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2691 Janelia Publications

Showing 801-810 of 2691 results
Eddy/Rivas Lab
01/01/13 | Dfam: a database of repetitive DNA based on profile hidden Markov models.
Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AF, Finn RD
Nucleic Acids Research. 2013 Jan;41:D70-82. doi: 10.1093/nar/gks1265

We present a database of repetitive DNA elements, called Dfam (http://dfam.janelia.org). Many genomes contain a large fraction of repetitive DNA, much of which is made up of remnants of transposable elements (TEs). Accurate annotation of TEs enables research into their biology and can shed light on the evolutionary processes that shape genomes. Identification and masking of TEs can also greatly simplify many downstream genome annotation and sequence analysis tasks. The commonly used TE annotation tools RepeatMasker and Censor depend on sequence homology search tools such as cross_match and BLAST variants, as well as Repbase, a collection of known TE families each represented by a single consensus sequence. Dfam contains entries corresponding to all Repbase TE entries for which instances have been found in the human genome. Each Dfam entry is represented by a profile hidden Markov model, built from alignments generated using RepeatMasker and Repbase. When used in conjunction with the hidden Markov model search tool nhmmer, Dfam produces a 2.9% increase in coverage over consensus sequence search methods on a large human benchmark, while maintaining low false discovery rates, and coverage of the full human genome is 54.5%. The website provides a collection of tools and data views to support improved TE curation and annotation efforts. Dfam is also available for download in flat file format or in the form of MySQL table dumps.

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Svoboda Lab
09/01/11 | DIADEMchallenge.org: a compendium of resources fostering the continuous development of automated neuronal reconstruction.
Gillette TA, Brown KM, Svoboda K, Liu Y, Ascoli GA
Neuroinformatics. 2011 Sep;9(2-3):303-4. doi: 10.1007/s12021-011-9104-3

Concomitant with the publication of this Special Issue of Neuroinformatics, a substantially updated version of the DIADEM web site has been released at http://diademchallenge.org. This web site was originally designed to host the challenge for automating the digital reconstruction of axonal and dendritic morphology (hence the DIADEM acronym). This post-competition version features additional content for continued use as the access point for DIADEM-related material. From the very beginning, one of the spirits of DIADEM has been to share data and resources with the neuroscience research community at large. The resources available from or linked to the DIADEM website constitute a substantial scientific legacy of the 2009/2010 competition. The new content includes finalist algorithms, image stack data, gold standard reconstructions, an updated DIADEM metric, and a retrospective on the competition in text and images.

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07/01/20 | Dielectric confinement and excitonic effects in two-dimensional nanoplatelets.
Ji B, Rabani E, Efros AL, Vaxenburg R, Ashkenazi O, Azulay D, Banin U, Millo O
ACS Nano. 2020 Jul 01:. doi: 10.1021/acsnano.0c01950

Quasi-two-dimensional (2D) semiconductor nanoplatelets manifest strong quantum confinement with exceptional optical characteristics of narrow photoluminescence peaks with energies tunable by thickness with monolayer precision. We employed scanning tunneling spectroscopy (STS) in conjunction with optical measurements to probe the thickness-dependent band gap and density of excited states in a series of CdSe nanoplatelets. The tunneling spectra, measured in the double-barrier tunnel junction configuration, reveal the effect of quantum confinement on the band gap taking place mainly through a blue-shift of the conduction band edge, along with a signature of 2D electronic structure intermixed with finite lateral-size and/or defects effects. The STS fundamental band gaps are larger than the optical gaps as expected from the contributions of exciton binding in the absorption, as confirmed by theoretical calculations. The calculations also point to strong valence band mixing between the light- and split-off hole levels. Strikingly, the energy difference between the heavy-hole and light-hole levels in the tunneling spectra are significantly larger than the corresponding values extracted from the absorption spectra. Possible explanations for this, including an interplay of nanoplatelet charging, dielectric confinement, and difference in exciton binding energy for light and heavy holes, are analyzed and discussed.

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11/24/23 | Different spectral sensitivities of ON- and OFF-motion pathways enhance the detection of approaching color objects in Drosophila.
Longden KD, Rogers EM, Nern A, Dionne H, Reiser MB
Nature Communications. 2023 Nov 24;14(1):7693. doi: 10.1038/s41467-023-43566-8

Color and motion are used by many species to identify salient objects. They are processed largely independently, but color contributes to motion processing in humans, for example, enabling moving colored objects to be detected when their luminance matches the background. Here, we demonstrate an unexpected, additional contribution of color to motion vision in Drosophila. We show that behavioral ON-motion responses are more sensitive to UV than for OFF-motion, and we identify cellular pathways connecting UV-sensitive R7 photoreceptors to ON and OFF-motion-sensitive T4 and T5 cells, using neurogenetics and calcium imaging. Remarkably, this contribution of color circuitry to motion vision enhances the detection of approaching UV discs, but not green discs with the same chromatic contrast, and we show how this could generalize for systems with ON- and OFF-motion pathways. Our results provide a computational and circuit basis for how color enhances motion vision to favor the detection of saliently colored objects.

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11/24/23 | Different spectral sensitivities of ON- and OFF-motion pathways enhance the detection of approaching color objects in Drosophila.
Longden KD, Rogers EM, Nern A, Dionne H, Reiser MB
Nature Communications. 2023 Nov 24;14(1):7693. doi: 10.1038/s41467-023-43566-8

Color and motion are used by many species to identify salient objects. They are processed largely independently, but color contributes to motion processing in humans, for example, enabling moving colored objects to be detected when their luminance matches the background. Here, we demonstrate an unexpected, additional contribution of color to motion vision in Drosophila. We show that behavioral ON-motion responses are more sensitive to UV than for OFF-motion, and we identify cellular pathways connecting UV-sensitive R7 photoreceptors to ON and OFF-motion-sensitive T4 and T5 cells, using neurogenetics and calcium imaging. Remarkably, this contribution of color circuitry to motion vision enhances the detection of approaching UV discs, but not green discs with the same chromatic contrast, and we show how this could generalize for systems with ON- and OFF-motion pathways. Our results provide a computational and circuit basis for how color enhances motion vision to favor the detection of saliently colored objects.

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02/28/23 | Differential Encoding of Trace and Delay Fear Memory in the Entorhinal Cortex.
Kong M, Kim N, Jo KI, Kim S, Choi J
Experimental Neurobiology. 2023 Feb 28;32(1):20-30. doi: 10.5607/en22042

Trace fear conditioning is characterized by a stimulus-free trace interval (TI) between the conditioned stimulus (CS) and the unconditioned stimulus (US), which requires an array of brain structures to support the formation and storage of associative memory. The entorhinal cortex (EC) has been proposed to provide essential neural code for resolving temporal discontinuity in conjunction with the hippocampus. However, how the CS and TI are encoded at the neuronal level in the EC is not clear. In Exp. 1, we tested the effect of bilateral pre-training electrolytic lesions of EC on trace vs. delay fear conditioning using rats as subjects. We found that the lesions impaired the acquisition of trace but not delay fear conditioning confirming that EC is a critical brain area for trace fear memory formation. In Exp. 2, single-unit activities from EC were recorded during the pre-training baseline and post-training retention sessions following trace or delay conditioning. The recording results showed that a significant proportion of the EC neurons modulated their firing during TI after the trace conditioning, but not after the delay fear conditioning. Further analysis revealed that the majority of modulated units decreased the firing rate during the TI or the CS. Taken together, these results suggest that EC critically contributes to trace fear conditioning by modulating neuronal activity during the TI to facilitate the association between the CS and US across a temporal gap.

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08/29/19 | Differential nanoscale organisation of LFA-1 modulates T cell migration.
Shannon MJ, Pineau J, Griffié J, Aaron J, Peel T, Williamson DJ, Zamoyska R, Cope AP, Cornish GH, Owen DM
Journal of Cell Science. 2019 Aug 29;132(7):1-28. doi: 10.1242/jcs.232991
01/01/23 | Dimensionality reduction of calcium-imaged neuronal population activity
Tze Hui Koh , William E. Bishop , Takashi Kawashima , Brian B. Jeon , Ranjani Srinivasan , Sandra J. Kuhlman , Misha B. Ahrens , Steven M. Chase , Byron M. Yu
Nature Computational Science. 2023 Jan 01:. doi: 10.1038/s43588-022-00390-2

Calcium imaging has been widely adopted for its ability to record from large neuronal populations. To summarize the time course of neural activity, dimensionality reduction methods, which have been applied extensively to population spiking activity, may be particularly useful. However, it is unclear if the dimensionality reduction methods applied to spiking activity are appropriate for calcium imaging. We thus carried out a systematic study of design choices based on standard dimensionality reduction methods. We also developed a novel method to perform deconvolution and dimensionality reduction simultaneously (termed CILDS). CILDS most accurately recovered the single-trial, low-dimensional time courses from calcium imaging that would have been recovered from spiking activity. CILDS also outperformed the other methods on calcium imaging recordings from larval zebrafish and mice. More broadly, this study represents a foundation for summarizing calcium imaging recordings of large neuronal populations using dimensionality reduction in diverse experimental settings.

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09/01/21 | Direct detection of SARS-CoV-2 RNA using high-contrast pH-sensitive dyes.
Timothy A. Brown , Katherine S. Schaefer , Arthur Tsang , Hyun Ah Yi , Jonathan B. Grimm , Andrew L. Lemire , Fadi M. Jradi , Charles Kim , Kevin McGowan , Kimberly Ritola , Derek T. Armstrong , Heba H. Mostafa , Wyatt Korff , Ronald D. Vale , Luke D. Lavis
Journal of Biomolecular Techniques. 2021 Sep 01;32(3):121-133. doi: https://doi.org/10.1101/2020.12.26.20248878

The worldwide COVID-19 pandemic has had devastating effects on health, healthcare infrastructure, social structure, and economics. One of the limiting factors in containing the spread of this virus has been the lack of widespread availability of fast, inexpensive, and reliable methods for testing of individuals. Frequent screening for infected and often asymptomatic people is a cornerstone of pandemic management plans. Here, we introduce two pH sensitive ‘LAMPshade’ dyes as novel readouts in an isothermal RT- LAMP amplification assay for SARS-CoV-2 RNA. The resulting JaneliaLAMP (jLAMP) assay is robust, simple, inexpensive, has low technical requirements and we describe its use and performance in direct testing of contrived and clinical samples without RNA extraction.

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Looger LabKeller Lab
12/15/15 | Direct in vivo manipulation and imaging of calcium transients in neutrophils identify a critical role for leading-edge calcium flux.
Beerman RW, Matty MA, Au GG, Looger LL, Choudhury KR, Keller PJ, Tobin DM
Cell Reports. 2015 Dec 15;13(10):2107-17. doi: 10.1016/j.celrep.2015.11.010

Calcium signaling has long been associated with key events of immunity, including chemotaxis, phagocytosis, and activation. However, imaging and manipulation of calcium flux in motile immune cells in live animals remain challenging. Using light-sheet microscopy for in vivo calcium imaging in zebrafish, we observe characteristic patterns of calcium flux triggered by distinct events, including phagocytosis of pathogenic bacteria and migration of neutrophils toward inflammatory stimuli. In contrast to findings from ex vivo studies, we observe enriched calcium influx at the leading edge of migrating neutrophils. To directly manipulate calcium dynamics in vivo, we have developed transgenic lines with cell-specific expression of the mammalian TRPV1 channel, enabling ligand-gated, reversible, and spatiotemporal control of calcium influx. We find that controlled calcium influx can function to help define the neutrophil's leading edge. Cell-specific TRPV1 expression may have broad utility for precise control of calcium dynamics in other immune cell types and organisms.

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