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2363 Janelia Publications

Showing 111-120 of 2363 results
05/02/23 | Meta-learning in head fixed mice navigating in virtual reality: A Behavioral Analysis
Xinyu Zhao , Rachel Gattoni , Andrea Kozlosky , Angela Jacobs , Colin Morrow , Sarah Lindo , Nelson Spruston
bioRxiv. 2023 May 02:. doi: 10.1101/2023.05.01.538936

Animals can learn general task structures and use them to solve new problems with novel sensory specifics. This capacity of ‘learning to learn’, or meta-learning, is difficult to achieve in artificial systems, and the mechanisms by which it is achieved in animals are unknown. As a step toward enabling mechanistic studies, we developed a behavioral paradigm that demonstrates meta-learning in head-fixed mice. We trained mice to perform a two-alternative forced-choice task in virtual reality (VR), and successively changed the visual cues that signaled reward location. Mice showed increased learning speed in both cue generalization and serial reversal tasks. During reversal learning, behavior exhibited sharp transitions, with the transition occurring earlier in each successive reversal. Analysis of motor patterns revealed that animals utilized similar motor programs to execute the same actions in response to different cues but modified the motor programs during reversal learning. Our study demonstrates that mice can perform meta-learning tasks in VR, thus opening up opportunities for future mechanistic studies.

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Sternson Lab
05/01/23 | Modulation of calcium signaling “on demand” to decipher the molecular mechanisms responsible for primary aldosteronism
Fedlaoui B, Cosentino T, Al Sayed ZR, Fernandes-Rosa FL, Hulot J, Magnus C, Sternson SM, Travers-Allard S, Baron S, Giscos-Douriez I, Zennaro MC, Boulkroun S
Archives of Cardiovascular Diseases Supplements. 2023 May 01;15(2):188. doi: 10.1016/j.acvdsp.2023.03.021

Primary aldosteronism (PA) is the most frequent form of secondary hypertension. Over the past two decades, major advances have been made in our understanding of the disease with the identification of germline or somatic mutations in ion channels and pumps. These mutations enhance calcium signaling, the main trigger of aldosterone biosynthesis.

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05/01/23 | Time-tagged ticker tapes for intracellular recordings.
Lin D, Li X, Moult E, Park P, Tang B, Shen H, Grimm JB, Falco N, Jia BZ, Baker D, Lavis LD, Cohen AE
Nature Biotechnology. 2023 May 01;41(5):631-9. doi: 10.1038/s41587-022-01524-7

Recording transcriptional histories of a cell would enable deeper understanding of cellular developmental trajectories and responses to external perturbations. Here we describe an engineered protein fiber that incorporates diverse fluorescent marks during its growth to store a ticker tape-like history. An embedded HaloTag reporter incorporates user-supplied dyes, leading to colored stripes that map the growth of each individual fiber to wall clock time. A co-expressed eGFP tag driven by a promoter of interest records a history of transcriptional activation. High-resolution multi-spectral imaging on fixed samples reads the cellular histories, and interpolation of eGFP marks relative to HaloTag timestamps provides accurate absolute timing. We demonstrate recordings of doxycycline-induced transcription in HEK cells and cFos promoter activation in cultured neurons, with a single-cell absolute accuracy of 30-40 minutes over a 12-hour recording. The protein-based ticker tape design we present here could be generalized to achieve massively parallel single-cell recordings of diverse physiological modalities.

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04/26/23 | The power of peer networking for improving STEM faculty job applications: a successful pilot programme.
Guardia CM, Kane E, Tebo AG, Sanders AA, Kaya D, Grogan KE
Proceedings. Biological Sciences. 2023 Apr 26;290(1997):20230124. doi: 10.1098/rspb.2023.0124

To attain a faculty position, postdoctoral fellows submit job applications that require considerable time and effort to produce. Although mentors and colleagues review these applications, postdocs rarely receive iterative feedback from reviewers with the breadth of expertise typically found on an academic search committee. To address this gap, we describe an international peer-reviewing programme for postdocs across disciplines to receive reciprocal, iterative feedback on faculty applications. A participant survey revealed that nearly all participants would recommend the programme to others. Furthermore, our programme was more likely to attract postdocs who struggled to find mentoring, possibly because of their identity as a woman or member of an underrepresented population in STEM or because they changed fields. Between 2018 and 2021, our programme provided nearly 150 early career academics with a diverse and supportive community of peer mentors during the difficult search for a faculty position and continues to do so today. As the transition from postdoc to faculty represents the largest 'leak' in the academic pipeline, implementation of similar programmes by universities or professional societies would provide psycho-social support necessary to prevent attrition of individuals from underrepresented populations as well as increase the chances of success for early career academics in their search for independence.

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04/25/23 | PEELing: an integrated and user-centric platform for cell-surface proteomics analysis
Xi Peng , Jody Clements , Zuzhi Jiang , Stephan Preibisch , Jiefu Li
bioRxiv. 2023 Apr 25:. doi: 10.1101/2023.04.21.537871

Proteins localized at the cellular interface mediate cell-cell communication and thus control many aspects of physiology in multicellular organisms. Cell-surface proteomics allows biologists to comprehensively identify proteins on the cell surface and survey their dynamics in physiological and pathological conditions. PEELing provides an integrated package and user-centric web service for analyzing cell-surface proteomics data. With a streamlined and automated workflow, PEELing evaluates data quality using curated references, performs cutoff analysis to remove contaminants, connects to databases for functional annotation, and generates data visualizations. Together with chemical and transgenic tools, PEELing completes a pipeline making cell-surface proteomics analysis handy for every lab.

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04/25/23 | Simultaneous photoactivation and high-speed structural tracking reveal diffusion-dominated motion in the endoplasmic reticulum
Matteo Dora , Christopher J. Obara , Tim Abel , Jennifer Lippincott-Schwarz , David Holcman
bioRxiv. 2023 Apr 25:. doi: 10.1101/2023.04.23.537908

The endoplasmic reticulum (ER) is a structurally complex, membrane-enclosed compartment that stretches from the nuclear envelope to the extreme periphery of eukaryotic cells. The organelle is crucial for numerous distinct cellular processes, but how these processes are spatially regulated within the structure is unclear. Traditional imaging-based approaches to understanding protein dynamics within the organelle are limited by the convoluted structure and rapid movement of molecular components. Here, we introduce a combinatorial imaging and machine learning-assisted image analysis approach to track the motion of photoactivated proteins within the ER of live cells. We find that simultaneous knowledge of the underlying ER structure is required to accurately analyze fluorescently-tagged protein redistribution, and after appropriate structural calibration we see all proteins assayed show signatures of Brownian diffusion-dominated motion over micron spatial scales. Remarkably, we find that in some cells the ER structure can be explored in a highly asymmetric manner, likely as a result of uneven connectivity within the organelle. This remains true independently of the size, topology, or folding state of the fluorescently-tagged molecules, suggesting a potential role for ER connectivity in driving spatially regulated biology in eukaryotes.

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04/25/23 | The big warp: Registration of disparate retinal imaging modalities and an example overlay of ultrawide-field photos and en-face OCTA images.
Thuma TB, Bogovic JA, Gunton KB, Jimenez H, Negreiros B, Pulido JS
PLoS One. 2023 Apr 25;18(4):e0284905. doi: 10.1371/journal.pone.0284905

PURPOSE: To develop an algorithm and scripts to combine disparate multimodal imaging modalities and show its use by overlaying en-face optical coherence tomography angiography (OCTA) images and Optos ultra-widefield (UWF) retinal images using the Fiji (ImageJ) plugin BigWarp.

METHODS: Optos UWF images and Heidelberg en-face OCTA images were collected from various patients as part of their routine care. En-face OCTA images were generated and ten (10) images at varying retinal depths were exported. The Fiji plugin BigWarp was used to transform the Optos UWF image onto the en-face OCTA image using matching reference points in the retinal vasculature surrounding the macula. The images were then overlayed and stacked to create a series of ten combined Optos UWF and en-face OCTA images of increasing retinal depths. The first algorithm was modified to include two scripts that automatically aligned all the en-face OCTA images.

RESULTS: The Optos UWF image could easily be transformed to the en-face OCTA images using BigWarp with common vessel branch point landmarks in the vasculature. The resulting warped Optos image was then successfully superimposed onto the ten Optos UWF images. The scripts more easily allowed for automatic overlay of the images.

CONCLUSIONS: Optos UWF images can be successfully superimposed onto en-face OCTA images using freely available software that has been applied to ocular use. This synthesis of multimodal imaging may increase their potential diagnostic value. Script A is publicly available at and Script B is available at

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04/19/23 | DNA-initiated epigenetic cascades driven by C9orf72 hexanucleotide repeat.
Liu Y, Huang Z, Liu H, Ji Z, Arora A, Cai D, Wang H, Liu M, Simko EA, Zhang Y, Periz G, Liu Z, Wang J
Neuron. 2023 Apr 19;111(8):1205-21. doi: 10.1016/j.neuron.2023.01.022

The C9orf72 hexanucleotide repeat expansion (HRE) is the most frequent genetic cause of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here, we describe the pathogenic cascades that are initiated by the C9orf72 HRE DNA. The HRE DNA binds to its protein partner DAXX and promotes its liquid-liquid phase separation, which is capable of reorganizing genomic structures. An HRE-dependent nuclear accumulation of DAXX drives chromatin remodeling and epigenetic changes such as histone hypermethylation and hypoacetylation in patient cells. While regulating global gene expression, DAXX plays a key role in the suppression of basal and stress-inducible expression of C9orf72 via chromatin remodeling and epigenetic modifications of the promoter of the major C9orf72 transcript. Downregulation of DAXX or rebalancing the epigenetic modifications mitigates the stress-induced sensitivity of C9orf72-patient-derived motor neurons. These studies reveal a C9orf72 HRE DNA-dependent regulatory mechanism for both local and genomic architectural changes in the relevant diseases.

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04/17/23 | Extracellular matrix assembly stress initiates Drosophila central nervous system morphogenesis.
Serna-Morales E, Sánchez-Sánchez BJ, Marcotti S, Nichols A, Bhargava A, Dragu A, Hirvonen LM, Diaz-de-la-Loza M, Mink M, Cox S, Rayfield E, Lee RM, Hobson CM, Chew T, Stramer BM
Developmental Cell. 2023 Apr 17:. doi: 10.1016/j.devcel.2023.03.019

Forces controlling tissue morphogenesis are attributed to cellular-driven activities, and any role for extracellular matrix (ECM) is assumed to be passive. However, all polymer networks, including ECM, can develop autonomous stresses during their assembly. Here, we examine the morphogenetic function of an ECM before reaching homeostatic equilibrium by analyzing de novo ECM assembly during Drosophila ventral nerve cord (VNC) condensation. Asymmetric VNC shortening and a rapid decrease in surface area correlate with the exponential assembly of collagen IV (Col4) surrounding the tissue. Concomitantly, a transient developmentally induced Col4 gradient leads to coherent long-range flow of ECM, which equilibrates the Col4 network. Finite element analysis and perturbation of Col4 network formation through the generation of dominant Col4 mutations that affect assembly reveal that VNC morphodynamics is partially driven by a sudden increase in ECM-driven surface tension. These data suggest that ECM assembly stress and associated network instabilities can actively participate in tissue morphogenesis.

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04/16/23 | A neural basis of choking under pressure
Adam L. Smoulder , Patrick J. Marino , Emily R. Oby , Sam E. Snyder , Hiroo Miyata , Nick P. Pavlovsky , William E. Bishop , Byron M. Yu , Steven M. Chase , Aaron P. Batista
bioRxiv. 2023 Apr 16:. doi: 10.1101/2023.04.16.537007

Incentives tend to drive improvements in performance. But when incentives get too high, we can “choke under pressure” and underperform when it matters most. What neural processes might lead to choking under pressure? We studied Rhesus monkeys performing a challenging reaching task in which they underperform when an unusually large “jackpot” reward is at stake. We observed a collapse in neural information about upcoming movements for jackpot rewards: in the motor cortex, neural planning signals became less distinguishable for different reach directions when a jackpot reward was made available. We conclude that neural signals of reward and motor planning interact in the motor cortex in a manner that can explain why we choke under pressure.

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