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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 1,171 records · Page 65Linked to original sources

bioRxiv2018

Gastrocnemius fascicles are shorter and more pennate immediately following acute Achilles tendon rupture

The purpose of this study was to characterize the short-term effects of Achilles tendon ruptures on medial gastrocnemius. We hypothesized that the fascicles of the medial gastrocnemius muscle of the injured Achilles tendon would be shorter and more pennate immediately following the injury and would persist throughout 4 weeks post-injury. B-mode longitudinal ultrasound images of the medial gastrocnemius were acquired in 10 adults who suffered acute Achilles tendon ruptures and were treated non-operatively. Ultrasound images were acquired during the initial clinical visit following injury as well as two and four weeks following this initial clinical visit. Resting muscle structure was characterized by measuring fascicle length, pennation angle, muscle thickness, and muscle echo intensity in both the injured and contralateral (control) limbs. Fascicle length was 15% shorter (P < 0.001) and pennation angle was 21% greater (P < 0.001) in the injured muscle compared to the uninjured (control) muscle at the presentation of injury (week 0). These differences in fascicle length and pennation angle persisted throughout the 4 weeks after the injury (P < 0.008). Muscle thickness changes were not detected at any of the post-injury visits (difference < 4%, P > 0.04). Echo intensity of the injured limb was 8% lower at the presentation of the injury and 11% lower (P = 0.008) than the contralateral muscle at 2 weeks following injury (P < 0.001) but returned to within 1% by 4 weeks (P = 0.393). Our results suggest that Achilles tendon ruptures elicit rapid changes in the configuration and quality of the medial gastrocnemius, which may explain long-term functional deficits.

bioengineering↗

bioRxiv2018

A normalized template matching method for improving spike detection in extracellular voltage recordings

Spike sorting is the process of detecting and clustering action potential waveforms from extracellular voltage recordings to identify spikes of putative single neurons. Typically, spike detection is done using a fixed voltage threshold and shadow period, but this approach can lead to missed spikes during high firing rate epochs or noisy conditions. We developed a novel spike detection method utilizing a computationally simple form of template matching that efficiently detects spikes from candidate single units and is tolerant of high firing rates and electrical noise without a whitening filter. Template matching was based on a sliding cosine similarity between mean spike waveforms of candidate single units and the extracellular voltage signal. Performance was tested in whisker somatosensory cortex (S1) of anesthetized mice in vivo. The method consistently detected whisker-evoked spikes that were missed by a standard fixed voltage threshold. Detection was most improved for spikes evoked by strong stimuli (40-70% increase), less improved for weaker stimuli, and unchanged for spontaneous spiking. This reflected the failure of standard detection during spatiotemporally dense spiking. Template-based detection revealed higher signal-to-noise ratio for sensory responses and sharper sensory tuning. Thus, this template matching method (and other model-based spike detection methods) critically improve the quantification of single-unit spiking activity.

neuroscience↗

bioRxiv2018

Errors in RNA-seq transcript abundance estimates

RNA-sequencing data is widely used to identify disease biomarkers and therapeutic targets. Here, using data from five RNA-seq processing pipelines applied to 6,690 human tumor and normal tissues, we show that for >12% of protein-coding genes, in at least 1% of samples, current best-in-class RNA-seq processing pipelines differ in their abundance estimates by more than four-fold using the same samples and the same set of RNA-seq reads, raising clinical concern.

bioinformatics↗

bioRxiv2018

Predicting natural behavior from whole-brain neural dynamics

The activity of an animals brain contains information about that animals actions and movements. We investigated the neural representation of locomotion in the nematode C. elegans by recording population calcium activity during unrestrained movement. We report that a neural population more accurately decodes locomotion than any single neuron. Relevant signals are distributed across neurons with diverse tunings to locomotion. Two distinct subpopulations are informative for decoding velocity and body curvature, and different neurons activities contribute features relevant for different instances of behavioral motifs. We labeled neurons AVAL and AVAR and found their activity was highly correlated with one another. They exhibited expected transients during backward locomotion, although they were not always the most informative neurons for decoding velocity. Finally, we compared population neural activity during movement and immobilization. Immobilization alters the correlation structure of neural activity and its dynamics. Some neurons previously correlated with AVA become anti-correlated and vice versa. The activity of an animals brain contains information about that animals actions and movements. We investigated the neural representation of locomotion in the nematode C. elegans by recording brain-wide neural dynamics in freely moving animals. We report that a population of neurons more accurately decodes the animals locomotion than any single neuron. Neural signals are distributed across neurons in the population with a diversity of tuning to locomotion. Two distinct subpopulations are most informative for decoding velocity and body curvature, and different neurons activities contribute features relevant for different instances of behavioral motifs within these subpopulations. We additionally labeled the AVA neurons within our population recordings. AVAL and AVAR exhibit activity that is highly correlated with one another, and they exhibit the expected responses to locomotion, although we find that AVA is not always the most informative neuron for decoding velocity. Finally, we compared brain-wide neural activity during movement and immobilization and observe that immobilization alters the correlation structure of neural activity and its dynamics. Some neurons that were previously correlated with AVA become anti-correlated and vice versa during immobilization. We conclude that neural population codes are important for understanding neural dynamics of behavior in moving animals.

neuroscience↗

bioRxiv2018

Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog, Dendrobates auratus

Color and pattern phenotypes have clear implications for survival and reproduction in many species. However, the mechanisms that produce this coloration are still poorly characterized, especially at the genomic level. Here we have taken a transcriptomics-based approach to elucidate the underlying genetic mechanisms affecting color and pattern in a highly polytypic poison frog. We sequenced RNA from the skin from four different color morphs during the final stage of metamorphosis and assembled a de novo transcriptome. We then investigated differential gene expression, with an emphasis on examining candidate color genes from other taxa. Overall, we found differential expression of a suite of genes that control melanogenesis, melanocyte differentiation, and melanocyte proliferation (e.g., tyrpl, lefl, leol, and mitf) as well as several differentially expressed genes involved in purine synthesis and iridophore development (e.g., arfgapl, arfgap2, airc, and gairt). Our results provide evidence that several gene networks known to affect color and pattern in vertebrates play a role in color and pattern variation in this species of poison frog.

evolutionary biology↗

bioRxiv2018

Large-scale neuron cell classification of single-channel and multi-channel extracellular recordings in the anterior lateral motor cortex

Identification of neuron cell type helps us connect neural circuitry and behavior; greater specificity in cell type and subtype classification provides a clearer picture of specific relationships between the brain and behavior. With the advent of high-density probes, large-scale neuron classification is needed, as typical extracellular recordings are identity-blind to the neurons they record. Current methods for identification of neurons include optogenetic tagging and intracellular recordings, but are limited in that they are expensive, time-consuming, and have a limited scope. Therefore, a more automated, real-time method is needed for large-scale neuron identification. Data from two recordings was incorporated into this research; the single-channel recording included data from three neuron types in the motor cortex: FS, IT, and PT neurons. The multi-channel recording contained data from two neuron subtypes also in the motor cortex: PT_L and PT_U neurons. This allowed for an examination of both general neuron classification and more specific subtype classification, which was done via artificial neural networks (ANNs) and machine learning (ML) algorithms. For the single-channel neuron classification, the ANNs achieved 91% accuracy, while the ML algorithms achieved 98% accuracy, using the raw electrical waveform. The multi-channel classification, which was significantly more difficult due to the similarity between the neuron types, yielded an ineffective ANN, reaching 68% accuracy, while the ML algorithms reached 81% using 8 calculated features from the waveform. Thus, to distinguish between different neuron cell types and subtypes in the motor cortex, both ANNs and specific ML algorithms can facilitate rapid and accurate near real-time large-scale classification.

neuroscience↗

bioRxiv2018

Cold-Induced Thermogenesis Increases Acetylation on the Brown Fat Proteome and Metabolome

Stimulating brown adipose tissue (BAT) energy expenditure could be a therapy for obesity and related metabolic diseases. Achieving this requires a systems-level understanding of the biochemical underpinnings of thermogenesis. To identify novel metabolic features of active BAT, we measured protein abundance, protein acetylation, and metabolite levels in BAT isolated from mice living in their thermoneutral zone or in colder environments. We find that the enzymes which synthesize lipids from cytosolic acetyl-coA are among the most robustly increased proteins after cold acclimation, consistent with recent studies highlighting the importance of anabolic de novo lipogenesis in BAT. In addition, many mitochondrial proteins are hyperacetylated by cold acclimation, including several sites on UCP1, which may have functional relevance. Metabolomics analysis further reveals cold-dependent increases to acetylated carnitine and several amino acids. This BAT multi-omics resource highlights widespread proteomic and metabolic changes linked to acetyl-CoA synthesis and utilization that may be useful in unraveling the remarkable metabolic properties of active BAT.

systems biology↗

bioRxiv2018

Independent mechanisms for acquired salt tolerance versus growth resumption induced by mild ethanol pretreatment in Saccharomyces cerevisiae

All living organisms must recognize and respond to various environmental stresses throughout their lifetime. In natural environments, cells frequently encounter fluctuating concentrations of different stressors that can occur in combination or sequentially. Thus, the ability to anticipate an impending stress is likely ecologically relevant. One possible mechanism for anticipating future stress is acquired stress resistance, where cells pre-exposed to a mild sub-lethal dose of stress gain the ability to survive an otherwise lethal dose of stress. We have been leveraging wild strains of Saccharomyces cerevisiae to investigate natural variation in the yeast ethanol stress response and its role in acquired stress resistance. Here, we report that a wild vineyard isolate possesses ethanol-induced cross-protection against severe concentrations of salt. Because this phenotype correlates with ethanol-dependent induction of the ENA genes, which encode sodium efflux pumps already associated with salt resistance, we hypothesized that variation in ENA expression was responsible for differences in acquired salt tolerance across strains. Surprisingly, we found that the ENA genes were completely dispensable for ethanol-induced survival of high salt concentrations in the wild vineyard strain. Instead, the ENA genes were necessary for the ability to resume growth on high concentrations of salt following a mild ethanol pretreatment. Surprisingly, this growth acclimation phenotype was also shared by the lab yeast strain despite lack of ENA induction under this condition. This study underscores that cross protection can affect both viability and growth through distinct mechanisms, both of which likely confer fitness effects that are ecologically relevant.\n\nIMPORTANCEMicrobes in nature frequently experience \"boom or bust\" cycles of environmental stress. Thus, microbes that can anticipate the onset of stress would have an advantage. One way microbes anticipate future stress is through acquired stress resistance, where cells exposed to a mild dose of one stress gain the ability survive an otherwise lethal dose of a subsequent stress. In the budding yeast Saccharomyces cerevisiae, certain stressors can cross protect against high salt concentrations, though the mechanisms governing this acquisition of higher stress resistance are not well understood. In this study, we took advantage of wild yeast strains to understand the mechanism underlying ethanol-induced cross protection against high salt concentrations. We found that mild ethanol stress allows cells to resume growth on high salt, which involves a novel role for a well-studied salt transporter. Overall, this discovery highlights how leveraging natural variation can provide new insights into well-studied stress defense mechanisms.

microbiology↗

bioRxiv2018

Evaluation of North American Asian citrus psyllid (Hemiptera: Liviidae) population genetics by cytochrome P450 melt curve analysis

The Asian Citrus Psyllid (ACP) (Diaphorina citri) is a Hemipteran which feeds on Citrus and is the principal vector of the pathogen Candidatus Liberibacter asiaticus (Las); the primary causal agent of Huanglongbing (HLB) or citrus greening disease. Currently HLB is the single greatest threat to the American citrus industry. Previous work has shown that that Cytochrome P450 (CYP4) genes are associated with insecticidal resistance to neonicotinoid insecticides. Infection by Las has also been shown to affect the expression of CYP4 genes. In this study the genetic relationships of ACP populations was evaluated using melting curve analysis of CYP4 genes. Principal component analysis shows the presence of two potential haplotypes. The groups identified by principal component analysis are significantly different from each other (P < 0.05) for all CYP4 genes tested. All populations are most likely within 2-3 mutations of each other. The existence of these mutations sheds light on the potential evolution of ACP in North America. Indicating either coevolution with Las or difference in imidacloprid basal selective pressure in the United States and Mexico.

evolutionary biology↗

bioRxiv2018

Cytoarchitecture and Layer Estimation in High-Resolution Neuroanatomical Images

Robust methods for characterizing the cellular architecture (cytoarchitecture) of the brain are needed to differentiate brain areas, identify neurological diseases, and model architectural differences across species. Current methods for mapping the cytoarchitecture and, in particular, identifying laminar (layer) divisions in tissue samples require the expertise of trained neuroanatomists to manually annotate the various regions-of-interest and cells within an image. However, as neuroanatomical datasets grow in volume, manual annotations become inefficient, impractical, and risk the potential of biasing results. In this paper, we propose an automated framework for cellular detection and density estimation that enables the detection of laminar divisions within retinal and neocortical histology datasets. Our approach for layer detection uses total variation minimization to find a small number of change points in the density that signify the beginning and end of each layer. We apply these methods to micron-scale histology images from a variety of cortical areas of the mouse brain and retina, as well as synthetic datasets. Our results demonstrate the feasibility of using automation to reveal the cytoarchitecture of neurological samples in high-resolution images.

neuroscience↗

bioRxiv2018

Individual variation in the dear enemy phenomenon via territorial vocalizations in red squirrels

Territoriality arises when the benefits of resources exceed the costs of defending them. The dear enemy phenomenon, where familiar territorial neighbours refrain from intruding on one another and mutually reduce their defensive efforts, allows for reduction of these costs but requires discrimination between conspecifics. We hypothesized that territorial vocalizations in red squirrels (Tamiasciurus hudsonicus) are used for this discrimination. We performed a speaker replacement experiment where red squirrels (n = 41) were temporarily removed from their territories and replaced with a speaker broadcasting their own call, an unfamiliar call, or silence. Contrary to our prediction, there were no differences in overall intrusion risk among our three playbacks, but the identity of intruders did vary. Existing variation in familiarity within territorial neighbourhoods should be considered, rather than the binary classification of familiar or stranger, when studying dear enemy effects. We also discuss the variable importance of silence in acoustic territorial populations.

animal behavior and cognition↗

bioRxiv2018

Predicting Intra- and Intertypic Recombination in Enterovirus 71

Enteroviruses are well known for their ability to cause neurological damage and paralysis. The model enterovirus is poliovirus (PV), the causative agent of poliomyelitis, a condition characterized by acute flaccid paralysis. A related virus, enterovirus 71 (EV-A71), causes similar clinical outcomes in recurrent outbreaks throughout Asia. Retrospective phylogenetic analysis has shown that recombination between circulating strains of EV-A71 produces the outbreak-associated strains which exhibit increased virulence and/or transmissibility. While studies on the mechanism(s) of recombination in PV are ongoing in several laboratories, little is known about factors that influence recombination in EV-A71. We have developed a cell-based assay to study recombination of EV-A71 based upon previously reported assays for poliovirus recombination. Our results show that: (1) EV-A71 strain-type and RNA sequence diversity impacts recombination frequency in a predictable manner that mimics the observations found in nature; (2) recombination is primarily a replicative process mediated by the RNA-dependent RNA polymerase (RdRp); (3) a mutation shown to reduce recombination in PV (L420A) similarly reduces EV-A71 recombination suggesting conservation in mechanism(s); and (4) sequencing of intertypic recombinant genomes indicates that template-switching is by a mechanism that requires some sequence homology at the recombination junction and that the triggers for template-switching may be sequence independent. The development of this recombination assay will permit further investigation on the interplay between replication, recombination and disease.

microbiology↗

bioRxiv2018

Processing of grassland soil C-N compounds into soluble and volatile molecules is depth stratified and mediated by genomically novel bacteria and archaea

Soil microbial activity drives the carbon and nitrogen cycles and is an important determinant of atmospheric trace gas turnover, yet most soils are dominated by organisms with unknown metabolic capacities. Even Acidobacteria, among the most abundant bacteria in soil, remain poorly characterized, and functions across groups such as Verrucomicrobia, Gemmatimonadetes, Chloroflexi, Rokubacteria are understudied. Here, we resolved sixty metagenomic, and twenty proteomic datasets from a grassland soil ecosystem and recovered 793 near-complete microbial genomes from 18 phyla, representing around one third of all organisms detected. Importantly, this enabled extensive genomics-based metabolic predictions for these understudied communities. Acidobacteria from multiple previously unstudied classes have genomes that encode large enzyme complements for complex carbohydrate degradation. Alternatively, most organisms we detected encode carbohydrate esterases that strip readily accessible methyl and acetyl groups from polymers like pectin and xylan, forming methanol and acetate, the availability of which could explain high prevalences of C1 metabolism and acetate utilization in genomes. Organism abundances among samples collected at three soil depths and under natural and amended rainfall regimes indicate statistically higher associations of inorganic nitrogen metabolism and carbon degradation in deep and shallow soils, respectively. This partitioning decreased in samples under extended spring rainfall indicating long term climate alteration can affect both carbon and nitrogen cycling. Overall, by leveraging natural and experimental gradients with genome-resolved metabolic profiles, we link organisms lacking prior genomic characterization to specific roles in complex carbon, C1, nitrate, and ammonia transformations and constrain factors that impact their distributions in soil.

microbiology↗

bioRxiv2018

The RNA-binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria

PlWI-interacting RNAs (piRNAs) silence transposons in Drosophila ovaries, ensuring female fertility. Two coupled pathways generate germline piRNAs: the ping-pong cycle, in which the PIWI proteins Aubergine and Ago3 increase the abundance of pre-existing piRNAs, and the phased piRNA pathway, which generates strings of tail-to-head piRNAs, one after another. Proteins acting in the ping-pong cycle localize to nuage, whereas phased piRNA production requires Zucchini, an endonuclease on the mitochondrial surface. Here, we report that Armitage (Armi), an RNA-binding ATPase localized to both nuage and mitochondria, links the ping-pong cycle to the phased piRNA pathway. Mutations that block phased piRNA production deplete Armi from nuage. Armi ATPase mutants cannot support phased piRNA production and inappropriately bind mRNA instead of piRNA precursors. We propose that Armi shuttles between nuage and mitochondria, feeding precursor piRNAs generated by Ago3 cleavage into the Zucchini-dependent production of Aubergine- and Piwi-bound piRNAs on the mitochondrial surface.

genetics↗

bioRxiv2018

The glucocorticoid receptor ligand-binding domain confers drug-gated protein regulation in C. elegans

Controlling protein activity and localization is a key tool in modern biology. Mammalian steroid receptor ligand-binding domains (LBDs) fusions have been used in a range of organisms and cell-types to inactivate proteins of interest until the cognate steroid ligand is applied. Here, we demonstrate that the glucocorticoid receptor LBD confers ligand-gated control of a heterologous gene expression system (Q system) and the DAF-16 transcription factor in C. elegans. These experiments demonstrate provide a powerful tool for temporal control of protein activity, and will bolster existing tools used to modulate gene expression and protein activity in this animal.

genetics↗

bioRxiv2018

Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change

Microorganisms are critical in terrestrial carbon cycling because their growth, activity and interactions with the environment largely control the fate of recent plant carbon inputs, as well as the stability of assimilated carbon (Gleixner, 2013; Schimel and Schaeffer, 2012). Soil carbon stocks reflect a balance between microbial decomposition and stabilization of organic carbon. The balance can shift under altered environmental conditions (Davidson and Janssens, 2006), and new research suggests that knowledge of microbial physiology may be critical for projecting changes in soil carbon and improving the prognosis of climate change feedbacks (Allison et al., 2010; Bradford et al., 2016; Liang et al., 2017; Wieder et al., 2015). Still, predicting the ecosystem implications of microbial processes remains a challenge. Here we argue that this challenge can be m ...

ecology↗

bioRxiv2018

Comparative genetic architectures of schizophrenia in East Asian and European populations

Author summarySchizophrenia is a severe psychiatric disorder with a lifetime risk of about 1% world-wide. Most large schizophrenia genetic studies have studied people of primarily European ancestry, potentially missing important biological insights. Here we present a study of East Asian participants (22,778 schizophrenia cases and 35,362 controls), identifying 21 genome-wide significant schizophrenia associations in 19 genetic loci. Over the genome, the common genetic variants that confer risk for schizophrenia have highly similar effects in those of East Asian and European ancestry (rg=0.98), indicating for the first time that the genetic basis of schizophrenia and its biology are broadly shared across these world populations. A fixed-effect meta-analysis including individuals from East Asian and European ancestries revealed 208 genome-wide significant schizophrenia associations in 176 genetic loci (53 novel). Trans-ancestry fine-mapping more precisely isolated schizophrenia causal alleles in 70% of these loci. Despite consistent genetic effects across populations, polygenic risk models trained in one population have reduced performance in the other, highlighting the importance of including all major ancestral groups with sufficient sample size to ensure the findings have maximum relevance for all populations.

genetics↗

bioRxiv2018

Using long-read sequencing to detect imprinted DNA methylation

Systematic variation in the methylation of cytosines at CpG sites plays a critical role in early development of humans and other mammals. Of particular interest are regions of differential methylation between parental alleles, as these often dictate monoallelic gene expression, resulting in parent of origin specific control of the embryonic transcriptome and subsequent development, in a phenomenon known as genomic imprinting. Using long-read nanopore sequencing we show that, with an average genomic coverage of approximately ten, it is possible to determine both the level of methylation of CpG sites and the haplotype from which each read arises. The long-read property is exploited to characterise, using novel methods, both methylation and haplotype for reads that have reduced basecalling precision compared to Sanger sequencing. We validate the analysis both through comparison of nanopore-derived methylation patterns with those from Reduced Representation Bisulfite Sequencing data and through comparison with previously reported data. Our analysis successfully identifies known imprinting control regions as well as some novel differentially methylated regions which, due to their proximity to hitherto unknown monoallelically expressed genes, may represent new imprinting control regions.

genomics↗