used in live cells.

}, issn = {1551-5044}, doi = {10.1369/0022155410395760}, author = {Lavis, Luke D} } @article {4302, title = {HMMER web server: interactive sequence similarity searching.}, journal = {Nucleic Acids Research}, volume = {39}, year = {2011}, month = {2011 Jul}, pages = {W29-37}, abstract = {

HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them.

}, keywords = {Internet, Protein, Sequence Alignment, Sequence Analysis, Software}, issn = {1362-4962}, doi = {10.1093/nar/gkr367}, author = {Finn, Robert D and Clements, Jody and Eddy, Sean R.} } @article {6358, title = {Hox gene Ultrabithorax regulates distinct sets of target genes at successive stages of Drosophila haltere morphogenesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Feb 15}, pages = {2855-60}, abstract = {

Hox genes encode highly conserved transcription factors that regionalize the animal body axis by controlling complex developmental processes. Although they are known to operate in multiple cell types and at different stages, we are still missing the batteries of genes targeted by any one Hox gene over the course of a single developmental process to achieve a particular cell and organ morphology. The transformation of wings into halteres by the Hox gene Ultrabithorax (Ubx) in Drosophila melanogaster presents an excellent model system to study the Hox control of transcriptional networks during successive stages of appendage morphogenesis and cell differentiation. We have used an inducible misexpression system to switch on Ubx in the wing epithelium at successive stages during metamorphosis{\textendash}in the larva, prepupa, and pupa. We have then used extensive microarray expression profiling and quantitative RT-PCR to identify the primary transcriptional responses to Ubx. We find that Ubx targets range from regulatory genes like transcription factors and signaling components to terminal differentiation genes affecting a broad repertoire of cell behaviors and metabolic reactions. Ubx up- and down-regulates hundreds of downstream genes at each stage, mostly in a subtle manner. Strikingly, our analysis reveals that Ubx target genes are largely distinct at different stages of appendage morphogenesis, suggesting extensive interactions between Hox genes and hormone-controlled regulatory networks to orchestrate complex genetic programs during metamorphosis.

}, keywords = {Animals, Cluster Analysis, Developmental, Drosophila, Drosophila Proteins, Fluorescent Antibody Technique, Gene Expression Regulation, Gene Regulatory Networks, Homeodomain Proteins, In Situ Hybridization, Life Cycle Stages, Microarray Analysis, Morphogenesis, Reverse Transcriptase Polymerase Chain Reaction, Transcription Factors, Wing}, issn = {1091-6490}, doi = {10.1073/pnas.1015077108}, author = {Pavlopoulos, Anastasios and Akam, Michael} } @article {46424, title = {Hts/Adducin controls synaptic elaboration and elimination.}, journal = {Neuron}, volume = {69}, year = {2011}, month = {2011 Mar 24}, pages = {1114-31}, abstract = {

Neural development requires both synapse elaboration and elimination, yet relatively little is known about how these opposing activities are coordinated. Here, we provide evidence Hts/Adducin can serve this function. We show that Drosophila Hts/Adducin is enriched both pre- and postsynaptically at the NMJ. We then demonstrate that presynaptic Hts/Adducin is necessary and sufficient to control two opposing processes associated with synapse remodeling: (1) synapse stabilization as determined by light level and ultrastructural and electrophysiological assays and (2) the elaboration of actin-based, filopodia-like protrusions that drive synaptogenesis and growth. Synapse remodeling is sensitive to Hts/Adducin levels, and we provide evidence that the synaptic localization of Hts/Adducin is controlled via phosphorylation. Mechanistically, Drosophila Hts/Adducin protein has actin-capping activity. We propose that phosphorylation-dependent regulation of Hts/Adducin controls the level, localization, and activity of Hts/Adducin, influencing actin-based synapse elaboration and spectrin-based synapse stabilization. Hts/Adducin may define a mechanism to switch between synapse stability and dynamics.

}, keywords = {Actins, Animals, Animals, Genetically Modified, Biological Transport, Blotting, Western, Calmodulin-Binding Proteins, Cytoskeleton, Drosophila, Drosophila Proteins, Electrophysiology, Immunohistochemistry, Microscopy, Electron, Transmission, Phosphorylation, Spectrin, Synapses, Synaptic Transmission}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.02.007}, author = {Pielage, Jan and Bulat, Victoria and Zuchero, J Bradley and Fetter, Richard D and Davis, Graeme W} } @article {3975, title = {Hunger states switch a flip-flop memory circuit via a synaptic AMPK-dependent positive feedback loop.}, journal = {Cell}, volume = {146}, year = {2011}, month = {2011 Sep 16}, pages = {992-1003}, abstract = {

Synaptic plasticity in response to changes in physiologic state is coordinated by hormonal signals across multiple neuronal cell types. Here, we combine cell-type-specific electrophysiological, pharmacological, and optogenetic techniques to dissect neural circuits and molecular pathways controlling synaptic plasticity onto AGRP neurons, a population that regulates feeding. We find that food deprivation elevates excitatory synaptic input, which is mediated by\ a presynaptic positive feedback loop involving AMP-activated protein kinase. Potentiation of glutamate release was triggered by the orexigenic hormone ghrelin and exhibited hysteresis, persisting for hours after ghrelin removal. Persistent activity was reversed by the anorexigenic hormone leptin, and optogenetic photostimulation demonstrated involvement of opioid release from POMC neurons. Based on these experiments, we propose a memory storage device for physiological state constructed from bistable synapses that are flipped between two sustained activity states by transient exposure to hormones signaling energy levels.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2011.07.039}, author = {Yang, Yunlei and Atasoy, Deniz and Su, Helen H and Sternson, Scott M} } @article {46410, title = {The heparin-binding domain of HB-EGF mediates localization to sites of cell-cell contact and prevents HB-EGF proteolytic release.}, journal = {Journal of Cell Science}, volume = {123}, year = {2010}, month = {2010 Jul 1}, pages = {2308-18}, abstract = {

Heparin-binding EGF-like growth factor (HB-EGF) is a ligand for EGF receptor (EGFR) and possesses the ability to signal in juxtacrine, autocrine and/or paracrine mode, with these alternatives being governed by the degree of proteolytic release of the ligand. Although the spatial range of diffusion of released HB-EGF is restricted by binding heparan-sulfate proteoglycans (HSPGs) in the extracellular matrix and/or cellular glycocalyx, ascertaining mechanisms governing non-released HB-EGF localization is also important for understanding its effects. We have employed a new method for independently tracking the localization of the extracellular EGF-like domain of HB-EGF and the cytoplasmic C-terminus. A striking observation was the absence of the HB-EGF transmembrane pro-form from the leading edge of COS-7 cells in a wound-closure assay; instead, this protein localized in regions of cell-cell contact. A battery of detailed experiments found that this localization derives from a trans interaction between extracellular HSPGs and the HB-EGF heparin-binding domain, and that disruption of this interaction leads to increased release of soluble ligand and a switch in cell phenotype from juxtacrine-induced growth inhibition to autocrine-induced proliferation. Our results indicate that extracellular HSPGs serve to sequester the transmembrane pro-form of HB-EGF at the point of cell-cell contact, and that this plays a role in governing the balance between juxtacrine versus autocrine and paracrine signaling.

}, keywords = {Amino Acid Sequence, Amphiregulin, Animals, Cell Communication, Cell Proliferation, Cercopithecus aethiops, COS Cells, EGF Family of Proteins, Glycoproteins, Heparan Sulfate Proteoglycans, Heparin, Heparin-binding EGF-like Growth Factor, Intercellular Junctions, Intercellular Signaling Peptides and Proteins, Mice, Molecular Sequence Data, Mutation, Peptides, Protein Precursors, Protein Structure, Tertiary}, issn = {1477-9137}, doi = {10.1242/jcs.058321}, author = {Prince, Robin N and Schreiter, Eric R and Zou, Peng and Wiley, H Steven and Ting, Alice Y and Lee, Richard T and Lauffenburger, Douglas A} } @article {4286, title = {Hidden Markov model speed heuristic and iterative HMM search procedure.}, journal = {BMC Bioinformatics}, volume = {11}, year = {2010}, month = {2010}, pages = {431}, abstract = {

Profile hidden Markov models (profile-HMMs) are sensitive tools for remote protein homology detection, but the main scoring algorithms, Viterbi or Forward, require considerable time to search large sequence databases.

}, keywords = {Algorithms, Artificial Intelligence, Base Sequence, Databases, Markov Chains, Protein, Proteins, Sequence Alignment, Software}, issn = {1471-2105}, doi = {10.1186/1471-2105-11-431}, author = {Johnson, L Steven and Eddy, Sean R. and Portugaly, Elon} } @article {5691, title = {A high-level 3D visualization API for Java and ImageJ.}, journal = {BMC Bioinformatics}, volume = {11}, year = {2010}, month = {2010}, pages = {274}, abstract = {

Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set.

}, keywords = {Automated, Computer Graphics, Computer-Assisted, Confocal, Image Interpretation, Imaging, Microscopy, Pattern Recognition, Programming Languages, Software, Three-Dimensional}, issn = {1471-2105}, doi = {10.1186/1471-2105-11-274}, author = {Schmid, Benjamin and Schindelin, Johannes and Cardona, Albert and Longair, Mark and Heisenberg, Martin.} } @article {5481, title = {Happyhour, a Ste20 family kinase, implicates EGFR signaling in ethanol-induced behaviors.}, journal = {Cell}, volume = {137}, year = {2009}, month = {2009 May 29}, pages = {949-60}, abstract = {

The consequences of alcohol use disorders (AUDs) are devastating to individuals and society, yet few treatments are currently available. To identify genes regulating the behavioral effects of ethanol, we conducted a genetic screen in Drosophila and identified a mutant, happyhour (hppy), due to its increased resistance to the sedative effects of ethanol. Hppy protein shows strong homology to mammalian Ste20 family kinases of the GCK-1 subfamily. Genetic and biochemical experiments revealed that the epidermal growth factor (EGF)-signaling pathway regulates ethanol sensitivity in Drosophila and that Hppy functions as an inhibitor of the pathway. Acute pharmacological inhibition of the EGF receptor (EGFR) in adult animals altered acute ethanol sensitivity in both flies and mice and reduced ethanol consumption in a preclinical rat model of alcoholism. Inhibitors of the EGFR or components of its signaling pathway are thus potential pharmacotherapies for AUDs.

}, keywords = {Alcohol-Induced Disorders, Animal, Animals, Crosses, Disease Models, Dopamine, Drosophila melanogaster, Drosophila Proteins, Epidermal Growth Factor, Ethanol, Female, Genetic, Insulin, Male, Mice, Mutation, Phosphorylation, Protein-Serine-Threonine Kinases, Receptor, Signal Transduction}, issn = {1097-4172}, doi = {10.1016/j.cell.2009.03.020}, author = {Corl, Ammon B and Berger, Karen H and Ophir-Shohat, Galit and Gesch, Julie and Simms, Jeffrey A and Bartlett, Selena E and Heberlein, Ulrike} } @article {1343, title = {Head-anchored whole-cell recordings in freely moving rats.}, journal = {Nature Protocols}, volume = {4}, year = {2009}, month = {2009}, pages = {385-92}, abstract = {

Intracellular recordings are routinely used to study the synaptic and intrinsic properties of neurons in vitro. A key requirement for these recordings is a mechanically very stable preparation; thus their use in vivo had been limited previously to head-restrained animals. We have recently demonstrated that anchoring the electrode rigidly in place with respect to the skull provides sufficient stabilization for long-lasting, high-quality whole-cell recordings in awake, freely moving rats. This protocol describes our procedure in detail, adds specific instructions for targeting hippocampal CA1 pyramidal neurons and updates it with changes that facilitate patching and improve the success rate. The changes involve combining a standard, nonhead-mounted micromanipulator with a gripper to firmly hold the recording pipette during the anchoring process then gently release it afterwards. The procedure from the beginning of surgery to the end of a recording takes approximately 5 h. This technique allows new studies of the mechanisms underlying neuronal integration and cellular/synaptic plasticity in identified cells during natural behaviors.

}, keywords = {Animals, Brain, Electrodes, Implanted, Neurology, Neurons, Patch-Clamp Techniques, Rats, Wakefulness}, issn = {1750-2799}, doi = {10.1038/nprot.2009.5}, author = {Lee, Albert K and Epsztein, J{\'e}r{\^o}me and Brecht, Michael} } @article {5758, title = {High-throughput ethomics in large groups of Drosophila.}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 Jun}, pages = {451-7}, abstract = {

We present a camera-based method for automatically quantifying the individual and social behaviors of fruit flies, Drosophila melanogaster, interacting in a planar arena. Our system includes machine-vision algorithms that accurately track many individuals without swapping identities and classification algorithms that detect behaviors. The data may be represented as an ethogram that plots the time course of behaviors exhibited by each fly or as a vector that concisely captures the statistical properties of all behaviors displayed in a given period. We found that behavioral differences between individuals were consistent over time and were sufficient to accurately predict gender and genotype. In addition, we found that the relative positions of flies during social interactions vary according to gender, genotype and social environment. We expect that our software, which permits high-throughput screening, will complement existing molecular methods available in Drosophila, facilitating new investigations into the genetic and cellular basis of behavior.

}, keywords = {Animal, Animals, Artificial Intelligence, Automated, Behavior, Computer-Assisted, Drosophila melanogaster, Humans, Image Interpretation, Monitoring, Movement, Pattern Recognition, Physiologic, Posture, Social Behavior}, issn = {1548-7105}, doi = {10.1038/nmeth.1328}, author = {Branson, Kristin and Robie, Alice A and Bender, John and Perona, Pietro and Dickinson, Michael H} } @article {4409, title = {How different are recently diverged species?: more than 150 phenotypic differences have been reported for the D. melanogaster species subgroup.}, journal = {Fly}, volume = {3}, year = {2009}, month = {2009 Apr-Jun}, pages = {117}, keywords = {Animals, Drosophila melanogaster, Genetic Speciation, Phenotype, Species Specificity}, issn = {1933-6942}, author = {Orgogozo, Virginie and Stern, David L} } @article {5237, title = {Hydrogen peroxide stimulates activity and alters behavior in Drosophila melanogaster.}, journal = {PLoS One}, volume = {4}, year = {2009}, month = {2009 Oct 28}, pages = {e7580}, abstract = {

Circadian rhythms in animals are regulated at the level of individual cells and by systemic signaling to coordinate the activities of multiple tissues. The circadian pacemakers have several physiological outputs, including daily locomotor rhythms. Several redox-active compounds have been found to function in regulation of circadian rhythms in cells, however, how particular compounds might be involved in regulating specific animal behaviors remains largely unknown. Here the effects of hydrogen peroxide on Drosophila movement were analyzed using a recently developed three-dimensional real-time multiple fly tracking assay. Both hydrogen peroxide feeding and direct injection of hydrogen peroxide caused increased adult fly locomotor activity. Continuous treatment with hydrogen peroxide also suppressed daily locomotor rhythms. Conditional over-expression of the hydrogen peroxide-producing enzyme superoxide dismutase (SOD) also increased fly activity and altered the patterns of locomotor activity across days and weeks. The real-time fly tracking system allowed for detailed analysis of the effects of these manipulations on behavior. For example, both hydrogen peroxide feeding and SOD over-expression increased all fly motion parameters, however, hydrogen peroxide feeding caused relatively more erratic movement, whereas SOD over-expression produced relatively faster-moving flies. Taken together, the data demonstrate that hydrogen peroxide has dramatic effects on fly movement and daily locomotor rhythms, and implicate hydrogen peroxide in the normal control of these processes.

}, keywords = {Animal, Animals, Behavior, Biological, Crosses, Drosophila melanogaster, Flight, Fluorescence, Genetic, Genetically Modified, Hydrogen Peroxide, Microscopy, Models, Movement, Oxidants, Oxidation-Reduction, Seasons, Superoxide Dismutase, Time Factors}, issn = {1932-6203}, doi = {10.1371/journal.pone.0007580}, author = {Grover, Dhruv and Ford, Daniel and Brown, Christopher and Hoe, Nicholas and Erdem, Aysen and Tavar{\'e}, Simon and Tower, John} } @conference {3298, title = {High speed action recognition and localization in compressed domain videos.}, booktitle = {IEEE Transactions on Circuits and Systems for Video Technology: Special issue on Video Surveillance}, year = {2008}, month = {2008 Aug}, abstract = {

We present a compressed domain scheme that is able to recognize and localize actions at high speeds. The recognition problem is posed as performing an action video query on a test video sequence. Our method is based on computing motion similarity using compressed domain features which can be extracted with low complexity. We introduce a novel motion correlation measure that takes into account differences in motion directions and magnitudes. Our method is appearance invariant, requires no prior segmentation, alignment or stabilization, and is able to localize actions in both space and time. We evaluated our method on a benchmark action video database consisting of 6 actions performed by 25 people under 3 different scenarios. Our proposed method achieved a classification accuracy of 90\%, comparing favorably with existing methods in action classification accuracy, and is able to localize a template video of 80 x 64 pixels with 23 frames in a test video of 368 x 184 pixels with 835 frames in just 11 seconds, easily outperforming other methods in localization speed. We also perform a systematic investigation of the effects of various encoding options on our proposed approach. In particular, we present results on the compression-classification trade-off, which would provide valuable insight into jointly designing a system that performs video encoding at the camera front-end and action classification at the processing backend.

}, author = {Yeo, C and Ahammad, Parvez and Ramchandran, K and Sastry, S} } @article {2080, title = {High-density mapping of single-molecule trajectories with photoactivated localization microscopy. (With commentary)}, journal = {Nature Methods}, volume = {5}, year = {2008}, month = {2008 Feb}, pages = {155-7}, abstract = {

We combined photoactivated localization microscopy (PALM) with live-cell single-particle tracking to create a new method termed sptPALM. We created spatially resolved maps of single-molecule motions by imaging the membrane proteins Gag and VSVG, and obtained several orders of magnitude more trajectories per cell than traditional single-particle tracking enables. By probing distinct subsets of molecules, sptPALM can provide insight into the origins of spatial and temporal heterogeneities in membranes.

Commentary: As a stepping stone to true live cell PALM (see above), our collaborator Jennifer Lippincott-Schwartz suggested using the sparse photoactivation principle of PALM to track the nanoscale motion of thousands of individual molecules within a single living cell. Termed single particle tracking PALM (sptPALM), Jennifer{\textquoteright}s postdocs Suliana Manley and Jen Gillette used the method in our PALM rig to create spatially resolved maps of diffusion rates in the plasma membrane of live cells. sptPALM is a powerful tool to study the active cytoskeletal or passive diffusional transport of individual molecules with far more measurements per cell than is possible without sparse photoactivation.

}, keywords = {Animals, Cercopithecus aethiops, COS Cells, Fluorescence, Image Enhancement, Membrane Proteins, Microscopy}, issn = {1548-7105}, doi = {10.1038/nmeth.1176}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18193054}, author = {Manley, Suliana and Gillette, Jennifer M and Patterson, George H and Shroff, Hari and Hess, Harald F and Betzig, Eric and Lippincott-Schwartz, Jennifer} } @article {1098, title = {A highly sensitive fluorogenic probe for cytochrome P450 activity in live cells.}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {18}, year = {2008}, month = {2008 Nov 15}, pages = {5864-6}, abstract = {

A derivative of rhodamine 110 has been designed and assessed as a probe for cytochrome P450 activity. This probe is the first to utilize a {\textquoteright}trimethyl lock{\textquoteright} that is triggered by cleavage of an ether bond. In vitro, fluorescence was manifested by the CYP1A1 isozyme with k(cat)/K(M)=8.8x10(3)M(-1)s(-1) and K(M)=0.09microM. In cellulo, the probe revealed the induction of cytochrome P450 activity by the carcinogen 2,3,7,8-tetrachlorodibenzo-p-dioxin, and its repression by the chemoprotectant resveratrol.

}, keywords = {Cytochrome P-450 CYP1A1, Cytochrome P-450 Enzyme System, Fluorescent Dyes, Humans, Isoenzymes, Molecular Structure, Prodrugs, Rhodamines, Stilbenes, Structure-Activity Relationship, Tetrachlorodibenzodioxin}, issn = {1464-3405}, doi = {10.1016/j.bmcl.2008.06.015}, author = {Yatzeck, Melissa M and Lavis, Luke D and Chao, Tzu-Yuan and Chandran, Sunil S and Raines, Ronald T} } @article {2081, title = {High-speed, low-photodamage nonlinear imaging using passive pulse splitters. (With commentary)}, journal = {Nature Methods}, volume = {5}, year = {2008}, month = {2008 Feb}, pages = {197-202}, abstract = {

Pulsed lasers are key elements in nonlinear bioimaging techniques such as two-photon fluorescence excitation (TPE) microscopy. Typically, however, only a percent or less of the laser power available can be delivered to the sample before photoinduced damage becomes excessive. Here we describe a passive pulse splitter that converts each laser pulse into a fixed number of sub-pulses of equal energy. We applied the splitter to TPE imaging of fixed mouse brain slices labeled with GFP and show that, in different power regimes, the splitter can be used either to increase the signal rate more than 100-fold or to reduce the rate of photobleaching by over fourfold. In living specimens, the gains were even greater: a ninefold reduction in photobleaching during in vivo imaging of Caenorhabditis elegans larvae, and a six- to 20-fold decrease in the rate of photodamage during calcium imaging of rat hippocampal brain slices.

Commentary: Na Ji came to me early in her postdoc with an idea to reduce photodamage in nonlinear microscopy by splitting the pulses from an ultrafast laser into multiple subpulses of reduced energy. In six weeks, we constructed a prototype pulse splitter and obtained initial results confirming the validity of her vision. Further experiments with Jeff Magee demonstrated that the splitter could be used to increase imaging speed or reduce photodamage in two photon microscopy by one to two orders of magnitude. This project is a great example of how quickly one can react and exploit new ideas in the Janelia environment.

}, keywords = {Animals, Caenorhabditis elegans, Cell Survival, Cells, Cultured, Equipment Design, Equipment Failure Analysis, Fluorescence, Image Enhancement, Lasers, Light, Lighting, Mice, Microscopy, Nonlinear Dynamics, Rats}, issn = {1548-7105}, doi = {10.1038/nmeth.1175}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18204458}, author = {Ji, Na and Magee, Jeffrey C and Betzig, Eric} } @article {3916, title = {High-speed, low-photodamage nonlinear imaging using passive pulse splitters.}, journal = {Nature Methods}, volume = {5}, year = {2008}, month = {2008 Feb}, pages = {197-202}, abstract = {

Pulsed lasers are key elements in nonlinear bioimaging techniques such as two-photon fluorescence excitation (TPE) microscopy. Typically, however, only a percent or less of the laser power available can be delivered to the sample before photoinduced damage becomes excessive. Here we describe a passive pulse splitter that converts each laser pulse into a fixed number of sub-pulses of equal energy. We applied the splitter to TPE imaging of fixed mouse brain slices labeled with GFP and show that, in different power regimes, the splitter can be used either to increase the signal rate more than 100-fold or to reduce the rate of photobleaching by over fourfold. In living specimens, the gains were even greater: a ninefold reduction in photobleaching during in vivo imaging of Caenorhabditis elegans larvae, and a six- to 20-fold decrease in the rate of photodamage during calcium imaging of rat hippocampal brain slices.

}, keywords = {Animals, Caenorhabditis elegans, Cell Survival, Cells, Cultured, Equipment Design, Equipment Failure Analysis, Fluorescence, Image Enhancement, Lasers, Light, Lighting, Mice, Microscopy, Nonlinear Dynamics, Rats}, issn = {1548-7105}, doi = {10.1038/nmeth.1175}, author = {Ji, Na and Magee, Jeffrey C and Betzig, Eric} } @article {4047, title = {HCN1 channels constrain synaptically evoked Ca2+ spikes in distal dendrites of CA1 pyramidal neurons.}, journal = {Neuron}, volume = {56}, year = {2007}, month = {2007 Dec 20}, pages = {1076-89}, abstract = {

HCN1 hyperpolarization-activated cation channels act as an inhibitory constraint of both spatial learning and synaptic integration and long-term plasticity in the distal dendrites of hippocampal CA1 pyramidal neurons. However, as HCN1 channels provide an excitatory current, the mechanism of their inhibitory action remains unclear. Here we report that HCN1 channels also constrain CA1 distal dendritic Ca2+ spikes, which have been implicated in the induction of LTP at distal excitatory synapses. Our experimental and computational results indicate that HCN1 channels provide both an active shunt conductance that decreases the temporal integration of distal EPSPs and a tonic depolarizing current that increases resting inactivation of T-type and N-type voltage-gated Ca2+ channels, which contribute to the Ca2+ spikes. This dual mechanism may provide a general means by which HCN channels regulate dendritic excitability.

}, keywords = {Animals, Calcium, Calcium Channel Blockers, Computer Simulation, Cyclic Nucleotide-Gated Cation Channels, Dendrites, Dose-Response Relationship, Electric Stimulation, Excitatory Amino Acid Antagonists, Excitatory Postsynaptic Potentials, Hippocampus, Knockout, Mice, Newborn, Patch-Clamp Techniques, Potassium Channels, Pyramidal Cells, Pyrimidines, Radiation, Reaction Time, Synapses}, issn = {0896-6273}, doi = {10.1016/j.neuron.2007.11.015}, author = {Tsay, David and Dudman, Joshua T and Siegelbaum, Steven A} } @article {4050, title = {HCN1 channels control resting and active integrative properties of stellate cells from layer II of the entorhinal cortex.}, journal = {The Journal of Neuroscience}, volume = {27}, year = {2007}, month = {2007 Nov 14}, pages = {12440-51}, abstract = {

Whereas recent studies have elucidated principles for representation of information within the entorhinal cortex, less is known about the molecular basis for information processing by entorhinal neurons. The HCN1 gene encodes ion channels that mediate hyperpolarization-activated currents (I(h)) that control synaptic integration and influence several forms of learning and memory. We asked whether hyperpolarization-activated, cation nonselective 1 (HCN1) channels control processing of information by stellate cells found within layer II of the entorhinal cortex. Axonal projections from these neurons form a major component of the synaptic input to the dentate gyrus of the hippocampus. To determine whether HCN1 channels control either the resting or the active properties of stellate neurons, we performed whole-cell recordings in horizontal brain slices prepared from adult wild-type and HCN1 knock-out mice. We found that HCN1 channels are required for rapid and full activation of hyperpolarization-activated currents in stellate neurons. HCN1 channels dominate the membrane conductance at rest, are not required for theta frequency (4-12 Hz) membrane potential fluctuations, but suppress low-frequency (\<4 Hz) components of spontaneous and evoked membrane potential activity. During sustained activation of stellate cells sufficient for firing of repeated action potentials, HCN1 channels control the pattern of spike output by promoting recovery of the spike afterhyperpolarization. These data suggest that HCN1 channels expressed by stellate neurons in layer II of the entorhinal cortex are key molecular components in the processing of inputs to the hippocampal dentate gyrus, with distinct integrative roles during resting and active states.

}, keywords = {Action Potentials, Animals, Cyclic Nucleotide-Gated Cation Channels, Dentate Gyrus, Entorhinal Cortex, Female, Ion Channel Gating, Knockout, Male, Membrane Potentials, Memory, Mice, Neural Inhibition, Neural Pathways, Neurons, Organ Culture Techniques, Patch-Clamp Techniques, Potassium Channels, Synaptic Membranes, Synaptic Transmission, Theta Rhythm}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2358-07.2007}, author = {Nolan, Matthew F and Dudman, Joshua T and Dodson, Paul D and Santoro, Bina} } @article {6362, title = {Hox go omics: insights from Drosophila into Hox gene targets.}, journal = {Genome Biology}, volume = {8}, year = {2007}, month = {2007}, pages = {208}, abstract = {

Genetic studies of the targets of the Hox genes have revealed only the tip of the iceberg. Recent microarray studies that have identified hundreds more transcriptional responses to Hox genes in Drosophila will help elucidate the role of Hox genes in development and evolution.

}, keywords = {Animals, Drosophila, Genes, Genetic, Homeobox, Microarray Analysis, Transcription}, issn = {1465-6914}, doi = {10.1186/gb-2007-8-3-208}, author = {Pavlopoulos, Anastasios and Akam, Michael} } @article {2670, title = {Huntingtin-interacting protein 14, a palmitoyl transferase required for exocytosis and targeting of CSP to synaptic vesicles.}, journal = {The Journal of Cell Biology}, volume = {179}, year = {2007}, month = {2007 Dec 31}, pages = {1481-96}, abstract = {

Posttranslational modification through palmitoylation regulates protein localization and function. In this study, we identify a role for the Drosophila melanogaster palmitoyl transferase Huntingtin-interacting protein 14 (HIP14) in neurotransmitter release. hip14 mutants show exocytic defects at low frequency stimulation and a nearly complete loss of synaptic transmission at higher temperature. Interestingly, two exocytic components known to be palmitoylated, cysteine string protein (CSP) and SNAP25, are severely mislocalized at hip14 mutant synapses. Complementary DNA rescue and localization experiments indicate that HIP14 is required solely in the nervous system and is essential for presynaptic function. Biochemical studies indicate that HIP14 palmitoylates CSP and that CSP is not palmitoylated in hip14 mutants. Furthermore, the hip14 exocytic defects can be suppressed by targeting CSP to synaptic vesicles using a chimeric protein approach. Our data indicate that HIP14 controls neurotransmitter release by regulating the trafficking of CSP to synapses.

}, keywords = {Acyltransferases, Adaptor Proteins, Animals, Drosophila melanogaster, Drosophila Proteins, Exocytosis, Ganglia, Invertebrate, Nerve Tissue Proteins, Nervous System, Neuromuscular Junction, Neurotransmitter Agents, Post-Translational, Protein Processing, Protein Transport, Signal Transducing, Synaptic Transmission, Synaptic Vesicles}, issn = {1540-8140}, doi = {10.1083/jcb.200710061}, author = {Ohyama, Tomoko and Verstreken, Patrik and Ly, Cindy V and Rosenmund, Tanja and Rajan, Akhila and Tien, An-Chi and Haueter, Claire and Schulze, Karen L and Bellen, Hugo J} } @article {4440, title = {Hysteresis phenomena of the intelligent driver model for traffic flow.}, journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics}, volume = {76}, year = {2007}, month = {2007 Jul}, pages = {016105}, abstract = {

We present hysteresis phenomena of the intelligent driver model for traffic flow in a circular one-lane roadway. We show that the microscopic structure of traffic flow is dependent on its initial state by plotting the fraction of congested vehicles over the density, which shows a typical hysteresis loop, and by investigating the trajectories of vehicles on the velocity-over-headway plane. We find that the trajectories of vehicles on the velocity-over-headway plane, which usually show a hysteresis loop, include multiple loops. We also point out the relations between these hysteresis loops and the congested jams or high-density clusters in traffic flow.

}, issn = {1539-3755}, author = {Dahui, Wang and Ziqiang, Wei and Ying, Fan} } @article {45749, title = {High-resolution quantitative trait locus mapping reveals sign epistasis controlling ovariole number between two Drosophila species.}, journal = {Genetics}, volume = {173}, year = {2006}, month = {2006 May}, pages = {197-205}, abstract = {

Identifying the genes underlying genetically complex traits is of fundamental importance for medicine, agriculture, and evolutionary biology. However, the level of resolution offered by traditional quantitative trait locus (QTL) mapping is usually coarse. We analyze here a trait closely related to fitness, ovariole number. Our initial interspecific mapping between Drosophila sechellia (8 ovarioles/ovary) and D. simulans (15 ovarioles/ovary) identified a major QTL on chromosome 3 and a minor QTL on chromosome 2. To refine the position of the major QTL, we selected 1038 additional recombinants in the region of interest using flanking morphological markers (selective phenotyping). This effort generated approximately one recombination event per gene and increased the mapping resolution by approximately seven times. Our study thus shows that using visible markers to select for recombinants can efficiently increase the resolution of QTL mapping. We resolved the major QTL into two epistatic QTL, QTL3a and QTL3b. QTL3a shows sign epistasis: it has opposite effects in two different genetic backgrounds, the presence vs. the absence of the QTL3b D. sechellia allele. This property of QTL3a allows us to reconstruct the probable order of fixation of the QTL alleles during evolution.

}, keywords = {Animals, Chromosome Mapping, Chromosomes, Crosses, Genetic, Drosophila, Epistasis, Genetic, Evolution, Molecular, Female, Ovary, Quantitative Trait Loci}, issn = {0016-6731}, doi = {10.1534/genetics.105.054098}, author = {Orgogozo, Virginie and Broman, Karl W and Stern, David L} } @article {48655, title = {High-speed pollen release in the white mulberry tree, Morus alba L.}, journal = {Sexual Plant Reproduction}, volume = {19}, year = {2006}, month = {2006 Mar}, pages = {19-24}, abstract = {

Anemophilous plants described as catapulting pollen explosively into the air have rarely attracted detailed examination. We investigated floral anthesis in a male mulberry tree with high-speed video and a force probe. The stamen was inflexed within the floral bud. Exposure to dry air initially resulted in a gradual movement of the stamen. This caused fine threads to tear at the stomium, ensuring dehiscence of the anther, and subsequently enabled the anther to slip off a restraining pistillode. The sudden release of stored elastic energy in the spring-like filament drove the stamen to straighten in less than 25\ μs, and reflex the petals to velocities in excess of half the speed of sound. This is the fastest motion yet observed in biology, and approaches the theoretical physical limits for movements in plants.

}, doi = {10.1007/s00497-005-0018-9}, author = {Taylor, Philip E and Card, Gwyneth M and House, James and Dickinson, Michael H and Flagan, Richard C} } @article {6353, title = {Hyperpolarization-activated cation current (Ih) is an ethanol target in midbrain dopamine neurons of mice.}, journal = {Journal of Neurophysiology}, volume = {95}, year = {2006}, month = {2006 Feb}, pages = {619-26}, abstract = {

Ethanol stimulates the firing activity of midbrain dopamine (DA) neurons, leading to enhanced dopaminergic transmission in the mesolimbic system. This effect is thought to underlie the behavioral reinforcement of alcohol intake. Ethanol has been shown to directly enhance the intrinsic pacemaker activity of DA neurons, yet the cellular mechanism mediating this excitation remains poorly understood. The hyperpolarization-activated cation current, Ih, is known to contribute to the pacemaker firing of DA neurons. To determine the role of Ih in ethanol excitation of DA neurons, we performed patch-clamp recordings in acutely prepared mouse midbrain slices. Superfusion of ethanol increased the spontaneous firing frequency of DA neurons in a reversible fashion. Treatment with ZD7288, a blocker of Ih, irreversibly depressed basal firing frequency and significantly attenuated the stimulatory effect of ethanol on firing. Furthermore, ethanol reversibly augmented Ih amplitude and accelerated its activation kinetics. This effect of ethanol was accompanied by a shift in the voltage dependence of Ih activation to more depolarized potentials and an increase in the maximum Ih conductance. Cyclic AMP mediated the depolarizing shift in Ih activation but not the increase in the maximum conductance. Finally, repeated ethanol treatment in vivo induced downregulation of Ih density in DA neurons and an accompanying reduction in the magnitude of ethanol stimulation of firing. These results suggest an important role of Ih in the reinforcing actions of ethanol and in the neuroadaptations underlying escalation of alcohol consumption associated with alcoholism.

}, keywords = {Action Potentials, Animals, Antiporters, Biological Clocks, Dopamine, Ethanol, Inbred C57BL, Ion Channel Gating, Membrane Potentials, Mesencephalon, Mice, Neurons}, issn = {0022-3077}, doi = {10.1152/jn.00682.2005}, author = {Okamoto, Takashi and Harnett, Mark T and Morikawa, Hitoshi} } @article {5489, title = {The hangover gene defines a stress pathway required for ethanol tolerance development.}, journal = {Nature}, volume = {436}, year = {2005}, month = {2005 Aug 11}, pages = {845-7}, abstract = {

Repeated alcohol consumption leads to the development of tolerance, simply defined as an acquired resistance to the physiological and behavioural effects of the drug. This tolerance allows increased alcohol consumption, which over time leads to physical dependence and possibly addiction. Previous studies have shown that Drosophila develop ethanol tolerance, with kinetics of acquisition and dissipation that mimic those seen in mammals. This tolerance requires the catecholamine octopamine, the functional analogue of mammalian noradrenaline. Here we describe a new gene, hangover, which is required for normal development of ethanol tolerance. hangover flies are also defective in responses to environmental stressors, such as heat and the free-radical-generating agent paraquat. Using genetic epistasis tests, we show that ethanol tolerance in Drosophila relies on two distinct molecular pathways: a cellular stress pathway defined by hangover, and a parallel pathway requiring octopamine. hangover encodes a large nuclear zinc-finger protein, suggesting a role in nucleic acid binding. There is growing recognition that stress, at both the cellular and systemic levels, contributes to drug- and addiction-related behaviours in mammals. Our studies suggest that this role may be conserved across evolution.

}, keywords = {Alcoholism, Animals, Drosophila melanogaster, Drosophila Proteins, Drug Tolerance, Ethanol, Heat-Shock Response, Mutation, Physiological, Stress, Zinc Fingers}, issn = {1476-4687}, doi = {10.1038/nature03864}, author = {Scholz, Henrike and Franz, Mirjam and Heberlein, Ulrike} } @article {1251, title = {Highly nonrandom features of synaptic connectivity in local cortical circuits.}, journal = {PLoS Biology}, volume = {3}, year = {2005}, month = {2005 Mar}, pages = {e68}, abstract = {

How different is local cortical circuitry from a random network? To answer this question, we probed synaptic connections with several hundred simultaneous quadruple whole-cell recordings from layer 5 pyramidal neurons in the rat visual cortex. Analysis of this dataset revealed several nonrandom features in synaptic connectivity. We confirmed previous reports that bidirectional connections are more common than expected in a random network. We found that several highly clustered three-neuron connectivity patterns are overrepresented, suggesting that connections tend to cluster together. We also analyzed synaptic connection strength as defined by the peak excitatory postsynaptic potential amplitude. We found that the distribution of synaptic connection strength differs significantly from the Poisson distribution and can be fitted by a lognormal distribution. Such a distribution has a heavier tail and implies that synaptic weight is concentrated among few synaptic connections. In addition, the strengths of synaptic connections sharing pre- or postsynaptic neurons are correlated, implying that strong connections are even more clustered than the weak ones. Therefore, the local cortical network structure can be viewed as a skeleton of stronger connections in a sea of weaker ones. Such a skeleton is likely to play an important role in network dynamics and should be investigated further.

}, keywords = {Animals, Cell Communication, Neural Pathways, Neuronal Plasticity, Neurons, Rats, Signal Transduction, Synapses, Visual Cortex}, issn = {1545-7885}, doi = {10.1016/j.tins.2005.05.006}, author = {Song, Sen and Sj{\"o}str{\"o}m, Per Jesper and Reigl, Markus and Nelson, Sacha and Chklovskii, Dmitri B} } @article {2369, title = {How to find decision makers in neural networks.}, journal = {Biological Cybernetics}, volume = {93}, year = {2005}, month = {2005 Dec}, pages = {447-62}, abstract = {

Nervous systems often face the problem of classifying stimuli and making decisions based on these classifications. The neurons involved in these tasks can be characterized as sensory or motor, according to their correlation with sensory stimulus or motor response. In this study we define a third class of neurons responsible for making perceptual decisions. Our mathematical formalism enables the weighting of neuronal units according to their contribution to decision making, thus narrowing the field for more detailed studies of underlying mechanisms. We develop two definitions of a contribution to decision making. The first definition states that decision making activity can be found at the points of emergence for behavioral correlations in the system. The second definition involves the study of propagation of noise in the network. The latter definition is shown to be equivalent to the first one in the cases when they can be compared. Our results suggest a new approach to analyzing decision making networks.

}, keywords = {Animals, Computer Simulation, Decision Making, Electric Stimulation, Humans, Models, Nerve Net, Neural Networks (Computer), Neurological, Neurons, Nonlinear Dynamics, Stochastic Processes}, issn = {0340-1200}, doi = {10.1523/JNEUROSCI.3613-08.2008}, author = {Koulakov, Alexei A and Rinberg, Dmitry A and Tsigankov, Dmitry N} } @article {46634, title = {Habituation of an odorant-induced startle response in Drosophila.}, journal = {Genes, Brain, and Behavior}, volume = {3}, year = {2004}, month = {2004 Jun}, pages = {127-37}, abstract = {

Habituation is a fundamental form of behavioral plasticity that permits organisms to ignore inconsequential stimuli. Here we describe the habituation of a locomotor response to ethanol and other odorants in Drosophila, measured by an automated high-throughput locomotor tracking system. Flies exhibit an immediate and transient startle response upon exposure to a novel odor. Surgical removal of the antennae, the fly{\textquoteright}s major olfactory organs, abolishes this startle response. With repeated discrete exposures to ethanol vapor, the startle response habituates. Habituation is reversible by a mechanical stimulus and is not due to the accumulation of ethanol in the organism, nor to non-specific mechanisms. Ablation or inactivation of the mushroom bodies, central brain structures involved in olfactory and courtship conditioning, results in decreased olfactory habituation. In addition, olfactory habituation to ethanol generalizes to odorants that activate separate olfactory receptors. Finally, habituation is impaired in rutabaga, an adenylyl cyclase mutant isolated based on a defect in olfactory associative learning. These data demonstrate that olfactory habituation operates, at least in part, through central mechanisms. This novel model of olfactory habituation in freely moving Drosophila provides a scalable method for studying the molecular and neural bases of this simple and ubiquitous form of learning.

}, keywords = {Adenylate Cyclase, Animals, Chemoreceptor Cells, Denervation, Drosophila melanogaster, Ethanol, Female, Habituation, Psychophysiologic, Learning, Male, Models, Animal, Motor Activity, Mushroom Bodies, Mutation, Odors, Physical Stimulation, Reflex, Startle, Smell}, issn = {1601-1848}, doi = {10.1111/j.1601-183x.2004.00061.x}, author = {Cho, W and Heberlein, U and Wolf, F W} } @article {2139, title = {Haploinsufficiency at the Nkx3.1 locus. A paradigm for stochastic, dosage-sensitive gene regulation during tumor initiation.}, journal = {Cancer Cell}, volume = {3}, year = {2003}, month = {2003 Mar}, pages = {273-83}, abstract = {

Tumorigenesis requires sequential accumulation of multiple genetic lesions. In the prostate, tumor initiation is often linked to loss of heterozygosity at the Nkx3.1 locus. In mice, loss of even one Nkx3.1 allele causes prostatic epithelial hyperplasia and eventual prostatic intraepithelial neoplasia (PIN) formation. Here we demonstrate that Nkx3.1 allelic loss extends the proliferative stage of regenerating luminal cells, leading to epithelial hyperplasia. Microarray analysis identified Nkx3.1 target genes, many of which show exquisite dosage sensitivity. The number of Nkx3.1 alleles determines the relative probabilities of stochastic activation or inactivation of a given target gene. Thus, loss of a single Nkx3.1 allele likely results in hyperplasia and PIN by increasing the probability of completely inactivating select Nkx3.1-regulated pathways within a subset of affected cells.

}, keywords = {Alleles, Animals, Biological, Cell Division, Gene Deletion, Gene Dosage, Gene Expression Profiling, Gene Expression Regulation, Gene Targeting, Genes, Genetic Predisposition to Disease, Loss of Heterozygosity, Male, Mice, Models, Mutant Strains, Neoplastic, Orchiectomy, Prostatic Intraepithelial Neoplasia, Prostatic Neoplasms, Testosterone, Tumor Suppressor}, issn = {1535-6108}, doi = {10.1002/cbic.201000254}, author = {Magee, Jeffrey A and Abdulkadir, Sarki A and Milbrandt, Jeffrey} } @article {45764, title = {The Hox gene Ultrabithorax modulates the shape and size of the third leg of Drosophila by influencing diverse mechanisms.}, journal = {Dev Biol}, volume = {256}, year = {2003}, month = {2003 Apr 15}, pages = {355-66}, abstract = {

The developmental mechanisms that regulate the relative size and shape of organs have remained obscure despite almost a century of interest in the problem and the fact that changes in relative size represent the dominant mode of evolutionary change. Here, I investigate how the Hox gene Ultrabithorax (Ubx) instructs the legs on the third thoracic segment of Drosophila melanogaster to develop with a different size and shape from the legs on the second thoracic segment. Through loss-of-function and gain-of-function experiments, I demonstrate that different segments of the leg, the femur and the first tarsal segment, and even different regions of the femur, regulate their size in response to Ubx expression through qualitatively different mechanisms. In some regions, Ubx acts autonomously to specify shape and size, whereas in other regions, Ubx influences size through nonautonomous mechanisms. Loss of Ubx autonomously reduces cell size in the T3 femur, but this reduction seems to be partially compensated by an increase in cell numbers, so that it is unclear what effect cell size and number directly have on femur size. Loss of Ubx has both autonomous and nonautonomous effects on cell number in different regions of the basitarsus, but again there is not a strong correlation between cell size or number and organ size. Total organ size appears to be regulated through mechanisms that operate at the level of the entire leg segment (femur or basitarsus) relatively independently of the behavior of individual subpopulations of cells within the segment.

}, keywords = {Animals, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Extremities, Gene Expression Regulation, Developmental, Homeodomain Proteins, Pupa, Transcription Factors}, issn = {0012-1606}, author = {Stern, David L} } @article {2321, title = {The hyperpolarization-activated HCN1 channel is important for motor learning and neuronal integration by cerebellar Purkinje cells.}, journal = {Cell}, volume = {115}, year = {2003}, month = {2003 Nov 26}, pages = {551-64}, abstract = {

In contrast to our increasingly detailed understanding of how synaptic plasticity provides a cellular substrate for learning and memory, it is less clear how a neuron{\textquoteright}s voltage-gated ion channels interact with plastic changes in synaptic strength to influence behavior. We find, using generalized and regional knockout mice, that deletion of the HCN1 channel causes profound motor learning and memory deficits in swimming and rotarod tasks. In cerebellar Purkinje cells, which are a key component of the cerebellar circuit for learning of correctly timed movements, HCN1 mediates an inward current that stabilizes the integrative properties of Purkinje cells and ensures that their input-output function is independent of the previous history of their activity. We suggest that this nonsynaptic integrative function of HCN1 is required for accurate decoding of input patterns and thereby enables synaptic plasticity to appropriately influence the performance of motor activity.

}, keywords = {Action Potentials, Afferent Pathways, Animals, Cells, Conditioning (Psychology), Cultured, Cyclic Nucleotide-Gated Cation Channels, Ion Channels, Knockout, Learning, Maze Learning, Mice, Motor Skills, Movement, Nerve Tissue Proteins, Neuronal Plasticity, Potassium Channels, Purkinje Cells, Synapses, Synaptic Transmission}, issn = {0092-8674}, doi = {10.3389/fnana.2010.00147}, author = {Nolan, Matthew F and Malleret, Ga{\"e}l and Lee, Ka Hung and Gibbs, Emma and Dudman, Joshua T and Santoro, Bina and Yin, Deqi and Thompson, Richard F and Siegelbaum, Steven A and Kandel, Eric R and Morozov, Alexei} } @article {2293, title = {Haemozoin as a marker of placental parasitization.}, journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene}, volume = {96}, year = {2002}, month = {2002 Nov-Dec}, pages = {644-6}, abstract = {

Both Plasmodium vivax and P. falciparum malaria can cause the delivery of low birthweight babies. In this report, we have quantitated haemozoin levels in placentas from women living on the Thai-Burmese border in a region of low transmission for both P. falciparum and P. vivax malaria from June 1995 to January 2000. P. falciparum malaria infections during pregnancy lead to the accumulation of haemozoin (malaria pigment) in the placenta, especially in infections near term and in primigravid pregnancies. Haemozoin concentration was not associated with adverse birth outcomes. Women with P. vivax infections during pregnancy do not have measurable levels of placental haemozoin suggesting that P. vivax-infected erythrocytes do not accumulate in the placenta as much as P. falciparum-infected ones.

}, keywords = {Analysis of Variance, Biological Markers, Falciparum, Female, Hemeproteins, Humans, Infant, Low Birth Weight, Malaria, Newborn, Parasitemia, Parasitic, Placenta, Placenta Diseases, Pregnancy, Pregnancy Complications, Regression Analysis, Vivax}, issn = {0035-9203}, author = {McGready, Rose and Brockman, Alan and Cho, Thein and Levesque, Martin A and Tkachuk, Ariana N and Meshnick, Steven R and Nosten, Fran\c cois} } @article {5492, title = {High-resolution analysis of ethanol-induced locomotor stimulation in Drosophila.}, journal = {The Journal of Neuroscience: The Official Journal of the Society for Neuroscience}, volume = {22}, year = {2002}, month = {2002 Dec 15}, pages = {11035-44}, abstract = {

Understanding how ethanol influences behavior is key to deciphering the mechanisms of ethanol action and alcoholism. In mammals, low doses of ethanol stimulate locomotion, whereas high doses depress it. The acute stimulant effect of ethanol has been proposed to be a manifestation of its rewarding effects. In Drosophila, ethanol exposure transiently potentiates locomotor activity in a biphasic dose- and time-dependent manner. An initial short-lived peak of activity corresponds to an olfactory response to ethanol. A second, longer-lasting period of increased activity coincides with rising internal ethanol concentrations; these closely parallel concentrations that stimulate locomotion in mammals. High-resolution analysis of the walking pattern of individual flies revealed that locomotion consists of bouts of activity; bout structure can be quantified by bout frequency, bout length, and the time spent walking at high speeds. Ethanol exposure induces both dramatic and dynamic changes in bout structure. Mutants with increased ethanol sensitivity show distinct changes in ethanol-induced locomotor behavior, as well as genotype-specific changes in activity bout structure. Thus, the overall effect of ethanol on locomotor behavior in Drosophila is caused by changes in discrete quantifiable parameters of walking pattern. The effects of ethanol on locomotion are comparable in flies and mammals, suggesting that Drosophila is a suitable model system to study the underlying mechanisms.

}, keywords = {Afferent Pathways, Animal, Animals, Automation, Behavior, Cyclic AMP, Dose-Response Relationship, Drosophila, Drug, Ethanol, Kinetics, Locomotion, Male, Mutation, Sensitivity and Specificity}, issn = {1529-2401}, author = {Wolf, Fred W and Rodan, Aylin R and Tsai, Linus T-Y and Heberlein, Ulrike} } @article {2430, title = {Human CRSP interacts with RNA polymerase II CTD and adopts a specific CTD-bound conformation.}, journal = {Genes \& Development}, volume = {16}, year = {2002}, month = {2002 Jun 1}, pages = {1339-44}, abstract = {

Activation of gene transcription in mammalian cells requires several classes of coactivators that participate in different steps of the activation cascade. Using conventional and affinity chromatography, we have isolated a human coactivator complex that interacts directly with the C-terminal domain (CTD) of RNA polymerase II (Pol II). The CTD-binding complex is structurally and functionally indistinguishable from our previously isolated CRSP coactivator complex. The closely related, but transcriptionally inactive, ARC-L complex failed to interact with the CTD, indicating a significant biochemical difference between CRSP and ARC-L that may, in part, explain their functional divergence. Electron microscopy and three-dimensional single-particle reconstruction reveals a conformation for CTD-CRSP that is structurally distinct from unliganded CRSP or CRSP bound to SREBP-1a, but highly similar to CRSP bound to the VP16 activator. Together, our findings suggest that the human CRSP coactivator functions, at least in part, by mediating activator-dependent recruitment of RNA Pol II via the CTD.

}, keywords = {Binding Sites, Chromatin, Electron, Electrophoresis, Genetic, Glutathione Transferase, Hela Cells, Humans, Immunoblotting, Ligands, Microscopy, Models, Molecular, Polyacrylamide Gel, Protein Binding, Protein Conformation, Protein Structure, Recombinant Fusion Proteins, RNA Polymerase II, Tertiary, Trans-Activators, Transcription}, issn = {0890-9369}, doi = {10.1073/pnas.1100640108}, author = {N{\"a}{\"a}r, Anders M and Taatjes, Dylan J and Zhai, Weiguo and Nogales, Eva and Tjian, Robert} } @article {2516, title = {Hormonal regulation and patterning of the broad-complex in the epidermis and wing discs of the tobacco hornworm, Manduca sexta.}, journal = {Developmental Biology}, volume = {231}, year = {2001}, month = {2001 Mar 1}, pages = {125-37}, abstract = {

Expression of Manduca Broad-Complex (BR-C) mRNA in the larval epidermis is under the dual control of ecdysone and juvenile hormone (JH). Immunocytochemistry with antibodies that recognize the core, Z2, and Z4 domains of Manduca BR-C proteins showed that BR-C appearance not only temporally correlates with pupal commitment of the epidermis on day 3 of the fifth (final) larval instar, but also occurs in a strict spatial pattern within the abdominal segment similar to that seen for the loss of sensitivity to JH. Levels of Z2 and Z4 BR-C proteins shift with Z2 predominating at pupal commitment and Z4 dominant during early pupal cuticle synthesis. Both induction of BR-C mRNA in the epidermis by 20-hydroxyecdysone (20E) and its suppression by JH were shown to be independent of new protein synthesis. For suppression JH must be present during the initial exposure to 20E. When JH was given 6 h after 20E, suppression was only seen in those regions that had not yet expressed BR-C. In the wing discs BR-C was first detected earlier 1.5 days after ecdysis, coincident with the pupal commitment of the wing. Our findings suggest that BR-C expression is one of the first molecular events underlying pupal commitment of both epidermis and wing discs.

}, keywords = {Animals, Biological, Drosophila Proteins, Ecdysone, Epidermis, Juvenile Hormones, Manduca, Messenger, Metamorphosis, RNA, Transcription Factors, Wing, Zinc Fingers}, issn = {0012-1606}, doi = {10.1006/dbio.2000.0143}, author = {Zhou, B and Riddiford, L M} } @article {3088, title = {Hippocampal damage induced by carbon monoxide poisoning and spreading depression is alleviated by chronic treatment with brain derived polypeptides.}, journal = {Brain Research}, volume = {816}, year = {1999}, month = {1999 Jan 23}, pages = {618-27}, abstract = {

A model of acute carbon monoxide poisoning combined with spreading depression (SD) induced metabolic stress was used to examine the protective effects of cerebrolysin (CL) on the development of electrophysiological, behavioral and morphological signs of hypoxic damage. Capillary electrodes were implanted into the neocortex and hippocampus of anesthetized rats which were then exposed for 90 min to breathing of 0.8\% to 0.5\% CO, while 3 to 4 waves of cortical and hippocampal SD were elicited by microinjections of 5\% KCl. Duration of SD-provoked depolarization of cerebral cortex and hippocampus was noted. Nine and 18 to 19 days later propagation of SD waves was recorded with the same electrodes and decrease of their amplitude was used as an index of brain damage which was significant in the hippocampus but not in the cortex. CL-treatment (2.5 ml/kg per day) started after CO administration and continued for 14 days significantly improved hippocampal recovery manifested by increased amplitude of SD waves. Behavioral tests performed 10 and 20 days after CO poisoning in the Morris water maze revealed better performance (escape latency 7 s) in the CL-treated than in untreated animals (14 s). Morphological analysis showed marked damage in the hippocampus consonant with electrophysiological and behavioral findings in the same animals. No apparent histological damage was found in rats exposed to CO inhalation alone without the additional SD-provoked depolarization. It is concluded that chronic CL-treatment enhances recovery of hippocampal tissue after hypoxic damage of intermediate severity.

}, keywords = {Acute Disease, Analysis of Variance, Animals, Brain, Carbon Monoxide Poisoning, Cortical Spreading Depression, Electrodes, Hippocampus, Hypoxia, Implanted, Long-Evans, Male, Maze Learning, Membrane Potentials, Neuropeptides, Rats, Reaction Time}, issn = {0006-8993}, author = {Koroleva, V I and Korolev, O S and Mares, V and Pastalkova, E and Bures, J} } @article {2704, title = {Human whole-genome shotgun sequencing.}, journal = {Genome Research}, volume = {7}, year = {1997}, month = {1997 May}, pages = {401-9}, keywords = {Cloning, DNA, Forecasting, Genetic, Genome, Human, Human Genome Project, Humans, Molecular, Polymorphism, Sequence Analysis, Sequence Tagged Sites}, issn = {1088-9051}, author = {Weber, J L and Myers, E W} } @article {1171, title = {A human mitochondrial transcriptional activator can functionally replace a yeast mitochondrial HMG-box protein both in vivo and in vitro.}, journal = {Molecular and Cellular Biology}, volume = {13}, year = {1993}, month = {1993 Mar}, pages = {1951-61}, abstract = {

Human mitochondrial transcription factor A is a 25-kDa protein that binds immediately upstream of the two major mitochondrial promoters, thereby leading to correct and efficient initiation of transcription. Although the nature of yeast mitochondrial promoters is significantly different from that of human promoters, a potential functional homolog of the human transcriptional activator protein has been previously identified in yeast mitochondria. The importance of the yeast protein in yeast mitochondrial DNA function has been shown by inactivation of its nuclear gene (ABF2) in Saccharomyces cerevisiae cells resulting in loss of mitochondrial DNA. We report here that the nuclear gene for human mitochondrial transcription factor A can be stably expressed in yeast cells devoid of the yeast homolog protein. The human protein is imported efficiently into yeast mitochondria, is processed correctly, and rescues the loss-of-mitochondrial DNA phenotype in a yeast abf2 strain, thus functionally substituting for the yeast protein. Both human and yeast proteins affect yeast mitochondrial transcription initiation in vitro, suggesting that the two proteins may have a common role in this fundamental process.

}, keywords = {Amino Acid, Amino Acid Sequence, Base Sequence, Biological Transport, Cell Compartmentation, DNA-Binding Proteins, Genes, Genetic, Humans, Mitochondria, Mitochondrial Proteins, Molecular Sequence Data, Nuclear Proteins, Oxygen Consumption, Post-Translational, Protein Processing, Protein Sorting Signals, Saccharomyces cerevisiae, Sequence Alignment, Sequence Homology, Transcription, Transcription Factors, Transformation}, issn = {0270-7306}, doi = {10.1101/gad.1352105}, author = {Parisi, M A and Xu, B and Clayton, D A} } @article {969, title = {The homeo domain protein rough is expressed in a subset of cells in the developing Drosophila eye where it can specify photoreceptor cell subtype.}, journal = {Genes \& Development}, volume = {4}, year = {1990}, month = {1990 May}, pages = {712-27}, abstract = {

The Drosophila homeo box gene rough is required in photoreceptor cells R2 and R5 for normal eye development. We show here that rough protein expression is limited to a subset of cells in the developing retina where it is transiently expressed for 30-60 hr. The rough protein is first expressed broadly in the morphogenetic furrow but is rapidly restricted to the R2, R3, R4, and R5 precursor cells. Ubiquitous expression of rough under the control of the hsp70 promoter in third-instar larvae suppresses the initial steps of ommatidial assembly. Structures derived from other imaginal discs are not affected. Ectopic expression of rough in the R7 precursor, through the use of the sevenless promoter, causes this cell to develop into an R1-6 photoreceptor subtype; however, this cell still requires sevenless function for its neural differentiation. Taken together with previous analyses of the rough mutant phenotype, these results suggest that the normal role of rough is to establish the unique cell identity of photoreceptors R2 and R5.

}, keywords = {Animals, Base Sequence, Cell Cycle Proteins, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Eye, Gene Expression, Genes, Genetic, Heat-Shock Proteins, Homeobox, Hot Temperature, Microtubule-Associated Proteins, Molecular Sequence Data, Morphogenesis, Phenotype, Photoreceptor Cells, Promoter Regions, Transcription Factors}, issn = {0890-9369}, doi = {10.1186/gb-2007-8-7-r145}, author = {Kimmel, B E and Heberlein, U and Rubin, G M} } @article {2519, title = {Hormonal control of insect epidermal cell commitment in vitro.}, journal = {Nature}, volume = {259}, year = {1976}, month = {1976 Jan 15}, pages = {115-7}, keywords = {Age Factors, Animals, Cell Differentiation, Ecdysone, Insect Hormones, Invertebrate Hormones, Juvenile Hormones, Larva, Lepidoptera, Moths, Pupa, Skin}, issn = {0028-0836}, author = {Riddiford, L M} }