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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 70,230 bioRxiv papers from 306,630 authors.

Most tweeted bioRxiv papers, last 24 hours

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

1: A standardized and reproducible method to measure decision-making in mice
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Posted to bioRxiv 17 Jan 2020

A standardized and reproducible method to measure decision-making in mice
210 tweets neuroscience

The International Brain Laboratory, Valeria Aguillon, Dora E. Angelaki, Hannah M. Bayer, Niccolo Bonacchi, Matteo Carandini, Fanny Cazettes, Anne K. Churchland, Gaelle Chapuis, Yang Dan, Eric Dewitt, Mayo Faulkner, Forrest Hamish, Laura Haetzel, Michael Hausser, Sonja Hofer, Fei Hu, Anup Khanal, Christopher Krasniak, Inês Laranjeira, Zachary Mainen, Guido Meijer, Nathaniel Miska, Thomas Mrsic-Flogel, Jean-Paul Noel, Alejandro Pan-Vazquez, Josh Sanders, Karolina Socha, Rebecca Terry, A.E. Urai, Hernando Martinez Vergara, Miles Wells, Christian Wilson, Ilana Witten, Lauren Wool, Anthony Zador

Progress in neuroscience is hindered by poor reproducibility of mouse behavior. Here we show that in a visual decision making task, reproducibility can be achieved by automating the training protocol and by standardizing experimental hardware, software, and procedures. We trained 101 mice in this task across nine laboratories at seven research institutions in three countries, and obtained 3 million mouse choices. In trained mice, variability in behavior between labs was indistinguishable from variability within labs. Psychometric curves showed no significant differences in visual threshold, bias, or lapse rates across labs. Moreover, mice across laboratories adopted similar strategies when stimulus location had asymmetrical probability that changed over time. We provide detailed instructions and open-source tools to set up and implement our method in other laboratories. These results establish a new standard for reproducibility of rodent behavior and provide accessible tools for the study of decision making in mice.

2: Non-essential function of KRAB zinc finger gene clusters in retrotransposon suppression
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Posted to bioRxiv 17 Jan 2020

Non-essential function of KRAB zinc finger gene clusters in retrotransposon suppression
51 tweets genetics

Gernot Wolf, Alberto de Iaco, Ming-An Sun, Melania Bruno, Matthew Tinkham, Don Hoang, Apratim Mitra, Shery Ralls, Didier Trono, Todd Macfarlan

The Kruppel-associated box zinc finger protein (KRAB-ZFP) family amplified and diversified in mammals by segmental duplications, but the function of the majority of this gene family remains largely unexplored due to the inaccessibility of the gene clusters to conventional gene targeting. We determined the genomic binding sites of 61 murine KRAB-ZFPs and genetically deleted in mouse embryonic stem (ES) cells five large KRAB-ZFP gene clusters encoding nearly one tenth of the more than 700 mouse KRAB-ZFPs. We demonstrate that clustered KRAB-ZFPs directly bind and silence retrotransposons and block retrotransposon-borne enhancers from gene activation in ES cells. Homozygous knockout mice generated from ES cells deleted in one of two KRAB-ZFP clusters were born at sub-mendelian frequencies in some matings, but heterozygous intercrosses could also yield knockout progeny with no overt phenotype. We further developed a retrotransposon capture-sequencing approach to assess mobility of the MMETn family of endogenous retrovirus like elements, which are transcriptionally activated in KRAB-ZFP cluster KOs, in a pedigree of KRAB-ZFP cluster KO and WT mice. We identified numerous somatic and several germ-line MMETn insertions, and found a modest increase in activity in mutant animals, but these events were detected in both wild-type and KO mice in stochastic and highly variable patterns. Our data suggests that the majority of young KRAB-ZFPs play a non-essential role in transposon silencing, likely due to the large redundancy with other KRAB-ZFPs and other transposon restriction pathways in mice.

3: Distinguishing the neural correlates of perceptual awareness and post-perceptual processing
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Posted to bioRxiv 16 Jan 2020

Distinguishing the neural correlates of perceptual awareness and post-perceptual processing
45 tweets neuroscience

Michael A Cohen, Kevin Ortego, Andrew Kyroudis, Michael Pitts

To identify the neural correlates of perceptual awareness, researchers often compare the differences in neural activation between conditions in which an observer is or is not aware of a target stimulus. While intuitive, this approach often contains a critical limitation: In order to link brain activity with perceptual awareness, observers traditionally report the contents of their perceptual experience. However, relying on observers reports is problematic because it makes it difficult to know if the neural responses being measured are associated with conscious perception per se or with post-perceptual processes involved in the reporting task (i.e., working memory, decision-making, etc.). To address this issue, we combined a standard visual masking paradigm with a recently developed no-report paradigm. In the visual masking paradigm, observers saw images of animals and objects that were visible or invisible depending on their proximity to masks. Meanwhile, on half of the trials, observers reported the contents of their perceptual experience (i.e., report condition), while on the other half of trials they refrained from reporting about their experiences (i.e., no-report condition). We used electroencephalography (EEG) to examine how visibility interacts with reporting by measuring the P3b event related potential (ERP), one of the proposed canonical signatures of conscious processing. Overall, we found a robust P3b in the report condition, but no P3b whatsoever in the no-report condition. This finding suggests that the P3b itself is not a neural signature of conscious processing and highlights the importance of carefully distinguishing the neural correlates of perceptual awareness from post-perceptual processing.

4: Synthesis of geological and comparative phylogeographic data point to climate, not mountain uplift, as driver of divergence across the Eastern Andean Cordillera
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Posted to bioRxiv 15 Jan 2020

Synthesis of geological and comparative phylogeographic data point to climate, not mountain uplift, as driver of divergence across the Eastern Andean Cordillera
43 tweets evolutionary biology

Erika Rodriguez-Munoz, Camilo Montes, Andrew J. Crawford

Aim: To evaluate the potential role of the orogeny of the Eastern Cordillera (EC) of the Colombian Andes and the Merida Andes (MA) of Venezuela as drivers of vicariance between populations of 37 tetrapod lineages codistributed on both flanks, through geological reconstruction and comparative phylogeographic analyses. Location: Northwestern South America. Methods: We first reviewed and synthesized published geological data on the timing of uplift for the EC MA. We then combined newly generated mitochondrial DNA sequence data with published datasets to create a comparative phylogeographic dataset for 37 independent tetrapod lineages. We reconstructed time calibrated molecular phylogenies for each lineage under Bayesian inference to estimate divergence times between lineages located East and West of the Andes. We performed a comparative phylogeographic analysis of all lineages within each class of tetrapod using hierarchical approximate Bayesian computation (hABC) to test for synchronous vicariance across the EC MA. To evaluate the potential role of life history in explaining variation in divergence times among lineages, we evaluated 13 general linear models (GLM) containing up to six variables each (maximum elevation, range size, body length, thermoregulation, type of dispersal, and taxonomic class). Results: Our synthesis of geological evidence suggested that the EC MA reached significant heights by 38 to 33 million years ago (Ma) along most of its length, and we reject the oft cited date of 2 to 5 Ma. Based on mtDNA divergence from 37 lineages, however, the median estimated divergence time across the EC MA was 3.26 Ma (SE = 2.84) in amphibians, 2.58 Ma (SE = 1.81) in birds, 2.99 Ma (SE = 4.68) in reptiles and 1.43 Ma (SE = 1.23) in mammals. Using Bayes Factors, the hypothesis for a single temporal divergence interval containing synchronous divergence events was supported for mammals and but not supported for amphibians, non avian reptiles, or birds. Among the six life history variables tested, only thermoregulation successfully explained variation in divergence times (minimum AICc, R2 = 0.10), with homeotherms showing more recent divergence relative to poikilotherms. Main conclusions: Our results reject the hypothesis of the rise Andean Cordillera as driver of vicariance of lowland population because divergence dates are too recent and too asynchronous. We discuss alternative explanations, including dispersal through mountain passes, and suggest that changes in the climatic conditions during the Pliocene and Pleistocene interacted with tetrapod physiology, promoting older divergences in amphibians and reptiles relative to mammals and birds on an already established orogeny.

5: Stability and dynamics of the human gut microbiome and its association with systemic immune traits
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Posted to bioRxiv 17 Jan 2020

Stability and dynamics of the human gut microbiome and its association with systemic immune traits
42 tweets microbiology

Allyson L Byrd, Menghan Liu, Kei E Fujimura, Svetlana Lyalina, Deepti R Nagarkar, Bruno Charbit, Etienne Patin, Oliver J Harrison, Lluis Quintana-Murci, Darragh Duffy, Matthew L. Albert, The Milieu Interieur Consortium

Analysis of 1,363 deeply sequenced gut microbiome samples from 946 healthy donors of the Milieu Intérieur cohort provides new opportunities to discover how the gut microbiome is associated with host factors and lifestyle parameters. Using a genome-based taxonomy to achieve higher resolution analysis, we found an enrichment of Prevotella species in males, and that bacterial profiles are dynamic across five decades of life (20-69), with Bacteroidota species consistently increased with age while Actinobacteriota species, including Bifidobacterium, decreased. Longitudinal sampling revealed short-term stability exceeds inter-individual differences; however, the degree of stability was variable between donors and influenced by their baseline community composition. We then integrated the microbiome results with systemic immunophenotypes to show that host/microbe associations discovered in animal models, such as T regulatory cells and short chain fatty acids, could be validated in human data. These results will enable personalized medicine approaches for microbial therapeutics and biomarkers.

6: Improvement of phycocyanobilin synthesis for genetically encoded phytochrome-based optogenetics.
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Posted to bioRxiv 16 Jan 2020

Improvement of phycocyanobilin synthesis for genetically encoded phytochrome-based optogenetics.
39 tweets synthetic biology

Youichi Uda, Haruko Miura, Yuhei Goto, Kazuhiro Aoki

Optogenetics is a powerful technique using photoresponsive proteins, and light-inducible dimerization (LID) systems, an optogenetic tool, allow to manipulate intracellular signaling pathways. One of the red/far-red responsive LID system, phytochrome B (PhyB)-phytochrome interacting factor (PIF), has a unique property of controlling both association and dissociation by light on the second time scale, but PhyB requires a linear tetrapyrrole chromophore such as phytochromobilin or phycocyanobilin (PCB), and such chromophores are present only in higher plants and cyanobacteria. Here, we report that we further improved our previously developed PCB synthesis system (synPCB), and successfully established a stable cell line containing a genetically encoded PhyB-PIF LID system. First, four genes responsible for PCB synthesis, namely, PcyA, HO1, Fd, and Fnr, were replaced with their counterparts derived from thermophilic cyanobacteria. Second, Fnr was truncated, followed by fusion with Fd to generate a chimeric protein, tFnr-Fd. Third, these genes were concatenated with P2A peptide cDNAs for polycistronic expression, resulting in an approximately 4-fold increase in PCB synthesis compared with the previous version. Finally, we incorporated PhyB-PIF and synPCB into drug inducible lentiviral and transposon vectors, which enabled us to induce PCB synthesis and PhyB-PIF LID system by doxycycline treatment. These tools provide a new opportunity to advance our understanding of the causal relationship between intracellular signaling and cellular functions.

7: Encoding of 3D Head Orienting Movements in Primary Visual Cortex
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Posted to bioRxiv 17 Jan 2020

Encoding of 3D Head Orienting Movements in Primary Visual Cortex
39 tweets neuroscience

Grigori Guitchounts, Javier Alejandro Masis, Steffen B.E. Wolff, David Cox

Animals actively sample from the sensory world by generating complex patterns of movement that evolve in three dimensions. At least some of these movements have been shown to influence neural codes in sensory areas. For example, in primary visual cortex (V1), locomotion-related neural activity influences sensory gain, encodes running speed, and predicts the direction of visual flow. As most experiments exploring movement-related modulation of V1 have been performed in head-fixed animals, it remains unclear whether or how the naturalistic movements used to interact with sensory stimuli--like head orienting--influence visual processing. Here we show that 3D head orienting movements modulate V1 neuronal activity in a direction-specific manner that also depends on the presence or absence of light. We identify two largely independent populations of movement-direction-tuned neurons that support this modulation, one of which is direction-tuned in the dark and the other in the light. Finally, we demonstrate that V1 gains access to a motor efference copy related to orientation from secondary motor cortex, which has been shown to control head orienting movements. These results suggest a mechanism through which sensory signals generated by purposeful movement can be distinguished from those arising in the outside world, and reveal a pervasive role of 3D movement in shaping sensory cortical dynamics.

8: URMAP, an ultra fast read mapper
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Posted to bioRxiv 14 Jan 2020

URMAP, an ultra fast read mapper
39 tweets bioinformatics

Robert C. Edgar

Mapping of reads to reference sequences is an essential step in a wide range of biological studies. The large size of datasets generated with next-generation sequencing technologies motivates the development of fast mapping software. Here, I describe URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA and Bowtie2 with comparable accuracy on a benchmark test using simulated paired 150nt reads of a well-studied human genome. Software is freely available at https://drive5.com/urmap.

9: A bright and high-performance genetically encoded Ca2+ indicator based on mNeonGreen fluorescent protein
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Posted to bioRxiv 17 Jan 2020

A bright and high-performance genetically encoded Ca2+ indicator based on mNeonGreen fluorescent protein
39 tweets molecular biology

Landon Zarowny, Abhi Aggarwal, Virginia Rutten, Ilya Kolb, The GENIE Project, Ronak Patel, Hsin-Yi Huang, Yu-Fen Chang, Tiffany Phan, Richard Kanyo, Misha Ahrens, W. Ted Allison, Kaspar Podgorski, Robert E. Campbell

Genetically encodable calcium ion (Ca2+) indicators (GECIs) based on green fluorescent proteins (GFP) are powerful tools for imaging of cell signaling and neural activity in model organisms. Following almost two decades of steady improvements in the Aequorea victoria GFP (avGFP)-based GCaMP series of GECIs, the performance of the most recent generation (i.e., GCaMP7) may have reached its practical limit due to the inherent properties of GFP. In an effort to sustain the steady progression towards ever-improved GECIs, we undertook the development of a new GECI based on the bright monomeric GFP, mNeonGreen (mNG). The resulting indicator, mNG-GECO1, is 60% brighter than GCaMP6s in vitro and provides comparable performance as demonstrated by imaging Ca2+ dynamics in cultured cells, primary neurons, and in vivo in larval zebrafish. These results suggest that mNG-GECO1 is a promising next-generation GECI that could inherit the mantle of GCaMP and allow the steady improvement of GECIs to continue for generations to come.

10: Biases and Blind-Spots in Genome-Wide CRISPR Knockout Screens
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Posted to bioRxiv 17 Jan 2020

Biases and Blind-Spots in Genome-Wide CRISPR Knockout Screens
38 tweets systems biology

Merve Dede, Eiru Kim, Traver Hart

It is widely accepted that pooled library CRISPR knockout screens offer greater sensitivity and specificity than prior technologies in detecting genes whose disruption leads to fitness defects, a critical step in identifying candidate cancer targets. However, the assumption that CRISPR screens are saturating has been largely untested. Through integrated analysis of screen data in cancer cell lines generated by the Cancer Dependency Map, we show that a typical CRISPR screen has a ~20% false negative rate, beyond library-specific false negatives previously described. Replicability falls sharply as gene expression decreases, while cancer subtype-specific genes within a tissue show distinct profiles compared to false negatives. Cumulative analyses across tissues suggest only a small number of lineage-specific essential genes and that these genes are highly enriched for transcription factors that define pathways of tissue differentiation. In addition, we show that half of all constitutively-expressed genes are never hits in any CRISPR screen, and that these never-essentials are highly enriched for paralogs. Together these observations strongly suggest that functional buffering masks single knockout phenotypes for a substantial number of genes, describing a major blind spot in CRISPR-based mammalian functional genomics approaches.

11: The structure and global distribution of the endoplasmic reticulum network is actively regulated by lysosomes
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Posted to bioRxiv 15 Jan 2020

The structure and global distribution of the endoplasmic reticulum network is actively regulated by lysosomes
35 tweets cell biology

Meng Lu, Francesca W. van Tartwijk, Julie Qiaojin Lin, Wilco Nijenhuis, Pierre Parutto, Marcus Fantham, Charles N. Christensen, Edward Avezov, Christine E. Holt, Alan Tunnacliffe, David Holcman, Lukas Kapitein, Gabriele Kaminski Schierle, Clemens F. Kaminski

The endoplasmic reticulum (ER) comprises morphologically and functionally distinct domains, sheets and interconnected tubules. These domains undergo dynamic reshaping, in response to changes in the cellular environment. However, the mechanisms behind this rapid remodeling within minutes are largely unknown. Here, we report that ER remodeling is actively driven by lysosomes, following lysosome repositioning in response to changes in nutritional status. The anchorage of lysosomes to ER growth tips is critical for ER tubule elongation and connection. We validate this causal link via the chemo- and optogenetically driven re-positioning of lysosomes, which leads to both a redistribution of the ER tubules and its global morphology. Lysosomes sense metabolic change in the cell and regulate ER tubule distribution accordingly. Dysfunction in this mechanism during axonal extension may lead to axonal growth defects. Our results demonstrate a critical role of lysosome-regulated ER dynamics and reshaping in nutrient responses and neuronal development.

12: A single bacterial genus maintains root development in a complex microbiome
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Posted to bioRxiv 23 May 2019

A single bacterial genus maintains root development in a complex microbiome
34 tweets microbiology

Omri M. Finkel, Isai Salas-Gonzalez, Gabriel Castrillo, Jonathan M. Conway, Theresa F Law, Paulo José Pereira Lima Teixeira, Ellie D. Wilson, Connor R. Fitzpatrick, Corbin D. Jones, Jeffery L. Dangl

Plants grow within a complex web of species interacting with each other and with the plant. Many of these interactions are governed by a wide repertoire of chemical signals, and the resulting chemical landscape of the rhizosphere can strongly affect root health and development. To understand how microbe-microbe interactions influence root development in Arabidopsis, we established a model system for plant-microbe-microbe-environment interactions. We inoculated seedlings with a 185-member bacterial synthetic community (SynCom), manipulated the abiotic environment, and measured bacterial colonization of the plant. This enabled classification of the SynCom into four modules of co-occurring strains. We deconstructed the SynCom based on these modules, identifying microbe-microbe interactions that determine root phenotypes. These interactions primarily involve a single bacterial genus, Variovorax, which completely reverts severe root growth inhibition (RGI) induced by a wide diversity of bacterial strains as well as by the entire 185-member community. We demonstrate that Variovorax manipulate plant hormone levels to balance this ecologically realistic root community's effects on root development. We identify a novel auxin degradation operon in the Variovorax genome that is necessary and sufficient for RGI reversion. Therefore, metabolic signal interference shapes bacteria-plant communication networks and is essential for maintaining the root's developmental program. Optimizing the feedbacks that shape chemical interaction networks in the rhizosphere provides a promising new ecological strategy towards the development of more resilient and productive crops.

13: Iterative Refinement of Cellular Identity from Single-Cell Data Using Online Learning
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Posted to bioRxiv 17 Jan 2020

Iterative Refinement of Cellular Identity from Single-Cell Data Using Online Learning
31 tweets bioinformatics

Chao Gao, Joshua D. Welch

Recent experimental advances have enabled high-throughput single-cell measurement of gene expression, chromatin accessibility and DNA methylation. We previously used integrative nonnegative matrix factorization (iNMF) to jointly learn interpretable low-dimensional representations from multiple single-cell datasets using dataset-specific and shared metagene factors. These factors provide a principled, quantitative definition of cellular identity and how it varies across biological contexts. However, datasets exceeding 1 million cells are now widely available, creating computational barriers to scientific discovery. For instance, it is no longer feasible to use the entire available datasets as inputs to implement standard pipelines on a personal computer with limited memory capacity. Moreover, there is a need for an algorithm capable of iteratively refining the definition of cellular identity as efforts to create a comprehensive human cell atlas continually sequence new cells. To address these challenges, we developed an online learning algorithm for integrating massive and continually arriving single-cell datasets. We extended previous online learning approaches for NMF to minimize the expected cost of a surrogate function for the iNMF objective. We also derived a novel hierarchical alternating least squares algorithm for iNMF and incorporated it into an efficient online algorithm. Our online approach accesses the training data as mini-batches, decoupling memory usage from dataset size and allowing on-the-fly incorporation of new data as it is generated. The online implementation of iNMF converges much more quickly using a fraction of the memory required for the batch implementation, without sacrificing solution quality. Our new approach enables factorization of 939489 single cells from 9 regions of the mouse brain on a standard laptop in ~30 minutes. Furthermore, we construct a multi-modal cell atlas of the mouse motor cortex by iteratively incorporating seven single-cell datasets from three different modalities generated by the BRAIN Initiative Cell Census Network over a period of two years. Our approach obviates the need to recompute results each time additional cells are sequenced, dramatically increases convergence speed, and allows processing of datasets too large to fit in memory. Most importantly, it facilitates continual refinement of cell identity as new single-cell datasets from different biological contexts and data modalities are generated.

14: What is the test-retest reliability of common task-fMRI measures? New empirical evidence and a meta-analysis
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Posted to bioRxiv 24 Jun 2019

What is the test-retest reliability of common task-fMRI measures? New empirical evidence and a meta-analysis
30 tweets neuroscience

Maxwell L Elliott, Annchen R. Knodt, David Ireland, Meriwether L Morris, Richie Polton, Sandhya Ramrakha, Maria L Sison, Terrie E. Moffitt, Avshalom Caspi, Ahmad Hariri

Identifying brain biomarkers of disease risk is a growing priority in neuroscience. The ability to identify meaningful biomarkers is limited by measurement reliability; unreliable measures are unsuitable for predicting clinical outcomes. Measuring brain activity using task-fMRI is a major focus of biomarker development; however, the reliability of task-fMRI has not been systematically evaluated. We present converging evidence demonstrating poor reliability of task-fMRI measures. First, a meta-analysis of 90 experiments (N=1,008) revealed poor overall reliability (mean ICC=.397). Second, the test-retest reliabilities of activity in a priori regions of interest across 11 common fMRI tasks collected in the context of the Human Connectome Project (N=45) and the Dunedin Study (N=20) were poor (ICCs=.067-.485). Collectively, these findings demonstrate that common task-fMRI measures are not currently suitable for brain biomarker discovery or individual differences research. We review how this state of affairs came to be and highlight avenues for improving task-fMRI reliability.

15: Ancestral Haplotype Reconstruction in Endogamous Populations using Identity-By-Descent
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Posted to bioRxiv 16 Jan 2020

Ancestral Haplotype Reconstruction in Endogamous Populations using Identity-By-Descent
30 tweets bioinformatics

Kelly Finke, Michael Kourakos, Gabriela Brown, Yuval B. Simons, Alejandro A. Schaffer, Rachel L. Kember, Maja Bucan, Sara Mathieson

In this work we develop a novel algorithm for reconstructing the genomes of ancestral individuals, given genotype or sequence data from contemporary individuals and an extended pedigree of family relationships. A pedigree with complete genomes for every individual enables the study of allele frequency dynamics and haplotype diversity across generations, including deviations from neutrality such as transmission distortion. When studying heritable diseases, ancestral haplotypes can be used to augment genome-wide association studies or compute polygenic risk scores for the reconstructed individuals. The building blocks of our reconstruction algorithm are segments of Identity-By-Descent (IBD) shared between two or more genotyped individuals. The method alternates between finding a source for each IBD segment and assembling IBD segments placed within each ancestral individual. After each iteration we perform conflict resolution to remove IBD segments that do not align with well- reconstructed haplotypes and upweight the probability that these segments should be placed in other individuals. We repeat this process until we are no longer successfully reconstructing additional ancestral haplotypes. Unlike previous approaches, our method is able to accommodate complex pedigree structures with hundreds of individuals genotyped at millions of SNPs. We apply our method to an Old Order Amish pedigree from Lancaster, Pennsylvania, whose founders came to the United States from Europe during the early 18th century. The pedigree includes 1338 individuals from the past 10 generations, 394 with genotype data. The motivation for reconstruction is to understand the genetic basis of diseases segregating in the family through tracking haplotype transmission over time. Using our algorithm thread, we are able to reconstruct an average of 230 ancestral individuals per autosome. thread was developed for endogamous populations, but can be applied to any extensive pedigree with the recent generations genotyped. We anticipate that this type of practical ancestral reconstruction will become more common and necessary to understand rare and complex heritable diseases in extended families.

16: Morphological profiling of human T and NK lymphocytes identifies actin-mediated control of the immunological synapse
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Posted to bioRxiv 17 Jan 2020

Morphological profiling of human T and NK lymphocytes identifies actin-mediated control of the immunological synapse
26 tweets immunology

Yolla German, Loan Vulliard, Aude Rubio, Kaan Boztug, Audrey Ferrand, Joerg Menche, Loic Dupre

he detection and neutralization of infected cells and tumors by cytotoxic lymphocytes is a vital immune defense mechanism. The immunological synapse orchestrates the target recognition process and the subsequent cytotoxic activity. Here, we present an integrated experimental and computational strategy to systematically characterize the morphological properties of the immunological synapse of human cytotoxic lymphocytes. Our approach combines high-content imaging with an unbiased, data-driven identification of high-resolution morphological profiles. Such profiling discriminates with high accuracy immunological synapse perturbations induced by an array of actin drugs in both model cell lines and primary lymphocytes. It reveals inter-individual heterogeneity in lymphocyte morphological traits. Furthermore, it uncovers immunological synapse alterations in functionally defective CD8+ T cells from immunodeficient patients carrying ARPC1B mutations. Our study thus provides a foundation for the application of morphological profiling as a powerful and scalable approach to monitor lymphocyte activation status in experimental and disease settings.

17: Multiplexed Single-cell Metabolic Profiles Organize the Spectrum of Human Cytotoxic T Cells
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Posted to bioRxiv 17 Jan 2020

Multiplexed Single-cell Metabolic Profiles Organize the Spectrum of Human Cytotoxic T Cells
25 tweets immunology

Felix J Hartmann, Dunja Mrdjen, Erin McCaffrey, David R Glass, Noah F Greenwald, Anusha Bharadwaj, Zumana Khair, Alex Baranski, Reema Baskar, Michael Angelo, Sean C Bendall

Cellular metabolism regulates immune cell activation, differentiation and effector functions to the extent that its perturbation can augment immune responses. However, the analytical technologies available to study cellular metabolism lack single-cell resolution, obscuring metabolic heterogeneity and its connection to immune phenotype and function. To that end, we utilized high-dimensional, antibody-based technologies to simultaneously quantify the single-cell metabolic regulome in combination with phenotypic identity. Mass cytometry (CyTOF)-based application of this approach to early human T cell activation enabled the comprehensive reconstruction of the coordinated metabolic remodeling of naive CD8+ T cells and aligned with conventional bulk assays for glycolysis and oxidative phosphorylation. Extending this analysis to a variety of tissue-resident immune cells revealed tissue-restricted metabolic states of human cytotoxic T cells, including metabolically repressed subsets that expressed CD39 and PD1 and that were enriched in colorectal carcinoma versus healthy adjacent tissue. Finally, combining this approach with multiplexed ion beam imaging by time-of-flight (MIBI-TOF) demonstrated the existence of spatially enriched metabolic neighborhoods, independent of cell identity and additionally revealed exclusion of metabolically repressed cytotoxic T cell states from the tumor-immune boundary in human colorectal carcinoma. Overall, we provide an approach that permits the robust approximation of metabolic states in individual cells along with multimodal analysis of cell identity and functional characteristics that can be applied to human clinical samples to study cellular metabolism how it may be perturbed to affect immunological outcomes.

18: Protocol for Community-created Public MS/MS Reference Library Within the GNPS Infrastructure
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Posted to bioRxiv 15 Oct 2019

Protocol for Community-created Public MS/MS Reference Library Within the GNPS Infrastructure
24 tweets bioinformatics

Fernando Vargas, Kelly Weldon, Nicole Sikora, Mingxun Wang, Zheng Zhang, Emily C. Gentry, Morgan W. Panitchpakdi, Andres Mauricio Caraballo Rodriguez, Pieter C. Dorrestein, Alan K. Jarmusch

Rationale: A major hurdle in identifying chemicals in mass spectrometry experiments is the availability of MS/MS reference spectra in public databases. Currently, scientists purchase databases or use public databases such as GNPS. The MSMS-Chooser workflow empowers the creation of MS/MS reference spectra directly in the GNPS infrastructure. Methods: An MSMS-Chooser sample template was completed with the required information and sequence tables were generated programmatically. Standards in methanol-water (1:1) solution (1 uM) were placed into wells individually. An LC-MS/MS system using data-dependent acquisition in positive and negative modes was used. Species that may be generated under typical ESI conditions are chosen. The MS/MS spectra and MSMS-Chooser sample template were subsequently uploaded to MSMS-Chooser in GNPS for automatic MS/MS spectral annotation. Results: Data acquisition quickly and effectively collected MS/MS spectra. MSMS-Chooser was able to accurately annotate 99.2% of the manually validated MS/MS scans that were generated from the chemical standards. The output of MSMS-Chooser includes a table ready for inclusion in the GNPS library (after inspection) as well as the ability to directly launch searches via MASST. Altogether, the data acquisition, processing, and upload to GNPS took ~2 hours for our proof-of-concept results. Conclusions: The MSMS-Chooser workflow enables the rapid data acquisition, analysis, and annotation of chemical standards, and uploads the MS/MS spectra to community-driven GNPS. MSMS-Chooser democratizes the creation of MS/MS reference spectra in GNPS which will improve annotation and strengthen the tools which use the annotation information.

19: Expanded Phylogenetic Diversity and Metabolic Flexibility of Microbial Mercury Methylation
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Posted to bioRxiv 17 Jan 2020

Expanded Phylogenetic Diversity and Metabolic Flexibility of Microbial Mercury Methylation
23 tweets microbiology

Elizabeth A McDaniel, Benjamin Peterson, Sarah LR Stevens, Patricia Q. Tran, Karthik Anantharaman, Katherine McMahon

Methylmercury is a potent, bioaccumulating neurotoxin that is produced by specific microorganisms by methylation of inorganic mercury released from anthropogenic sources. The hgcAB genes were recently discovered to be required for microbial methylmercury production in diverse anaerobic bacteria and archaea. However, the full phylogenetic and metabolic diversity of mercury methylating microorganisms has not been fully explored due to the limited number of cultured, experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury methylating microorganisms identified by hgcA sequence identity from publicly available isolate genomes and metagenome-assembled genomes (MAGs), as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known, and the distribution of hgcA is most likely due to several independent horizontal gene transfer events. Identified methylating microorganisms possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. Using a metatranscriptomic survey of a thawing permafrost gradient from which we identified 111 putative mercury methylators, we demonstrate that specific methylating populations may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify methylators based upon hgcA presence and describe their putative functions in the environment.

20: The npBAF to nBAF Chromatin Switch Regulates Cell Cycle Exit in the Developing Mammalian Cortex
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Posted to bioRxiv 17 Jan 2020

The npBAF to nBAF Chromatin Switch Regulates Cell Cycle Exit in the Developing Mammalian Cortex
19 tweets developmental biology

Simon Braun, Ralitsa Petrova, Jiong Tang, Andrey Krokhotin, Erik Miller, Yitai Tang, Georgia Panagiotakos, Gerald Crabtree

Nervous system development is orchestrated by tightly-regulated progenitor cell divisions, followed by differentiation at precise but varying times across different regions. As progenitors exit the cell cycle, they initiate a subunit switch of the mSWI/SNF or npBAF complex to generate neuron-specific nBAF complexes. These chromatin regulatory complexes play dosage-sensitive roles in neural development and are frequently mutated in neurodevelopmental disorders. Here we manipulated the timing of BAF subunit exchange in the developing mouse brain and find that deletion of the npBAF subunit BAF53a blocks progenitor proliferation, leading to impaired neurogenesis. We show that npBAF complexes regulate cell cycle progression by antagonizing Polycomb complexes to promote chromatin accessibility at cell cycle and NPC identity genes. Replacement of the actin-related protein, Actl6a (BAF53a) by the neuron-specific actin-related protein, Actl6b (BAF53b), but not other regulators of proliferation, rescues progenitors by promoting neuronal differentiation. We propose that the function of the npBAF to nBAF chromatin switch is to control progenitor cell cycle exit and promote synchronous neural differentiation.

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