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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 reproductive mode in which the offspring inherits its entire nuclear genome from the father, is often reported as a strictly clonal reproductive mode. Androgenesis is the predominant reproductive mode within the hermaphroditic, invasive lineages of the mollusk genus Corbicula. Their ability to reproduce clonally through androgenesis has been determinant in their invasive success, having colonized during the 20th century American and European freshwater systems, where they became notorious invaders with a widespread, global distribution. However, in androgenetic Corbicula clams, occasional genetic mixing between distinct lineages has also been observed when the sperm of one lineage fertilizes the oocyte of another one. Because of these occasional introgressions, the genetic relationships between Corbicula species remained unclear, and the biogeographic origins of the invasive androgenetic lineages have been challenging to identify. To address these issues, we analyzed the patterns of allele sharing for several nuclear and mitochondrial molecular markers among Corbicula individuals collected across both the native and invasive range. Our results show the occurrence of an allelic pool encompassing all Corbicula freshwater species worldwide, including sexual and androgenetic ones, which highlights the substantial genetic mixing within this genus. However, the differences in allele sharing patterns between invasive lineages, and the low diversity within each lineage, suggest recent, distinct biogeographic origins of invasive Corbicula androgenetic lineages. Finally, the polyploidy, high heterozygosity, and hybrid phenotypes and genotypes found in our study probably originated from hybridization events following egg parasitism between distinct Corbicula lineages. This extensive cross-lineage mixing found in Corbicula may generate nuclear diversity in an otherwise asexually reproducing species. | evolutionary biology |
10.1101/592543 | Rate-limiting transport of positive charges through the Sec-machinery is integral to the mechanism of protein transport | Transport of proteins across and into membranes is a fundamental biological process with the vast majority being conducted by the ubiquitous Sec machinery. In bacteria, this is usually achieved when the SecY-complex engages the cytosolic ATPase SecA (secretion) or translating ribosomes (insertion). Great strides have been made towards understanding the mechanism of protein translocation. Yet, important questions remain - notably, the nature of the individual steps that constitute transport, and how the proton-motive force (PMF) across the plasma membrane contributes. Here, we apply a recently developed high-resolution protein transport assay to explore these questions. We find that pre-protein transport is limited primarily by the diffusion of arginine residues across the membrane, particularly in the context of bulky hydrophobic sequences. This specific effect of arginine, caused by its positive charge, is mitigated for lysine which can be deprotonated and transported across the membrane in its neutral form. These observations have interesting implications for the mechanism of protein secretion, suggesting a simple mechanism by which PMF can aid transport, and enabling a proton ratchet, wherein re-protonation of exiting lysine residues prevents channel re-entry, biasing transport in the outward direction. | biochemistry |
10.1101/593129 | Single cell transcriptomics identifies master regulators of dysfunctional pathways in SOD1 ALS motor neurons | BackgroundBulk RNA-Seq has been extensively utilized to investigate the molecular changes accompanying motor neuron degeneration in Amyotrophic Lateral Sclerosis (ALS). However, due to the heterogeneity and degenerating phenotype of the neurons, it has proved difficult to assign specific changes to neuronal subtypes and identify which factors drive these changes. Consequently, we have utilized single cell transcriptomics of degenerating motor neurons derived from ALS patients to uncover key transcriptional drivers of dysfunctional pathways.
ResultsSingle cell analysis of spinal neuronal cultures derived from SOD1 E100G ALS and isogenic iPSCs allowed us to classify cells into neural subtypes including motor neurons and interneurons. Differential expression analysis between disease and control motor neurons revealed downregulation of genes involved in synaptic structure, neuronal cytoskeleton, mitochondrial function and autophagy. Interestingly, interneurons did not show similar suppression of these homeostatic functions. Single cell expression data enabled us to derive a context-specific transcriptional network relevant to ALS neurons. Master regulator analysis based on this network identified core transcriptional factors driving the ALS MN gene dysregulation. Specifically, we identified activation of SMAD2, a downstream mediator of the TGF-{beta} signalling pathway as a potential driving factor of ALS motor neuron degeneration. Our phenotypic analysis further confirmed that an activated TGF-{beta} signalling is major driver of motor neuron loss in SOD1 ALS. Importantly, expression analysis of TGF{beta} target genes and computational analysis of publicly available datasets indicates that activation of TGF{beta} signalling may be a common mechanism shared between SOD1, FUS and sporadic ALS.
ConclusionsOur results demonstrate the utility of single cell transcriptomics in mapping disease-relevant gene regulatory networks driving neurodegeneration in ALS motor neurons. We find that ALS-associated mutant SOD1 targets transcriptional networks that perturb motor neuron homeostasis. | genomics |
10.1101/593608 | Population receptive fields of human primary visual cortex organised as DC-balanced bandpass filters. | The response to visual stimulation of population receptive fields (pRF) in the human visual cortex can be accurately modelled with a Difference of Gaussians model, yet many aspects of their organisation remain poorly understood. Here, we examined the theoretical underpinnings of this model and argue that the DC-balanced Difference of Gaussians (DoG) holds a number of advantages over a DC-biased DoG. Through functional magnetic resonance imaging (fMRI) pRF mapping, we compared performance of DC-balanced and DC-biased models in human primary visual cortex and found that when model complexity is taken into account, the DC-balanced model is preferred. Finally, we present evidence indicating that the BOLD signal DC-offset contains information related to the processing of visual stimuli. Taken together, the results indicate that V1 neurons are at least frequently organised in the exact constellation that allows them to function as bandpass-filters, which allows for the separation of stimulus contrast and luminance. We further speculate that if the DoG models stimulus contrast, the DC-offset may reflect stimulus luminance. These findings suggest that it may be possible to separate contrast and luminance processing in fMRI experiments and this could lead to new insights on the haemodynamic response. | neuroscience |
10.1101/595769 | CRISPR-SID: identifying EZH2 as a druggable target for desmoid tumors via in vivo dependency mapping | Cancer precision medicine implies identification of tumor-specific vulnerabilities associated with defined oncogenic pathways. Desmoid tumors are soft-tissue neoplasms strictly driven by Wnt signaling network hyperactivation. Despite this clearly defined genetic etiology and the strict and unique implication of the Wnt/{beta}-catenin pathway, no specific molecular targets for these tumors have been identified. To address this caveat, we developed fast and semi-high throughput genetic Xenopus tropicalis desmoid tumor models to identify and characterize novel drug targets. We used multiplexed CRISPR/Cas9 genome editing in these models to simultaneously target a tumor suppressor gene (apc) and candidate dependency genes. Our methodology CRISPR/Cas9 Selection mediated Identification of Dependencies (CRISPR-SID) uses calculated deviations between experimentally observed gene editing outcomes and deep-learning-predicted double strand break repair patterns, to identify genes under negative selection during tumorigenesis. This revealed EZH2 and SUZ12, both encoding polycomb repressive complex 2 components, and the transcription factor CREB3L1, as genetic dependencies for desmoid tumors. In vivo EZH2 inhibition by Tazemetostat induced partial regression of established autochthonous tumors. In vitro models of patient desmoid tumor cells revealed a direct effect of Tazemetostat on Wnt pathway activity. CRISPR-SID represents a potent novel approach for in vivo mapping of tumor vulnerabilities and drug target identification.
Significance StatementCRISPR-SID was established in the diploid frog Xenopus tropicalis for in vivo elucidation of cancer cell vulnerabilities. CRISPR-SID uses deep learning predictions and binomial theory to identify genes under positive or negative selection during autochthonous tumor development. Using CRISPR-SID in a genetic model for desmoid tumors, treatment-recalcitrant mesenchymal tumors driven by hyper-activation of the Wnt signaling pathway, we identified EZH2 and SUZ12, both encoding critical components of the polycomb repressive complex 2, as dependency genes for desmoid. Finally, we demonstrate the promise of EZH2 inhibition as a novel therapeutic strategy for desmoid tumors. With the simplicity of CRISPR sgRNA multiplexing in Xenopus embryos the CRISPR-SID method may be applicable to reveal vulnerabilities in other tumor types. | cancer biology |
10.1101/596627 | OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions | Chromatin accessibility, as a powerful marker of active DNA regulatory elements, provides valuable information for understanding regulatory mechanisms. The revolution in high-throughput methods has accumulated massive chromatin accessibility profiles in public repositories. Nevertheless, utilization of these data is hampered by cumbersome collection, time-consuming processing, and manual chromatin accessibility (openness) annotation of genomic regions. To fill this gap, we developed OpenAnnotate (http://health.tsinghua.edu.cn/openannotate/) as the first web server for efficiently annotating openness of massive genomic regions across various biosample types, tissues, and biological systems. In addition to the annotation resource from 2729 comprehensive profiles of 614 biosample types of human and mouse, OpenAnnotate provides user-friendly functionalities, ultra-efficient calculation, real-time browsing, intuitive visualization, and elaborate application notebooks. We show its unique advantages compared to existing databases and toolkits by effectively revealing cell type-specificity, identifying regulatory elements and 3D chromatin contacts, deciphering gene functional relationships, inferring functions of transcription factors, and unprecedentedly promoting single-cell data analyses. We anticipate OpenAnnotate will provide a promising avenue for researchers to construct a more holistic perspective to understand regulatory mechanisms. | bioinformatics |
10.1101/596486 | Rapid label-free identification of pathogenic bacteria species from a minute quantity 1 exploiting three-dimensional quantitative phase imaging and artificial neural network | The healthcare industry is in dire need for rapid microbial identification techniques. Microbial infection is a major healthcare issue with significant prevalence and mortality, which can be treated effectively during the early stages using appropriate antibiotics. However, determining the appropriate antibiotics for the treatment of the early stages of infection remains a challenge, mainly due to the lack of rapid microbial identification techniques. Conventional culture-based identification and matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy are the gold standard methods, but the sample amplification process is extremely time-consuming. Here, we propose an identification framework that can be used to measure minute quantities of microbes by incorporating artificial neural networks with three-dimensional quantitative phase imaging. We aimed to accurately identify the species of bacterial bloodstream infection pathogens based on a single colony-forming unit of the bacteria. The successful distinction between a total of 19 species, with the accuracy of 99.9% when ten bacteria were measured, suggests that our framework can serve as an effective advisory tool for clinicians during the initial antibiotic prescription.
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org.highwire.dtl.DTLVardef@786668org.highwire.dtl.DTLVardef@8b4eb4org.highwire.dtl.DTLVardef@1dc2452org.highwire.dtl.DTLVardef@1d4888c_HPS_FORMAT_FIGEXP M_FIG C_FIG | microbiology |
10.1101/600254 | Quality control of large genome datasets using genome fingerprints | The 1000 Genomes Project (TGP) is a foundational resource which serves the biomedical community as a standard reference cohort for human genetic variation. There are now seven public versions of these genomes. The TGP Consortium produced the first by mapping its final data release against human reference sequence GRCh37, then "lifted over these genomes to the improved reference sequence (GRCh38) when it was released, and remapped the original data to GRCh38 with two similar pipelines. As best practice quality validation, the pipelines that generated these versions were benchmarked against the Genome In A Bottle Consortiums platinum quality genome (NA12878). The New York Genome Center recently released the results of independently resequencing the cohort at greater depth (30X), a phased version informed by the inclusion of related individuals, and independently remapped the original variant calls to GRCh38. We evaluated all seven versions using genome fingerprinting, which supports ultrafast genome comparison even across reference versions. We noted multiple issues including discrepancies in cohort membership, disagreement on the overall level of variation, evidence of substandard pipeline performance on specific genomes and in specific regions of the genome, cryptic relationships between individuals, inconsistent phasing, and annotation distortions caused by the history of the reference genome itself. We therefore recommend global quality assessment by rapid genome comparisons, using genome fingerprints and other metrics, alongside benchmarking as part of best practice quality assessment of large genome datasets. Our observations also help inform the decision of which version to use, to support analyses by individual researchers. | genomics |
10.1101/600106 | Tumor-targeted delivery of childhood vaccine recall antigens by attenuated Listeria reduces pancreatic cancer | Pancreatic ductal adenocarcinoma is highly metastatic, poorly immunogenic, and immune suppression prevents T cell activation in the tumor microenvironment. We developed a microbial-based immunotherapeutic concept for selective delivery of a highly immunogenic tetanus toxoid protein (TT856-1313), into tumor cells by attenuated Listeria monocytogenes, and reactivation of pre-existing TT-specific memory T cells (generated during childhood) to kill infected tumor cells. Thus, TT here functions as an alternative for neoantigens. Treatment of KPC mice with Listeria-TT resulted in TT accumulation in tumors and inside tumor cells, and attraction of predominantly TT-specific memory CD4 T cells. Moreover, gemcitabine (GEM) combined with Listeria-TT significantly improved the migration of CD4 T cells into tumors and the production of perforin and granzyme B, turning cold tumors into immunological hot tumors. In vivo depletion of T cells in Listeria-TT+GEM-treated mice demonstrated CD4 T cell-mediated eradication of tumors and metastases (Mann-Whitney p<0.05). In addition, peritumoral lymph node like structures (LNS) were observed in close contact with the pancreatic tumors displaying CD4 T cells and CD8 T cells of KPC mice treated with Listeria-TT or Listeria-TT+GEM. The production of perforin and granzyme B was observed in LNS of KPC mice that received Listeria-TT+GEM. This combination not only reduced tumor burden (80%) and metastases (87%) significantly (p<0.05, Mann-Whitney), but also improved the survival time of KPC mice with advanced pancreatic cancer substantially (Mantel-Cox p<0.0001). Our results unveil new mechanisms of Listeria and GEM improving immunotherapy for PDAC. | immunology |
10.1101/600106 | Tumor-targeted delivery of childhood vaccine recall antigens by attenuated Listeria reduces pancreatic cancer | Pancreatic ductal adenocarcinoma is highly metastatic, poorly immunogenic, and immune suppression prevents T cell activation in the tumor microenvironment. We developed a microbial-based immunotherapeutic concept for selective delivery of a highly immunogenic tetanus toxoid protein (TT856-1313), into tumor cells by attenuated Listeria monocytogenes, and reactivation of pre-existing TT-specific memory T cells (generated during childhood) to kill infected tumor cells. Thus, TT here functions as an alternative for neoantigens. Treatment of KPC mice with Listeria-TT resulted in TT accumulation in tumors and inside tumor cells, and attraction of predominantly TT-specific memory CD4 T cells. Moreover, gemcitabine (GEM) combined with Listeria-TT significantly improved the migration of CD4 T cells into tumors and the production of perforin and granzyme B, turning cold tumors into immunological hot tumors. In vivo depletion of T cells in Listeria-TT+GEM-treated mice demonstrated CD4 T cell-mediated eradication of tumors and metastases (Mann-Whitney p<0.05). In addition, peritumoral lymph node like structures (LNS) were observed in close contact with the pancreatic tumors displaying CD4 T cells and CD8 T cells of KPC mice treated with Listeria-TT or Listeria-TT+GEM. The production of perforin and granzyme B was observed in LNS of KPC mice that received Listeria-TT+GEM. This combination not only reduced tumor burden (80%) and metastases (87%) significantly (p<0.05, Mann-Whitney), but also improved the survival time of KPC mice with advanced pancreatic cancer substantially (Mantel-Cox p<0.0001). Our results unveil new mechanisms of Listeria and GEM improving immunotherapy for PDAC. | immunology |
10.1101/601971 | Heterologous Cas9 and non-homologous end joining as a Potentially Organism-Agnostic Knockout (POAK) system in bacteria | Making targeted gene deletions is essential for studying organisms, but is difficult in many prokaryotes due to the inefficiency of homologous recombination based methods. Here, I describe an easily modifiable, single-plasmid system that can be used to make rapid, sequence targeted, markerless knockouts in both a Gram-negative and a Gram-positive organism. The system is comprised of targeted DNA cleavage by Cas9 and error-prone repair by Non-Homologous End Joining (NHEJ) proteins. I confirm previous results showing that Cas9 and NHEJ can make knockouts when NHEJ is expressed before Cas9. Then, I show that Cas9 and NHEJ can be used to make knockouts when expressed simultaneously. I term the new method Potentially Organism-Agnostic Knockout (POAK) system and characterize its function in Escherichia coli and Weissella confusa. First, I develop a novel transformation protocol for W. confusa. Next, I show that, as in E. coli, POAK can create knockouts in W. confusa. Characterization of knockout efficiency across galK in both E. coli and W. confusa showed that while all gRNAs are effective in E. coli, only some gRNAs are effective in W. confusa, and cut site position within a gene does not determine knockout efficiency for either organism. I examine the sequences of knockouts in both organisms and show that POAK produces similar edits in both E. coli and W. confusa. Finally, as an example of the importance of being able to make knockouts quickly, I target W. confusa sugar metabolism genes to show that two sugar importers are not necessary for metabolism of their respective sugars. Having demonstrated that simultaneous expression of Cas9 and NHEJ is sufficient for making knockouts in two minimally related bacteria, POAK represents a hopeful avenue for making knockouts in other under-utilized bacteria. | synthetic biology |
10.1101/603613 | Heterochromatin renewal after release from growth arrest controls genome-wide transcription re-activation in S.cerevisiae | The budding yeast SIR complex (Silent Information Regulator) is the principal actor in heterochromatin formation, which causes epigenetically regulated gene silencing phenotypes. The dynamics of the SIR complex during the cell cycle are however not well understood. It is consequently still not known how the SIR complex is maintained and/or restored after genome replication and cell division, and how the underlying silenced state is transmitted form one cell generation to the next. We used the tag switch RITE system to measure genome wide turnover rates of the SIR subunit Sir3p during and after exit from growth arrest caused by nutrient depletion. Our results show that Sir3p subunits have high rates of exchange immediately after release from growth arrest. "Maternal" Sir3p is consequently almost completely replaced with newly synthesized Sir3p in subtelomeric regions by the end of the first cell cycle after release from growth arrest. The sudden increase in the off rate of Sir3 upon release from growth arrest leads to SIR complex instability that is exacerbated in strains with sub optimal amounts of newly synthesized Sir3p. Unexpectedly, heightened SIR complex instability in these Sir3p "hypo-morphs" has global effects on gene expression with faster reactivation of hundreds of euchromatic genes upon exit from growth arrest. | molecular biology |
10.1101/605550 | MetaNovo: a probabilistic approach to peptide discovery in complex mass spectrometry datasets | BackgroundMicrobiome research is providing important new insights into the metabolic interactions of complex microbial ecosystems involved in fields as diverse as the pathogenesis of human diseases, agriculture and climate change. Poor correlations typically observed between RNA and protein expression datasets make it hard to accurately infer microbial protein synthesis from metagenomic data. Additionally, mass spectrometry-based metaproteomic analyses typically rely on focussed search libraries based on prior knowledge for protein identification that may not represent all the proteins present in a set of samples. Metagenomic 16S rRNA sequencing will only target the bacterial component, while whole genome sequencing is at best an indirect measure of expressed proteomes. We describe a novel approach, MetaNovo, that combines existing open-source software tools to perform scalable de novo sequence tag matching with a novel algorithm for probabilistic optimization of the entire UniProt knowledgebase to create tailored databases for target-decoy searches directly at the proteome level, enabling analyses without prior expectation of sample composition or metagenomic data generation, and compatible with standard downstream analysis pipelines.
ResultsWe compared MetaNovo to published results from the MetaPro-IQ pipeline on 8 human mucosal-luminal interface samples, with comparable numbers of peptide and protein identifications, many shared peptide sequences and a similar bacterial taxonomic distribution compared to that found using a matched metagenome database - but simultaneously identified many more non-bacterial peptides than the previous approaches. MetaNovo was also benchmarked on samples of known microbial composition against matched metagenomic and whole genomic database workflows, yielding many more MS/MS identifications for the expected taxa, with improved taxonomic representation, while also highlighting previously described genome sequencing quality concerns for one of the organisms, and identifying a known sample contaminant without prior expectation.
ConclusionsBy estimating taxonomic and peptide level information directly on microbiome samples from tandem mass spectrometry data, MetaNovo enables the simultaneous identification of peptides from all domains of life in metaproteome samples, bypassing the need for curated sequence search databases. We show that the MetaNovo approach to mass spectrometry metaproteomics is more accurate than current gold standard approaches of tailored or matched genomic database searches, can identify sample contaminants without prior expectation and yields insights into previously unidentified metaproteomic signals, building on the potential for complex mass spectrometry metaproteomic data to speak for itself. The pipeline source code is available on GitHub1 and documentation is provided to run the software as a singularity-compatible docker image available from the Docker Hub2. | bioinformatics |
10.1101/606954 | An Integrated Platform for High-Throughput Nanoscopy | Diffraction-unlimited single-molecule techniques like STORM and (F)PALM enable three-dimensional (3D) fluorescence imaging at tens of nanometer resolution and are invaluable to investigate sub-cellular organization. The multitude of camera frames required to reconstruct a super-resolved image limits the typical throughput of these techniques to tens of cells per day, rendering these methods incompatible with large-scale cell biological or clinical application. STORM acquisition rates can be increased by over an order of magnitude, however the data volumes of about 40 TB a day and concomitant analysis burdens exceed the capacity of existing workflows. Here we present an integrated platform which transforms SMLM from a trick-pony technique into a work horse for cell biology. We leverage our developments in microscopy-specific data compression, distributed storage, and distributed analysis to automatically perform real-time localization analysis, which enable SMLM at throughputs of 10,000 cells a day. We implemented these advances in a fully-integrated environment that supports a highly-flexible architecture for distributed analysis, enabling quickly- and graphically-reconfigurable analyses to be automatically initiated from the microscope during acquisition, remotely executed, and even feedback and queue new acquisition tasks on the microscope. We demonstrate the utility of this framework by imaging hundreds of cells per well in multi-well sample formats. Our platform, the PYthon-Microscopy Environment (PYME), is easily configurable for hardware control on custom microscopes, and includes a plugin framework so users can readily extend all components of their imaging, visualization, and analysis pipeline. PYME is cross-platform, open source, and efficiently puts high-caliber visualization and analysis tools into the hands of both microscope developers and users. | biophysics |
10.1101/607101 | Inter-subunit coupling enables fast CO2-fixation by reductive carboxylases | Enoyl-CoA carboxylases/reductases (ECRs) belong to the most efficient CO2-fixing enzymes described to date. However, the molecular mechanisms underlying ECRs extraordinary catalytic activity on the level of the protein assembly remain elusive. Here we used a combination of ambient temperature X-ray Free Electron Laser (XFEL) and cryogenic synchrotron experiments to study the structural organization of the ECR from Kitasatospora setae. K. setae ECR is a homo-tetramer that differentiates into a dimer of dimers of open- and closed-form subunits in the catalytically active state. Using molecular dynamics simulations and structure-based mutagenesis, we show that catalysis is synchronized in K. setae ECR across the pair of two dimers. This conformational coupling of catalytic domains is conferred by individual amino acids to achieve high CO2-fixation rates. Our results provide unprecedented insights into the dynamic organization and synchronized inter- and intra-subunit communications of this remarkably efficient CO2-fixing enzyme during catalysis.
Significance StatementFixation of CO2 offers real potential for reaching negative CO2 emissions in bioenergy, and bioproduct utilization. The capture and conversion of atmospheric CO2 remains a challenging task. Existing biological systems can be exploited and optimized for this use. Bacterial enoyl-CoA carboxylases/reductases (ECRs) encompass the fastest CO2-fixing enzymes found in nature to date. However, the mechanisms underlying ECRs extraordinary catalytic activity remain elusive. Our structural, computational, and biochemical results elucidate the dynamic structural organization of the ECR complex and describe how coupled motions of catalytic domains in the ECR tetramer drive carboxylation. This mechanistic understanding is critical for engineering highly efficient CO2-fixing biocatalysts for bioenergy and bioproduct applications. | biophysics |
10.1101/608646 | Network science inspires novel tree shape statistics | 1The shape of phylogenetic trees can be used to gain evolutionary insights. A trees shape specifies the connectivity of a tree, while its branch lengths reflect either the time or genetic distance between branching events; well-known measures of tree shape include the Colless and Sackin imbalance, which describe the asymmetry of a tree. In other contexts, network science has become an important paradigm for describing structural features of networks and using them to understand complex systems, ranging from protein interactions to social systems. Network science is thus a potential source of many novel ways to characterize tree shape, as trees are also networks. Here, we tailor tools from network science, including diameter, average path length, and betweenness, closeness, and eigenvector centrality, to summarize phylogenetic tree shapes. We thereby propose tree shape summaries that are complementary to both asymmetry and the frequencies of small configurations. These new statistics can be computed in linear time and scale well to describe the shapes of large trees. We apply these statistics, alongside some conventional tree statistics, to phylogenetic trees from three very different viruses (HIV, dengue fever and measles), from the same virus in different epidemiological scenarios (influenza A and HIV) and from simulation models known to produce trees with different shapes. Using mutual information and supervised learning algorithms, we find that the statistics adapted from network science perform as well as or better than conventional statistics. We describe their distributions and prove some basic results about their extreme values in a tree. We conclude that network science-based tree shape summaries are a promising addition to the toolkit of tree shape features. All our shape summaries, as well as functions to select the most discriminating ones for two sets of trees, are freely available as an R package at http://github.com/Leonardini/treeCentrality. | bioinformatics |
10.1101/608729 | A suite of rare microbes interacts with a dominant, heritable, fungal endophyte to influence plant trait expression | Endophytes are microbes that live, for at least a portion of their life history, within plant tissues. Endophyte assemblages are often composed of a few abundant taxa and many infrequently-observed, rare taxa. The ways in which most endophytes affect host phenotype are unknown; however, certain dominant endophytes can influence plants in ecologically meaningful ways-including by affecting growth and contributing to immune responses. In contrast, the effects of rare endophytes have been unexplored, and how rare and common endophytes might interact is also unknown. Here, we manipulate both the suite of rare foliar endophytes (including both fungi and bacteria) and Alternaria fulva-a dominant, vertically- transmitted fungus-within the fabaceous forb Astragalus lentiginosus. We report that rare, low-biomass endophytes affected host size and foliar %N, but only when the dominant fungal endophyte (A. fulva) was not present. A. fulva also reduced plant size and %N, but these deleterious effects on the host could be offset by a striking antagonism we observed between this heritable fungus and a foliar pathogen. These results are unusual in that they are derived from experimental manipulation in a non-crop or non-grass system and demonstrate that interactions among taxa determine the net effect of endophytic assemblages on their hosts. We suggest that the myriad infrequently-observed endophytes within plant leaves may be more than a collection of uninfluential, commensal organisms, but instead have meaningful ecological roles. | ecology |
10.1101/608729 | A suite of rare microbes interacts with a dominant, heritable, fungal endophyte to influence plant trait expression | Endophytes are microbes that live, for at least a portion of their life history, within plant tissues. Endophyte assemblages are often composed of a few abundant taxa and many infrequently-observed, rare taxa. The ways in which most endophytes affect host phenotype are unknown; however, certain dominant endophytes can influence plants in ecologically meaningful ways-including by affecting growth and contributing to immune responses. In contrast, the effects of rare endophytes have been unexplored, and how rare and common endophytes might interact is also unknown. Here, we manipulate both the suite of rare foliar endophytes (including both fungi and bacteria) and Alternaria fulva-a dominant, vertically- transmitted fungus-within the fabaceous forb Astragalus lentiginosus. We report that rare, low-biomass endophytes affected host size and foliar %N, but only when the dominant fungal endophyte (A. fulva) was not present. A. fulva also reduced plant size and %N, but these deleterious effects on the host could be offset by a striking antagonism we observed between this heritable fungus and a foliar pathogen. These results are unusual in that they are derived from experimental manipulation in a non-crop or non-grass system and demonstrate that interactions among taxa determine the net effect of endophytic assemblages on their hosts. We suggest that the myriad infrequently-observed endophytes within plant leaves may be more than a collection of uninfluential, commensal organisms, but instead have meaningful ecological roles. | ecology |
10.1101/610188 | Stabilising effects of competition and diversity determine vaccine impact on antibiotic resistance evolution | Bacterial vaccines can protect recipients from contracting potentially antibiotic-resistant infections. But by altering the selective balance between sensitive and resistant strains, vaccines may also suppress--or spread--antibiotic resistance among unvaccinated individuals. Predicting the outcome requires knowing what drives selection for resistance in bacterial pathogens, and in particular, what maintains the circulation of both antibiotic-sensitive and resistant strains of bacteria. Using mathematical modelling, we show that the frequency of penicillin resistance in Streptococcus pneumoniae (pneumococcus) across 27 European countries can be explained by between-host diversity in antibiotic use, heritable diversity in pneumococcal carriage duration, or frequency-dependent selection brought about by within-host competition between resistant and sensitive strains. We use our calibrated models to predict the impact of non-serotype-specific pneumococcal vaccination upon the prevalence of carriage, incidence of disease, and frequency of resistance for S. pneumoniae. We find that the relative strength and directionality of competition between resistant and sensitive pneumococcal strains is the most important determinant of whether vaccination promotes, inhibits, or has little effect upon the evolution of antibiotic resistance. Finally, we show that country-specific differences in pathogen transmission substantially alter the predicted impact of vaccination, highlighting that policies for managing resistance with vaccines must be tailored to a specific pathogen and setting.
One sentence summaryFrequency-dependent competition and extrinsically-maintained diversity shape selection for antibiotic resistance following vaccination. | evolutionary biology |
10.1101/609537 | Reward motivation increases univariate activity but has limited effect on coding of task-relevant information across the frontoparietal cortex | Selection and integration of information based on current goals is fundamental for goal-directed behavior. Reward motivation has been shown to improve behavioral performance, yet the neural mechanisms that link motivation and control processes, and in particular its effect on context-dependent information processing, remain unclear. We used functional magnetic resonance imaging (fMRI) in 24 human volunteers (13 females) to test whether reward motivation enhances the coding of task-relevant information across the frontoparietal cortex, as would be predicted based on previous experimental evidence and theoretical accounts. In a cued target detection task, participants detected whether an object from a cued visual category was present in a subsequent display. The combination of the cue and the object visual category determined the behavioral status of the objects. To manipulate reward motivation, half of all trials offered the possibility of a monetary reward. We observed an increase with reward in overall univariate activity across the frontoparietal control network when the cue and subsequent object were presented. Multivariate pattern analysis (MVPA) showed that behavioral status information for the objects was conveyed across the network. However, in contrast to our prediction, reward did not increase the discrimination between behavioral status conditions in the stimulus epoch of a trial when object information was processed depending on a current context. In the high-level general-object visual region, the lateral occipital complex, the representation of behavioral status was driven by visual differences and was not modulated by reward. Our study provides useful evidence for the limited effects of reward motivation on task-related neural representations and highlights the necessity to unravel the diverse forms and extent of these effects. | neuroscience |
10.1101/611848 | Reference plasmid pHXB2_D is an HIV-1 molecular clone that exhibits identical LTRs and a single integration site indicative of an HIV provirus | ObjectiveTo compare long-read nanopore DNA sequencing (DNA-seq) with short-read sequencing-by-synthesis for sequencing a full-length (e.g., non-deletion, nor reporter) HIV-1 model provirus in plasmid pHXB2_D.
DesignWe sequenced pHXB2_D and a control plasmid pNL4-3_gag-pol({Delta}1443-4553)_EGFP with long- and short-read DNA-seq, evaluating sample variability with resequencing (sequencing and mapping to reference HXB2) and de novo viral genome assembly.
MethodsWe prepared pHXB2_D and pNL4-3_gag-pol({Delta}1443-4553)_EGFP for long-read nanopore DNA-seq, varying DNA polymerases Taq (Sigma-Aldrich) and Long Amplicon (LA) Taq (Takara). Nanopore basecallers were compared. After aligning reads to the reference HXB2 to evaluate sample coverage, we looked for variants. We next assembled reads into contigs, followed by finishing and polishing. We hired an external core to sequence-verify pHXB2_D and pNL4-3_gag-pol({Delta}1443-4553)_EGFP with single-end 150 base-long Illumina reads, after masking sample identity.
ResultsWe achieved full-coverage (100%) of HXB2 HIV-1 from 5 to 3 long terminal repeats (LTRs), with median per-base coverage of over 9000x in one experiment on a single MinION flow cell. The longest HIV-spanning read to-date was generated, at a length of 11,487 bases, which included full-length HIV-1 and plasmid backbone with flanking host sequences supporting a single HXB2 integration event. We discovered 20 single nucleotide variants in pHXB2_D compared to reference, verified by short-read DNA sequencing. There were no variants detected in the HIV-1 segments of pNL4-3_gag-pol({Delta}1443-4553)_EGFP.
ConclusionsNanopore sequencing performed as-expected, phasing LTRs, and even covering full-length HIV. The discovery of variants in a reference plasmid demonstrates the need for sequence verification moving forward, in line with calls from funding agencies for reagent verification. These results illustrate the utility of long-read DNA-seq to advance the study of HIV at single integration site resolution. | genomics |
10.1101/611848 | Reference plasmid pHXB2_D is an HIV-1 molecular clone that exhibits identical LTRs and a single integration site indicative of an HIV provirus | ObjectiveTo compare long-read nanopore DNA sequencing (DNA-seq) with short-read sequencing-by-synthesis for sequencing a full-length (e.g., non-deletion, nor reporter) HIV-1 model provirus in plasmid pHXB2_D.
DesignWe sequenced pHXB2_D and a control plasmid pNL4-3_gag-pol({Delta}1443-4553)_EGFP with long- and short-read DNA-seq, evaluating sample variability with resequencing (sequencing and mapping to reference HXB2) and de novo viral genome assembly.
MethodsWe prepared pHXB2_D and pNL4-3_gag-pol({Delta}1443-4553)_EGFP for long-read nanopore DNA-seq, varying DNA polymerases Taq (Sigma-Aldrich) and Long Amplicon (LA) Taq (Takara). Nanopore basecallers were compared. After aligning reads to the reference HXB2 to evaluate sample coverage, we looked for variants. We next assembled reads into contigs, followed by finishing and polishing. We hired an external core to sequence-verify pHXB2_D and pNL4-3_gag-pol({Delta}1443-4553)_EGFP with single-end 150 base-long Illumina reads, after masking sample identity.
ResultsWe achieved full-coverage (100%) of HXB2 HIV-1 from 5 to 3 long terminal repeats (LTRs), with median per-base coverage of over 9000x in one experiment on a single MinION flow cell. The longest HIV-spanning read to-date was generated, at a length of 11,487 bases, which included full-length HIV-1 and plasmid backbone with flanking host sequences supporting a single HXB2 integration event. We discovered 20 single nucleotide variants in pHXB2_D compared to reference, verified by short-read DNA sequencing. There were no variants detected in the HIV-1 segments of pNL4-3_gag-pol({Delta}1443-4553)_EGFP.
ConclusionsNanopore sequencing performed as-expected, phasing LTRs, and even covering full-length HIV. The discovery of variants in a reference plasmid demonstrates the need for sequence verification moving forward, in line with calls from funding agencies for reagent verification. These results illustrate the utility of long-read DNA-seq to advance the study of HIV at single integration site resolution. | genomics |
10.1101/612549 | Coupling Metastasis to pH-Sensing GPR68 Using a Novel Small Molecule Inhibitor | An acidic milieu is a hallmark of the glycolytic metabolism that occurs in cancerous cells. The acidic environment is known to promote cancer progression, but the underlying signaling and cell biological underpinnings of these phenomena are not well understood. Here, we describe ogremorphin, a first-in-class small-molecule inhibitor of GPR68, an extracellular proton-sensing and mechanosensing G protein-coupled receptor. Ogremorphin was discovered in a chemical genetic zebrafish screen for its ability to perturb neural crest development, which shares basic cell behaviors of migration and invasion with cancer metastasis. Ogremorphin also inhibited migration and invasive behavior of neural crest-derived human melanoma cells in vitro. Furthermore, in phenome-wide association studies (PheWAS), we identified an aberrantly activated variant of GPR68, which is associated with cancer metastasis in vivo and promotes invasive phenotypes of cancer cells in vitro. Thus, extracellular proton-sensing GPR68 signaling promotes cell migration and invasion during embryonic development and may do likewise in cancer progression. | cancer biology |
10.1101/608935 | Untangling the Indonesian tangle net fishery: describing a data-poor fishery targeting large threatened rays (Order Batoidea) | O_LIShark-like rays (Order Rhinopristiformes) are among the most threatened families of marine fish. Yet little is known about their populations, as these rays are normally taken as opportunistic catch in fisheries targeting other species and are thus poorly reported. One exception is the Indonesian tangle net fishery, which targets shark-like rays.
C_LIO_LIMarket surveys of Muara Angke landing site in Jakarta, north-western Java (including one frozen shipment from Benoa Harbour, Bali), were conducted between 2001 and 2005, and recorded landed catch for this fishery. Recent catch data from Indonesian Capture Fisheries (2017 - 2018) were also examined to provide contemporary information about landed catch.
C_LIO_LI1,559 elasmobranchs (sharks and rays) were recorded, comprised of 24 species of rays and nine species of sharks. The most abundant species landed were the pink whipray Pateobatis fai and the bottlenose wedgefish Rhynchobatus australiae, the latter being the main target species.
C_LIO_LICatch composition varied based on differences in species catchability and may also be indicative of localized declines. The fishery was highly selective for larger sized individuals, however smaller size classes of target species were also caught in other Indonesian fisheries resulting in fishing pressure across all age classes.
C_LIO_LIEvidence of substantial declines in global landings of wedgefish species, and the observed shift in catch composition in the Indonesian tangle net fishery, increases concerns about the status of shark-like rays and stingrays in Indonesia.
C_LI | zoology |
10.1101/611939 | On the efficacy of restoration in stream networks: comments, critiques, and prospective recommendations | Swan and Brown (2017) recently addressed the effects of restoration on stream communities under the meta-community framework. Using a combination of headwater and mainstem streams, Swan and Brown (2017) evaluated how position within a stream network affected the outcome of restoration on invertebrate communities. Ostensibly, their hypotheses were partially supported as restoration had stronger effects in headwater streams: invertebrate taxonomic richness was increased and temporal variability decreased in restored reaches; however, these results were not consistent upon closer scrutiny for both the original paper (Swan and Brown 2017) and the later erratum (Swan and Brown 2018). Here, I provide a secondary analysis of the data, with hypotheses and interpretations in the context of stream, meta-community, and restoration ecology. Swan and Brown (2017, 2018) evaluated the effect of restoration on sites receiving various combinations of in-channel manipulation and riparian reforestation treatments. Given the difference in the relative importance of environmental filtering and dispersal between headwaters and mainstems and the structure of river networks, I contend that different restoration treatments have differential effects between headwaters and mainstems. I hypothesized in-channel manipulations would have more consistent effects between headwaters and mainstems compared to riparian reforestation, and I used this hypothesis to guide site selection in the re-analysis. I then compared results from the re-analysis to those presented by Swan and Brown (2017, 2018). I did not find any effects of restoration on local diversity, spatial dissimilarity, or temporal variability, let alone differential effects of restoration between headwaters and mainstems; these results are contrary Swan and Brown (2017, 2018), who reported that restoration increased taxonomic richness, increased spatial dissimilarity, and decreased temporal variability in restored headwater streams. I demonstrate further that the statistical tests conducted by Swan and Brown (2017, 2018) were invalid and, therefore, recommend the use of the results presented here. More broadly, I suggest, in agreement with Swan and Brown (2017, 2018) and a growing body of research, that river and stream restoration will likely have greater success if a regional approach is taken to designing and implementing restoration projects. | ecology |
10.1101/614529 | Integrase-mediated differentiation circuits improve evolutionary stability of burdensome and toxic functions in E. coli | Advances in synthetic biology, bioengineering, and computation allow us to rapidly and reliably program cells with increasingly complex and useful functions. However, because the functions we engineer cells to perform are typically unnecessary for cellular survival and burdensome to cell growth, they can be rapidly lost due to the processes of mutation and natural selection. To improve the evolutionary stability of engineered functions in a general manner, we developed an integrase-recombination-based differentiation gene circuit in Escherichia coli. In this system, differentiated cells uniquely carry out burdensome or toxic engineered functions but have limited capacity to grow (terminal differentiation), preventing the propagation of selectively advantageous loss of function mutations that inevitably arise. To experimentally implement terminal differentiation, we co-opted the R6K plasmid system, using differentiation to simultaneously activate T7 RNAP-driven expression of arbitrary engineered functions, and inactivate expression of {pi} protein (an essential factor for R6K plasmid replication), thereby allowing limitation of differentiated cell growth through antibiotic selection. We experimentally demonstrate terminal differentiation increases both duration and magnitude of high-burden T7 RNAP-driven expression, and that its evolutionary stability can be further improved with strategic redundancy. Using burdensome overexpression of a fluorescent protein as a model engineered function, our terminal differentiation circuit results in a ~2.8-fold (single-cassette) and ~4.2-fold (two-cassette) increase of total fluorescent protein produced compared to high-burden naive expression in which all cells inducibly express T7 RNAP. Finally, we demonstrate that differentiation can enable the expression of even toxic functions, a feat not achieved to our knowledge by any other strategy for addressing long-term evolutionary stability. Overall, this study provides an effective generalizable strategy for protecting engineered functions from evolutionary degradation. | synthetic biology |
10.1101/614529 | Integrase-mediated differentiation circuits improve evolutionary stability of burdensome and toxic functions in E. coli | Advances in synthetic biology, bioengineering, and computation allow us to rapidly and reliably program cells with increasingly complex and useful functions. However, because the functions we engineer cells to perform are typically unnecessary for cellular survival and burdensome to cell growth, they can be rapidly lost due to the processes of mutation and natural selection. To improve the evolutionary stability of engineered functions in a general manner, we developed an integrase-recombination-based differentiation gene circuit in Escherichia coli. In this system, differentiated cells uniquely carry out burdensome or toxic engineered functions but have limited capacity to grow (terminal differentiation), preventing the propagation of selectively advantageous loss of function mutations that inevitably arise. To experimentally implement terminal differentiation, we co-opted the R6K plasmid system, using differentiation to simultaneously activate T7 RNAP-driven expression of arbitrary engineered functions, and inactivate expression of {pi} protein (an essential factor for R6K plasmid replication), thereby allowing limitation of differentiated cell growth through antibiotic selection. We experimentally demonstrate terminal differentiation increases both duration and magnitude of high-burden T7 RNAP-driven expression, and that its evolutionary stability can be further improved with strategic redundancy. Using burdensome overexpression of a fluorescent protein as a model engineered function, our terminal differentiation circuit results in a ~2.8-fold (single-cassette) and ~4.2-fold (two-cassette) increase of total fluorescent protein produced compared to high-burden naive expression in which all cells inducibly express T7 RNAP. Finally, we demonstrate that differentiation can enable the expression of even toxic functions, a feat not achieved to our knowledge by any other strategy for addressing long-term evolutionary stability. Overall, this study provides an effective generalizable strategy for protecting engineered functions from evolutionary degradation. | synthetic biology |
10.1101/611517 | Regulatory network-based imputation of dropouts in single-cell RNA sequencing data | Single-cell RNA sequencing (scRNA-seq) methods are typically unable to quantify the expression levels of all genes in a cell, creating a need for the computational prediction of missing values ( dropout imputation). Most existing dropout imputation methods are limited in the sense that they exclusively use the scRNA-seq dataset at hand and do not exploit external gene-gene relationship information. Further, it is unknown if all genes equally benefit from imputation or which imputation method works best for a given gene.
Here, we show that a transcriptional regulatory network learned from external, independent gene expression data improves dropout imputation. Using a variety of human scRNA-seq datasets we demonstrate that our network-based approach outperforms published state-of-the-art methods. The network-based approach performs particularly well for lowly expressed genes, including cell-type-specific transcriptional regulators. Further, the cell-to-cell variation of 12.6% to 48.2% of the genes could not be adequately imputed by any of the methods that we tested. In those cases gene expression levels were best predicted by the mean expression across all cells, i.e. assuming no measurable expression variation between cells. These findings suggest that different imputation methods are optimal for different genes. We thus implemented an R-package called ADImpute (available via Bioconductor https://bioconductor.org/packages/release/bioc/html/ADImpute.html) that automatically determines the best imputation method for each gene in a dataset.
Our work represents a paradigm shift by demonstrating that there is no single best imputation method. Instead, we propose that imputation should maximally exploit external information and be adapted to gene-specific features, such as expression level and expression variation across cells.
Author summarySingle-cell RNA-sequencing (scRNA-seq) allows for gene expression to be quantified in individual cells and thus plays a critical role in revealing differences between cells within tissues and characterizing them in healthy and pathological conditions. Because scRNA-seq captures the RNA content of individual cells, lowly expressed genes, for which few RNA molecules are present in the cell, are easily missed. These events are called dropouts and considerably hinder analysis of the resulting data. In this work, we propose to make use of gene-gene relationships, learnt from external and more complete datasets, to estimate the true expression of genes that could not be quantified in a given cell. We show that this approach generally outperforms previously published methods, but also that different genes are better estimated with different methods. To allow the community to use our proposed method and combine it with existing ones, we created the R package ADImpute, available through Bioconductor. | bioinformatics |
10.1101/615336 | Resistance to aztreonam in combination with non-β-lactam β-lactamase inhibitors due to the layering of mechanisms in Escherichia coli identified following mixed culture selection. | Using mixed culture selection, we show how reduced envelope permeability, reduced target-site affinity, and increased {beta}-lactamase production layer to confer aztreonam/{beta}-lactamase inhibitor resistance in Escherichia coli. We report a clinical isolate producing CTX-M-15 and CMY-4, lacking OmpF, and carrying a PBP3 mutation. It is resistant to aztreonam plus the inhibitors avibactam, relebactam and vaborbactam. Mobilisation of blaSHV-12 into this isolate generated a derivative additionally resistant to aztreonam plus the bicyclic boronate inhibitors 2 and taniborbactam. | microbiology |
10.1101/615229 | Attention Decorrelates Sensory and Motor Signals in the Mouse Visual Cortex | Visually-guided behaviors depend on the activity of cortical networks receiving visual inputs and transforming these signals to guide appropriate actions. However, non-retinal inputs, carrying motor signals as well as cognitive and attentional modulatory signals, also activate these cortical regions. How these networks avoid interference between coincident signals ensuring reliable visual behaviors is poorly understood. Here, we observed neural responses in the dorsal-parietal cortex of mice during a visual discrimination task driven by visual stimuli and movements. We found that visual and motor signals interacted according to two canonical mechanisms: divisive normalization and response demixing. Interactions were contextually modulated by the animals state of attention, with attention amplifying visual and motor signals and decorrelating them in a low-dimensional space of neural activations. These findings reveal canonical computational principles operating in dorsal-parietal networks that enable separation of incoming signals for reliable visually-guided behaviors during interactions with the environment. | neuroscience |
10.1101/617936 | A developmental framework linking neurogenesis and circuit formation in the Drosophila CNS | The mechanisms specifying neuronal diversity are well-characterized, yet it remains unclear how or if these mechanisms regulate neural circuit assembly. To address this, we mapped the developmental origin of 160 interneurons from seven bilateral neural progenitors (neuroblasts), and identify them in a synapse-scale TEM reconstruction of the Drosophila larval CNS. We find that lineages concurrently build the sensory and motor neuropils by generating sensory and motor hemilineages in a Notch-dependent manner. Neurons in a hemilineage share common synaptic targeting within the neuropil, which is further refined based on neuronal temporal identity. Connectome analysis shows that hemilineage-temporal cohorts share common connectivity. Finally, we show that proximity alone cannot explain the observed connectivity structure, suggesting hemilineage/temporal identity confers an added layer of specificity. Thus, we demonstrate that the mechanisms specifying neuronal diversity also govern circuit formation and function, and that these principles are broadly applicable throughout the nervous system. | neuroscience |
10.1101/618082 | Fitness-related traits are maximized in recently introduced, slow-growing populations of an invasive clam: is this a response to strong r-selection? | Many species are shifting their ranges being forced to rapidly respond to novel stressful environmental conditions. Colonizing individuals experience strong selective forces that favor the expression of life history traits notably affecting dispersal and reproductive rates in newly invaded habitats. Limited information is currently available on trait variation within the invasive range despite being critical for understanding ecological and evolutionary factors that drive the process of range expansion of invasive species. Here we evaluated life history shifts of the widely introduced Asian clam Corbicula, within its invaded range. Through an exhaustive literature search, we obtained data for 17 invasive Corbicula populations from different ecosystems worldwide. We tested the relationship between population and individual parameters relevant to the process of range expansion. Our main results are that recently introduced Corbicula populations were characterized by (i) low density and low rate of population increase, (ii) clams reproduced earlier in slow-growing populations, and (iii) density had no effect on population increase. All Corbicula populations analyzed in this study, which are fixed for one genotype (lineage Form A/R), experienced different selective environments in the introduced range. These findings support the perspective that adaptive phenotypic plasticity favored the expression of traits that maximize fitness in recently established populations, which faced stronger r-selective forces relative to long-established ones. We discuss the role of plasticity in facilitating rapid adaptation and increasing the likelihood of populations to overcome difficulties associated with low densities and low population increase in newly invaded areas. | ecology |
10.1101/618082 | Fitness-related traits are maximized in recently introduced, slow-growing populations of a global invasive clam | Many species are shifting their ranges being forced to rapidly respond to novel stressful environmental conditions. Colonizing individuals experience strong selective forces that favor the expression of life history traits notably affecting dispersal and reproductive rates in newly invaded habitats. Limited information is currently available on trait variation within the invasive range despite being critical for understanding ecological and evolutionary factors that drive the process of range expansion of invasive species. Here we evaluated life history shifts of the widely introduced Asian clam Corbicula, within its invaded range. Through an exhaustive literature search, we obtained data for 17 invasive Corbicula populations from different ecosystems worldwide. We tested the relationship between population and individual parameters relevant to the process of range expansion. Our main results are that recently introduced Corbicula populations were characterized by (i) low density and low rate of population increase, (ii) clams reproduced earlier in slow-growing populations, and (iii) density had no effect on population increase. All Corbicula populations analyzed in this study, which are fixed for one genotype (lineage Form A/R), experienced different selective environments in the introduced range. These findings support the perspective that adaptive phenotypic plasticity favored the expression of traits that maximize fitness in recently established populations, which faced stronger r-selective forces relative to long-established ones. We discuss the role of plasticity in facilitating rapid adaptation and increasing the likelihood of populations to overcome difficulties associated with low densities and low population increase in newly invaded areas. | ecology |
10.1101/618082 | Fitness-related traits are maximized in recently introduced, slow-growing populations of a global invasive clam | Many species are shifting their ranges being forced to rapidly respond to novel stressful environmental conditions. Colonizing individuals experience strong selective forces that favor the expression of life history traits notably affecting dispersal and reproductive rates in newly invaded habitats. Limited information is currently available on trait variation within the invasive range despite being critical for understanding ecological and evolutionary factors that drive the process of range expansion of invasive species. Here we evaluated life history shifts of the widely introduced Asian clam Corbicula, within its invaded range. Through an exhaustive literature search, we obtained data for 17 invasive Corbicula populations from different ecosystems worldwide. We tested the relationship between population and individual parameters relevant to the process of range expansion. Our main results are that recently introduced Corbicula populations were characterized by (i) low density and low rate of population increase, (ii) clams reproduced earlier in slow-growing populations, and (iii) density had no effect on population increase. All Corbicula populations analyzed in this study, which are fixed for one genotype (lineage Form A/R), experienced different selective environments in the introduced range. These findings support the perspective that adaptive phenotypic plasticity favored the expression of traits that maximize fitness in recently established populations, which faced stronger r-selective forces relative to long-established ones. We discuss the role of plasticity in facilitating rapid adaptation and increasing the likelihood of populations to overcome difficulties associated with low densities and low population increase in newly invaded areas. | ecology |
10.1101/618744 | O-glycosylation regulates plant developmental transitions downstream of miR156 | The timing of plant developmental transitions is decisive for reproductive success and thus tightly regulated. The transition from juvenile to adult vegetative and later to the reproductive phase is controlled by an endogenous pathway regulated by miR156, targeting the SQUAMOSA PROMOTER BINDING PROTEIN (SBP/SPL) family of transcription factors. SPLs regulate a number of developmental processes, such as trichome formation, leaf shape and floral transition. Such complex regulatory pathways often involve post-translational modifications (PTMs), integrating a range of internal and external signals. One of these PTMs is O-glycosylation, the attachment of a single monosaccharide to serine or threonine of nuclear and cytoplasmic proteins, which is found on a number of very diverse proteins. O-GlcNAcylation is the most common type of cytosolic O-glycosylation, but in plants also O-fucose modification occurs. Here we show that mutants defective in the O-fucosyltransferase SPINDLY (SPY) show accelerated developmental transitions. Genetic analysis shows that this effect is independent of miR156 levels, but partly dependent on functional SPLs. In a phenotyping analysis, we found that SPY and SPLs also control leaf growth, as loss of function mutants showed defects in cell expansion, while SPL9 also regulates cell division in rosette leaves. Moreover, SPLs interact directly with SPY and are O-glycosylated. Our results show that O-glycosylation is involved at several steps in the regulation of developmental transitions and organ growth in Arabidopsis thaliana. | plant biology |
10.1101/619650 | An Optimized Registration Workflow and Standard Geometric Space for Small Animal Brain Imaging | The reliability of scientific results critically depends on reproducible and transparent data processing. Cross-subject and cross-study comparability of imaging data in general, and magnetic resonance imaging (MRI) data in particular, is contingent on the quality of registration to a standard reference space. In small animal MRI this is not adequately provided by currently used processing workflows, which utilize high-level scripts optimized for human data, and adapt animal data to fit the scripts, rather than vice-versa. In this fully reproducible article we showcase a generic workflow optimized for the mouse brain, alongside a standard reference space suited to harmonize data between analysis and operation. We introduce four separate metrics for automated quality control (QC), and a visualization method to aid operator inspection. Benchmarking this workflow against common legacy practices reveals that it performs more consistently, better preserves variance across subjects while minimizing variance across sessions, and improves both volume and smoothness conservation RMSE approximately 2-fold. We propose this open source workflow and the QC metrics as a new standard for small animal MRI registration, ensuring workflow robustness, data comparability, and region assignment validity, all of which are indispensable prerequisites for the comparability of scientific results across experiments and centers. | neuroscience |
10.1101/620963 | Uncovering the effects of Müllerian mimicry on the evolution of conspicuousness in colour patterns | Variation in the conspicuousness of colour patterns is observed within and among defended prey species. The evolution of conspicuous colour pattern in defended species can be strongly impaired because of increased detectability by predators. Nevertheless, such evolution of the colour pattern can be favoured if changes in conspicuousness result in Mullerian mimicry with other defended prey. Here, we develop a model describing the population dynamics of a conspicuous defended prey species, and we assess the invasion conditions of derived phenotypes that differ from the ancestral phenotype by their conspicuousness. Such change in conspicuousness may then modify their level of mimicry with the local community of defended species. Derived colour pattern displayed in this focal population can therefore be either exactly similar, partially resembling or completely dissimilar to the local mimicry ring displaying the ancestral colour pattern. We assume that predation risk depends (1) on the number of individuals sharing a given colour pattern within the population, (2) on the occurrence of co-mimetic defended species, and (3) on the availability of alternative edible prey. Using a combination of analytical derivations and numerical simulations, we show that less conspicuous colour patterns are generally favoured within mimicry rings, unless reduced conspicuousness impairs mimicry. By contrast, when a mutation affecting the colour pattern leads to a shift toward a better protected mimicry ring, crypsis is no longer necessarily beneficial and a more conspicuous colour pattern can be favoured. The selected aposematic pattern then depends on the local composition of mimetic communities, as well as on the detectability, memorability and level of mimicry of the colour patterns. | evolutionary biology |
10.1101/621458 | On the cortical mapping function -- visual space, cortical space, and crowding | The retino-cortical visual pathway is retinotopically organized: Neighbourhood relationships on the retina are preserved in the mapping to the cortex. Size relationships in that mapping are also highly regular: The size of a patch in the visual field that maps onto a cortical patch of fixed size follows, along any radius and in a wide range, simply a linear function with retinal eccentricity. As a consequence, and under simplifying assumptions, the mapping of retinal to cortical locations follows a logarithmic function along that radius. While this has already been shown by Fischer (1973), the link between the linear function - which describes the local behaviour by the cortical magnification factor M - and the logarithmic location function for the global behaviour, has never been made fully explicit. The present paper provides such a link as a set of ready-to-use equations using Levi and Kleins E2 nomenclature, and examples for their validity and applicability in the retinotopic mapping literature are discussed. The equations allow estimating M in the retinotopic centre and values thus derived from the literature are provided. A new structural parameter, d2, is proposed to characterize the cortical map, as a cortical counterpart to E2, and typical values for it are given. One pitfall is discussed and spelt out as a set of equations, namely the common myth that a pure logarithmic function will give an adequate map: The popular omission of a constant term renders the equations ill defined in, and around, the retinotopic centre. The correct equations are finally extended to describe the cortical map of Boumas law on visual crowding. The result contradicts recent suggestions that critical crowding distance corresponds to a constant cortical distance. | neuroscience |
10.1101/621292 | Memory for Individual Items is Related to Non-Reinforced Preference Change | It is commonly assumed that memories contribute to value-based decisions. Nevertheless, most theories of value-based decision-making do not account for memory influences on choice. Recently, new interest has emerged in the interactions between these two fundamental processes, mainly using reinforcement-based paradigms. Here, we aimed to study the role memory processes play in preference change following the non-reinforced cue-approach training (CAT) paradigm. In CAT, the mere association of cued items with a speeded motor response influences choices. Previous studies with this paradigm showed that a single training session induces a long-lasting effect of enhanced preferences for high-value trained stimuli, that is maintained for several months. We hypothesized that CAT influences memory accessibility for trained items, leading to enhanced accessibility of their positive associative memories and in turn to preference changes. In two pre-registered experiments, we tested whether memory for trained items was enhanced following CAT, in the short and in the long-term, and whether memory modifications were related to choices. We found that memory was enhanced for trained items and that better memory was correlated with enhanced preferences at the individual item level, both immediately and one month following CAT. Our findings show that memory plays a central role in value-based decision-making following CAT, even in the absence of external reinforcements. These findings contribute to new theories relating memory and value-based decision-making and set the groundwork for the implementation of novel behavioral interventions that lead to long-lasting behavioral change. | neuroscience |
10.1101/621490 | Predation strategies of the bacterium Bdellovibrio bacteriovorus result in overexploitation and bottlenecks | With increasing antimicrobial resistance, alternatives for treating infections or removing resistant bacteria are urgently needed, such as the bacterial predator Bdellovibrio bacteriovorus or bacteriophage. Therefore, we need to better understand microbial predator-prey dynamics. We developed mass-action mathematical models of predation for chemostats, which capture the low substrate concentration and slow growth typical for intended application areas of the predators such as wastewater treatment, aquaculture or the gut. Our model predicted that predator survival required a minimal prey size, explaining why Bdellovibrio is much smaller than its prey. A too good predator (attack rate too high, mortality too low) overexploited its prey leading to extinction (tragedy of the commons). Surprisingly, a predator taking longer to produce more offspring outcompeted a predator producing fewer offspring more rapidly (rate versus yield trade-off). Predation was only efficient in a narrow region around optimal parameters. Moreover, extreme oscillations under a wide range of conditions led to severe bottlenecks. A bacteriophage outcompeted Bdellovibrio due to its higher burst size and faster life cycle. Together, results suggest that Bdellovibrio would struggle to survive on a single prey, explaining why it must be a generalist predator and suggesting it is better suited than phage to environments with multiple prey.
ImportanceThe discovery of antibiotics led to a dramatic drop in deaths due to infectious disease. Increasing levels of antimicrobial resistance, however, threaten to reverse this progress. There is thus a need for alternatives, such as therapies based on phage and predatory bacteria that kill bacteria regardless of whether they are pathogens or resistant to antibiotics. To best exploit them, we need to better understand what determines their effectiveness. By using a mathematical model to study bacterial predation in realistic slow growth conditions, we found that the generalist predator Bdellovibrio is most effective within a narrow range of conditions for each prey. For example, a minimum prey size is required, and the predator should not be too good as this would result in over-exploitation risking extinction. Together these findings give insights into the ecology of microbial predation and help explain why Bdellovibrio needs to be a generalist predator. | microbiology |
10.1101/622019 | In the absence of reproductive isolation - Extensive gene flow after speciation | In the conventional view, species are separate gene pools delineated by reproductive isolation (RI). However, species may also be delineated by merely a small set of "speciation genes" without full RI. It is thus important to know whether "good species" (defined by the "secondary sympatry" test) do continue to exchange genes. Here, we carry out sequencing and de novo high-quality assembly of the genomes of two closely related mangrove species (Rhizophora mucronata and R. stylosa). Whole-genome re-sequencing of individuals across their range on the tropical coasts shows their genomes to be well delineated in allopatry. They became sympatric in northeastern Australia but remain distinct species in contact. Nevertheless, their genomes harbor [~] 4,000 to 10,000 introgression blocks, each averaging only about 3-4 Kb. These fine-grained introgressions indicate that gene flow has continued long after speciation. Non-introgressable "genomic islets," averaging only 1.4 Kb, may contribute to speciation as they often harbor diverging genes underlying flower development and gamete production. In conclusion, RI needs not be the main criterion of species delineation even though all species would eventually be fully reproductively isolated. | evolutionary biology |
10.1101/614032 | tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes | tRNAscan-SE has been widely used for transfer RNA (tRNA) gene prediction for over twenty years, developed just as the first genomes were decoded. With the massive increase in quantity and phylogenetic diversity of genomes, the accurate detection and functional prediction of tRNAs has become more challenging. Utilizing a vastly larger training set, we created nearly one hundred specialized isotype-and clade-specific models, greatly improving tRNAscan-SEs ability to identify and classify both typical and atypical tRNAs. We employ a new comparative multi-model strategy where predicted tRNAs are scored against a full set of isotype-specific covariance models, allowing functional prediction based on both the anticodon and the highest-scoring isotype model. Comparative model scoring has also enhanced the programs ability to detect tRNA-derived SINEs and other likely pseudogenes. For the first time, tRNAscan-SE also includes fast and highly accurate detection of mitochondrial tRNAs using newly developed models. Overall, tRNA detection sensitivity and specificity is improved for all isotypes, particularly those utilizing specialized models for selenocysteine and the three subtypes of tRNA genes encoding a CAU anticodon. These enhancements will provide researchers with more accurate and detailed tRNA annotation for a wider variety of tRNAs, and may direct attention to tRNAs with novel traits. | bioinformatics |
10.1101/623827 | The neuronal calcium sensor Synaptotagmin-1 and SNARE proteins cooperate to dilate fusion pores | All membrane fusion reactions proceed through an initial fusion pore, including calcium-triggered release of neurotransmitters and hormones. Expansion of this small pore to release cargo is energetically costly and regulated by cells, but the mechanisms are poorly understood. Here we show that the neuronal/exocytic calcium sensor Synaptotagmin-1 (Syt1) promotes expansion of fusion pores induced by SNARE proteins. Pore dilation relied on calcium-induced insertion of the tandem C2 domain hydrophobic loops of Syt1 into the membrane, previously shown to reorient the C2 domain. Mathematical modelling suggests that C2B reorientation rotates a bound SNARE complex so that it exerts force on the membranes in a mechanical lever action that increases the height of the fusion pore, provoking pore dilation to offset the bending energy penalty. We conclude that Syt1 exerts novel non-local calcium-dependent mechanical forces on fusion pores that dilate pores and assist neurotransmitter and hormone release.
SIGNIFICANCE STATEMENTDuring neurotransmitter release, calcium-induced membrane insertion of the C2B domain of Synaptotagmin re-orients the bound SNARE complex which dilates the fusion pore in a mechanical lever action. | biophysics |
10.1101/623983 | Low centrosome numbers correlate with higher aggressivity in ovarian cancer | Centrosome amplification, the presence of more than two centrosomes in a cell is a common feature of most human cancer cell lines. However, little is known about centrosome numbers of human cancers and whether amplification or other numerical aberrations are frequently present. To address this question, we have analyzed a large cohort of human epithelial ovarian cancers (EOCs) from 100 patients. Using state-of-the-art microscopy, we have determined the Centrosome-Nucleus Index (CNI) of each tumor. We found that EOCs show infrequent centrosome amplifications. Strikingly, the large majority of these tumors presented low CNIs. We show that low CNI tumors are enriched in the mesenchymal subgroup and correlate with poor patient survival. Our findings highlight a novel paradigm linking low centrosome number with highly aggressive behavior in ovarian cancers and show that the CNI signature may be used to stratify ovarian cancers. | cancer biology |
10.1101/629543 | Protein and Lipid Mass Concentration Measurement in Tissues by Stimulated Raman Scattering Microscopy | Cell mass and its chemical composition are important aggregate cellular variables for physiological processes including growth control and tissue homeostasis. Despite their central importance, it has been difficult to quantitatively measure these quantities from single cells in intact tissue. Here, we introduce Normalized Raman Imaging (NoRI), a Stimulated Raman Scattering (SRS) microscopy method that provides the local concentrations of protein, lipid and water from live or fixed tissue samples with high spatial resolution. Using NoRI, we demonstrate that single cell protein, lipid and water concentrations are maintained in a tight range in cells under same physiological conditions and are altered in different physiological states such as cell cycle stages, attachment to substrates of different stiffness, or by entering senescence. In animal tissues, protein and lipid concentration varies with cell types, yet an unexpected cell-to-cell heterogeneity was found in cerebellar Purkinje cells. Protein and lipid concentration profile provides a new means to quantitatively compare disease-related pathology as demonstrated using models of Alzheimers disease. Our demonstration shows that NoRI is a broadly applicable tool for probing the biological regulation of protein mass, lipid mass and water in cellular and tissue growth, homeostasis, and disease. | bioengineering |
10.1101/632497 | Cholinergic modulation of dentate gyrus processing through dynamic reconfiguration of inhibitory circuits | The dentate gyrus (DG) of the hippocampus plays a key role in memory formation and it is known to be modulated by septal projections. By performing electrophysiology and optogenetics we evaluated the role of cholinergic modulation in the processing of afferent inputs in the DG. We showed that mature granule cells (GCs), but not adult-born immature neurons, have increased responses to afferent perforant path stimuli upon cholinergic modulation. This is due to a highly precise reconfiguration of inhibitory circuits, differentially affecting Parvalbumin and Somatostatin interneurons, resulting in a nicotinic-dependent perisomatic disinhibition of GCs. This circuit reorganization provides a mechanism by which mature GCs could escape the strong inhibition they receive, creating a window of opportunity for plasticity. Indeed, coincident activation of perforant path inputs with optogenetic release of acetylcholine produced a long-term potentiated response in GCs, essential for memory formation. | neuroscience |
10.1101/617670 | Estimation of biodiversity metrics by environmental DNA metabarcoding compared with visual and capture surveys of river fish communities | O_LIInformation on alpha (local), beta (between habitats), and gamma (regional) diversity is fundamental to understanding biodiversity as well as the function and stability of community dynamics. Methods like environmental DNA (eDNA) metabarcoding are currently considered useful to investigate biodiversity.
C_LIO_LIWe compared the performance of eDNA metabarcoding with visual and capture surveys for estimating alpha and gamma diversity of river fish communities, and nestedness and turnover in particular.
C_LIO_LIIn five rivers across west Japan, by comparison to visual/capture surveys, eDNA metabarcoding detected more species in the study sites (i.e., alpha diversity). Consequently the overall number of species in the region (i.e., gamma diversity) was higher. In particular, the species found by visual/capture surveys were encompassed by those detected by eDNA metabarcoding.
C_LIO_LIEstimates of community diversity within rivers differed between survey methods. Although we found that the methods show similar levels of community nestedness and turnover within the rivers, visual/capture surveys showed more distinct community differences from upstream to downstream. Our results suggest that eDNA metabarcoding may be a suitable method for community assemblage analysis, especially for understanding regional community patterns, for fish monitoring in rivers.
C_LI | ecology |
10.1101/634782 | Complex community-wide consequences of consumer sexual dimorphism | Sexual dimorphism is a ubiquitous source of within-species variation, yet the communitylevel consequences of sex differences remain poorly understood. Here, we analyze a bitrophic model of two competing resource species and a sexually-reproducing consumer species. We show that consumer sex differences in resource acquisition can have striking consequences for consumer-resource coexistence, abundance, and dynamics. Under both direct interspecific competition and apparent competition between two resource species, sexual dimorphism in consumers attack rates can mediate coexistence of the resource species, while in other cases can lead to exclusion when stable coexistence is typically expected. Slight sex differences in total resource acquisition also can reverse competitive outcomes and lead to density cycles. These effects are expected whenever both consumer sexes require different amounts or types of resources to reproduce. Our results suggest that consumer sexual dimorphism, which is common, has wide-reaching implications for the assembly and dynamics of natural communities.
Statement of authorshipDB SD and SJS designed the study, SJS performed the mathematical analysis, SD performed the simulations and drafted the manuscript. All authors revised the manuscript.
Data accessibility statementNo data is used | ecology |
10.1101/634782 | Complex community-wide consequences of consumer sexual dimorphism | Sexual dimorphism is a ubiquitous source of within-species variation, yet the communitylevel consequences of sex differences remain poorly understood. Here, we analyze a bitrophic model of two competing resource species and a sexually-reproducing consumer species. We show that consumer sex differences in resource acquisition can have striking consequences for consumer-resource coexistence, abundance, and dynamics. Under both direct interspecific competition and apparent competition between two resource species, sexual dimorphism in consumers attack rates can mediate coexistence of the resource species, while in other cases can lead to exclusion when stable coexistence is typically expected. Slight sex differences in total resource acquisition also can reverse competitive outcomes and lead to density cycles. These effects are expected whenever both consumer sexes require different amounts or types of resources to reproduce. Our results suggest that consumer sexual dimorphism, which is common, has wide-reaching implications for the assembly and dynamics of natural communities.
Statement of authorshipDB SD and SJS designed the study, SJS performed the mathematical analysis, SD performed the simulations and drafted the manuscript. All authors revised the manuscript.
Data accessibility statementNo data is used | ecology |
10.1101/635805 | The regenerating skeletal muscle niche guides muscle stem cell self-renewal | Skeletal muscle stem cells (MuSCs) are essential for muscle regeneration and maintenance. While MuSCs typically are quiescent and reside in an asymmetric niche between the basal lamina and myofiber membrane: to repair or maintain muscle, MuSCs activate, proliferate and differentiate to repair injured tissue, and self-renew to replenish MuSCs. Little is known about the timing of MuSC self-renewal during muscle regeneration and the cellular processes that direct MuSC self-renewal fate decisions. Using DNA-based lineage tracing, we find that during muscle regeneration most MuSCs self-renew from 5-7 days post-injury, following fusion of myogenic cells to regenerate myofibers. Single cell sequencing of the myogenic cells in regenerating muscle reveals that non-cell autonomous signaling networks regulate MuSC self-renewal allowing identification of asymmetrically distributed proteins in self-renewing MuSCs. Cell transplantation experiments verified that the regenerating environment signals MuSC self-renewal. Our results define the critical window for MuSC self-renewal emphasizing the temporal contribution of the regenerative muscle environment on MuSC fate, establishing a new paradigm for restoring the MuSC pool during muscle regeneration. | cell biology |
10.1101/635839 | Synthetic design of farnesyl-electrostatic peptides for development of a protein kinase A membrane translocation switch | Molecular switches that respond to a biochemical stimulus in cells have proven utility as a foundation for developing molecular sensors and actuators that could be used to address important biological questions. Developing a molecular switch unfortunately remains difficult as it requires elaborate coordination of sensing and actuation mechanisms built into a single molecule. Here, we rationally designed a molecular switch that changes its subcellular localization in response to an intended stimulus such as an activator of protein kinase A (PKA). By arranging the sequence for Kemptide in tandem, we designed a farnesylated peptide whose localization can dramatically change upon phosphorylation by PKA. After testing a different valence number of Kemptide as well as modulating the linker sequence connecting them, we identified an efficient peptide switch that exhibited dynamic translocation between plasma membranes and internal endomembranes in a PKA activity dependent manner. Due to the modular design and small size, our PKA switch can have versatile utility in future studies as a platform for visualizing and perturbing signal transduction pathways, as well as for performing synthetic operations in cells. | cell biology |
10.1101/636043 | First report of marine sponge Chelonaplysilla delicata (Demospongiae: Darwinellidae) from the Andaman Sea/Indian Ocean with a baseline information of epifauna on a mesophotic shipwreck | During a biodiversity assessment on a wreck located in the Andaman Sea (Andaman Islands), a single specimen of sponge Chelonaplysilla delicata was recorded. Our finding confirms the species taxonomy and highlights the current observation as a first report from the Andaman Sea/ Indian Ocean. The baseline information of epifauna is further stated in this study. | ecology |
10.1101/637298 | Quantitative analysis of ZFY and CTCF reveals dependent recognition of tandem zinc finger proteins. | The human genome contains around 800 C2H2 Zinc Finger Proteins (ZFPs), and many of them are composed of long tandem arrays of zinc fingers. Current motif prediction models assume longer finger arrays correspond to longer DNA-binding motifs and higher specificity. However, recent experimental efforts to identify ZFP binding sites in vivo contradict this assumption, with many having short motifs. Here, we systematically test how multiple zinc fingers contribute to binding for three model ZFPs: Zinc Finger Y (ZFY), CTCF, and ZNF343. Using ZFY, which contains 13 fingers, we quantitatively characterize its binding specificity with several methods, including Affinity-seq, HT-SELEX, Spec-seq and fluorescence anisotropy, and find evidence for dependent recognition where downstream fingers can recognize some extended motifs only in the presence of an intact core site. For the genomic insulator CTCF, additional high-throughput affinity measurements reveal that its upstream specificity profile depends on the strength of the core, violating presumed additivity and positionindependence. Moreover, the effect of different epigenetic modifications within the core site depends on the strength of flanking upstream site, providing new insight into how the previously identified intellectual disability-causing and cancer-related mutant R567W disrupts upstream recognition and deregulates CTCFs methylation sensitivity. Lastly, we used ZNF343 as example to show that a simple iterative motif analysis strategy based on a small set of prefixed cores can reveal the dependent relationship between cores and upstream motifs. These results establish that the current underestimation of ZFPs motif lengths is due to our lack of understanding of intrinsic properties of tandem zinc finger recognition, including irregular motif structure, variable spacing, and dependent recognition between sub-motifs. These results also motivate a need for better recognition models beyond additive, position-weight matrix to predict ZFP specificities, occupancies, and the molecular mechanisms of disease mutations. | genetics |
10.1101/637512 | Gene-experience correlation during cognitive development: Evidence from the Adolescent Brain Cognitive Development (ABCD) StudySM | BackgroundFindings in adults have shown more culturally sensitive crystallized measures of intelligence have greater heritability, these results were not able to be shown in children.
MethodsWith data from 8,518 participants, aged 9 to 11, from the Adolescent Brain Cognitive Development (ABCD) Study(R), we used polygenic predictors of intelligence test performance (based on genome-wide association meta-analyses of data from 269,867 individuals) and of educational attainment (based on data from 1.1 million individuals), associating these predictors with neurocognitive performance. We then assessed the extent of mediation of these associations by a measure of recreational reading.
Resultsmore culturally sensitive crystallized measures were more strongly associated with the polygenic predictors than were less culturally sensitive fluid measures. This mirrored heritability differences reported previously in adults and suggests similar associations in children. Recreational reading more strongly statistically mediated the genetic associations with crystallized than those with fluid measures of cognition.
ConclusionThis is consistent with a prominent role of gene-environment correlation in cognitive development measured by "crystallized" intelligence tests. Such experiential mediators may represent malleable targets for improving cognitive outcomes. | neuroscience |
10.1101/639468 | Role of Water-bridged Interactions in Metal Ion Coupled Protein Allostery | Allosteric communication between distant parts of proteins controls many cellular functions, in which metal ions are widely utilized as effectors to trigger the allosteric cascade. Due to the involvement of strong coordination interactions, the energy landscape dictating the metal ion binding is intrinsically rugged. How metal ions achieve fast binding by overcoming the landscape ruggedness and thereby efficiently mediate protein allostery is elusive. By performing molecular dynamics simulations for the Ca2+ binding mediated allostery of the calmodulin (CaM) domains, each containing two Ca2+ binding helix-loop-helix motifs (EF-hands), we revealed the key role of water-bridged interactions in Ca2+ binding and protein allostery. The bridging water molecules between Ca2+ and binding residue reduces the ruggedness of ligand exchange landscape by acting as a lubricant, facilitating the Ca2+ coupled protein allostery.
Calcium-induced rotation of the helices in the EF-hands, with the hydrophobic core serving as the pivot, leads to exposure of hydrophobic sites for target binding. Intriguingly, despite being structurally similar, the response of the two symmetrically arranged EF-hands upon Ca2+ binding is asymmetric. Breakage of symmetry is needed for efficient allosteric communication between the EF-hands. The key roles that water molecules play in driving allosteric transitions are likely to be general in other metal ion mediated protein allostery. | biochemistry |
10.1101/640276 | An automated model reduction tool to guide the design and analysis of synthetic biological circuits | We present an automated model reduction algorithm that uses quasi-steady state approximation to minimize the error between the desired outputs. Additionally, the algorithm minimizes the sensitivity of the error with respect to parameters to ensure robust performance of the reduced model in the presence of parametric uncertainties. We develop the theory for this model reduction algorithm and present the implementation of the algorithm that can be used to perform model reduction of given SBML models. To demonstrate the utility of this algorithm, we consider the design of a synthetic biological circuit to control the population density and composition of a consortium consisting of two different cell strains. We show how the model reduction algorithm can be used to guide the design and analysis of this circuit. | synthetic biology |
10.1101/641340 | Metacognitive awareness of difficulty in action selection: the role of the cingulo-opercular network | The question whether and how we are able to monitor our own cognitive states (metacognition) has been a matter of debate for decades. Do we have direct access to our cognitive processes or can we only infer them indirectly based on their consequences? In the current study, we wanted to investigate the brain circuits that underlie the metacognitive experience of fluency in action selection. To manipulate action-selection fluency we used a subliminal response priming paradigm. On each trial, both male and female human participants additionally engaged in the metacognitive process of rating how hard they felt it was to respond to the target stimulus. Despite having no conscious awareness of the prime, results showed that participants rated incompatible trials (during which subliminal primes interfered with the required response) to be more difficult than compatible trials (where primes facilitated the required response) reflecting metacognitive awareness of difficulty. This increased sense of subjective difficulty was mirrored by increased activity in the rostral cingulate zone (RCZ) and the anterior insula, two regions that are functionally closely connected. Importantly, this reflected activations that were unique to subjective difficulty ratings and were not explained by reaction times or prime-response compatibility. We interpret these findings in light of a possible grounding of the metacognitive judgement of fluency in action selection in interoceptive signals resulting from increased effort. | neuroscience |
10.1101/639674 | An optimized tissue clearing protocol for rat brain labeling, imaging, and high throughput analysis | The advent of whole brain clearing and imaging methods extends the breadth and depth at which brain-wide neural populations and structures can be studied. However, these methods have yet to be applied to larger brains, such as the brains of the common laboratory rat, despite the importance of these models in behavioral neuroscience research. Here we introduce AdipoClear+, an optimized immunolabeling and clearing methodology for application to adult rat brain hemispheres, and validate its application through the testing of common antibodies and electrode tract visualization. In order to extend the accessibility of this methodology for general use, we have developed an open source platform for the registration of rat brain volumes to standard brain atlases for high throughput analysis. | neuroscience |
10.1101/641449 | Increasing plant group productivity through latent genetic variation for cooperation | Historic yield advances in the major crops have to a large part been achieved by selection for improved productivity of groups of plant individuals such as high-density stands. Research suggests that such improved group productivity depends on "cooperative" traits (e.g. erect leaves, short stems) that - while beneficial to the group - decrease individual fitness under competition. This poses a problem for some traditional breeding approaches, especially when selection occurs at the level of individuals, because "selfish" traits will be selected for and reduce yields in high-density monocultures. One approach therefore has been to select individuals based on ideotypes with traits expected to promote group productivity. However, this approach is limited to architectural and physiological traits whose effects on growth and competition are relatively easy to anticipate.
Here, we developed a general and simple method for the discovery of alleles promoting cooperation in plant stands. Our method is based on the game-theoretical premise that alleles increasing cooperation incur a cost to the individual but benefit the monoculture group. Testing the approach using the model plant Arabidopsis thaliana, we found a major effect locus where the rarer allele was associated with increased cooperation and productivity in high-density stands. The allele likely affects a pleiotropic gene, since we find that it is also associated with reduced root competition but higher resistance against disease. Thus, even though cooperation is considered evolutionarily unstable, conflicting selective forces acting on a pleiotropic gene might maintain latent genetic variation for it in nature. Such variation, once identified in a crop, could be rapidly leveraged in modern breeding programs and provide efficient routes to increase yields. | plant biology |
10.1101/642272 | Muscle torques provide more sensitive measures of post-stroke movement deficits than joint angles. | The whole repertoire of complex human motion is enabled by forces applied by our muscles and controlled by the nervous system. The of stroke on the complex multi-joint motor control is difficult to quantify in a meaningful way that informs about the underlying deficit in the active motor control and intersegmental coordination. We tested the idea that post-stroke deficit can be quantified with high sensitivity using motion capture and inverse modeling of a broad range of reaching movements. Our hypothesis is that muscle moments estimated based on active joint torques provide a more sensitive measure of post-stroke motor deficits than joint angle and angular velocity. The motion of twenty-two participants was captured while performing reaching movements in a center-out task, presented in virtual reality. We used inverse dynamics analysis to derive active joint torques that were the result of muscle contractions, termed muscle torques, that caused the recorded multi-joint motion. We then applied a novel analysis to separate the component of muscle torque related to gravity compensation from that related to intersegmental dynamics. Our results show that individual reaching movements can be characterized with higher information content using muscle torques rather than joint angles. Moreover, muscle torques allow for distinguishing between the individual motor deficits due to aging or stroke from the typical differences in reaching between healthy individuals. This novel quantitative assessment method may be used in conjunction with home-based gaming motion-capture technology for remote monitoring of motor deficits and inform the development of evidence-based robotic therapy interventions.
New and NoteworthyFunctional deficits seen in task performance have biomechanical underpinnings, seen only through the analysis of forces. Our study has shown that estimating muscle moments can quantify with high sensitivity post-stroke deficits in intersegmental coordination. An assessment developed based on this method could help quantify less observable deficits in mildly affected stroke patients. It may also bridge the gap between evidence from studies of constrained or robotically manipulated movements and research with functional and unconstrained movements. | neuroscience |
10.1101/643973 | Influenza-specific effector memory B cells predict long-lived antibody responses to vaccination in humans | Seasonal influenza vaccination elicits hemagglutinin (HA)-specific CD27+ memory B cells (Bmem) that differ in expression of T-bet, BACH2 and TCF7. T-bethiBACH2loTCF7lo Bmem are transcriptionally similar to effector-like memory cells while T-betloBACH2+TCF7+ Bmem exhibit stem-like central memory properties. T-bethi Bmem do not express plasma cell-specific transcription factors but do exhibit transcriptional, epigenetic, metabolic and functional changes that poise the cells for antibody production. Consistent with these changes, D7 HA+ T-bethi Bmem express intracellular immunoglobulin and T-bethi Bmem differentiate more rapidly into ASCs in vitro. The T-bethi Bmem response positively correlates with long-lived humoral immunity and clonotypes from T-bethi Bmem are represented in the early secondary ASC response to repeat vaccination, suggesting that this effector-like population can be used to predict vaccine durability and recall potential. | immunology |
10.1101/643585 | Mutators drive evolution of multi-resistance to antibiotics | Combination drug treatments are an approach used to counter the evolution of resistance-the guiding principle being that they can prevent multiple independent resistance mutations from arising sequentially in the same genome. Here, we show that bacterial populations with mutators, organisms defective in DNA repair, can evolve multi-resistance under conditions where purely wild-type populations cannot. We exposed experimental populations of Escherichia coli to rising concentrations of single-drug and combination antibiotic treatments. Introducing mutators at low-to-intermediate frequencies permitted the evolution of multi-resistance. Notably, the evolution of multi-resistance did not require direct selection for both resistance mutations, as the elevated mutation rates allowed it to evolve under single-drug and combination treatments alike. Using eco-evolutionary simulations, we show that hitch-hiking with single resistance mutations allowed the mutator allele to sweep to fixation. The resulting increase in mutation supply was the key to evolving multi-resistance sequentially. While simulations also demonstrated that multi-resistance can arise in large populations, the size required exceeded those typical of infection. Ultimately, our results suggest that the utility of combination therapy may be limited when mutators are present, and when achieving or maintaining therapeutic antibiotic concentrations is difficult. | evolutionary biology |
10.1101/645317 | A Hessian-based decomposition characterizes how performance in complex motor skills depends on individual strategy and variability | In complex real-life motor skills such as unconstrained throwing, performance depends on how accurate is on average the outcome of noisy, high-dimensional, and redundant actions. What characteristics of the action distribution relate to performance and how different individuals select specific action distributions are key questions in motor control. Previous computational approaches have highlighted that variability along the directions of first order derivatives of the action-to-outcome mapping affects performance the most, that different mean actions may be associated to regions of the actions space with different sensitivity to noise, and that action covariation in addition to noise magnitude matters. However, a method to relate individual high-dimensional action distribution and performance is still missing. Here we introduce a de-composition of performance into a small set of indicators that compactly and directly characterize the key performance-related features of the distribution of high-dimensional redundant actions. Central to the method is the observation that, if performance is quantified as a mean score, the Hessian (second order derivatives) of the action-to-score function determines how the noise of the action distribution affects the average score. We can then approximate the mean score as the sum of the score of the mean action and a tolerance-variability index which depends on both Hessian and action covariance. Such index can be expressed as the product of three terms capturing noise magnitude, noise sensitivity, and alignment of the most variable and most noise sensitive directions. We apply this method to the analysis of unconstrained throwing actions by non-expert participants and show that, consistently across four different throwing targets, each participant shows a specific selection of mean action score and tolerance-variability index as well as specific selection of noise magnitude and alignment indicators. Thus, participants with different strategies may display the same performance because they can trade off suboptimal mean action for better tolerance-variability and higher action variability for better alignment with more tolerant directions in action space.
Author summaryWhy do people differ in their performance of complex motor skills? In many real-life motor tasks achieving a goal requires selecting an appropriate high-dimensional action out of infinitely many goal-equivalent actions. Because of sensorimotor noise, we are unable to execute the exact same movement twice and our performance depends on how accurate we are on average. Thus, to understand why people perform differently we need to characterize how their action distribution relates to their mean task score. While better performance is often associated to smaller variability around a more accurate mean action, performance also depends on the relationship between the directions of highest variability in action space and the directions in which action variability affects the most the outcome of the action. However, characterizing such geometric relationship when actions are high dimensional is challenging. In this work we introduce a method that allows to characterize the key performance-related features of the distribution of high-dimensional actions by a small set of indicators. We can then compare such indicators in different people performing a complex task (such as unconstrained throwing) and directly characterize the most skilled ones but also identify different strategies that distinguish people with similar performance. | neuroscience |
10.1101/645747 | Comparing statistical and mechanistic models to identify the drivers of mortality within a rear-edge beech population | AO_SCPLOWBSTRACTC_SCPLOWSince several studies have been reporting an increase in the decline of forests, a major issue in ecology is to better understand and predict tree mortality. The interactions between the different factors and the physiological processes giving rise tree mortality, as well as the inter-individual variability in mortality risk, still need to be better assessed.
This study investigates mortality in a rear-edge population of European beech (Fagus sylvatica L.) using a combination of statistical and process-based modelling approaches. Based on a survey of 4323 adult beeches since 2002 within a natural reserve, we first used statistical models to quantify the effects of competition, tree growth, size, defoliation and fungi presence on mortality. Secondly, we used an ecophysiological process-based model (PBM) to separate out the different mechanisms giving rise to temporal and inter-individual variations in mortality by simulating depletion of carbon stocks, loss of hydraulic conductance and damage due to late frosts in response to climate.
The combination of all these simulated processes was associated with the temporal variations in the population mortality rate. The individual probability of mortality decreased with increasing mean growth, and increased with increasing crown defoliation, earliness of budburst, fungi presence and increasing competition, in the statistical model. Moreover, the interaction between tree size and defoliation was significant, indicating a stronger increase in mortality associated to defoliation in smaller than larger trees. Finally, the PBM predicted a higher conductance loss together with a higher level of carbon reserves for trees with earlier budburst, while the ability to defoliate the crown was found to limit the impact of hydraulic stress at the expense of the accumulation of carbon reserves.
We discuss the convergences and divergences obtained between statistical and process-based approaches and we highlight the importance of combining them to characterize the different processes underlying mortality, and the factors modulating individual vulnerability to mortality. | ecology |
10.1101/645747 | Comparing statistical and mechanistic models to identify the drivers of mortality within a rear-edge beech population | AO_SCPLOWBSTRACTC_SCPLOWSince several studies have been reporting an increase in the decline of forests, a major issue in ecology is to better understand and predict tree mortality. The interactions between the different factors and the physiological processes giving rise tree mortality, as well as the inter-individual variability in mortality risk, still need to be better assessed.
This study investigates mortality in a rear-edge population of European beech (Fagus sylvatica L.) using a combination of statistical and process-based modelling approaches. Based on a survey of 4323 adult beeches since 2002 within a natural reserve, we first used statistical models to quantify the effects of competition, tree growth, size, defoliation and fungi presence on mortality. Secondly, we used an ecophysiological process-based model (PBM) to separate out the different mechanisms giving rise to temporal and inter-individual variations in mortality by simulating depletion of carbon stocks, loss of hydraulic conductance and damage due to late frosts in response to climate.
The combination of all these simulated processes was associated with the temporal variations in the population mortality rate. The individual probability of mortality decreased with increasing mean growth, and increased with increasing crown defoliation, earliness of budburst, fungi presence and increasing competition, in the statistical model. Moreover, the interaction between tree size and defoliation was significant, indicating a stronger increase in mortality associated to defoliation in smaller than larger trees. Finally, the PBM predicted a higher conductance loss together with a higher level of carbon reserves for trees with earlier budburst, while the ability to defoliate the crown was found to limit the impact of hydraulic stress at the expense of the accumulation of carbon reserves.
We discuss the convergences and divergences obtained between statistical and process-based approaches and we highlight the importance of combining them to characterize the different processes underlying mortality, and the factors modulating individual vulnerability to mortality. | ecology |
10.1101/647156 | Deconstructing taxa x taxa x environment interactions in the microbiota: A theoretical examination | O_LIA major objective of microbial ecology is to identify how the composition of gut microbial taxa shapes host phenotypes. However, most studies focus solely on community-level patterns and pairwise interactions and ignore the potentially significant effects of higher-order interactions involving three or more component taxa.
C_LIO_LIStudies on higher-order interactions among microbial taxa are scarce for many reasons, including experimental intractability, daunting diversity and complexity of many microbial systems, and the potential confounding role of the environment. Moreover, we still lack the empirical and statistical tools to isolate and understand the role of higher-order interactions on the host.
C_LIO_LIHere, we apply a mathematical approach to quantifying the effects of higher-order interactions among taxa on host infection risk. To do so, we adapt the Hadamard-Walsh method recently used in evolutionary genetics to quantify the nonlinear effects of mutations on fitness. We apply our approach to an in silico dataset built to resemble a population of insect hosts with gut-associated microbial communities at risk of infection from an intestinal parasite. Critically, we examine these interactions across a breadth of environmental contexts, using nutrient content of the insect diet as a model for context.
C_LIO_LIWe find that the effect of higher-order interactions is considerable and can change appreciably across environmental contexts. Strikingly, the relative eminence of different orders (pairwise vs. third order, fourth order, and fifth order) changes as a function of environmental context. Furthermore, we show-in our theoretical microcosm-that higher-order interactions can stabilize community structure thereby reducing host susceptibility to parasite invasion.
C_LIO_LIOur approach illustrates how incorporating the effects of higher-order interactions among gut microbiota across environments can be essential for understanding their effects on host phenotypes. We conclude that higher-order interactions among taxa can profoundly shape important organismal phenotypes, and they deserve greater attention in host-associated microbiome studies.
C_LI | ecology |
10.1101/649392 | Damped oscillations of the probability of random events followed by absolute refractory period: exact analytical results | There are numerous examples of natural and artificial processes that represent stochastic sequences of events followed by an absolute refractory period during which the occurrence of a subsequent event is impossible. In the simplest case of a generalized Bernoulli scheme for uniform random events followed by the absolute refractory period, the event probability as a function of time can exhibit damped transient oscillations. Using stochastically-spiking point neuron as a model example, we present an exact and compact analytical description for the oscillations without invoking the standard renewal theory. The resulting formulas stand out for their relative simplicity, allowing one to analytically obtain the amplitude damping of the 2nd and 3rd peaks of the event probability. | neuroscience |
10.1101/646695 | Estimations of the weather effects on brain functions using functional MRI: a cautionary note | The influences of environmental factors such as weather on the human brain are still largely unknown. A few neuroimaging studies have demonstrated seasonal effects, but were limited by their cross-sectional design or sample sizes. Most importantly, the stability of the MRI scanner hasnt been taken into account, which may also be affected by environments. In the current study, we analyzed longitudinal resting-state functional MRI (fMRI) data from eight individuals, where the participants were scanned over months to years. We applied machine learning regression to use different resting-state parameters, including the amplitude of low-frequency fluctuations (ALFF), regional homogeneity (ReHo), and functional connectivity matrix, to predict different weather and environmental parameters. For careful control, the raw EPI and the anatomical images were also used for predictions. We first found that daylight length and air temperatures could be reliably predicted with cross-validation using the resting-state parameters. However, similar prediction accuracies could also be achieved by using one frame of EPI image, and even higher accuracies could be achieved by using segmented or raw anatomical images. Finally, the signals outside of the brain in the anatomical images and signals in phantom scans could also achieve higher prediction accuracies, suggesting that the predictability may be due to the baseline signals of the MRI scanner. After all, we did not identify detectable influences of weather on brain functions other than the influences on the baseline signals of MRI scanners. The results highlight the difficulty of studying long-term effects using MRI. | neuroscience |
10.1101/651315 | Secondary Structure Motifs Made Searchable to Facilitate the Functional Peptide Design | To ensure a physicochemically desired sequence motif to adapt a specific type of secondary structures, we compile an -helix database allowing complicate search patterns to facilitate a data-driven design of therapeutic peptides. Nearly 1.7 million helical peptides in >130 thousand proteins are extracted along with their interacting partners from the protein data bank (PDB). The sequences of the peptides are indexed with patterns and gaps and deposited in our Therapeutic Peptide Design dataBase (TP-DB). We here demonstrate its utility in three medicinal design cases. By our pattern-based search engine but not PHI-BLAST, we can identify a pathogenic protein, Helicobacter pylori neutrophil-activating protein (HP-NAP), a virulence factor of H. pylori, which contains a motif DYKYLE that belongs to the affinity determinant motif DYKXX[DE] of the FLAG-tag and can be recognized by the anti-FLAG M2 antibody. By doing so, the known purification-tag-specific antibody is repurposed into a diagnostic kit for H. pylori. Also by leveraging TP-DB, we discovered a stretch of helical peptide matching the potent membrane-insertion pattern WXXWXXW, elucidated by MD simulations. The newly synthesized peptide has a better minimal inhibitory concentration (MIC) and much lower cytotoxicity against Candida albicans (fungus) than that of previously characterized homologous antimicrobial peptides. In a similar vein, taking the discontinued anchoring residues in the helix-helix interaction interface as the search pattern, TP-DB returns several helical peptides as potential tumor suppressors of hepatocellular carcinoma (HCC) whose helicity and binding affinity were examined by MD simulations. Taken together, we believe that TP-DB and its pattern-based search engine provide a new opportunity for a (secondary-)structure-based design of peptide drugs and diagnostic kits for pathogens without inferring evolutionary homology between sequences sharing the same pattern. TP-DB is made available at http://dyn.life.nthu.edu.tw/design/. | bioinformatics |
10.1101/652040 | Mitigating biomass composition uncertainties in flux balance analysis using ensemble representations | The biomass equation is a critical component in genome-scale metabolic models (GEMs): it is used as the de facto objective function in flux balance analysis (FBA). This equation accounts for the quantities of all known biomass precursors that are required for cell growth based on the macromolecular and monomer compositions measured at certain conditions. However, it is often reported that the macromolecular composition of cells could change across different environmental conditions; the use of the same single biomass equation in FBA, under multiple conditions, is questionable. Thus, we first investigated the qualitative and quantitative variations of macromolecular compositions of three representative host organisms, Escherichia coli, Saccharomyces cerevisiae and Cricetulus griseus, across different environmental/genetic variations. While macromolecular building blocks such as DNA, RNA, protein, and lipid composition vary notably, variations in fundamental biomass monomer units such as nucleotides and amino acids are not appreciable. We further observed that while macromolecular compositions are similar across taxonomically closer species, certain monomers, especially fatty acids, vary substantially. Based on the analysis results, we subsequently propose a new extension to FBA, named "Flux Balance Analysis with Ensemble Biomass (FBAwEB)", to embrace the natural variation in selected components of the biomass equation. The current study clearly highlights that certain components of the biomass equation are very sensitive to different conditions, and the ensemble representation of biomass equation in the FBA framework enables us to account for such natural variations accurately during GEM-guided in silico simulations. | systems biology |
10.1101/654889 | Molecular Determinants of μ-Conotoxin KIIIA interaction with the Voltage-Gated Sodium Channel Nav1.7 | The voltage-gated sodium (Nav) channel subtype Nav1.7 plays a critical role in pain signaling, making it an important drug target. Here we studied the molecular interactions between -conotoxin KIIIA (KIIIA) and the human Nav1.7 channel (hNav1.7). We developed a structural model of hNav1.7 using Rosetta computational modeling and performed in silico docking of KIIIA using RosettaDock to predict residues forming specific pairwise contacts between KIIIA and hNav1.7. We experimentally validated these contacts using mutant cycle analysis. Comparison between our KIIIA-hNav1.7 model and the cryo-EM structure of KIIIA-hNav1.2 revealed key similarities and differences between Nav channel subtypes with potential implications for the molecular mechanism of toxin block. The accuracy of our integrative approach, combining structural data with computational modeling, experimental validation, and molecular dynamics simulations, suggests that Rosetta structural predictions will be useful for rational design of novel biologics targeting specific Nav channels. | biophysics |
10.1101/653907 | Deep learning does not outperform classical machine learning for cell-type annotation | Deep learning has revolutionized image analysis and natural language processing with remarkable accuracies in prediction tasks, such as image labeling and semantic segmentation or named-entity recognition and semantic role labeling. Specifically, the combination of algorithmic and hardware advances with the appearance of large and well-labeled datasets has led up to seminal contributions in these fields.
The emergence of large amounts of data from single-cell RNA-seq and the recent global effort to chart all cell types in the Human Cell Atlas has attracted an interest in deep-learning applications. However, all current approaches are unsupervised, i.e., learning of latent spaces without using any cell labels, even though supervised learning approaches are often more powerful in feature learning and the most popular approach in the current AI revolution by far. Here, we ask why this is the case. In particular we ask whether supervised deep learning can be used for cell annotation, i.e. to predict cell-type labels from single-cell gene expression profiles. After evaluating 10 classification methods across 14 datasets, we notably find that deep learning does not outperform classical machine-learning methods in the task. Thus, cell-type prediction based on gene-signature derived cell-type labels is potentially too simplistic a task for complex non-linear methods, which demands better labels of functional single-cell readouts. | bioinformatics |
10.1101/655225 | Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila | BackgroundVariation in gene expression underlies interindividual variability in relevant traits including immune response. However, the genetic variation responsible for these gene expression changes remain largely unknown. Among the non-coding variants that could be relevant, transposable element insertions are promising candidates as they have been shown to be a rich and diverse source of cis-regulatory elements.
ResultsIn this work, we used a population genetics approach to identify transposable element insertions likely to increase the tolerance of Drosophila melanogaster to bacterial infection by affecting the expression of immune-related genes. We identified 12 insertions associated with allele-specific expression changes in immune-related genes. We experimentally validated three of these insertions including one likely to be acting as a silencer, one as an enhancer, and one with a dual role as enhancer and promoter. The direction in the change of gene expression associated with the presence of several of these insertions was consistent with an increased survival to infection. Indeed, for one of the insertions, we showed that this is the case by analyzing both natural populations and CRISPR/Cas9 mutants in which the insertion was deleted from its native genomic context.
ConclusionsWe showed that transposable elements contribute to gene expression variation in response to infection in D. melanogaster and that this variation is likely to affect their survival capacity. Because the role of transposable elements as regulatory elements is not restricted to Drosophila, TEs are likely to play a role in immune response in other organisms as well. | evolutionary biology |
10.1101/655084 | Neural pathways linking hypoxia with pectoral fin movements in Danio rerio | Zebrafish larvae respond to hypoxia by increasing a number of ventilatory behaviors. During development, these animals switch from skin-resident to gill-resident neuroendocrine cells around 7 days post fertilization (d.p.f.) to detect hypoxia and drive adaptive behaviors. Here, we probe the neural pathways that receive inputs from skin-resident neuroendocrine cells and alter pectoral fin movements. We first show that a 5 d.p.f. larva increases its pectoral fin movements and heart activity upon hypoxia exposure. Next, we map the downstream neural circuitry and show that individual vagal sensory neurons receive inputs from multiple oxygen-sensing neuroendocrine cells. We then use calcium imaging to show that neurons in the second, but not third, vagal sensory ganglia show increases in the magnitude of their hypoxia-evoked responses. Finally, we link purinergic signaling between neuroendocrine cells and second vagal sensory neurons to increases in pectoral fin movements. Collectively, we suggest that vagal sensory neurons transform hypoxic stimuli into respiratory behaviors. | neuroscience |
10.1101/653196 | Re-treatment with direct-acting antivirals policy is needed to eliminate Hepatitis C among persons who inject drugs | Background and AimsHepatitis C virus (HCV) infection is a leading cause of chronic liver disease and mortality worldwide. Direct-acting antiviral (DAA) therapy leads to high cure rates. However, persons who inject drugs (PWID) are at risk for reinfection after cure and may require DAA retreatment to reach the World Health Organizations (WHO) goal of HCV elimination by 2030. We aim to project the frequency of retreatment and DAA cost needed to achieve WHO goals.
DesignWe use an agent-based model (ABM) that accounts for the complex interplay of demographic factors, risk behaviors, social networks, and geographic location for HCV transmission among PWID.
Setting and participants32,000 in-silico PWID in metropolitan Chicago.
Intervention and comparatorPossible treatment adherence rates (i.e., DAA cure rates) of 60%-90% with DAA treatment enrollment rates of 2.5%-10% and retreatments per PWID of 0 (retreatment prohibited), 1, 2, 3, or no retreatment restriction were simulated. DAA cost is assumed $25,000 (USD) per treatment.
FindingsModeling results indicate that prohibition of retreatment in PWID would jeopardize achieving the WHO goal of reducing the incidence of new chronic HCV infections by 90% by 2030. We predict that with a DAA treatment rate of >7.5% per year and high (90%) adherence, 75%, 19%, 5% and <2% of PWID will require 1, 2, 3, and 4 treatment courses with overall DAA cost of $325 million to achieve the WHO goal in metropolitan Chicago. We estimate a 28% increase in the overall DAA cost under low adherence (70%) compared to high adherence (90%).
ConclusionsModeling results predict the frequency of DAA retreatment needed to achieve the WHO goal and underscore the importance of retreatment of HCV re-infections. | epidemiology |
10.1101/655340 | Amyloid-β induced membrane damage instigates tunneling nanotubes by exploiting PAK1 dependent actin remodulation | Alzheimers disease (AD) pathology progresses gradually via anatomically connected brain regions. Earlier studies have shown that amyloid-{beta}1-42 oligomers (oA{beta}) can be directly transferred between connected neurons. However, the mechanism of transfer is not fully revealed. We observed formation of oA{beta} induced tunneling nanotubes (TNTs), nanoscaled f-actin containing membrane conduit, in differentially differentiated SH-SY5Y neuronal models. Time-lapse images showed that TNTs propagate oligomers from one cell to another. Preceding the TNT-formation, we detected oA{beta} induced plasma membrane (PM) damage and calcium-dependent repair through lysosomal-exocytosis and significant membrane surface expansion, followed by massive endocytosis to re-establish the PM. Massive endocytosis was monitored by an influx of the membrane-impermeable dye TMA-DPH and PM damage was quantified by propidium iodide influx in the absence of calcium. The massive endocytosis eventually caused accumulation of internalized oA{beta} in Lamp1 positive multi vesicular bodies/lysosomes via the actin cytoskeleton remodulating p21-activated kinase1 (PAK1) dependent endocytic pathway. Three dimensional quantitative and qualitative confocal imaging, structured illumination superresolution microscopy (SIM) and flowcytometry data revealed that oA{beta} induces activated phospho-PAK1, which modulates the formation of long stretched f-actin extensions between cells. Moreover, formation of TNTs can be inhibited by preventing PAK1 dependent internalization of oA{beta} using small-molecule inhibitor IPA-3, a highly selective cell permeable auto-regulatory inhibitor of PAK1. The present study gives insight that the TNTs are probably instigated as a consequence of oA{beta} induced PM damage and repair process, followed by PAK1 dependent endocytosis and actin remodeling, probably to maintain cell surface expansion and/or membrane tension in equilibrium. | cell biology |
10.1101/655340 | Amyloid-β induced membrane damage instigates tunneling nanotubes by exploiting PAK1 dependent actin remodulation | Alzheimers disease (AD) pathology progresses gradually via anatomically connected brain regions. Earlier studies have shown that amyloid-{beta}1-42 oligomers (oA{beta}) can be directly transferred between connected neurons. However, the mechanism of transfer is not fully revealed. We observed formation of oA{beta} induced tunneling nanotubes (TNTs), nanoscaled f-actin containing membrane conduit, in differentially differentiated SH-SY5Y neuronal models. Time-lapse images showed that TNTs propagate oligomers from one cell to another. Preceding the TNT-formation, we detected oA{beta} induced plasma membrane (PM) damage and calcium-dependent repair through lysosomal-exocytosis and significant membrane surface expansion, followed by massive endocytosis to re-establish the PM. Massive endocytosis was monitored by an influx of the membrane-impermeable dye TMA-DPH and PM damage was quantified by propidium iodide influx in the absence of calcium. The massive endocytosis eventually caused accumulation of internalized oA{beta} in Lamp1 positive multi vesicular bodies/lysosomes via the actin cytoskeleton remodulating p21-activated kinase1 (PAK1) dependent endocytic pathway. Three dimensional quantitative and qualitative confocal imaging, structured illumination superresolution microscopy (SIM) and flowcytometry data revealed that oA{beta} induces activated phospho-PAK1, which modulates the formation of long stretched f-actin extensions between cells. Moreover, formation of TNTs can be inhibited by preventing PAK1 dependent internalization of oA{beta} using small-molecule inhibitor IPA-3, a highly selective cell permeable auto-regulatory inhibitor of PAK1. The present study gives insight that the TNTs are probably instigated as a consequence of oA{beta} induced PM damage and repair process, followed by PAK1 dependent endocytosis and actin remodeling, probably to maintain cell surface expansion and/or membrane tension in equilibrium. | cell biology |
10.1101/655217 | Universal latent axes capturing Parkinson's patient deep phenotypic variation reveals patients with a high genetic risk for Alzheimer's disease are more likely to develop a more aggressive form of Parkinson's. | The generation of deeply phenotyped patient cohorts offers an enormous potential to identify disease subtypes but are currently limited by the cohort size and the heterogeneity of the clinical assessments collected across different cohorts. Identifying the universal axes of clinal severity and progression is key to accelerating our understanding of how disease manifests and progresses. These universal axes would accelerate our understanding of how Parkinsons disease (PD) manifests and progresses through which patients may be appropriately compared appropriately stratified, and personalised therapeutic strategies and treatments can be developed and targeted. We developed a Bayesian multiple phenotype mixed model incorporating the genetic relationships between individuals which is able to reduce a wide-array of different clinical measurements into a smaller number of continuous underlying factors named phenotypic axis. We identify three principal axes of PD patient phenotypic variation which are reproducibly found across three independent, deeply and diversely phenotyped cohorts. Together they explain over 75% of the observed clinical variation and remain robustly captured with a fraction of the clinically-recorded features. The most influential axis was associated with the genetic risk of Alzheimers disease (AD) and involves genetic pathways associated with neuroinflammation. Our results suggest PD patients with a high genetic risk for AD are more likely to develop a more aggressive form of PD including, but not limited to, dementia. | neuroscience |
10.1101/656355 | Oxazepam and cognitive reappraisal: a randomised experiment | BackgroundCognitive reappraisal is a strategy for emotional regulation, important in the context of anxiety disorders. It is not known whether anxiolytic effects of benzodiazepines affect cognitive reappraisal.
AimsWe aimed to investigate the effect of 25 mg oxazepam on cognitive reappraisal.
MethodsIn a preliminary investigation, 33 healthy male volunteers were randomised to oxazepam or placebo, and then underwent an experiment where they were asked to use cognitive reappraisal to upregulate or downregulate their emotional response to images with negative or neutral emotional valence. We recorded unpleasantness ratings, skin conductance, superciliary corrugator muscle activity, and heart rate. Participants completed rating scales measuring empathy (Interpersonal Reactivity Index, IRI), anxiety (State-Trait Anxiety Inventory, STAI), alexithymia (Toronto Alexithymia Scale-20, TAS-20), and psychopathy (Psychopathy Personality Inventory-Revised, PPI-R).
ResultsUpregulation to negative-valence images in the cognitive reappraisal task caused increased unpleasantness ratings, corrugator activity, and heart rate compared to downregulation. Upregulation to both negative- and neutral-valence images caused increased skin conductance responses. Oxazepam caused lower unpleasantness ratings to negative-valence stimuli, but did not interact with reappraisal instruction on any outcome. Self-rated trait empathy was associated with stronger responses to negative-valence stimuli, whereas self-rated psychopathic traits were associated with weaker responses to negative-valence stimuli.
ConclusionsWhile 25 mg oxazepam caused lower unpleasantness ratings in response to negative-valence images, we did not observe an effect of 25 mg oxazepam on cognitive reappraisal. | neuroscience |
10.1101/658658 | Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition | The human brain differs from that of other primates, but the genetic basis of these differences remains unclear. We investigated the evolutionary pressures acting on almost all human protein-coding genes (N=11,667; 1:1 orthologs in primates) based on their divergence from those of early hominins, such as Neanderthals, and non-human primates. We confirm that genes encoding brain-related proteins are among the most strongly conserved protein-coding genes in the human genome. Combining our evolutionary pressure metrics for the protein-coding genome with recent datasets, we found that this conservation applied to genes functionally associated with the synapse and expressed in brain structures such as the prefrontal cortex and the cerebellum. Conversely, several genes presenting signatures commonly associated with positive selection appear as causing brain diseases or conditions, such as micro/macrocephaly, Joubert syndrome, dyslexia, and autism. Among those, a number of DNA damage response genes associated with microcephaly in humans such as BRCA1, NHEJ1, TOP3A, and RNF168 show strong signs of positive selection and might have played a role in human brain size expansion during primate evolution. We also showed that cerebellum granule neurons express a set of genes also presenting signatures of positive selection and that may have contributed to the emergence of fine motor skills and social cognition in humans. This resource is available online and can be used to estimate evolutionary constraints acting on a set of genes and to explore their relative contributions to human traits. | genetics |
10.1101/657908 | Simplified high-throughput methods for deep proteome analysis on the timsTOF Pro | Recent advances in mass spectrometry technology have seen remarkable increases in proteomic sequencing speed, while improvements to dynamic range have remained limited. An exemplar of this is the new timsTOF Pro instrument, which thanks to its trapped ion mobility, pushes effective fragmentation rates beyond 100Hz and provides accurate CCS values as well as impressive sensitivity. Established data dependent methodologies underutilize these advances by relying on long analytical columns and extended LC gradients to achieve comprehensive proteome coverage from biological samples. Here we describe the implementation of methods for short packed emitter columns that fully utilize instrument speed and CCS values by combining rapid generation of deep peptide libraries with enhanced matching of single shot data dependent sample analysis. Impressively, with only a 17 minute separation gradient (50 samples per day), the combination of high performance chromatography and CCS enhanced library based matching resulted in an average of 5,931 protein identifications within individual samples, and 7,244 proteins cumulatively across replicates from HeLa cell tryptic digests. Additionally, an ultra-high throughput setup utilizing 5 min gradients (180 samples per day) yielded an average of 3,666 protein identifications within individual samples and 4,659 proteins cumulatively across replicates. These workflows are simple to implement on available technology and do not require complex software solutions or custom-made consumables to achieve high throughput and deep proteome analysis from biological samples. | biochemistry |
10.1101/649582 | From spikes to intercellular waves: tuning intercellular Ca2+ signaling dynamics modulates organ size control | Information flow within and between cells depends in part on calcium (Ca2+) signaling dynamics. However, the biophysical mechanisms that govern emergent patterns of Ca2+ signaling dynamics at the organ level remain elusive. Recent experimental studies in developing Drosophila wing imaginal discs demonstrate the emergence of four distinct patterns of Ca2+ activity: Ca2+ spikes, intercellular Ca2+ transients, tissue-level Ca2+ waves, and a global "fluttering" state. Here, we used a combination of computational modeling and experimental approaches to identify two different populations of cells within tissues that are connected by gap junctional proteins. We term these two subpopulations "initiator cells" defined by elevated levels of Phospholipase C (PLC) activity and "standby cells," which exhibit baseline activity. We found that the strength of hormonal stimulation and extent of gap junctional communication jointly determine the predominate class of Ca2+ signaling activity. Further, single-cell Ca2+ spikes are stimulated by insulin, while intercellular Ca2+ waves depend on Gq activity. Our computational model successfully recapitulates how the dynamics of Ca2+ transients varies during organ growth. Phenotypic analysis of perturbations to Gq and insulin signaling support an integrated model of cytoplasmic Ca2+ as a dynamic reporter of overall tissue growth. Further, we show that perturbations to Ca2+signaling tune the final size of organs. This work provides a platform to further study how organ size regulation emerges from the crosstalk between biochemical growth signals and heterogeneous cell signaling states.
Author SummaryCalcium (Ca2+) is a universal second messenger that regulates a myriad of cellular processes such as cell division, cell proliferation and apoptosis. Multiple patterns of Ca2+ signaling including single cell spikes, multicellular Ca2+ transients, large-scale Ca2+ waves, and global "fluttering" have been observed in epithelial systems during organ development. Key molecular players and biophysical mechanisms involved in formation of these patterns during organ development are not well understood. In this work, we developed a generalized multicellular model of Ca2+ that captures all the key categories of Ca2+ activity as a function of key hormonal signals. Integration of model predictions and experiments reveals two subclasses of cell populations and demonstrates that Ca2+ signaling activity at the organ scale is defined by a general decrease in gap junction communication as organ growth. Our experiments also reveal that a "goldilocks zone" of optimal Ca2+ activity is required to achieve optimal growth at the organ level. | systems biology |
10.1101/659557 | Dynamic pneumococcal genetic adaptations support bacterial growth and inflammation during coinfection with influenza | Streptococcus pneumoniae (pneumococcus) is one of the primary bacterial pathogens that complicates influenza virus infections. These bacterial coinfections increase influenza-associated morbidity and mortality through a number of immunological and viral-mediated mechanisms, but the specific bacterial genes that contribute to post-influenza pathogenicity are not known. Here, we used genome-wide transposon mutagenesis (Tn-Seq) to reveal bacterial genes that confer improved fitness in influenza-infected hosts. The majority of the 32 identified genes are involved in bacterial metabolism, including nucleotide biosynthesis, amino acid biosynthesis, protein translation, and membrane transport. We generated single-gene deletion (SGD) mutants of five identified genes: SPD1414, SPD2047 (cbiO1), SPD0058 (purD), SPD1098, and SPD0822 (proB), to investigate their effect on in vivo fitness, disease severity, and host immune responses. Growth of SGD mutants was slightly attenuated in vitro and in vivo, but each still grew to high titers in the lungs of mock- and influenza-infected hosts. Despite high bacterial loads, mortality was significantly reduced or delayed with all SGD mutants. Time-dependent reductions in pulmonary neutrophils, inflammatory macrophages, and select proinflammatory cytokines and chemokines were also observed. Immunohistochemical staining further revealed that neutrophil phenotype and distribution was altered in the lungs of influenza-SGD coinfected animals. These studies demonstrate a critical role for specific bacterial genes and for bacterial metabolism in driving virulence and modulating immune function during influenza-associated bacterial pneumonia. | microbiology |
10.1101/658930 | Whole body regeneration deploys a rewired embryonic gene regulatory network logic | For over a century, researchers have been trying to understand the relationship between embryogenesis and regeneration. A long-standing hypothesis is that biological processes implicated in embryonic development are re-deployed during regeneration. In the past decade, we have begun to understand the relationships of genes and their organization into gene regulatory networks (GRN) driving embryonic development and regeneration in diverse taxa.
Here, we compare embryonic and regeneration GRNs in the same species to investigate how regeneration re-uses genetic interactions originally set aside for embryonic development. Using a well-suited embryonic development and whole-body regeneration model, the sea anemone Nematostella vectensis, we show that at the transcriptomic level the regenerative program partially re-uses elements of the embryonic gene network along with a small cohort of genes that are specifically activated during the process of regeneration. We further identified co-expression modules that are either i) highly conserved between these two developmental trajectories and involved in core biological processes (e.g., terminal differentiation) or ii) regeneration specific modules that drive cellular events, such as apoptosis, that are unique to regeneration.
Our global transcriptomic approach suggested that regeneration reactivates embryonic gene modules following regeneration-specific network logic. We thus verified this observation by functionally dissecting the role of MEK/ERK signaling during regeneration and established a first blueprint of the regeneration MEK/ERK-dependent GRN in Nematostella. Comparing the latter to the existing GRN underlying embryogenic development of the same species, we show at the network level that i) regeneration is a partial redeployment of the embryonic GRN, ii) embryonic gene modules are rewired during regeneration and iii) they are interconnected to novel down-stream targets, including "regeneration-specific" genes.
Significance statementIn this intra-species transcriptomic comparison of embryonic development and regeneration in a whole-body regeneration model, the sea anemone Nematostella vectensis, we identified that 1) regeneration is a transcriptionally modest event compared to embryonic development and 2) that although regeneration re-uses embryonic genetic interactions, it does so by using regeneration specific network logic. In addition to identifying that apoptosis is a regeneration-specific event in Nematostella, this study reveals that GRN modules are reshuffled from one developmental trajectory to the other, even when accomplishing the same task (e.g. forming a fully functional organism). These findings highlight the plasticity of network architecture and set the basis for determining and functionally dissecting regeneration-inducing regulatory elements. From an evolutionary perspective, our study sets the foundation for further comparative work and provides new opportunities to understand why certain organisms can regenerate while others cannot. | developmental biology |
10.1101/652826 | Eating in a losing cause: limited benefit of modified macronutrient consumption following infection in the oriental cockroach Blatta orientalis | BackgroundHost-pathogen interactions can lead to dramatic changes in host feeding behaviour. One aspect of this includes self-medication, where infected individuals consume substances such as toxins or alter their macronutrient consumption to enhance immune competence. Another widely adopted animal response to infection is illness-induced anorexia, which is thought to assist host immunity directly or by limiting the nutritional resources available to pathogens. Here, we recorded macronutrient preferences of the global pest cockroach, Blatta orientalis to investigate how shifts in host macronutrient dietary preference and quantity of carbohydrate (C) and protein (P) interact with immunity following bacterial infection.
ResultsWe find that B. orientalis avoids diets enriched for P under normal conditions, and that high P diets reduce cockroach survival in the long term. However, following bacterial challenge, cockroaches significantly reduced their overall nutrient intake, particularly of carbohydrates, and increased the relative ratio of protein (P:C) consumed. Surprisingly, these behavioural shifts had a limited effect on cockroach immunity and survival, with minor changes to immune protein abundance and antimicrobial activity between individuals placed on different diets, regardless of infection status.
ConclusionsWe show that cockroach feeding behaviour can be modulated by a pathogen, resulting in an illness-induced anorexia-like feeding response and a shift from a C-enriched to a more P:C equal diet. However, our results also indicate that such responses do not provide significant immune protection in B. orientalis, suggesting that the hosts dietary shift might also result from random rather than directed behaviour. The lack of an apparent benefit of the shift in feeding behaviour highlights a possible reduced importance for diet in immune regulation in these invasive animals, although further investigations employing pathogens with alternative infection strategies are warranted. | ecology |
10.1101/661660 | Temozolomide-induced guanine mutations create exploitable vulnerabilities of guanine-rich DNA and RNA regions in drug resistant gliomas | Temozolomide (TMZ) is a chemotherapeutic agent that has been the first-line standard of care for the aggressive brain cancer glioblastoma (GBM) since 2005. Though initially beneficial, TMZ- resistance is universal and second-line interventions are an unmet clinical need. Here we took advantage the mechanism of action of TMZ to target guanines (G) and investigated G-rich g- quadruplex (G4) and splice site changes that occur upon TMZ-resistance. We report TMZ-resistant GBM has guanine mutations that disrupt the G-rich DNA G4s and splice sites that lead to deregulated alternative splicing. These alterations create vulnerabilities, which are selectively targeted by either the G4 stabilizing drug TMPyP4 or a novel splicing kinase inhibitor of cdc2- like kinase. Finally, we show that the G4 and RNA-binding protein EWSR1 aggregates in the cytoplasm in TMZ-resistant GBM cells and patient samples. Together, our findings provide insight into targetable vulnerabilities of TMZ-resistant GBM and present cytoplasmic EWSR1 as a putative biomarker.
TeaserTargeting temozolomide mutations in drug resistant glioma via g-quadruplex and splicing modulators with a putative biomarker. | cancer biology |
10.1101/662049 | Analysis of meiosis in Pristionchus pacificus reveals plasticity in homolog pairing and synapsis in the nematode lineage | Meiosis is conserved across eukaryotes yet varies in the details of its execution. Here we describe a new comparative model system for molecular analysis of meiosis, the nematode Pristionchus pacificus, a distant relative of the widely studied model organism Caenorhabditis elegans. P. pacificus shares many anatomical and other features that facilitate analysis of meiosis in C. elegans. However, while C. elegans has lost the meiosis-specific recombinase Dmc1 and evolved a recombination-independent mechanism to synapse its chromosomes, P. pacificus expresses both DMC-1 and RAD-51. We find that SPO-11 and DMC-1 are required for stable homolog pairing, synapsis, and crossover formation, while RAD-51 is dispensable for these key meiotic processes. RAD-51 and DMC-1 localize sequentially to chromosomes during meiotic prophase and show nonoverlapping functions. We also present a new genetic map for P. pacificus that reveals a crossover landscape very similar to that of C. elegans, despite marked divergence in the regulation of synapsis and crossing-over between these lineages. | cell biology |
10.1101/662130 | Invariant Object Representation Based on Principle of Maximum Dependence Capturing | Sensory inputs conveying information about the environment are often noisy and incomplete, yet the brain can achieve remarkable consistency in object recognition. This cognitive robustness is thought to be enabled by transforming the varying input patterns into invariant representations of objects, but how this transformation occurs computationally remains unclear. Here we propose that sensory coding should follow a principle of maximal dependence capturing to encode associations among structural components that can uniquely identify objects. We show that a computational framework incorporating dimension expansion and a specific form of sparse coding can capture structures that contain maximum information about specific objects, allow redundancy coding, and enable consistent representation of object identities. Using symbol and face recognition, we demonstrate that a two-layer system can generate representations that remain invariant under conditions of occlusion, corruption, or high noise. | neuroscience |
10.1101/659649 | Staufen blocks autophagy in neurodegeneration | ObjectiveThe mechanistic target of rapamycin (mTOR) kinase is one of the master coordinators of cellular stress responses, regulating metabolism, autophagy, and apoptosis. We recently reported that Staufen1 (STAU1), a stress granule (SG) protein, was overabundant in fibroblast cell lines from patients with spinocerebellar ataxia type 2 (SCA2), amyotrophic lateral sclerosis, frontotemporal degeneration, Huntingtons, Alzheimers, and Parkinsons diseases as well as animal models, and patient tissues. STAU1 overabundance is associated with mTOR hyperactivation and links SG formation with autophagy. Our objective was to determine the mechanism of mTOR regulation by STAU1.
MethodsWe determined STAU1 abundance with disease- and chemical-induced cellular stressors in patient cells and animal models. We also used RNA binding assays to contextualize STAU1 interaction with MTOR mRNA.
ResultsSTAU1 and mTOR were overabundant in BAC-C9orf72, ATXN2Q127, and Thy1-TDP-43 transgenic mouse models. Reducing STAU1 levels in these mice normalized mTOR levels and activity and autophagy-related marker proteins. We also saw increased STAU1 levels in HEK293 cells transfected to express C9orf72-relevant dipeptide repeats (DPRs). Conversely, DPR accumulations were not observed in cells treated by STAU1 RNAi. Overexpression of STAU1 in HEK293 cells increased mTOR levels through direct MTOR mRNA interaction, activating downstream targets and impairing autophagic flux. Targeting mTOR by rapamycin or RNAi normalized STAU1 abundance in a SCA2 cellular model.
InterpretationSTAU1 interaction with mTOR drives its hyperactivation and inhibits autophagic flux in multiple models of neurodegeneration. Staufen, therefore, constitutes a novel target to modulate mTOR activity, autophagy, and for the treatment of neurodegenerative diseases. | neuroscience |
10.1101/660993 | The drug-induced phenotypic landscape of colorectal cancer organoids | Patient derived organoids resemble the biology of tissues and tumors, enabling ex vivo modeling of human diseases from primary patient samples. Organoids can be used as models for drug discovery and are being explored to guide clinical decision making. Patient derived organoids can have heterogeneous morphologies with unclear biological causes and relationship to treatment response. Here, we used high-throughput, image-based profiling to quantify phenotypes of over 5 million individual colorectal cancer organoids after treatment with more than 500 small molecules. Integration of data using a joint multi-omics modelling framework identified organoid size and cystic vs. solid organoid architecture as axes of morphological variation across organoids. Mechanistically, we found that organoid size was linked to IGF1 receptor signaling, while a cystic organoid architecture was associated with an LGR5+ stemness program. Treatment-induced organoid morphology reflected organoid viability, drug mechanism of action, and was biologically interpretable using joint modelling. Inhibition of MEK led to cystic reorganization of organoids and increased expression of LGR5, while inhibition of mTOR induced IGF1 receptor signaling. In conclusion, we identified shared axes of variation for colorectal cancer organoid morphology, their underlying biological mechanisms, and pharmacological interventions with the ability to move organoids along them. Image-based profiling of patient derived organoids coupled with multi-omics integration facilitates drug discovery by linking drug responses with underlying biological mechanisms. | genomics |
10.1101/662502 | iNetModels 2.0: an interactive visualization and database of multi-omics data | It is essential to reveal the associations between different omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics and metabolomics as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their own data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and diseases research. iNetModels can be accessed freely at https://inetmodels.com without any limitation. | bioinformatics |
10.1101/665208 | Pervasive Translation in Mycobacterium tuberculosis | Most bacterial ORFs are identified by automated prediction algorithms. However, these algorithms often fail to identify ORFs lacking canonical features such as a length of >50 codons or the presence of an upstream Shine-Dalgarno sequence. Here, we use ribosome profiling approaches to identify actively translated ORFs in Mycobacterium tuberculosis. Most of the ORFs we identify have not been previously described, indicating that the M. tuberculosis transcriptome is pervasively translated. The newly described ORFs are predominantly short, with many encoding proteins of [≤]50 amino acids. Codon usage of the newly discovered ORFs suggests that most have not been subject to purifying selection, and hence do not contribute to cell fitness. Nevertheless, we identify 90 new ORFs (median length of 52 codons) that bear the hallmarks of purifying selection. Thus, our data suggest that pervasive translation of short ORFs in Mycobacterium tuberculosis serves as a rich source for the evolution of new functional proteins. | microbiology |
10.1101/665448 | A simple pressure-assisted method for MicroED specimen preparation | Micro-crystal electron diffraction (MicroED) has shown great potential for structure determination of macromolecular crystals too small for X-ray diffraction. However, specimen preparation remains a major bottleneck. Here, we report a simple method for preparing MicroED specimens, named Preassis, in which excess liquid is removed through an EM grid with the assistance of pressure. We show the ice thicknesses can be controlled by tuning the pressure in combination with EM grids with appropriate hole sizes. Importantly, Preassis can handle a wide range of protein crystals grown in various buffer conditions including those with high viscosity, as well as samples with low crystal contents. Preassis is a simple and universal method for MicroED specimen preparation, and will significantly broaden the applications of MicroED. | molecular biology |
10.1101/668442 | Tipping-point analysis uncovers critical transition signals from gene expression profiles | Differentiation involves bifurcations between discrete cell states, each defined by a distinct gene expression profile. Single-cell RNA profiling allows the detection of bifurcations. However, while current methods capture these events, they do not identify characteristic gene signals. Here we show that BioTIP - a tipping-point theory-based analysis - can accurately, robustly, and reliably identify critical transition signals (CTSs). A CTS is a small group of genes with high covariance in expression that mark the cells approaching a bifurcation. We validated its accuracy in the cardiogenesis with known a tipping point and demonstrated the identified CTSs contain verified differentiation-driving transcription factors. We then demonstrated the application on a published mouse gastrulation dataset, validated the predicted CTSs using independent in-vivo samples, and inferred the key developing mesoderm regulator Etv2. Taken together, BioTIP is broadly applicable for the characterization of the plasticity, heterogeneity, and rapid switches in developmental processes, particularly in single-cell data analysis.
HighlightsO_LIIdentifying significant critical transition signals (CTSs) from expression noise
C_LIO_LIA significant CTS contains or is targeted by key transcription factors
C_LIO_LIBioTIP identifies CTSs accurately and independent of trajectory topologies
C_LIO_LISignificant CTSs reproducibly indicate bifurcations across datasets
C_LI | systems biology |
10.1101/668442 | Tipping-point analysis uncovers critical transition signals from gene expression profiles | Differentiation involves bifurcations between discrete cell states, each defined by a distinct gene expression profile. Single-cell RNA profiling allows the detection of bifurcations. However, while current methods capture these events, they do not identify characteristic gene signals. Here we show that BioTIP - a tipping-point theory-based analysis - can accurately, robustly, and reliably identify critical transition signals (CTSs). A CTS is a small group of genes with high covariance in expression that mark the cells approaching a bifurcation. We validated its accuracy in the cardiogenesis with known a tipping point and demonstrated the identified CTSs contain verified differentiation-driving transcription factors. We then demonstrated the application on a published mouse gastrulation dataset, validated the predicted CTSs using independent in-vivo samples, and inferred the key developing mesoderm regulator Etv2. Taken together, BioTIP is broadly applicable for the characterization of the plasticity, heterogeneity, and rapid switches in developmental processes, particularly in single-cell data analysis.
HighlightsO_LIIdentifying significant critical transition signals (CTSs) from expression noise
C_LIO_LIA significant CTS contains or is targeted by key transcription factors
C_LIO_LIBioTIP identifies CTSs accurately and independent of trajectory topologies
C_LIO_LISignificant CTSs reproducibly indicate bifurcations across datasets
C_LI | systems biology |
10.1101/669234 | The organizer of chromatin topology RIF1 ensures cellular resilience to DNA replication stress. | Eukaryotic genomes are duplicated from thousands of replication origins that fire sequentially forming a defined spatiotemporal pattern of replication clusters. The temporal order of DNA replication is determined by chromatin architecture and, more specifically, by chromatin contacts that are stabilized by RIF1. Here we show that RIF1 localizes in close proximity to newly synthesized DNA. In cells exposed to the DNA replication inhibitor aphidicolin, suppression of RIF1 markedly decreased the efficacy of protein isolation on nascent DNA (iPOND), suggesting that the iPOND procedure is biased by chromatin topology. RIF1 was required to limit the accumulation of DNA lesions induced by aphidicolin treatment and promoted the recruitment of cohesins in the vicinity of nascent DNA. Collectively, the data suggest that the stabilization of chromatin topology by RIF1 limits replication-associated genomic instability. | cell biology |
10.1101/668962 | Independent population coding of the past and the present in prefrontal cortex during learning | Medial prefrontal cortex (mPfC) activity represents information about the state of the world, including present behaviour, such as decisions, and the immediate past, such as short-term memory. Unknown is whether information about different states of the world are represented in the same mPfC neural population and, if so, how they are kept distinct. To address this, we analyse here mPfC population activity of rats learning rules in a Y-maze, with self-initiated choice trials to an arm-end followed by a self-paced return during the inter-trial interval (ITI). We find that trial and ITI population activity from the same population fall into different low-dimensional subspaces. These subspaces encode different states of the world: multiple features of the task can be decoded from both trial and ITI activity, but the decoding axes for the same feature are roughly orthogonal between the two task phases, and the decodings are predominantly of features of the present during the trial but features of the preceding trial during the ITI. These subspace distinctions are carried forward into sleep, where population activity is preferentially reactivated in post-training sleep, but differently for activity from the trial and ITI subspaces. Our results suggest that the problem of interference when representing different states of the world is solved in mPfC by population activity occupying different subspaces for the world states, which can be independently decoded by downstream targets and independently addressed by upstream inputs.
Significance statementActivity in the medial prefrontal cortex plays a roles in representing the current and past states of the world. We show that during a maze task the activity of a single population in medial prefrontal cortex represents at least two different states of the world. These representations were sequential and sufficiently distinct that a downstream population could separately read out either state from that activity. Moreover, the activity representing different states is differently reactivated in sleep. Different world states can thus be represented in the same medial prefrontal cortex population, but in such a way that prevents potentially catastrophic interference between them. | neuroscience |
10.1101/668962 | Independent population coding of the past and the present in prefrontal cortex during learning | Medial prefrontal cortex (mPfC) activity represents information about the state of the world, including present behaviour, such as decisions, and the immediate past, such as short-term memory. Unknown is whether information about different states of the world are represented in the same mPfC neural population and, if so, how they are kept distinct. To address this, we analyse here mPfC population activity of rats learning rules in a Y-maze, with self-initiated choice trials to an arm-end followed by a self-paced return during the inter-trial interval (ITI). We find that trial and ITI population activity from the same population fall into different low-dimensional subspaces. These subspaces encode different states of the world: multiple features of the task can be decoded from both trial and ITI activity, but the decoding axes for the same feature are roughly orthogonal between the two task phases, and the decodings are predominantly of features of the present during the trial but features of the preceding trial during the ITI. These subspace distinctions are carried forward into sleep, where population activity is preferentially reactivated in post-training sleep, but differently for activity from the trial and ITI subspaces. Our results suggest that the problem of interference when representing different states of the world is solved in mPfC by population activity occupying different subspaces for the world states, which can be independently decoded by downstream targets and independently addressed by upstream inputs.
Significance statementActivity in the medial prefrontal cortex plays a roles in representing the current and past states of the world. We show that during a maze task the activity of a single population in medial prefrontal cortex represents at least two different states of the world. These representations were sequential and sufficiently distinct that a downstream population could separately read out either state from that activity. Moreover, the activity representing different states is differently reactivated in sleep. Different world states can thus be represented in the same medial prefrontal cortex population, but in such a way that prevents potentially catastrophic interference between them. | neuroscience |
10.1101/668962 | Activity subspaces in medial prefrontal cortex distinguish states of the world | Medial prefrontal cortex (mPfC) activity represents information about the state of the world, including present behaviour, such as decisions, and the immediate past, such as short-term memory. Unknown is whether information about different states of the world are represented in the same mPfC neural population and, if so, how they are kept distinct. To address this, we analyse here mPfC population activity of rats learning rules in a Y-maze, with self-initiated choice trials to an arm-end followed by a self-paced return during the inter-trial interval (ITI). We find that trial and ITI population activity from the same population fall into different low-dimensional subspaces. These subspaces encode different states of the world: multiple features of the task can be decoded from both trial and ITI activity, but the decoding axes for the same feature are roughly orthogonal between the two task phases, and the decodings are predominantly of features of the present during the trial but features of the preceding trial during the ITI. These subspace distinctions are carried forward into sleep, where population activity is preferentially reactivated in post-training sleep, but differently for activity from the trial and ITI subspaces. Our results suggest that the problem of interference when representing different states of the world is solved in mPfC by population activity occupying different subspaces for the world states, which can be independently decoded by downstream targets and independently addressed by upstream inputs.
Significance statementActivity in the medial prefrontal cortex plays a roles in representing the current and past states of the world. We show that during a maze task the activity of a single population in medial prefrontal cortex represents at least two different states of the world. These representations were sequential and sufficiently distinct that a downstream population could separately read out either state from that activity. Moreover, the activity representing different states is differently reactivated in sleep. Different world states can thus be represented in the same medial prefrontal cortex population, but in such a way that prevents potentially catastrophic interference between them. | neuroscience |
10.1101/669333 | Compensating for a shifting world: evolving reference frames of visual and auditory signals across three multimodal brain areas | Stimulus locations are detected differently by different sensory systems, but ultimately they yield similar percepts and behavioral responses. How the brain transcends initial differences to compute similar codes is unclear. We quantitatively compared the reference frames of two sensory modalities, vision and audition, across three interconnected brain areas involved in generating saccades, namely the frontal eye fields (FEF), lateral and medial parietal cortex (M/LIP), and superior colliculus (SC). We recorded from single neurons in head-restrained monkeys performing auditory- and visually-guided saccades from variable initial fixation locations, and evaluated whether their receptive fields were better described as eye-centered, head-centered, or hybrid (i.e. not anchored uniquely to head- or eye-orientation). We found a progression of reference frames across areas and across time, with considerable hybrid-ness and persistent differences between modalities during most epochs/brain regions. For both modalities, the SC was more eye-centered than the FEF, which in turn was more eye-centered than the predominantly hybrid M/LIP. In all three areas and temporal epochs from stimulus onset to movement, visual signals were more eye-centered than auditory signals. In the SC and FEF, auditory signals became more eye-centered at the time of the saccade than they were initially after stimulus onset, but only in the SC at the time of the saccade did the auditory signals become predominantly eye-centered. The results indicate that visual and auditory signals both undergo transformations, ultimately reaching the same final reference frame but via different dynamics across brain regions and time.
New and NoteworthyModels for visual-auditory integration posit that visual signals are eye-centered throughout the brain, while auditory signals are converted from head-centered to eye-centered coordinates. We show instead that both modalities largely employ hybrid reference frames: neither fully head-nor eye-centered. Across three hubs of the oculomotor network (intraparietal cortex, frontal eye field and superior colliculus) visual and auditory signals evolve from hybrid to a common eye-centered format via different dynamics across brain areas and time. | neuroscience |