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10.1101/498378 | Species Tree Inference on Data with Paralogs is Accurate Using Methods Intended to Deal with Incomplete Lineage Sorting | AO_SCPLOWBSTRACTC_SCPLOWMany recent phylogenetic methods have focused on accurately inferring species trees when there is gene tree discordance due to incomplete lineage sorting (ILS). For almost all of these methods, and for phylogenetic methods in general, the data for each locus is assumed to consist of orthologous,... | evolutionary biology |
10.1101/501221 | Neurocomputational underpinnings of expected surprise | Predictive coding accounts of brain functions profoundly influence current approaches to perceptual synthesis. However, a fundamental paradox has emerged, that may be very relevant for understanding hallucinations, psychosis or cognitive inflexibility. This paradox is that in some situations surprise or prediction erro... | neuroscience |
10.1101/502328 | Visual exposure enhances stimulus encoding and persistence in primary cortex | The brain adapts to the sensory environment. For example, simple sensory exposure can modify the response properties of early sensory neurons. How these changes affect the overall encoding and maintenance of stimulus information across neuronal populations remains unclear. We perform parallel recordings in the primary ... | neuroscience |
10.1101/501627 | Sensory coding and causal impact of mouse cortex in a visual decision | Correlates of sensory stimuli and motor actions are found in multiple cortical areas, but such correlates do not indicate whether these areas are causally relevant to task performance. We trained mice to discriminate visual contrast and report their decision by turning a wheel. Widefield calcium imaging and Neuropixels... | neuroscience |
10.1101/501627 | Sensory coding and causal impact of mouse cortex in a visual decision | Correlates of sensory stimuli and motor actions are found in multiple cortical areas, but such correlates do not indicate whether these areas are causally relevant to task performance. We trained mice to discriminate visual contrast and report their decision by turning a wheel. Widefield calcium imaging and Neuropixels... | neuroscience |
10.1101/500108 | Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics | Cancer stem cells drive disease progression and relapse in many types of cancer. Despite this, a thorough characterization of these cells remains elusive and with i the ability to eradicate cancer at its source. In acute myeloid leukemia (AML), leukemic stem cells (LSCs) underlie mortality but are difficult to isolate ... | genomics |
10.1101/504332 | Differential dominance of an allele of the Drosophila tbetah gene challenges standard genetic techniques | The biogenic amine octopamine (OA) and its precursor tyramine (TA) are involved in controlling a plethora of different physiological and behavioral processes. The tyramine-{beta}-hydroxylase (t{beta}h) gene encodes the enzyme catalyzing the last synthesis step from TA to OA. Here, we report differential dominance (from... | genetics |
10.1101/506261 | Feedback between a retinoid-related nuclear receptor and the let-7 microRNAs controls the pace and number of molting cycles in C. elegans. | Animal development requires coordination among cyclic processes, sequential cell fate specifications, and once-a-lifetime morphogenic events, but the underlying mechanisms are not well understood. C. elegans undergo four molts at regular 8-10 h intervals. The pace of the cycle is governed by PERIOD/lin-42 and other as-... | developmental biology |
10.1101/508572 | Cyclic Nucleotide-Gated Ion Channel 2 modulates auxin homeostasis and signaling | Cyclic Nucleotide Gated Ion Channels (CNGCs) have been firmly established as Ca2+-conducting ion channels that regulate a wide variety of physiological responses in plants. CNGC2 has been implicated in plant immunity and Ca2+ signaling due to the autoimmune phenotypes exhibited by null mutants of CNGC2. However, cngc2 ... | plant biology |
10.1101/508242 | Identifying complex sequence patterns with a variable-convolutional layer effectively and efficiently | Motif identification is among the most common and essential computational tasks for bioinformatics and genomics. Here we proposed a novel convolutional layer for deep neural network, named Variable Convolutional (vConv) layer, for effective motif identification in high-throughput omics data by learning kernel length fr... | bioinformatics |
10.1101/508242 | Identifying complex sequence patterns in massive omics data with a variable-convolutional layer in deep neural network | Motif identification is among the most common and essential computational tasks for bioinformatics and genomics. Here we proposed a novel convolutional layer for deep neural network, named Variable Convolutional (vConv) layer, for effective motif identification in high-throughput omics data by learning kernel length fr... | bioinformatics |
10.1101/508242 | Identifying complex motifs in massive omics data with a variable-convolutional layer in deep neural network | Motif identification is among the most common and essential computational tasks for bioinformatics and genomics. Here we proposed a novel convolutional layer for deep neural network, named Variable Convolutional (vConv) layer, for effective motif identification in high-throughput omics data by learning kernel length fr... | bioinformatics |
10.1101/512780 | Rigorous equations for isothermal titration calorimetry: theoretical and practical consequences | The author has withdrawn his manuscript because:
The withdrawn preprint was about methodological aspects in Isothermal Titration Calorimetry (ITC) used to obtain thermodynamic information about reactions like A + B {rightleftarrows} C where A is initially in the cell and B injected from a syringe. The preprint conside... | biophysics |
10.1101/513572 | Discovering footprints of evolutionary chromatin response to transposons activity: merging biophysics with bioinformatics | Transposons are genome components that account for the majority of genome size in many organisms, behaving as parasitic entities and interfering with the translation mechanism. Chromatin structure influences the activity of transposons, by coordinating genome accessibility for the expression and insertion of these sequ... | biophysics |
10.1101/516443 | Chloroplasts alter their morphology and accumulate at the pathogen interface during infection by Phytophthora infestans | Upon immune activation, chloroplasts switch off photosynthesis, produce anti-microbial compounds, and associate with the nucleus through tubular extensions called stromules. Although it is well-established that chloroplasts alter their position in response to light, little is known about the dynamics of chloroplasts mo... | plant biology |
10.1101/516831 | Sequestration of RBM10 in Nuclear Bodies: Targeting Sequences and Biological Significance | RBM10 is an RNA-binding protein that regulates alternative splicing (AS). It localizes to the extra-nucleolar nucleoplasm and S1-1 nuclear bodies (NBs) in the nucleus. We investigated the biological significance of this localization in relation to its molecular function. Our analyses, employing deletion mutants, reveal... | molecular biology |
10.1101/518936 | Rbm10 facilitates heterochromatin assembly via the Clr6 HDAC complex | Splicing factors have recently been shown to be involved in heterochromatin formation, but their role in controlling heterochromatin structure and function remains poorly understood. In this study, we identified a fission yeast homologue of human splicing factor RBM10, which has been linked to TARP syndrome. Overexpres... | molecular biology |
10.1101/519629 | A Data-Driven Transcriptional Taxonomy of Adipogenic Chemicals to Identify White and Brite Adipogens | BackgroundChemicals in disparate structural classes activate specific subsets of PPAR{gamma}s transcriptional programs to generate adipocytes with distinct phenotypes.
ObjectivesOur objectives were to 1) establish a novel classification method to predict PPAR{gamma} ligands and modifying chemicals, and 2) create a tax... | pharmacology and toxicology |
10.1101/521369 | Stimulation of phospholipase Cβ1 by Gαq promotes the assembly of stress granule proteins | During adverse conditions, mammalian cells regulate protein production by sequestering the translational machinery in membrane-less organelles known as stress granules. Here, we found that activation of the G protein subunit Gq promoted the formation of particles that contained stress granule proteins through a mechani... | biochemistry |
10.1101/522441 | A neuroendocrine pathway modulating osmotic stress in Drosophila | Environmental factors challenge the physiological homeostasis in animals, thereby evoking stress responses. Various mechanisms have evolved to counter stress at the organism level, including regulation by neuropeptides. In recent years, much progress has been made on the mechanisms and neuropeptides that regulate respo... | neuroscience |
10.1101/522904 | Development and maintenance of synaptic structure is mediated by the alpha-tubulin acetyltransferase MEC-17/αTAT1 | The authors have withdrawn their manuscript whilst they perform additional experiments to test some of their conclusions further. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author | cell biology |
10.1101/520536 | The imprinted Igf2-Igf2r axis is critical for matching placental microvasculature expansion to fetal growth | In all eutherian mammals, growth of the fetus is dependent upon a functional placenta, but whether and how the latter adapts to putative fetal signals is currently unknown. Here we demonstrate, through fetal, endothelial, hematopoietic and trophoblast-specific genetic manipulations in the mouse, that endothelial and fe... | developmental biology |
10.1101/520536 | The imprinted Igf2-Igf2r axis is critical for matching placental microvasculature expansion to fetal growth | In all eutherian mammals, growth of the fetus is dependent upon a functional placenta, but whether and how the latter adapts to putative fetal signals is currently unknown. Here we demonstrate, through fetal, endothelial, hematopoietic and trophoblast-specific genetic manipulations in the mouse, that endothelial and fe... | developmental biology |
10.1101/521401 | Progressive domain segregation in early embryonic development and underlying correlation to genetic and epigenetic changes | Chromatin undergoes drastic structural organization and epigenetic reprogramming during embryonic development. We present here a consistent view of the chromatin structural change, epigenetic reprogramming and the corresponding sequence dependence in both mouse and human embryo development. The two types of domains, id... | developmental biology |
10.1101/527002 | Krüppel-like factor gene function in the ctenophore Mnemiopsis leidyi assessed by CRISPR/Cas9-mediated genome editing | The Kruppel-like factor (Klf) gene family encodes for transcription factors that play an important role in the regulation of stem cell proliferation, cell differentiation, and development in bilaterians. While Klf genes have been shown to functionally specify various cell types in non-bilaterian animals, their role in ... | developmental biology |
10.1101/525600 | Cellular transformation by combined lineage conversion and oncogene expression | Cancer is the most complex genetic disease known, with mutations implicated in more than 250 genes. However, it is still elusive which specific mutations found in human patients lead to tumorigenesis. Here we show that a combination of oncogenes that is characteristic of liver cancer (CTNNB1, TERT, MYC) induces senesce... | cancer biology |
10.1101/525600 | Cellular transformation by combined lineage conversion and oncogene expression | Cancer is the most complex genetic disease known, with mutations implicated in more than 250 genes. However, it is still elusive which specific mutations found in human patients lead to tumorigenesis. Here we show that a combination of oncogenes that is characteristic of liver cancer (CTNNB1, TERT, MYC) induces senesce... | cancer biology |
10.1101/527754 | Phosphorylation-dependent routing of RLP44 towards brassinosteroid or phytosulfokine signalling | Plants rely on a complex network of cell surface receptors to integrate developmental and environmental cues into behaviour adapted to the conditions. The largest group of these receptors, leucine-rich repeat receptor-like kinases, form a complex interaction network that is modulated and extended by receptor-like prote... | plant biology |
10.1101/529040 | Identification of sample mix-ups and mixtures in microbiome data in Diversity Outbred mice | In a Diversity Outbred mouse project with genotype data on 500 mice, including 297 with microbiome data, we identified three sets of sample mix-ups (two pairs and one trio) as well as at least 15 microbiome samples that appear to be mixtures of pairs of mice. The microbiome data consisted of shotgun sequencing reads fr... | genetics |
10.1101/529040 | Identification of sample mix-ups and mixtures in microbiome data in Diversity Outbred mice | In a Diversity Outbred mouse project with genotype data on 500 mice, including 297 with microbiome data, we identified three sets of sample mix-ups (two pairs and one trio) as well as at least 15 microbiome samples that appear to be mixtures of pairs of mice. The microbiome data consisted of shotgun sequencing reads fr... | genetics |
10.1101/529560 | Widespread latitudinal asymmetry in marginal population performance | AimRange shifts are expected to occur when populations at one range margin perform better than those at the other margin, yet no global trend in population performances at range margins has been demonstrated empirically across a wide range of taxa and biomes. Here we test the prediction that, if impacts of ongoing clim... | ecology |
10.1101/529719 | Chemogenetic inhibition of a monosynaptic projection from the basolateral amygdala to the ventral hippocampus reduces appetitive and consummatory alcohol drinking behaviors | Alcohol use disorder (AUD) and anxiety/stressor disorders frequently co-occur and this dual diagnosis represents a major health and economic problem worldwide. The basolateral amygdala (BLA) is a key brain region that is known to contribute to the etiology of both disorders. Although many studies have implicated BLA hy... | neuroscience |
10.1101/530329 | Thunor: Visualization and Analysis of High-Throughput Dose-response Datasets | High-throughput cell proliferation assays to quantify drug-response are becoming increasingly common and powerful with the emergence of improved automation and multi-time point analysis methods. However, pipelines for analysis of these datasets that provide reproducible, efficient, and interactive visualization and int... | pharmacology and toxicology |
10.1101/530220 | High-pass filtering artifacts in multivariate classification of neural time series data | 0.BackgroundTraditionally, EEG/MEG data are high-pass filtered and baseline-corrected to remove slow drifts. Minor deleterious effects of high-pass filtering in traditional time-series analysis have been well-documented, including temporal displacements. However, its effects on time-resolved multivariate pattern classi... | neuroscience |
10.1101/528638 | The HIV-1 ribonucleoprotein dynamically regulates its condensate behavior and drives acceleration of protease activity through membraneless granular phase separation | A growing number of studies indicate that mRNAs and long ncRNAs can affect protein populations by assembling dynamic ribonucleoprotein (RNP) granules. These phase separated molecular sponges, stabilized by quinary (transient and weak) interactions, control proteins involved in numerous biological functions. Retrovirus... | molecular biology |
10.1101/531822 | Long-term potentiation in neurogliaform cells modulates excitation-inhibition balance in the temporoammonic pathway | Apical dendrites of pyramidal neurons integrate information from higher-order cortex and thalamus, and gate signaling and plasticity at proximal synapses. In the hippocampus, neurogliaform cells and other interneurons located within stratum lacunosum-moleculare mediate powerful inhibition of CA1 pyramidal neuron distal... | neuroscience |
10.1101/532952 | Individual tree-crown detection in RGB imagery using semi-supervised deep learning neural networks | Remote sensing can transform the speed, scale, and cost of biodiversity and forestry surveys. Data acquisition currently outpaces the ability to identify individual organisms in high resolution imagery. We outline an approach for identifying tree-crowns in RGB imagery while using a semi-supervised deep learning detecti... | ecology |
10.1101/532952 | Individual tree-crown detection in RGB imagery using semi-supervised deep learning neural networks | Remote sensing can transform the speed, scale, and cost of biodiversity and forestry surveys. Data acquisition currently outpaces the ability to identify individual organisms in high resolution imagery. We outline an approach for identifying tree-crowns in RGB imagery while using a semi-supervised deep learning detecti... | ecology |
10.1101/533323 | Multi-omic analyses reveal a role for mammalian CIC in cell cycle regulation and mitotic fidelity | CIC encodes a transcriptional repressor that is inactivated by loss-of-function mutations in several cancer types, indicating that it may function as a tumor suppressor. Recent studies have indicated that CIC may regulate cell cycle genes in humans; however, a systematic investigation of this proposed role has not yet ... | cancer biology |
10.1101/534834 | Network Inference with Granger Causality Ensembles on Single-Cell Transcriptomic Data | Advances in single-cell transcriptomics enable measuring the gene expression of individual cells, allowing cells to be ordered by their state in a dynamic biological process. Many algorithms assign pseudotimes to each cell, representing the progress along the biological process. Ordering the expression data according ... | bioinformatics |
10.1101/534750 | Multiple sources of Shh are critical for the generation and scaling of ventral spinal cord oligodendrocyte precursor populations. | Graded Sonic Hedgehog (Shh) signaling emanating from notochord and floorplate patterns the early neural tube. Soon thereafter, Shh signaling strength within the ventricular zone becomes dis-contiguous and discontinuous along the ventral to dorsal axis suggesting a distribution of Shh that cannot be achieved by diffusio... | developmental biology |
10.1101/536078 | Microbial metabolism and adaptations in Atribacteria-dominated methane hydrate sediments | Gas hydrates harbor gigatons of natural gas, yet their microbiomes remain understudied. We bioprospected 16S rRNA amplicons, metagenomes, and metaproteomes from methane hydrate-bearing sediments under Hydrate Ridge (offshore Oregon, USA, ODP Site 1244, 2-69 mbsf) for novel microbial metabolic and biosynthetic potential... | microbiology |
10.1101/538165 | A Stomata Classification and Detection System in Microscope Images of Maize Cultivars | Research on stomata, i.e., morphological structures of plants, has increased in popularity in the last years. These structures (pores) are in charge of the interaction between the internal plant system and the environment, working on different processes such as photosynthesis and transpiration stream. Besides, a better... | plant biology |
10.1101/540971 | A scalar Poincare map for struggling in Xenopus tadpoles | Short-term synaptic plasticity is widely found in many areas of the central nervous system. In particular, it is believed that synaptic depression can act as a mechanism to allow simple networks to generate a range of different firing patterns. The locomotor circuit of hatchling Xenopus tadpoles produces two types of b... | neuroscience |
10.1101/542340 | Protein appetite drives macronutrient-related differences in ventral tegmental area neural activity | Control of protein intake is essential for numerous biological processes as several amino acids cannot be synthesized de novo, however, its neurobiological substrates are still poorly understood. In the present study, we combined in vivo fiber photometry with nutrient-conditioned flavor in a rat model of protein appeti... | neuroscience |
10.1101/544981 | Dot1L-dependent H3K79 methylation facilitates histone variant H2A.Z exchange at DNA double strand breaks and is required for high fidelity, homology-directed DNA repair | In eukaryotic cells, the homology-directed repair (HDR) and non-homologous end joining (NHEJ) pathways are required for the repair of DNA double strand breaks (DSB). The high-fidelity HDR pathway is particularly important for maintenance of genomic stability. In mammals, histone post-translational modifications and his... | molecular biology |
10.1101/541805 | Optical measurement of voltage sensing by endogenous ion channel | A primary goal of molecular physiology is to understand how conformational changes of proteins affect the function of cells, tissues, and organisms. Here, we describe an imaging method for measuring the conformational changes of the voltage sensors of endogenous ion channel proteins within live tissue, without genetic ... | biophysics |
10.1101/546309 | BLight: Efficient exact associative structure for k-mers | MotivationA plethora of methods and applications share the fundamental need to associate information to words for high throughput sequence analysis. Doing so for billions of k-mers is commonly a scalability problem, as exact associative indexes can be memory expensive. Recent works take advantage of overlaps between k-... | bioinformatics |
10.1101/548412 | Work Flows for Cellular Epidemiology, From Conception to Translation | The authors have withdrawn their manuscript after issues with the cell viability validation (Fig. 8) were found. In the interest of furthering science and ensuring that clinical decisions are based on best practices and evidence, the issue is described in more detail in the peer-reviewed, published paper: https://www.f... | physiology |
10.1101/547794 | Maize brace root mechanics vary by whorl, genotype, and reproductive stage | Root lodging is responsible for significant crop losses world-wide. During root lodging, roots fail by breaking, buckling, or pulling out of the ground. In maize, above-ground roots, called brace roots, have been shown to reduce root lodging susceptibility. However, the underlying structural-functional properties of br... | plant biology |
10.1101/549386 | Urinary glucocorticoids in harbour seal (Phoca vitulina) pups during rehabilitation | The glucocorticoid (GC) hormone cortisol is often measured in animals to indicate their welfare and stress levels. However, the levels of other naturally occurring GCs are usually overlooked. We aimed to investigate whether aspects of the care and conditions of harbour seal (Phoca vitulina) pups in rehabilitation centr... | zoology |
10.1101/550368 | The pharmacodynamic inoculum effect from the perspective of bacterial population modeling | SynopsisO_ST_ABSBackgroundC_ST_ABSThe quantitative determination of the effects of antimicrobials is essential for our understanding of pharmacodynamics and for their rational clinical application. However, common pharmacodynamic measures of antimicrobial efficacy, such as the MIC and the pharmacodynamic function, fail... | pharmacology and toxicology |
10.1101/551580 | Opposing steroid signals modulate protein homeostasis through deep changes in fat metabolism in Caenorhabditis elegans | Protein homeostasis is crucial for viability of all organisms, and mutations that enhance protein aggregation cause different human pathologies, including polyglutamine (polyQ) diseases, such as some spinocerebellar ataxias or Huntington disease. Here, we report that neuronal Stomatin-like protein UNC-1 protects agains... | genetics |
10.1101/547877 | Traces of transposable element in genome dark matter co-opted by flowering gene regulation networks. | AO_SCPLOWBSTRACTC_SCPLOWTransposable elements (TEs) are mobile, repetitive DNA sequences that make the largest contribution to genome bulk. They thus contribute to the so-called "dark matter of the genome", the part of the genome in which nothing is immediately recognizable as biologically functional.
We developed a n... | genomics |
10.1101/547877 | Traces of transposable element in genome dark matter co-opted by flowering gene regulation networks. | AO_SCPLOWBSTRACTC_SCPLOWTransposable elements (TEs) are mobile, repetitive DNA sequences that make the largest contribution to genome bulk. They thus contribute to the so-called "dark matter of the genome", the part of the genome in which nothing is immediately recognizable as biologically functional.
We developed a n... | genomics |
10.1101/550640 | Rabies virus with a destabilization domain added to its nucleoprotein spreads between neurons only if the domain is removed | Monosynaptic tracing using rabies virus is an important technique in neuroscience, allowing brain-wide labeling of neurons directly presynaptic to a targeted neuronal population. A 2017 article reported development of a noncytotoxic version - a major advance - based on attenuating the rabies virus by addition of a dest... | neuroscience |
10.1101/550640 | Rabies virus with a destabilization domain added to its nucleoprotein spreads between neurons only if the domain is removed | Monosynaptic tracing using rabies virus is an important technique in neuroscience, allowing brain-wide labeling of neurons directly presynaptic to a targeted neuronal population. A 2017 article reported development of a noncytotoxic version - a major advance - based on attenuating the rabies virus by addition of a dest... | neuroscience |
10.1101/555276 | Dynamically Linking Influenza Virus Infection Kinetics, Lung Injury, Inflammation, and Disease Severity | Influenza viruses cause a significant amount of morbidity and mortality. Understanding host immune control efficacy and how different factors influence lung injury and disease severity are critical. Here, we established dynamical connections between viral loads, infected cells, CD8+ T cell-mediated clearance, lung inju... | systems biology |
10.1101/556571 | Transcriptomic analysis of human and mouse muscle during hyperinsulinemia demonstrates insulin receptor downregulation as a mechanism for insulin resistance | Hyperinsulinemia is commonly viewed as a compensatory response to insulin resistance, yet studies have suggested that chronically elevated insulin may also drive insulin resistance. The molecular mechanisms underpinning this potentially cyclic process remain poorly defined, especially on a transcriptome-wide level. To ... | physiology |
10.1101/558890 | Endocytosis against high turgor pressure is made easier by partial protein coating and a freely rotating base | During clathrin-mediated endocytosis, a patch of flat plasma membrane is deformed into a vesicle. In walled cells, such as plants and fungi, the turgor pressure is high and pushes the membrane against the cell wall, thus hindering membrane internalization. In this paper, we study how a patch of membrane is deformed aga... | biophysics |
10.1101/560011 | Negative Affect Induces Rapid Learning of Counterfactual Representations: A Model-based Facial Expression Analysis Approach | Whether we are making life-or-death decisions or thinking about the best way to phrase an email, counterfactual emotions including regret and disappointment play an ever-present role in how we make decisions. Functional theories of counterfactual thinking suggest that the experience and future expectation of counterfac... | neuroscience |
10.1101/559948 | Coding Triplets in the Transfer RNA acceptor Arm and Their Role in Present and Past tRNA Recognition | The mechanism and evolution of the recognition scheme between key components of the translation system, i.e., tRNAs, synthetases and elongation factors, are fundamental issues in understanding the translation of genetic information into proteins. Statistical analysis of bacterial tRNA sequences reveals that for six ami... | genetics |
10.1101/561548 | Internal noise measures in coarse and fine motion direction discrimination tasks, and the correlation with autism traits | Motion perception is essential for visual guidance of behaviour and is known to be limited by both internal additive noise (arising from random fluctuations in neural activity), and by motion pooling (global integration of local motion signals across space). People with autism spectrum disorder (ASD) display abnormalit... | neuroscience |
10.1101/565796 | Polymer brush bilayers under stationary shear motion at linear response regime: A theoretical approach | Statistical mechanics is employed to tackle the problem of polymer brush bilayers under stationary shear motion. The article addresses, solely, the linear response regime in which the polymer brush bilayers behave very much similar to the Newtonian fluids. My approach to this long-standing problem split drastically fro... | biophysics |
10.1101/568626 | What the odor is not: Estimation by elimination | Olfactory systems use a small number of broadly sensitive receptors to combinatorially encode a vast number of odors. We propose a method of decoding such distributed representations by exploiting a statistical fact: receptors that do not respond to an odor carry more information than receptors that do because they sig... | neuroscience |
10.1101/571083 | The Cdc14 phosphatase controls resolution of recombination intermediates and crossover formation during meiosis | Meiotic defects derived from incorrect DNA repair during gametogenesis can lead to mutations, aneuploidies and infertility. Coordinated resolution of meiotic recombination intermediates is required for crossover formation, ultimately necessary for accurate completion of both rounds of chromosome segregation. Numerous m... | genetics |
10.1101/572156 | The solution structure of Dead End bound to AU-rich RNA reveals an unprecedented mode of tandem RRM-RNA recognition required for mRNA regulation | Dead End (DND1) is an RNA-binding protein essential for germline development through its role in post-transcriptional gene regulation. The molecular mechanisms behind selection and regulation of its targets are unknown. Here, we present the solution structure of DND1s tandem RNA Recognition Motifs (RRMs) bound to AU-ri... | molecular biology |
10.1101/570556 | Conserving unprotected important coastal habitats in the Yellow Sea: shorebird occurrence, distribution and food resources at Lianyungang | The authors have withdrawn their manuscript since this preprint contain errors which have been corrected in the version published in the journal Global Ecology and Conservation (doi: 10.1016/j.gecco.2019.e00724). Therefore, the authors do not wish this preprint to be cited as reference for the project. If you have any... | ecology |
10.1101/570580 | Eco-evolutionary dynamics further weakens mutualistic interaction and coexistence under population decline | AO_SCPLOWBSTRACTC_SCPLOWWith current environmental changes, evolution can rescue declining populations, but what happens to their interacting species? Mutualistic interactions can help species sustain each other when their environment worsens. However, mutualism is often costly to maintain, and evolution might counter-... | ecology |
10.1101/570580 | Eco-evolutionary dynamics further weakens mutualistic interaction and coexistence under population decline | AO_SCPLOWBSTRACTC_SCPLOWWith current environmental changes, evolution can rescue declining populations, but what happens to their interacting species? Mutualistic interactions can help species sustain each other when their environment worsens. However, mutualism is often costly to maintain, and evolution might counter-... | ecology |
10.1101/570580 | Eco-evolutionary dynamics further weakens mutualistic interaction and coexistence under population decline | AO_SCPLOWBSTRACTC_SCPLOWWith current environmental changes, evolution can rescue declining populations, but what happens to their interacting species? Mutualistic interactions can help species sustain each other when their environment worsens. However, mutualism is often costly to maintain, and evolution might counter-... | ecology |
10.1101/571380 | Event segmentation reveals working memory forgetting rate | We encounter the world as a continuous flow and effortlessly segment sequences of events into episodes. This process of event segmentation engages working memory (WM) for tracking the flow of events and impacts subsequent memory accuracy. WM is limited in how much information is retained (i.e., WM capacity) and for how... | neuroscience |
10.1101/573907 | Recombination-independent recognition of DNA homology for meiotic silencing in Neurospora crassa | Pairing of homologous chromosomes represents a critical step of meiosis in nearly all sexually reproducing species. While in some organisms meiotic pairing requires programmed DNA breakage and recombination, in many others it engages homologous chromosomes that remain apparently intact. The mechanistic nature of such r... | molecular biology |
10.1101/576116 | Publicly available transcriptomes provide the opportunity for dual RNA-Seq meta analysis in Plasmodium infection | Dual RNA-Seq is the simultaneous transcriptomic analysis of interacting symbionts, for example, in malaria. Potential cross-species interactions identified by correlated gene expression might highlight interlinked signaling, metabolic or gene regulatory pathways in addition to physically interacting proteins. Often, ma... | bioinformatics |
10.1101/576793 | Common variants associated with OSMR expression contribute to carotid plaque vulnerability, but not to cardiovascular disease in humans | Background and aimsOncostatin M (OSM) signaling is implicated in atherosclerosis, however the mechanism remains unclear. We investigated the impact of common genetic variants in OSM and its receptors, OSMR and LIFR, on overall plaque vulnerability, plaque phenotype, intraplaque OSMR and LIFR expression, coronary artery... | genetics |
10.1101/576793 | Common variants associated with OSMR expression contribute to carotid plaque vulnerability, but not to cardiovascular disease in humans | Background and aimsOncostatin M (OSM) signaling is implicated in atherosclerosis, however the mechanism remains unclear. We investigated the impact of common genetic variants in OSM and its receptors, OSMR and LIFR, on overall plaque vulnerability, plaque phenotype, intraplaque OSMR and LIFR expression, coronary artery... | genetics |
10.1101/577833 | Liver X Receptor; Controls Hepatic Stellate Cell Activation via Hedgehog Signaling | Liver X receptors (LXR) and {beta} serve important roles in cholesterol homeostasis, anti-inflammatory processes and the activation of hepatic stellate cells (HSCs). However, the development of therapies for liver fibrosis based on LXR agonists have been hampered due to side-effects such as liver steatosis. In this st... | cell biology |
10.1101/579151 | Balancing selection of the Intracellular Pathogen Response in natural Caenorhabditis elegans populations | Genetic variation in host populations may lead to differential viral susceptibilities. Here, we investigate the role of natural genetic variation in the Intracellular Pathogen Response (IPR), an important antiviral pathway in the model organism Caenorhabditis elegans against Orsay virus (OrV). The IPR involves transcri... | genetics |
10.1101/579151 | Balancing selection of the Intracellular Pathogen Response in natural Caenorhabditis elegans populations | Genetic variation in host populations may lead to differential viral susceptibilities. Here, we investigate the role of natural genetic variation in the Intracellular Pathogen Response (IPR), an important antiviral pathway in the model organism Caenorhabditis elegans against Orsay virus (OrV). The IPR involves transcri... | genetics |
10.1101/580258 | A candidate causal variant underlying both enhanced cognitive performance and increased risk of bipolar disorder | Bipolar disorder is a highly heritable mental illness, but the relevant genetic variants and molecular mechanisms are largely unknown. Recent GWASs have identified an intergenic region associated with both cognitive performance and bipolar disorder. This region contains dozens of putative fetal brain-specific enhancers... | genetics |
10.1101/581660 | PME-1 suppresses anoikis, and is associated with therapy relapse of PTEN-deficient prostate cancers | While organ-confined PCa is mostly therapeutically manageable, metastatic progression of PCa remains an unmet clinical challenge. Resistance to anoikis, a form of cell death initiated by cell detachment from the surrounding extracellular matrix, is one of the cellular processes critical for PCa progression towards aggr... | cancer biology |
10.1101/581827 | A stable pollination environment limits current but not potential evolution of floral traits | The vast variation in floral traits at a macroevolutionary level is often interpreted as the result of adaptation to pollinators. However, studies in wild populations often find no evidence of pollinator-mediated selection on flowers. Evolutionary theory predicts this could be the outcome of long periods of stasis unde... | evolutionary biology |
10.1101/582056 | Protein structure without structure determination: direct coupling analysis based on in vitro evolution | Protein structure is tightly inter-twined with function according to the laws of evolution. Understanding how structure determines function has been the aim of structural biology for decades. Here, we have wondered instead whether it is possible to exploit the function for which a protein was evolutionary selected to g... | evolutionary biology |
10.1101/581876 | Variations in Structural MRI Quality Significantly Impact Commonly-Used Measures of Brain Anatomy | Subject motion can introduce noise into neuroimaging data and result in biased estimations of brain structure. In-scanner motion can compromise data quality in a number of ways and varies widely across developmental and clinical populations. However, quantification of structural image quality is often limited to proxy ... | neuroscience |
10.1101/585133 | Rapid neural representations of personally relevant faces | The faces of those most personally relevant to us are our primary source of social information, making their timely perception a priority. Recent research indicates that gender, age and identity of faces can be decoded from EEG/MEG data within 100ms. Yet the time course and neural circuitry involved in representing the... | neuroscience |
10.1101/584409 | Single trial dynamics of attentional intensity in visual area V4 | Understanding how activity of visual neurons represents distinct components of attention and their dynamics that account for improved visual performance remains elusive because single-unit experiments have not isolated the intensive aspect of attention from attentional selectivity. We isolated attentional intensity and... | neuroscience |
10.1101/583880 | Quantifying Climatic and Socio-Economic Influences on Urban Malaria in Surat, India: A Modelling Study | BackgroundCities are becoming increasingly important habitats for mosquito-borne infections. The pronounced heterogeneity of urban landscapes challenges our understanding of the spatio-temporal dynamics of these diseases, and of the influence of climate and socio-economic factors at different spatial scales. Here, we q... | ecology |
10.1101/585687 | Genomic data and multi-species demographic modelling uncover past hybridization between currently allopatric freshwater species | Evidence for ancient interspecific gene flow through hybridization has been reported in many animal and plant taxa based on genetic markers. The study of genomic patterns of closely related species with allopatric distributions allow to assess the relative importance of vicariant isolating events and past gene flow. He... | evolutionary biology |
10.1101/586545 | Effective clustering for single cell sequencing cancer data | Single cell sequencing (SCS) technologies provide a level of resolution that makes it indispensable for inferring from a sequenced tumor, evolutionary trees or phylogenies representing an accumulation of cancerous mutations. A drawback of SCS is elevated false negative and missing value rates, resulting in a large spac... | cancer biology |
10.1101/586313 | Global mammalian zooregions reveal a signal of past human impacts | Ecologists have long documented that the worlds biota is spatially organized in regions with boundaries shaped by processes acting on geological and evolutionary timescales. Although growing evidence suggests that human impact has been key in how biodiversity is currently assembled, its role as a driver of the geograph... | ecology |
10.1101/586313 | Global mammalian zooregions reveal a signal of past human impacts | Ecologists have long documented that the worlds biota is spatially organized in regions with boundaries shaped by processes acting on geological and evolutionary timescales. Although growing evidence suggests that human impact has been key in how biodiversity is currently assembled, its role as a driver of the geograph... | ecology |
10.1101/588020 | Recovery of trait heritability from whole genome sequence data | Heritability, the proportion of phenotypic variance explained by genetic factors, can be estimated from pedigree data 1, but such estimates are uninformative with respect to the underlying genetic architecture. Analyses of data from genome-wide association studies (GWAS) on unrelated individuals have shown that for hum... | genetics |
10.1101/587030 | The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements | Transposable elements (TEs) are genomic parasites that can propagate by inserting copies of themselves into host genomes. Mammalian genomes are typically dominated by LINE retrotransposons and their associated SINEs, and their mobilization in the germline is a challenge to genome integrity. There are genomic defenses a... | evolutionary biology |
10.1101/589168 | Mammalian mitochondrial mutational spectrum as a hallmark of cellular and organismal aging. | Mutational spectrum of the mitochondrial genome (mtDNA) does not resemble signatures of any known mutagens and variation in mtDNA mutational spectra between different tissues and organisms is still incomprehensible. Since mitochondria is tightly involved in aerobic energy production, it is expected that mtDNA mutationa... | genomics |
10.1101/589002 | Familiar neighbours, but not relatives, enhance fitness in a territorial mammal | SummaryOne of the outstanding questions in evolutionary biology is the extent to which mutually beneficial interactions and kin-selection can facilitate the evolution of cooperation by mitigating conflict between interacting organisms. The indirect fitness benefits gained from associating with kin are an important path... | evolutionary biology |
10.1101/590463 | The degree of polymerization and sulfation patterns in heparan sulfate are critical determinants of cytomegalovirus entry into host cells | Several enveloped viruses, including herpesviruses attach to host cells by initially interacting with cell surface heparan sulfate (HS) proteoglycans followed by specific coreceptor engagement which culminates in virus-host membrane fusion and virus entry. Interfering with HS-herpesvirus interactions has long been know... | microbiology |
10.1101/592154 | Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes | Metagenomics is increasingly used to describe microbial communities in biological specimens. Ideally, the steps involved in the processing of the biological specimens should not change the microbiome composition in a way that it could lead to false interpretations of inferred microbial community composition. Common ste... | microbiology |
10.1101/589572 | Phylogenetic inference of changes in amino acid propensities with single-position resolution | Fitness conferred by the same allele may differ between genotypes, and these differences shape variation and evolution. Changes in amino acid propensities at protein sites over the course of evolution have been inferred from sequence alignments statistically, but the existing methods are data-intensive and aggregate mu... | evolutionary biology |
10.1101/590836 | Extensive genetic mixing within the clam genus Corbicula | AO_SCPLOWBSTRACTC_SCPLOW"Occasional" sexuality occurs when a species combines clonal reproduction and genetic mixing. This strategy is predicted to combine the advantages of both asexuality and sexuality, but its actual consequences on the genetic diversity and species longevity are poorly understood. Androgenesis, a r... | evolutionary biology |
10.1101/590836 | Substantial genetic mixing among sexual and androgenetic lineages within the clam genus Corbicula | AO_SCPLOWBSTRACTC_SCPLOW"Occasional" sexuality occurs when a species combines clonal reproduction and genetic mixing. This strategy is predicted to combine the advantages of both asexuality and sexuality, but its actual consequences on the genetic diversity and species longevity are poorly understood. Androgenesis, a r... | evolutionary biology |
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