@article {68832, title = {The Janelia Atalanta plasmids provide a simple and efficient CRISPR/Cas9-mediated homology directed repair platform for Drosophila}, journal = {bioRxiv}, year = {2023}, month = {2023 Jun 17}, abstract = {

Homology-directed repair (HDR) is a powerful tool for modifying genomes in precise ways to address many biological questions. Use of Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR)-Cas9 induced targeted DNA double-strand breakage has substantially simplified use of homology-directed repair to introduce specific perturbations in\ Drosophila, but existing platforms for CRISPR-Cas9-mediated HDR in\ Drosophila\ involve multiple cloning steps and have low efficiency. To simplify cloning of HDR plasmids, we designed a new plasmid platform, the Janelia Atalanta (pJAT) series, that exploits recent advances in dsDNA synthesis to facilitate Gateway cloning of gRNA sequences and homology arms in one step. Surprisingly, the pJAT plasmids yielded considerably higher HDR efficiency (approximately 25\%) than we have observed with other approaches. pJAT plasmids work in multiple\ Drosophila\ species and exhibited such high efficiency that previously impossible experiments in\ Drosophila, such as driving targeted chromosomal inversions, were made possible. We provide pJAT plasmids for a range of commonly performed experiments including targeted insertional mutagenesis, insertion of phiC31-mediated attP landing sites, generation of strains carrying a germ-line source of Cas9, and induction of chromosomal rearrangements. We also provide {\textquotedblleft}empty{\textquotedblright} pJAT plasmids with multiple cloning sites to simplify construction of plasmids with new functionality. The pJAT platform is generic and may facilitate improved efficiency CRISPR-Cas9 HDR in a wide range of model and non-model organisms.

}, doi = {10.1101/2023.06.17.545412}, url = {https://doi.org/10.1101/2023.06.17.545412}, author = {David L. Stern and Elizabeth Kim and Emily L. Behrman} } @article {67672, title = {jumps with greater velocity and acceleration than previously reported.}, journal = {MicroPublication Biology}, volume = {2021}, year = {2021}, month = {2021 Aug 02}, abstract = {

Infective juveniles of the insect-parastic nematode canjump greater than 6 times their height, a striking evolved novelty in some species of this genus. Using high-speed videography, we observed the kinematics of spontaneousjumping behavior. Our analysis places a lower bound on the velocity and acceleration of these worms.

}, issn = {2578-9430}, doi = {10.17912/micropub.biology.000435}, author = {Dillman, Adler R and Korff, Wyatt and Dickinson, Michael H and Sternberg, Paul W} } @article {65618, title = {jYCaMP: an optimized calcium indicator for two-photon imaging at fiber laser wavelengths.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 May 25}, pages = {694-97}, abstract = {

Femtosecond lasers at fixed wavelengths above 1,000 nm are powerful, stable and inexpensive, making them promising sources for two-photon microscopy. Biosensors optimized for these wavelengths are needed for both next-generation microscopes and affordable turn-key systems. Here we report jYCaMP1, a yellow variant of the calcium indicator jGCaMP7 that outperforms its parent in mice and flies at excitation wavelengths above 1,000 nm and enables improved two-color calcium imaging with red fluorescent protein-based indicators.

}, issn = {1548-7105}, doi = {10.1038/s41592-020-0835-7}, author = {Mohr, Manuel Alexander and Bushey, Daniel and Abhi Aggarwal and Marvin, Jonathan S and Kim, Jeong Jun and Marquez, Emiliano Jimenez and Liang, Yajie and Patel, Ronak and Macklin, John J and Lee, Chi-Yu and Tsang, Arthur and Tsegaye, Getahun and Ahrens, Allison M and Chen, Jerry L and Kim, Douglas S and Wong, Allan M and Looger, Loren L and Schreiter, Eric R and Podgorski, Kaspar} } @article {49177, title = {Joint deformable registration of large EM image volumes: a matrix solver approach.}, journal = {arXiv}, year = {2018}, month = {2018 Apr 26}, abstract = {

Large electron microscopy image datasets for connectomics are typically composed of thousands to millions of partially overlapping two-dimensional images (tiles), which must be registered into a coherent volume prior to further analysis. A common registration strategy is to find matching features between neighboring and overlapping image pairs, followed by a numerical estimation of optimal image deformation using a so-called solver program.\ 
Existing solvers are inadequate for large data volumes, and inefficient for small-scale image registration.\ 
In this work, an efficient and accurate matrix-based solver method is presented. A linear system is constructed that combines minimization of feature-pair square distances with explicit constraints in a regularization term. In absence of reliable priors for regularization, we show how to construct a rigid-model approximation to use as prior. The linear system is solved using available computer programs, whose performance on typical registration tasks we briefly compare, and to which future scale-up is delegated. Our method is applied to the joint alignment of 2.67 million images, with more than 200 million point-pairs and has been used for successfully aligning the first full adult fruit fly brain.

}, url = {https://arxiv.org/abs/1804.10019}, author = {Khairy, Khaled and Denisov, Gennady and Saalfeld, Stephan} } @article {49143, title = {Juvenile hormone reveals mosaic developmental programs in the metamorphosing optic lobe of Drosophila melanogaster.}, journal = {Biology Open}, year = {2018}, month = {2018 Apr 04}, abstract = {

The development of the adult optic lobe (OL) of is directed by a wave of ingrowth of the photoreceptors over a two day period at the outset of metamorphosis which is accompanied by the appearance of the pupal-specific transcription factor Broad-Z3 (Br-Z3) and expression of early drivers in OL neurons. During this time, there are pulses of ecdysteroids that time the metamorphic events. At the outset, the transient appearance of juvenile hormone (JH) prevents precocious development of the OL caused by the ecdysteroid peak that initiates pupariation, but the artificial maintenance of JH after this time misdirects subsequent development. Axon ingrowth, Br-Z3 appearance and the expression of early drivers were unaffected, but aspects of later development such as the dendritic expansion of the lamina monopolar neurons and the expression of late drivers were suppressed. This effect of the exogenous JH mimic (JHM) pyriproxifen is lost by 24 hr after pupariation. Part of this effect of JHM is due to its suppression of the appearance of ecdysone receptor EcR-B1 that occurs after pupation and during early adult development.

}, issn = {2046-6390}, doi = {10.1242/bio.034025}, author = {Riddiford, Lynn M and Truman, James W and Nern, Aljoscha} } @article {45190, title = {Juvenile hormone regulates body size and perturbs insulin signaling in Drosophila.}, journal = {Proceedings of the National Academy of Science of the United States of America}, volume = {111}, year = {2014}, month = {2014 May 13}, pages = {7018-23}, abstract = {

The role of juvenile hormone (JH) in regulating the timing and nature of insect molts is well-established. Increasing evidence suggests that JH is also involved in regulating final insect size. Here we elucidate the developmental mechanism through which JH regulates body size in developing Drosophila larvae by genetically ablating the JH-producing organ, the corpora allata (CA). We found that larvae that lack CA pupariated at smaller sizes than control larvae due to a reduced larval growth rate. Neither the timing of the metamorphic molt nor the duration of larval growth was affected by the loss of JH. Further, we show that the effects of JH on growth rate are dependent on the forkhead box O transcription factor (FOXO), which is negatively regulated by the insulin-signaling pathway. Larvae that lacked the CA had elevated levels of FOXO activity, whereas a loss-of-function mutation of FOXO rescued the effects of CA ablation on final body size. Finally, the effect of JH on growth appears to be mediated, at least in part, via ecdysone synthesis in the prothoracic gland. These results indicate a role of JH in regulating growth rate via the ecdysone- and insulin-signaling pathways.

}, keywords = {Animals, Basic Helix-Loop-Helix Transcription Factors, Body Size, Corpora Allata, Denervation, Drosophila melanogaster, Drosophila Proteins, Ecdysone, Forkhead Transcription Factors, Insulin, Juvenile Hormones, Larva, Signal Transduction}, issn = {1091-6490}, doi = {10.1073/pnas.1313058111}, author = {Mirth, C K and Tang, H Y and Makohon-Moore, S C and Salhadar, S and Gokhale, R H and Warner, R D and Koyama, T and Riddiford, L M and Shingleton, A W} } @article {5763, title = {JAABA: interactive machine learning for automatic annotation of animal behavior.}, journal = {Nature Methods}, volume = {10}, year = {2013}, month = {2012 Dec}, pages = {64-7}, abstract = {

We present a machine learning{\textendash}based system for automatically computing interpretable, quantitative measures of animal behavior. Through our interactive system, users encode their intuition about behavior by annotating a small set of video frames. These manual labels are converted into classifiers that can automatically annotate behaviors in screen-scale data sets. Our general-purpose system can create a variety of accurate individual and social behavior classifiers for different organisms, including mice and adult and larval Drosophila.

}, issn = {1548-7091}, author = {Kabra, Mayank and Robie, Alice A and Rivera-Alba, Marta and Branson, Steven and Branson, Kristin} } @article {6390, title = {Juvenile hormone and insulin suppress lipolysis between periods of lactation during tsetse fly pregnancy.}, journal = {Molecular and Cellular Endocrinology}, volume = {372}, year = {2013}, month = {2013 Jun 15}, pages = {30-41}, abstract = {

Tsetse flies are viviparous insects that nurture a single intrauterine progeny per gonotrophic cycle. The developing larva is nourished by the lipid-rich, milk-like secretions from a modified female accessory gland (milk gland). An essential feature of the lactation process involves lipid mobilization for incorporation into the milk. In this study, we examined roles for juvenile hormone (JH) and insulin/IGF-like (IIS) signaling pathways during tsetse pregnancy. In particular, we examined the roles for these pathways in regulating lipid homeostasis during transitions between non-lactating (dry) and lactating periods. The dry period occurs over the course of oogenesis and embryogenesis, while the lactation period spans intrauterine larvigenesis. Genes involved in the JH and IIS pathways were upregulated during dry periods, correlating with lipid accumulation between bouts of lactation. RNAi suppression of Forkhead Box Sub Group O (FOXO) expression impaired lipolysis during tsetse lactation and reduced fecundity. Similar reduction of the JH receptor Methoprene tolerant (Met), but not its paralog germ cell expressed (gce), reduced lipid accumulation during dry periods, indicating functional divergence between Met and gce during tsetse reproduction. Reduced lipid levels following Met knockdown led to impaired fecundity due to inadequate fat reserves at the initiation of milk production. Both the application of the JH analog (JHA) methoprene and injection of insulin into lactating females increased stored lipids by suppressing lipolysis and reduced transcripts of lactation-specific genes, leading to elevated rates of larval abortion. To our knowledge, this study is the first to address the molecular physiology of JH and IIS in a viviparous insect, and specifically to provide a role for JH signaling through Met in the regulation of lipid metabolism during insect lactation.

}, issn = {1872-8057}, doi = {10.1016/j.mce.2013.02.019}, author = {Baumann, Aaron A and Benoit, Joshua B and Michalkova, Veronika and Mireji, Paul O and Attardo, Geoffrey M and Moulton, John K and Wilson, Thomas G and Aksoy, Serap} } @article {5635, title = {The juvenile hormone signaling pathway in insect development.}, journal = {Annual Review of Entomology}, volume = {58}, year = {2013}, month = {2013 Jan 7}, pages = {181-204}, abstract = {

The molecular action of juvenile hormone (JH), a regulator of vital importance to insects, was until recently regarded as a mystery. The past few years have seen an explosion of studies of JH signaling, sparked by a finding that a JH-resistance gene, Methoprene-tolerant (Met), plays a critical role in insect metamorphosis. Here, we summarize the recently acquired knowledge on the capacity of Met to bind JH, which has been mapped to a particular ligand-binding domain, thus establishing this bHLH-PAS protein as a novel type of an intracellular hormone receptor. Next, we consider the significance of JH-dependent interactions of Met with other transcription factors and signaling pathways. We examine the regulation and biological roles of genes acting downstream of JH and Met in insect metamorphosis. Finally, we discuss the current gaps in our understanding of JH action and outline directions for future research.

}, issn = {1545-4487}, doi = {10.1146/annurev-ento-120811-153700}, author = {Jindra, Marek and Palli, Subba R and Riddiford, Lynn M} } @article {46603, title = {JNK pathway activation is controlled by Tao/TAOK3 to modulate ethanol sensitivity.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012 Dec 5}, pages = {e50594}, abstract = {

Neuronal signal transduction by the JNK MAP kinase pathway is altered by a broad array of stimuli including exposure to the widely abused drug ethanol, but the behavioral relevance and the regulation of JNK signaling is unclear. Here we demonstrate that JNK signaling functions downstream of the Sterile20 kinase family gene tao/Taok3 to regulate the behavioral effects of acute ethanol exposure in both the fruit fly Drosophila and mice. In flies tao is required in neurons to promote sensitivity to the locomotor stimulant effects of acute ethanol exposure and to establish specific brain structures. Reduced expression of key JNK pathway genes substantially rescued the structural and behavioral phenotypes of tao mutants. Decreasing and increasing JNK pathway activity resulted in increased and decreased sensitivity to the locomotor stimulant properties of acute ethanol exposure, respectively. Further, JNK expression in a limited pattern of neurons that included brain regions implicated in ethanol responses was sufficient to restore normal behavior. Mice heterozygous for a disrupted allele of the homologous Taok3 gene (Taok3Gt) were resistant to the acute sedative effects of ethanol. JNK activity was constitutively increased in brains of Taok3Gt/+ mice, and acute induction of phospho-JNK in brain tissue by ethanol was occluded in Taok3Gt/+ mice. Finally, acute administration of a JNK inhibitor conferred resistance to the sedative effects of ethanol in wild-type but not Taok3Gt/+ mice. Taken together, these data support a role of a TAO/TAOK3-JNK neuronal signaling pathway in regulating sensitivity to acute ethanol exposure in flies and in mice.

}, keywords = {Animals, Base Sequence, Behavior, Animal, DNA Primers, Drosophila, Drosophila Proteins, Ethanol, Immunohistochemistry, MAP Kinase Kinase 4, Mice, Mice, Inbred C57BL, Mutation, Protein-Serine-Threonine Kinases, Reverse Transcriptase Polymerase Chain Reaction}, issn = {1932-6203}, doi = {10.1371/journal.pone.0050594}, author = {Kapfhamer, David and King, Ian and Zou, Mimi E and Lim, Jana P and Heberlein, Ulrike and Wolf, Fred W} } @article {4886, title = {Joint control of Drosophila male courtship behavior by motion cues and activation of male-specific P1 neurons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 May 29}, pages = {10065-70}, abstract = {

Sexual behaviors in animals are governed by inputs from multiple external sensory modalities. However, how these inputs are integrated to jointly control animal behavior is still poorly understood. Whereas visual information alone is not sufficient to induce courtship behavior in Drosophila melanogaster males, when a subset of male-specific fruitless (fru)- and doublesex (dsx)-expressing neurons that respond to chemosensory cues (P1 neurons) were artificially activated via a temperature-sensitive cation channel (dTRPA1), males followed and extended their wing toward moving objects (even a moving piece of rubber band) intensively. When stationary, these objects were not courted. Our results indicate that motion input and activation of P1 neurons are individually necessary, and under our assay conditions, jointly sufficient to elicit early courtship behaviors, and provide insights into how courtship decisions are made via sensory integration.

}, issn = {1091-6490}, doi = {10.1073/pnas.1207107109}, author = {Pan, Yufeng and Meissner, Geoffrey W and Baker, Bruce S} } @article {6394, title = {Juvenile hormone action requires paralogous genes in Drosophila melanogaster.}, journal = {Genetics}, volume = {185}, year = {2010}, month = {2010}, pages = {1327-36}, author = {Baumann, Aaron and Barry, J and Wang, S and WIlson, TG} } @article {45964, title = {Junction-forming aquaporins.}, journal = {Current Opinion in Structural Biology}, volume = {18}, year = {2008}, month = {2008 Apr}, pages = {229-35}, abstract = {

Aquaporins (AQPs) are a family of ubiquitous membrane channels that conduct water and solutes across membranes. This review focuses on AQP0 and AQP4, which in addition to forming water channels also appear to play a role in cell adhesion. We discuss the recently determined structures of the membrane junctions mediated by these two AQPs, the mechanisms that regulate junction formation, and evidence that supports a role for AQP0 and AQP4 in cell adhesion.

}, keywords = {Animals, Aquaporin 4, Aquaporins, Eye Proteins, Humans, Intercellular Junctions, Models, Molecular, Protein Structure, Quaternary}, issn = {0959-440X}, doi = {10.1016/j.sbi.2007.11.003}, author = {Engel, Andreas and Fujiyoshi, Yoshinori and Gonen, Tamir and Walz, Thomas} } @article {2499, title = {Juvenile hormone action: a 2007 perspective.}, journal = {Journal of Insect Physiology}, volume = {54}, year = {2008}, month = {2008 Jun}, pages = {895-901}, abstract = {

Juvenile hormone (JH) is a key hormone in regulation of the insect{\textquoteright}s life history, both in maintaining the larval state during molts and in directing reproductive maturation. This short review highlights the recent papers of the past year that lend new insight into the role of this hormone in the larva and the mechanisms whereby it achieves this role.

}, keywords = {Animals, Basic Helix-Loop-Helix Transcription Factors, Biological, DNA-Binding Proteins, Drosophila Proteins, Insects, Juvenile Hormones, Larva, Metamorphosis, Response Elements, Transcription Factors}, issn = {0022-1910}, doi = {10.1016/j.jinsphys.2008.01.014}, author = {Riddiford, Lynn M} } @article {6289, title = {Janelia Farm: an experiment in scientific culture.}, journal = {Cell}, volume = {125}, year = {2006}, month = {2006 Apr 21}, pages = {209-12}, abstract = {

Janelia Farm, the new research campus of the Howard Hughes Medical Institute, is an ongoing experiment in the social engineering of research communities.

}, keywords = {Academies and Institutes, Biomedical Research, Culture, Humans, Laboratories, Research Personnel, Research Support as Topic, Residence Characteristics}, issn = {0092-8674}, doi = {10.1016/j.cell.2006.04.005}, author = {Rubin, Gerald M} } @article {2508, title = {Juvenile hormone is required to couple imaginal disc formation with nutrition in insects.}, journal = {Science }, volume = {312}, year = {2006}, month = {2006 Jun 2}, pages = {1385-8}, abstract = {

In starved larvae of the tobacco hornworm moth Manduca sexta, larval and imaginal tissues stop growing, the former because they lack nutrient-dependent signals but the latter because of suppression by juvenile hormone. Without juvenile hormone, imaginal discs form and grow despite severe starvation. This hormone inhibits the intrinsic signaling needed for disc morphogenesis and does so independently of ecdysteroid action. Starvation and juvenile hormone treatments allowed the separation of intrinsic and nutrient-dependent aspects of disc growth and showed that both aspects must occur during the early phases of disc morphogenesis to ensure normal growth leading to typical-sized adults.

}, keywords = {Animal Nutritional Physiological Phenomena, Animals, Ecdysteroids, Juvenile Hormones, Larva, Manduca, Morphogenesis, Pyridines}, issn = {1095-9203}, doi = {10.1126/science.1123652}, author = {Truman, J W and Hiruma, K and Allee, J P and Macwhinnie, S G B and Champlin, D T and Riddiford, L M} } @proceedings {3305, title = {Joint nonparametric alignment for analyzing spatial gene expression patterns of Drosophila imaginal discs.}, volume = {2}, year = {2005}, month = {2005 Jun 20}, pages = {755-60}, abstract = {

To compare spatial patterns of gene expression, one must analyze a large number of images as current methods are only able to measure a small number of genes at a time. Bringing images of corresponding tissues into alignment is a critical first step in making a meaningful comparative analysis of these spatial patterns. Significant image noise and variability in the shapes make it hard to pick a canonical shape model. In this paper, we address these problems by combining segmentation and unsupervised shape learning algorithms. We first segment images to acquire structures of interest, then jointly align the shapes of these acquired structures using an unsupervised nonparametric maximum likelihood algorithm along the lines of congealing, while simultaneously learning the underlying shape model and associated transformations. The learned transformations are applied to corresponding images to bring them into alignment in one step. We demonstrate the results for images of various classes of Drosophila imaginal discs and discuss the methodology used for a quantitative analysis of spatial gene expression patterns.

}, author = {Ahammad, Parvez and Harmon, C and Hammonds, Ann S and Sastry, S and Rubin, Gerald M} } @conference {3306, title = {Joint MRI bias removal using entropy minimization across images.}, booktitle = {Neural Information Processing Systems Conference}, year = {2004}, month = {2004}, abstract = {

The correction of bias in magnetic resonance images is an important problem in medical image processing. Most previous approaches have used a maximum likelihood method to increase the likelihood of the pixels in a single image by adaptively estimating a correction to the unknown image bias field. The pixel likelihoods are defined either in terms of a pre-existing tissue model, or non-parametrically in terms of the image{\textquoteright}s own pixel values. In both cases, the specific location of a pixel in the image is not used to calculate the likelihoods. We suggest a new approach in which we simultaneously eliminate the bias from a set of images of the same anatomy, but from different patients. We use the statistics from the same location across different images, rather than within an image, to eliminate bias fields from all of the images simultaneously. The method builds a multi-resolution non-parametric tissue model conditioned on image location while eliminating the bias fields associated with the original image set. We present experiments on both synthetic and real MR data sets, and present comparisons with other methods.

}, author = {Learned-Miller, EG and Ahammad, Parvez} }