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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 67,113 bioRxiv papers from 295,324 authors.

Most downloaded bioRxiv papers, since beginning of last month

65,750 results found. For more information, click each entry to expand.

521: The BELT and phenoSEED platforms: shape and colour phenotyping of seed samples
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Posted to bioRxiv 31 Oct 2019

The BELT and phenoSEED platforms: shape and colour phenotyping of seed samples
267 downloads plant biology

Keith Halcro, Kaitlin McNabb, Ashley Lockinger, Didier Socquet-Juglard, Kirstin Bett, Scott Noble

Background: Seed analysis is currently a bottleneck in phenotypic analysis of seeds. Measurements are slow and imprecise with potential for bias to be introduced when gathered manually. New acquisition tools were requested to improve phenotyping efficacy with an emphasis on obtaining colour information. Results: A portable imaging system (BELT) supported by image acquisition and analysis software (phenoSEED) was created for small-seed optical analysis. Lentil (Lens culinaris L.) phenotyping was used as the primary test case. Seeds were loaded into the system and all seeds in a sample were automatically and individually imaged to acquire top and side views as they passed through an imaging chamber. A Python analysis script applied a colour calibration and extracted quantifiable traits of seed colour, size and shape. Extraction of lentil seed coat patterning was implemented to further describe the seed coat. The use of this device was forecasted to eliminate operator biases, increase the rate of acquisition of traits, and capture qualitative information about traits that have been historically analyzed by eye. Conclusions: Increased precision and higher rates of data acquisition compared to traditional techniques will help breeders to develop more productive cultivars. The system presented is available as an open-source project for academic and non-commercial use.

522: GPCRmd uncovers the dynamics of the 3D-GPCRome
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Posted to bioRxiv 13 Nov 2019

GPCRmd uncovers the dynamics of the 3D-GPCRome
267 downloads biophysics

Ismael Rodríguez-Espigares, Mariona Torrens-Fontanals, Johanna K.S. Tiemann, David Aranda-García, Juan Manuel Ramírez-Anguita, Tomasz Maciej Stepniewski, Nathalie Worp, Alejandro Varela-Rial, Adrián Morales-Pastor, Brian Medel Lacruz, Gáspár Pándy-Szekeres, Eduardo Mayol, Rasmus Fonseca, Toni Giorgino, Jens Carlsson, Xavier Deupi, Slawomir Filipek, José Carlos Gómez-Tamayo, Angel Gonzalez, Hugo Gutierrez-de-Teran, Mireia Jimenez, Willem Jespers, Jon Kapla, Peter Kolb, Dorota Latek, Maria Marti-Solano, Pierre Matricon, Minos-Timotheos Matsoukas, Przemyslaw Miszta, Mireia Olivella, Laura Perez-Benito, Santiago Ríos, Iván Rodríguez-Torrecillas, Jessica Sallander, Agnieszka Sztyler, Silvana Vasile, Peter W. Hildebrand, Gianni De Fabritiis, David E. Gloriam, Arnau Cordomi, Ramon Guixà-González, Jana Selent

G protein-coupled receptors (GPCRs) are involved in numerous physiological processes and the most frequent targets of approved drugs. The striking explosion in the number of new 3D molecular structures of GPCRs (3D-GPCRome) during the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. While experimentally-resolved structures undoubtedly provide valuable snapshots of specific GPCR conformational states, they give only limited information on their flexibility and dynamics associated with function. Molecular dynamics (MD) simulations have become a widely established technique to explore the conformational landscape of proteins at an atomic level. However, the analysis and visualization of MD simulations requires efficient storage resources and specialized software, hence limiting the dissemination of these data to specialists in the field. Here we present the GPCRmd, an online platform with web-based visualization capabilities and a comprehensive analysis toolbox that allows scientists from any discipline to visualize, share, and analyse GPCR MD data. We describe the GPCRmd in the context of a community-driven effort to create the first open, interactive, and standardized database of GPCR MD simulations. We demonstrate the power of this resource by performing comparative analyses of multiple GPCR simulations on two mechanisms critical to receptor function: internal water networks and sodium ion interaction.

523: A better way to define and describe Morlet wavelets for time-frequency analysis
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Posted to bioRxiv 21 Aug 2018

A better way to define and describe Morlet wavelets for time-frequency analysis
267 downloads neuroscience

Michael X Cohen

Morlet wavelets are frequently used for time-frequency analysis of non-stationary time series data, such as neuroelectrical signals recorded from the brain. The crucial parameter of Morlet wavelets is the width of the Gaussian that tapers the sine wave. This width parameter controls the trade-off between temporal precision and frequency precision. It is typically defined as the "number of cycles," but this parameter is opaque, and often leads to uncertainty and suboptimal analysis choices, as well as being difficult to interpret and evaluate. The purpose of this paper is to present alternative formulations of Morlet wavelets in time and in frequency that allow parameterizing the wavelets directly in terms of the desired temporal and spectral smoothing (as full-width at half-maximum). This formulation provides clarity on an important data analysis parameter, and should facilitate proper analyses, reporting, and interpretation of results. MATLAB code is provided.

524: Dual indexed design of in-Drop single-cell RNA-seq libraries improves sequencing quality and throughput
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Posted to bioRxiv 08 Nov 2019

Dual indexed design of in-Drop single-cell RNA-seq libraries improves sequencing quality and throughput
267 downloads molecular biology

Austin N. Southard-Smith, Alan J Simmons, Bob Chen, Angela L. Jones, Marisol A Ramirez-Solano, Paige N Vega, Cherie' R Scurrah, Yue Zhao, Michael J Brenan, Jiekun Xuan, Ely B Porter, Xi Chen, Colin J.H. Brenan, Qi Liu, Lauren N.M. Quigley, Ken S Lau

The increasing demand of single-cell RNA-sequencing (scRNA-seq) experiments, such as the number of experiments and cells queried per experiment, necessitates higher sequencing depth coupled to high data quality. New high-throughput sequencers, such as the Illumina NovaSeq 6000, enables this demand to be filled in a cost-effective manner. However, current scRNA-seq library designs present compatibility challenges with newer sequencing technologies, such as index-hopping, and their ability to generate high quality data has yet to be systematically evaluated. Here, we engineered a new dual-indexed library structure, called TruDrop, on top of the inDrop scRNA-seq platform to solve these compatibility challenges, such that TruDrop libraries and standard Illumina libraries can be sequenced alongside each other on the NovaSeq. We overcame the index-hopping issue, demonstrated significant improvements in base-calling accuracy, and provided an example of multiplexing twenty-four scRNA-seq libraries simultaneously. We showed favorable comparisons in transcriptional diversity of TruDrop compared with prior library structures. Our approach enables cost-effective, high throughput generation of sequencing data with high quality, which should enable more routine use of scRNA-seq technologies.

525: Mapping polyclonal antibody responses in non-human primates vaccinated with HIV Env trimer subunit vaccines
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Posted to bioRxiv 07 Nov 2019

Mapping polyclonal antibody responses in non-human primates vaccinated with HIV Env trimer subunit vaccines
267 downloads immunology

Bartek Nogal, Matteo Bianchi, Christopher A Cottrell, Robert N. Kirchdoerfer, Leigh M Sewall, Hannah L Turner, Fangzhu Zhao, Devin Sok, Dennis Burton, Lars Hangartner, Andrew B Ward

Rational immunogen design aims to focus antibody responses to vulnerable sites on the primary antigens. Given the size of these antigens there is however potential for eliciting unwanted, off-target responses. Here, we used our electron microscopy polyclonal epitope mapping approach to describe the antibody specificities elicited by immunization of non-human primates with soluble HIV envelope trimers and subsequent repeated viral challenge. An increased diversity of epitopes recognized, and the approach angle by which these antibodies bound, constituted a hallmark of the humoral response in most protected animals. We also show that fusion peptide-specific antibodies are responsible for some neutralization breadth. Moreover, cryoEM analysis of a fully-protected animal revealed a high degree of clonality within a subset of putatively neutralizing antibodies, enabling a detailed molecular description of the antibody paratope. Our results provide important insights into the immune response against a vaccine candidate that entered into clinical trials earlier this year.

526: Fast and accurate long-read assembly with wtdbg2
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Posted to bioRxiv 26 Jan 2019

Fast and accurate long-read assembly with wtdbg2
267 downloads bioinformatics

Jue Ruan, Heng Li

Existing long-read assemblers require tens of thousands of CPU hours to assemble a human genome and are being outpaced by sequencing technologies in terms of both throughput and cost. We developed a novel long-read assembler wtdbg2 that, for human data, is tens of times faster than published tools while achieving comparable contiguity and accuracy. It represents a significant algorithmic advance and paves the way for population-scale long-read assembly in future.

527: Excitatory and inhibitory subnetworks are equally selective during decision-making and emerge simultaneously during learning
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Posted to bioRxiv 22 Jun 2018

Excitatory and inhibitory subnetworks are equally selective during decision-making and emerge simultaneously during learning
266 downloads neuroscience

Farzaneh Najafi, Gamaleldin F. Elsayed, Robin Cao, Eftychios Pnevmatikakis, Peter E Latham, John Cunningham, Anne K. Churchland

Inhibitory neurons, which play a critical role in decision-making models, are often simplified as a single pool of non-selective neurons lacking connection specificity. This assumption is supported by observations in primary visual cortex: inhibitory neurons are broadly tuned in vivo, and show non-specific connectivity in slice. Selectivity of excitatory and inhibitory neurons within decision circuits, and hence the validity of decision-making models, is unknown. We simultaneously measured excitatory and inhibitory neurons in posterior parietal cortex of mice judging multisensory stimuli. Surprisingly, excitatory and inhibitory neurons were equally selective for the animals choice, both at the single cell and population level. Further, both cell types exhibited similar changes in selectivity and temporal dynamics during learning, paralleling behavioral improvements. These observations, combined with modeling, argue against circuit architectures assuming non-selective inhibitory neurons. Instead, they argue for selective subnetworks of inhibitory and excitatory neurons that are shaped by experience to support expert decision-making.

528: The evolutionary history of 2,658 cancers
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Posted to bioRxiv 11 Jul 2017

The evolutionary history of 2,658 cancers
266 downloads cancer biology

Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, Stefan C. Dentro, Santiago Gonzalez Rosado, Daniel Rosebrock, Thomas J. Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu, Maxime Tarabichi, Amit Deshwar, Jeff Wintersinger, Kortine Kleinheinz, Ignacio Vázquez-García, Kerstin Haase, Lara Jerman, Subhajit Sengupta, Geoff Macintyre, Salem Malikic, Nilgun Donmez, Dimitri G. Livitz, Marek Cmero, Jonas Demeulemeester, Steven Schumacher, Yu Fan, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Paul C. Boutros, David D. Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, S. Cenk Sahinalp, Yuan Ji, Martin Peifer, Florian Markowetz, Ville Mustonen, Ke Yuan, Wenyi Wang, Quaid D Morris, Paul T. Spellman, David C. Wedge, Peter Van Loo, on behalf of the PCAWG Evolution and Heterogeneity Working Group, the PCAWG network

Cancer develops through a process of somatic evolution. Here, we reconstruct the evolutionary history of 2,778 tumour samples from 2,658 donors spanning 39 cancer types. Characteristic copy number gains, such as trisomy 7 in glioblastoma or isochromosome 17q in medulloblastoma, are found amongst the earliest events in tumour evolution. The early phases of oncogenesis are driven by point mutations in a restricted set of cancer genes, often including biallelic inactivation of tumour suppressors. By contrast, increased genomic instability, a more than three-fold diversification of driver genes, and an acceleration of mutational processes are features of later stages. Clock-like mutations yield estimates for whole genome duplications and subclonal diversification in chronological time. Our results suggest that driver mutations often precede diagnosis by many years, and in some cases decades. Taken together, these data reveal common and divergent trajectories of cancer evolution, pivotal for understanding tumour biology and guiding early cancer detection.

529: Small molecules for modulating protein driven liquid-liquid phase separation in treating neurodegenerative disease
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Posted to bioRxiv 05 Aug 2019

Small molecules for modulating protein driven liquid-liquid phase separation in treating neurodegenerative disease
265 downloads cell biology

Richard J Wheeler, Hyun O Lee, Ina Poser, Arun Pal, Thom Doeleman, Satoshi Kishigami, Sukhleen Kour, Eric Nathaniel Anderson, Lara Marrone, Anastasia C Murthy, Marcus Jahnel, Xiaojie Zhang, Edgar Boczek, Anatol Fritsch, Nicolas L Fawzi, Jared Sterneckert, Udai Pandey, Della C David, Benjamin G Davis, Andrew J. Baldwin, Andreas Hermann, Marc Bickle, Simon Alberti, Anthony A Hyman

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease with few avenues for treatment. Many proteins implicated in ALS associate with stress granules, which are examples of liquid-like compartments formed by phase separation. Aberrant phase transition of stress granules has been implicated in disease, suggesting that modulation of phase transitions could be a possible therapeutic route. Here, we combine cell-based and protein-based screens to show that lipoamide, and its related compound lipoic acid, reduce the propensity of stress granule proteins to aggregate in vitro. More significantly, they also prevented aggregation of proteins over the life time of Caenorhabditis elegans. Observations that they prevent dieback of ALS patient-derived (FUS mutant) motor neuron axons in culture and recover motor defects in Drosophila melanogaster expressing FUS mutants suggest plausibility as effective therapeutics. Our results suggest that altering phase behaviour of stress granule proteins in the cytoplasm could be a novel route to treat ALS.

530: Bright and photostable chemigenetic indicators for extended in vivo voltage imaging
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Posted to bioRxiv 06 Oct 2018

Bright and photostable chemigenetic indicators for extended in vivo voltage imaging
265 downloads neuroscience

Ahmed S. Abdelfattah, Takashi Kawashima, Amrita Singh, Ondrej Novak, Hui Liu, Yichun Shuai, Yi-Chieh Huang, Jonathan B. Grimm, Ronak Patel, Johannes Friedrich, Brett D. Mensh, Liam Paninski, John J Macklin, Kaspar Podgorski, Bei-Jung Lin, Tsai-Wen Chen, Glenn C. Turner, Zhe Liu, Minoru Koyama, Karel Svoboda, Misha B Ahrens, Luke D. Lavis, Eric R Schreiter

Imaging changes in membrane potential using genetically encoded fluorescent voltage indicators (GEVIs) has great potential for monitoring neuronal activity with high spatial and temporal resolution. Brightness and photostability of fluorescent proteins and rhodopsins have limited the utility of existing GEVIs. We engineered a novel GEVI, Voltron, that utilizes bright and photostable synthetic dyes instead of protein-based fluorophores, extending the combined duration of imaging and number of neurons imaged simultaneously by more than tenfold relative to existing GEVIs. We used Voltron for in vivo voltage imaging in mice, zebrafish, and fruit flies. In mouse cortex, Voltron allowed single-trial recording of spikes and subthreshold voltage signals from dozens of neurons simultaneously, over 15 minutes of continuous imaging. In larval zebrafish, Voltron enabled the precise correlation of spike timing with behavior.

531: Discovery and Engineering of a Therapeutic Interfering Particle (TIP): a combination self-renewing antiviral
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Posted to bioRxiv 30 Oct 2019

Discovery and Engineering of a Therapeutic Interfering Particle (TIP): a combination self-renewing antiviral
265 downloads synthetic biology

Elizabeth J Tanner, Seung-Yong Jung, Joshua J Glazier, Cassandra E Thompson, Yuqi Zhou, Benjamin Martin, Hye-In Son, James L Riley, Leor S. Weinberger

Population-level control of HIV-1 faces recognized challenges, including the evolution of viral resistance and adherence issues in resource-limited settings. It has long been proposed that viral deletion mutants that conditionally self-renew at the expense of the wild-type virus (i.e., Defective Interfering Particles, DIPs) could constitute a long-term intervention that circumvents adherence challenges and has a high genetic barrier to resistance. Theories predict that DIPs could be engineered into a therapy for HIV-1 (i.e., Therapeutic interfering particles or 'TIPs') provided they stably persist in patients (R>1) by spreading to new cells during active infection (hence, a self-replenishing antiviral). To date, DIPs amenable to such engineering have remained elusive for HIV-1. Here we report the discovery of an HIV-1 DIP and its subsequent engineering into a TIP. The TIP interferes with HIV-1 replication at multiple stages of the viral lifecycle, including genome packaging, virion maturation, and reverse transcription, essentially acting as a combination antiviral. In humanized mice, the TIP suppressed HIV-1 replication by ten-fold and significantly protected CD4+ T cells from HIV-1 mediated depletion. These data provide proof-of-concept for a class of biologic with the potential to circumvent significant barriers to HIV-1 control.

532: Microneedle manipulation of the mammalian spindle reveals specialized, short-lived reinforcement near chromosomes
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Posted to bioRxiv 15 Nov 2019

Microneedle manipulation of the mammalian spindle reveals specialized, short-lived reinforcement near chromosomes
265 downloads cell biology

Pooja Suresh, Alexandra F Long, Sophie Dumont

The spindle generates force to segregate chromosomes at cell division. In mammalian cells, kinetochore-fibers connect chromosomes to the spindle. The dynamic spindle anchors kinetochore-fibers in space and time to coordinate chromosome movement. Yet, how it does so remains poorly understood as we lack tools to directly challenge this anchorage. Here, we adapt microneedle manipulation to exert local forces on the spindle with spatiotemporal control. Pulling on kinetochore-fibers reveals that the spindle retains local architecture in its center on the seconds timescale. Upon pulling, sister, but not neighbor, kinetochore-fibers remain tightly coupled, restricting chromosome stretching. Further, pulled kinetochore-fibers freely pivot around poles but not around chromosomes, retaining their orientation within 3 μm of chromosomes. This local reinforcement has a 20 s lifetime, and requires the microtubule crosslinker PRC1. Together, these observations indicate short-lived, specialized reinforcement of the kinetochore-fiber in the spindle center. This could help the spindle protect local structure near chromosomes from transient forces while allowing its remodeling over longer timescales, thereby supporting robust chromosome attachments and movements.

533: High multiplex, digital spatial profiling of proteins and RNA in fixed tissue using genomic detection methods
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Posted to bioRxiv 22 Feb 2019

High multiplex, digital spatial profiling of proteins and RNA in fixed tissue using genomic detection methods
264 downloads pathology

Christopher R. Merritt, Giang T Ong, Sarah Church, Kristi Barker, Gary Geiss, Margaret Hoang, Jaemyeong Jung, Yan Liang, Jill McKay-Fleisch, Karen Nguyen, Kristina Sorg, Isaac Sprague, Charles Warren, Sarah Warren, Zoey Zhou, Daniel R. Zollinger, Dwayne L. Dunaway, Gordon B. Mills, Joseph M. Beechem

We have developed Digital Spatial Profiling (DSP), a non-destructive method for high-plex spatial profiling of proteins and RNA, using oligonucleotide detection technologies with unlimited multiplexing capability. The key breakthroughs underlying DSP are threefold: (1) multiplexed readout of proteins/RNA using oligo-tags; (2) oligo-tags attached to affinity reagents (antibodies/RNA probes) through a photocleavable (PC) linker; (3) photocleaving light projected onto the tissue sample to release PC-oligos in any spatial pattern. Here we show precise analyte reproducibility, validation, and cellular resolution using DSP. We also demonstrate biological proof-of-concept using lymphoid, colorectal tumor, and autoimmune tissue as models to profile immune cell populations, stroma, and cancer cells to identify factors specific for the diseased microenvironment. DSP utilizes the unlimited multiplexing capability of modern genomic approaches, while simultaneously providing spatial context of protein and RNA to examine biological questions based on analyte location and distribution.

534: Inference of CRISPR Edits from Sanger Trace Data
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Posted to bioRxiv 20 Jan 2018

Inference of CRISPR Edits from Sanger Trace Data
264 downloads bioinformatics

Tim Hsiau, David Conant, Nicholas Rossi, Travis Maures, Kelsey Waite, Joyce Yang, Sahil Joshi, Reed Kelso, Kevin Holden, Brittany L Enzmann, Rich Stoner

Efficient precision genome editing requires a quick, quantitative, and inexpensive assay of editing outcomes. Here we present ICE (Inference of CRISPR Edits), which enables robust analysis of CRISPR edits using Sanger data. ICE proposes potential outcomes for editing with guide RNAs (gRNAs) and then determines which are supported by the data via regression. Additionally, we develop a score called ICE-D (Discordance) that can provide information on large or unexpected edits. We empirically confirm through over 1,800 edits that the ICE algorithm is robust, reproducible, and can analyze CRISPR experiments within days after transfection. We also confirm that ICE strongly correlates with next-generation sequencing of amplicons (Amp-Seq). The ICE tool is free to use and offers several improvements over current analysis tools. For instance, ICE can analyze individual experiments as well as multiple experiments simultaneously (batch analysis). ICE can also detect a wider variety of outcomes, including multi-guide edits (multiple gRNAs per target) and edits resulting from homology-directed repair (HDR), such as knock-ins and base edits. ICE is a reliable analysis tool that can significantly expedite CRISPR editing workflows. It is available online at [ice.synthego.com][1], and the source code is at [github.com/synthego-open/ice][2] [1]: http://ice.synthego.com [2]: http://github.com/synthego-open/ice

535: Hormonal control of motivational circuitry orchestrates the transition to sexuality in Drosophila
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Posted to bioRxiv 23 Nov 2019

Hormonal control of motivational circuitry orchestrates the transition to sexuality in Drosophila
264 downloads neuroscience

Stephen X. Zhang, Ethan H. Glantz, Dragana Rogulja, Michael A. Crickmore

Newborns and hatchlings of many species perform incredibly sophisticated behaviors, but all vertebrates and many invertebrates selectively abstain from sexual activity at the beginning of life. Hormonal changes have long been associated with adolescence, but it is not clear how these circulating factors create a new motivation and drive its associated behaviors. We show that the transition to sexuality in male Drosophila is controlled by juvenile hormone, which spikes at eclosion and declines over days as the propensity for courtship gradually increases. Juvenile hormone directly inhibits the activity of at least three courtship-motivating circuit elements, ensuring the complete suppression of sexual motivation and behavior. Blocking or overriding these inhibitory mechanisms evokes immediate and robust sexual behavior from very young and otherwise asexual males. These results provide a first example of hormonal changes gating the transition to sexuality by activating latent, but largely developed and functional, motivational circuitry.

536: PBS3 and EPS1 complete salicylic acid biosynthesis from isochorismate in Arabidopsis
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Posted to bioRxiv 07 Apr 2019

PBS3 and EPS1 complete salicylic acid biosynthesis from isochorismate in Arabidopsis
264 downloads plant biology

Michael P Torrens-Spence, Anastassia Bobokalonova, Valentina Carballo, Christopher M. Glinkerman, Tomáš Pluskal, Amber Shen, Jing-Ke Weng

Salicylic acid (SA) is an important phytohormone mediating both local and systemic defense responses in plants. Despite over half a century of research, how plants biosynthesize SA remains unresolved. In Arabidopsis, a major part of SA is derived from isochorismate, a key intermediate produced by the isochorismate synthase (ICS), which is reminiscent of SA biosynthesis in bacteria. Whereas bacteria employ an isochorismate pyruvate lyase (IPL) that catalyzes the turnover of isochorismate to pyruvate and SA, plants do not contain an IPL ortholog and generate SA from isochorismate through an unknown mechanism. Combining genetic and biochemical approaches, we delineated the SA biosynthetic pathway downstream of isochorismate in Arabidopsis. We show that PBS3, a GH3 acyl adenylase-family enzyme important for SA accumulation, catalyzes ATP- and Mg2+-dependent conjugation of L -glutamate primarily to the 8-carboxyl of isochorismate and yields the key SA biosynthetic intermediate isochorismoyl-glutamate A. Moreover, EPS1, a BAHD acyltransferase-family protein with previously implicated role in SA accumulation upon pathogen attack, harbors a noncanonical active site and an unprecedented isochorismoyl-glutamate A pyruvoyl-glutamate lyase (IPGL) activity that produces SA from the isochorismoyl-glutamate A substrate. Together, PBS3 and EPS1 form a two-step metabolic pathway to produce SA from isochorismate in Arabidopsis, which is distinct from how SA is biosynthesized in bacteria. This study closes a major knowledge gap in plant SA metabolism and would help develop new strategies for engineering disease resistance in crop plants.

537: Establishment of Proximity-dependent Biotinylation Approaches in Different Plant Model Systems
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Posted to bioRxiv 14 Jul 2019

Establishment of Proximity-dependent Biotinylation Approaches in Different Plant Model Systems
263 downloads plant biology

Deepanksha Arora, Nikolaj B. Abel, Chen Liu, Petra Van Damme, Lam Dai Vu, Anna Tornkvist, Francis Impens, Dominique Eeckhout, Alain Goossens, Geert De Jaeger, Thomas Ott, Panagiotis Moschou, Daniel Van Damme

The use of proximity-dependent biotin labelling (PDL) approaches coupled with mass spectrometry recently greatly advanced the identification of protein-protein interactions and study of protein complexation. PDL is based on the expression of a promiscuous biotin ligase (PBL), e.g. BirA* or a peroxidase fused to a bait protein of interest. In the presence of biotin as substrate, PBL enables covalent biotin labelling of proteins in the vicinity of the PBL-fused bait in vivo, allowing the subsequent capture and identification of interacting and neighbouring proteins without the need for the protein complex to remain intact during purification. To date, PDL has not been extensively used in plants. Here we present the results of a systematic multi-lab study applying a variety of PDL approaches in several plant systems under various conditions and bait proteins. We show that TurboID is the most promiscuous variant for PDL in plants and establish protocols for its efficient application. We demonstrate the applicability of TurboID in capturing membrane protein interactomes using the Lotus japonicus symbiotically active receptor kinases RLKs NOD FACTOR RECEPTOR 5 (NFR5) and LRR-RLK SYMBIOTIC RECEPTOR-KINASE (SYMRK) as test-cases. Furthermore, we benchmark the efficiency of various PBLs using the octameric endocytic TPLATE complex and compare PDL with one-step AP-MS approaches. Our results indicate that different PDL approaches in plants may differ in signal-to-noise ratio and robustness. We present a straightforward strategy to identify both non-biotinylated as well as biotinylated proteins in plants in a single experimental setup. Finally, we provide initial evidence that this technique has potential to infer structural information of protein complexes. Our methods, tools and adjustable pipelines provide a useful resource for the plant research community.

538: Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana
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Posted to bioRxiv 17 Nov 2019

Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana
263 downloads plant biology

Andres Romanowski, Rubén G. Schlaen, Soledad Perez-Santangelo, Estefania Mancini, Marcelo Javier Yanovsky

The circadian clock of Arabidopsis thaliana controls many physiological and molecular processes, allowing plants to anticipate daily changes in its environment. However, a detailed understanding of how oscillations in mRNA levels are connected to oscillations in post-transcriptional processes, such as splicing, has remained a challenge. Here we applied a combined approach of deep transcriptome sequencing and bioinformatics tools to identify novel circadian regulated genes and splicing events. Using a stringent approach, we identified 109 intron retention, 35 exon skipping, 42 alternative 5’ splice site usage, and 63 alternative 3’ splice site usage events under circadian regulation. We also found 24 and 1765 novel alternative exonic and intronic events. Depletion of the circadian regulated splicing factor SPF30 homolog, resulted in the disruption of a subset of clock controlled splicing events, mainly at CT16. Altogether, our global circadian RNAseq coupled with an in silico , event centred, splicing analysis tool offers a new approach for studying the interplay between the circadian clock and the splicing machinery at a global scale. The identification of a large number of circadian regulated splicing events, broadens our current understanding of the level of control that the circadian clock has over this posttranscriptional regulatory layer.

539: Whole-genome sequencing of rare disease patients in a national healthcare system
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Posted to bioRxiv 01 Jan 2019

Whole-genome sequencing of rare disease patients in a national healthcare system
263 downloads genomics

The NIHR BioResource, on behalf of the 100,000 Genomes Project

Most patients with hereditary rare diseases do not receive a molecular diagnosis and the aetiological variants and mediating genes for half such disorders remain to be discovered. We implemented whole-genome sequencing (WGS) in a national healthcare system to streamline diagnosis and to discover unknown aetiological variants, in the coding and non-coding regions of the genome. In a pilot study for the 100,000 Genomes Project, we generated WGS data for 13,037 participants, of whom 9,802 had a rare disease, and provided a genetic diagnosis to 1,040 of the 7,065 patients with detailed phenotypic data. We identified 99 Mendelian associations between genes and rare diseases, of which at least 80 are confirmed aetiological. Using WGS of UK Biobank, we showed that rare alleles can explain the presence of some individuals in the tails of a quantitative red blood cell (RBC) trait. Finally, we reported novel non-coding variants which cause disease through the disruption of transcription of ARPC1B, GATA1, LRBA and MPL. Our study demonstrates a synergy by using WGS for diagnosis and aetiological discovery in routine healthcare.

540: High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing
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Posted to bioRxiv 17 Jun 2019

High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing
263 downloads genomics

Devika Ganesamoorthy, Mengjia Yan, Valentine Murigneux, Chenxi Zhou, Minh Duc Cao, Tania Duarte, Lachlan J. M. Coin

Tandem repeats (TRs) are highly prone to variation in copy numbers due to their repetitive and unstable nature, which makes them a major source of genomic variation between individuals. However, population variation of TRs have not been widely explored due to the limitations of existing tools, which are either low-throughput or restricted to a small subset of TRs. Here, we used SureSelect targeted sequencing approach combined with Nanopore sequencing to overcome these limitations. We achieved an average of 3062-fold target enrichment on a panel of 142 TR loci, generating an average of 97X sequence coverage on 7 samples utilizing 2 MinION flow-cells with 200ng of input DNA per sample. We identified a subset of 110 TR loci with length less than 2kb, and GC content greater than 25% for which we achieved an average genotyping rate of 75% and increasing to 91% for the highest-coverage sample. Alleles estimated from targeted long-read sequencing were concordant with gold standard PCR sizing analysis and moreover highly correlated with alleles estimated from whole genome long-read sequencing. We demonstrate a targeted long-read sequencing approach that enables simultaneous analysis of hundreds of TRs and accuracy is comparable to PCR sizing analysis. Our approach is feasible to scale for more targets and more samples facilitating large-scale analysis of TRs.

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