title: A bivariate zero-inflated negative binomial model and its applications to biomedical settings

abstract: SO_SCPLOWUMMARYC_SCPLOWThe zero-inflated negative binomial (ZINB) distribution has been widely used for count data analyses in various biomedical settings due to its capacity of modeling excess zeros and overdispersion. When there are correlated count variables, a bivariate model is essential for understanding their full distributional features. For this purpose, we develop a Bivariate Zero-Inflated Negative Binomial (BZINB) model that has a simple latent variable framework and parameters with intuitive interpretations. Using this model, we examine two biomedical data examples where the counts are zero-inflated--single cell RNA sequencing (scRNA-seq) data and dental caries count indices. In scRNA-seq data example, a correlation between a pair of genes is estimated after adjusting for the effects of dropout events represented by excess zeros. In the dental caries data, we analyze how the treatment with Xylitol mints affects the marginal mean and other patterns of response manifested in the two dental caries traits. An R package  bzinb is available on CRAN.


title: Long-read error correction: a survey and qualitative comparison

abstract: Third generation sequencing technologies Pacific Biosciences and Oxford Nanopore Technologies were respectively made available in 2011 and 2014. In contrast with second generation sequencing technologies such as Illumina, these new technologies allow the sequencing of long reads of tens to hundreds of kbp. These so called long reads are particularly promising, and are especially expected to solve various problems such as contig and haplotype assembly or scaffolding, for instance. However, these reads are also much more error prone than second generation reads, and display error rates reaching 10 to 30%, according to the sequencing technology and to the version of the chemistry. Moreover, these errors are mainly composed of insertions and deletions, whereas most errors are substitutions in Illumina reads. As a result, long reads require efficient error correction, and a plethora of error correction tools, directly targeted at these reads, were developed in the past ten years. These methods can adopt a hybrid approach, using complementary short reads to perform correction, or a self-correction approach, only making use of the information contained in the long reads sequences. Both these approaches make use of various strategies such as multiple sequence alignment, de Bruijn graphs, Hidden Markov Models, or even combine different strategies. In this paper, we describe a complete survey of long-read error correction, reviewing all the different methodologies and tools existing up to date, for both hybrid and self-correction. Moreover, the long reads characteristics, such as sequencing depth, length, error rate, or even sequencing technology, have huge impacts on how well a given tool or strategy performs, and can thus drastically reduce the correction quality. We thus also present an in-depth benchmark of available long-read error correction tools, on a wide variety of datasets, composed of both simulated and real data, with various error rates, coverages, and read lengths, ranging from small bacterial to large mammal genomes.

category: bioinformatics


title: Oligomeric amyloid beta prevents myelination in a clusterin-dependent manner

abstract: White matter loss has been described as a common occurrence in Alzheimers disease (AD) patients for multiple decades. However, it remains unclear why oligodendrocyte progenitor cells (OPCs) fail to repair myelin deficits in these patients. Here, we show that clusterin, a risk factor for late-onset AD, is produced by OPCs and inhibits their differentiation into oligodendrocytes. Specifically, we demonstrate that a unique subset of OPCs produces clusterin. We show that phagocytosis of debris, including amyloid beta (A{beta}) and myelin, drives the upregulation of clusterin in OPCs. We confirm, in vivo, that A{beta} oligomers drive clusterin upregulation and that OPCs phagocytose A{beta}. Furthermore, we show that clusterin is a potent inhibitor of OPC differentiation and prevents the production of myelin proteins. Finally, we demonstrate that clusterin inhibits OPC differentiation by significantly reducing the production of IL-9 by OPCs. Our data reveals that clusterin may be responsible for the lack of myelin repair observed in AD and is a promising therapeutic target for AD-associated cognitive decline.

category: neuroscience


title: A fast and efficient smoothing approach to Lasso regression and an application in statistical genetics: polygenic risk scores for chronic obstructive pulmonary disease (COPD)

abstract: High dimensional linear regression problems are often fitted using Lasso approaches. Although the Lasso objective function is convex, it is not differentiable everywhere, making the use of gradient descent methods for minimization not straightforward. To avoid this technical issue, we apply Nesterov smoothing to the original (unsmoothed) Lasso objective function. We introduce a closed-form smoothed Lasso which preserves the convexity of the Lasso function, is uniformly close to the unsmoothed Lasso, and allows us to obtain closed-form derivatives everywhere for efficient and fast minimization via gradient descent. Our simulation studies are focused on polygenic risk scores using genetic data from a genome-wide association study (GWAS) for chronic obstructive pulmonary disease (COPD). We compare accuracy and run-time of our approach to the current gold standard in the literature, the FISTA algorithm. Our results suggest that the proposed methodology provides estimates with equal or higher accuracy than the FISTA algorithm while having the same asymptotic runtime scaling. The proposed methodology is implemented in the R-package smoothedLasso, available on the Comprehensive R Archive Network (CRAN).


title: Homologous organization of cerebellar pathways to sensory, motor, and associative forebrain

abstract:
Cerebellar outputs take polysynaptic routes to reach the rest of the brain, impeding conventional tracing. Here we quantify pathways between cerebellum and forebrain using transsynaptic tracing viruses and a whole-brain quantitative analysis pipeline. Retrograde tracing found a majority of descending paths originating from somatomotor cortex. Anterograde tracing of ascending paths encompassed most thalamic nuclei, especially ventral posteromedial, lateral posterior, mediodorsal, and reticular nuclei; in neocortex, sensorimotor regions contained the most labeled neurons, but higher densities were found in associative areas, including orbital, anterior cingulate, prelimbic, and infralimbic cortex. Patterns of ascending expression correlated with c-Fos expression after optogenetic inhibition of Purkinje cells. Our results reveal homologous networks linking single areas of cerebellar cortex to diverse forebrain targets. We conclude that shared areas of cerebellum are positioned to provide sensory-motor information to regions implicated in both movement and nonmotor function.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/979153v3_ufig1.gif" ALT="Figure 1">
View larger version (45K):
org.highwire.dtl.DTLVardef@1bead0corg.highwire.dtl.DTLVardef@1531de2org.highwire.dtl.DTLVardef@1cf02f6org.highwire.dtl.DTLVardef@1cb6774_HPS_FORMAT_FIGEXP  M_FIG C_FIG


title: Intergenerational transmission of the patterns of functional and structural brain networks

abstract: There is clear evidence of intergenerational transmission of life values, cognitive traits, psychiatric disorders, and even aspects of daily decision making. To investigate biological substrates of this phenomenon, brain has received increasing attention as a measurable biomarker and potential target for intervention. However, no previous study has quantitatively and comprehensively investigated the effects of intergenerational transmission on functional and structural brain networks from parents to their children. Here, by employing an unusually large cohort dataset, we show that patterns of functional and structural brain networks are preserved over a generation. We also demonstrate that several demographic and behavioural phenotypes have effects on brain similarity. Collectively, our results provide a comprehensive picture of neurobiological substrates of parent-child similarity, and demonstrate the usability of our dataset for investigating the neurobiological substrates of intergenerational transmission.


title: pyrpipe: a python package for RNA-Seq workflows

abstract: The availability of terabytes of RNA-Seq data and continuous emergence of new analysis tools, enable unprecedented biological insight. However, implementing RNA-Seq analysis pipelines in a reproducible, flexible manner is challenging as data gets bigger and more complex. Thus, there is a pressing requirement for frameworks that allows for fast, efficient, easy-to-manage, and reproducibile analysis. Simple scripting has many challenges and drawbacks. We have developed a python package, python RNA-Seq Pipeliner (pyrpipe) that enables straightforward development of flexible, reproducible and easy-to-debug computational pipelines purely in python, in an object-oriented manner. pyrpipe provides access to popular RNA-Seq tools, within python, via easy-to-use high level APIs. Pipelines can be customized by integrating new python code, third-party programs, or python libraries. Users can create checkpoints in the pipeline or integrate pyrpipe into a workflow management system, thus allowing execution on multiple computing environments. pyrpipe produces detailed analysis, and benchmark reports which can be shared or included in publications. pyrpipe is implemented in python and is compatible with python versions 3.6 and higher. To illustrate the rich functionality of pyrpipe, we provide case studies using RNA-Seq data from GTEx, SARS-CoV-2-infected human cells, and Zea mays. All source code is freely available at https://github.com/urmi-21/pyrpipe; the package can be installed from the source or from PyPI (https://pypi.org/project/pyrpipe). Documentation is available at (http://pyrpipe.rtfd.io).


title: Tick infestation probability increases with human recreation and exploratory behaviour in great tits

abstract:
Ticks are parasites that feed on the blood of various vertebrate hosts, including many species of bird. Birds can disperse ticks over short and long distances, therefore impacting tick population dynamics. The likelihood that birds attract ticks should depend on their behaviour and the environment. We studied various key ecological variables (breeding density, human disturbance) and phenotypic traits (exploratory behaviour; body condition) proposed to predict tick burden in great tits (Parus major). Our study spanned over three years and 12 human-recreated plots, equipped with nest-boxes in southern Germany. Adult breeders were assessed for exploratory behaviour, tick burden, and body condition. For each plot, human disturbance was quantified as a human recreational pressure index during biweekly nest box inspections by scoring the number of recreants using the plots. Infestation probability but not tick burden increased with exploratory behaviour. We also found moderate support for a positive effect of recreational pressure on infestation probability. Further, body condition negatively predicted tick burden. Individuals were repeatable in tick burden across years. Our study implies that infestation probability and tick burden are governed by distinct ecological and phenotypic drivers. Our findings also highlight the importance of incorporating ecological and individual variation in host phenotypes to predict spatiotemporal distributions of ticks in nature. (207/250-word limit)

Lay SummaryTicks use many birds as hosts, but why do some individuals have more or fewer ticks? Using a data collected over three years on great tit adults inhabiting 12 different nest-box plots, we showed that more explorative birds and those in highly recreated habitats were more likely to be infested with ticks. Exploratory behaviour and human disturbance could modify great tit habitat choice and, therefore, impact how often a birds and ticks encounter each other.

category: ecology


title: Is male dimorphism under sexual selection in humans? A meta-analysis

abstract: Humans are sexually dimorphic: men and women differ in body build and composition, craniofacial structure, and voice pitch, likely mediated in part by developmental testosterone. Sexual selection hypotheses posit that, ancestrally, more  masculine men may have acquired more mates and/or sired more viable offspring. Thus far, however, evidence for either association is unclear. Here, we meta-analyze the relationships between six masculine traits and mating/reproductive outcomes (96 studies, 474 effects, N = 177,044). Voice pitch, height, and testosterone all predicted mating; however, strength/muscularity was the strongest and only consistent predictor of both mating and reproduction. Facial masculinity and digit ratios did not significantly predict either. There was no clear evidence for any effects of masculinity on offspring viability. Our findings support arguments that strength/muscularity can be considered sexually selected in humans, but raise concerns over other forms of masculinity and highlight the need to increase tests of evolutionary hypotheses outside of industrialized populations.

category: evolutionary biology


title: Evidence accumulation and associated error-related brain activity as computationally informed prospective predictors of substance use in emerging adulthood

abstract:
RationaleSubstance use peaks during the developmental period known as emerging adulthood (ages 18-25), but not every individual who uses substances during this period engages in frequent or problematic use. Although individual differences in neurocognition appear to predict use severity, mechanistic neurocognitive risk factors with clear links to both behavior and neural circuitry have yet to be identified. Here we aim to do so with an approach rooted in computational psychiatry, an emerging field in which formal models are used to identify candidate biobehavioral dimensions that confer risk for psychopathology.

ObjectivesWe test whether lower efficiency of evidence accumulation (EEA), a computationally-characterized individual difference variable that drives performance on the go/no-go and other neurocognitive tasks, is a risk factor for substance use in emerging adults.

Methods and ResultsIn an fMRI substudy within a sociobehavioral longitudinal study (n=106), we find that lower EEA and reductions in a robust neural-level correlate of EEA (error-related activations in salience network structures) measured at ages 18-21 are both prospectively related to greater substance use during ages 22-26, even after adjusting for other well-known risk factors. Results from Bayesian model comparisons corroborated inferences from conventional hypothesis testing and provided evidence that both EEA and its neuroimaging correlates contain unique predictive information about substance use involvement.

ConclusionsThese findings highlight EEA as a computationally-characterized neurocognitive risk factor for substance use during a critical developmental period, with clear links to both neuroimaging measures and well-established formal theories of brain function.


title: A transcriptomic census reveals that Rbfox contributes to a broad but selective recapitulation of peripheral tissue splicing patterns in the thymus

abstract: Thymic epithelial cells (TEC) control the selection of a T-cell repertoire reactive to pathogens but tolerant of self. While this process is known to involve the promiscuous expression of virtually the entire protein-coding gene repertoire the extent to which TEC recapitulate peripheral isoforms, and the mechanisms by which they do so, have remained largely unknown. We performed the first assembly-based transcriptomic census of transcript structures and splicing factor (SF) expression in mouse medullary TEC (mTEC) and 21 peripheral tissues. Mature mTEC expressed 60.1% of all protein-coding transcripts, more than was detected in any of the peripheral tissues. However, for genes with tissue-restricted expression, we found that mTEC produced fewer isoforms than did the relevant peripheral tissues. Analysis of exon inclusion revealed an absence of brain-specific micro-exons in mTEC. We did not find unusual numbers of novel transcripts in TEC and show that Aire, the facilitator of promiscuous gene expression, promotes usage of long transcripts but has only a limited impact on alternative splicing in mTEC. Comprehensive assessment of SF expression in mTEC identified a small set of non-promiscuously expressed SF genes amongst which we confirmed RBFOX to be present with AIRE in mTEC nuclei. Using a conditional loss of function approach, we show that Rbfox2 promotes mTEC development and regulates the alternative splicing of promiscuously expressed genes. These data indicate that TEC recommission a small number of peripheral SFs, including members of the Rbfox family, to generate a broad but selective representation of the peripheral splice isoform repertoire.

category: immunology


title: Coastal development and human recreation disturbance limit Australian Pied Oystercatcher Haematopus longirostris population sizes on E Australian beaches

abstract: Australian Pied Oystercatchers Haematopus longirostris and their habitat were surveyed on 72 beaches and 674 km of coastline, from Fraser Island, Queensland to near the New South Wales-Victoria state border, in 2015-2018. A grand total of 232 individual birds (the sum of mean beach counts) and 41 oystercatcher territories were counted. Regression models for mean oystercatcher count density indicated a positive response to the abundance of the surf clam Donax deltoides, a positive New South Wales Far North Coast regional effect and a negative response to the proportion of urban beach. Models for oystercatcher territory density indicated a positive Far North Coast effect and a negative response to pedestrian access density. This report upgrades the coastal development and human recreation disturbance threats for the species.


title: Ecological opportunity, radiation events and genomic innovations shaped the episodic evolutionary history of papillomaviruses

abstract:
Papillomaviruses (PVs) have a wide host range, infecting mammals, birds, turtles, and snakes. The recent discovery of PVs in different fish species allows for a more complete reconstruction of the evolutionary history of this viral family. In this study we perform phylogenetic dating to analyse evolutionary events that occurred during PV evolution, as well as to estimate speciation and evolutionary rates.

We have used four different data sets to explore and correct for potential biases that particular taxa combinations may introduce during molecular time inference. When considering the evolution of substitution rates we observed that short-term rate estimates are much higher than long-term rate estimates, also known as the time-dependent rate phenomenon. When considering the evolution of viral branching events (as a proxy for speciation rates), we show that these have not been constant through time, suggesting the occurrence of distinct evolutionary events such as adaptive radiations and/or changes in the available host niches. In a joint analysis with host speciation rates, we identified at least four different evolutionary periods, suggesting that the evolution of PVs has been multiphasic, and thus refining the previously suggested biphasic evolutionary scenario. Thanks to the discovery of novel PVs in basal hosts and to the implementation of a time-dependent rate model for molecular dating, our results provide new insights into the evolutionary history of PVs. In this updated evolutionary scenario, ecological opportunity appears as one main driving force for the different radiation and key-innovation events we observe.


title: Estimating plasmid conjugation rates: a new computational tool and a critical comparison of methods

abstract:
Plasmids are important vectors for the spread of genes among diverse populations of bacteria. However, there is no standard method to determine the rate at which they spread horizontally via conjugation. Here, we compare commonly used methods on simulated and experimental data, and show that the resulting conjugation rate estimates often depend strongly on the time of measurement, the initial population densities, or the initial ratio of donor to recipient populations. Differences in growth rate, e.g. induced by sub-lethal antibiotic concentrations or temperature, can also significantly bias conjugation rate estimates. We derive a new  end-point measure to estimate conjugation rates, which extends the well-known Simonsen method to include the effects of differences in population growth and conjugation rates from donors and transconjugants. We further derive analytical expressions for the parameter range in which these approximations remain valid. We present an easy to use R package and web interface which implement both new and previously existing methods to estimate conjugation rates. The result is a set of tools and guidelines for accurate and comparable measurement of plasmid conjugation rates.

HighlightsO_LIWe present an R package and Shiny app to estimate conjugation rates from experimental data
C_LIO_LIWe highlight the diversity of existing measures used to estimate conjugation rates
C_LIO_LIWe show these measures are biased for populations with differing growth and conjugation rates from donors or transconjugants
C_LIO_LIWe develop a new  end-point measure which accounts for such differences in growth and conjugation rates
C_LI

category: microbiology


title: In Vivo Transcriptomic Profiling using Cell Encapsulation Identifies Effector Pathways of Systemic Aging

abstract: Sustained exposure to a young systemic environment rejuvenates aged organisms and promotes cellular function. However, due to the intrinsic complexity of tissues it remains challenging to pinpoint niche-independent effects of circulating factors on specific cell populations. Here we describe a method for the encapsulation of human and mouse skeletal muscle progenitors in diffusible polyethersulfone hollow fiber capsules that can be used to profile systemic aging in vivo independent of heterogeneous short-range tissue interactions. We observed that circulating long-range signaling factors in the old systemic environment lead to an activation of Myc and E2F transcription factors, induce senescence and suppress myogenic differentiation. Importantly, in vitro profiling using young and old serum in 2D culture does not capture all pathways deregulated in encapsulated cells in aged mice. Thus, in vivo transcriptomic profiling using cell encapsulation allows for the characterization of effector pathways of systemic aging with unparalleled accuracy.

category: bioengineering


title: Identification of X-chromosomal genes that drive global X-dosage effects in embryonic stem cells

abstract: X-chromosomal genes contribute to sex differences, in particular during early development, when both X chromosomes are active in females. Here, double X-dosage shifts female pluripotent cells towards the naive stem cell state by increasing pluripotency factor expression, inhibiting the differentiation-promoting MAP kinase (MAPK) signalling pathway and delaying differentiation. To identify the genetic basis of these sex differences, we have performed a series of CRISPR knockout screens in murine embryonic stem cells to comprehensively identify X-linked genes that cause the female pluripotency phenotype. We found multiple genes that act in concert, among which Klhl13 plays a central role. We show that this E3 ubiquitin ligase substrate adaptor protein promotes pluripotency factor expression, delays differentiation and represses MAPK target genes, and we identify putative substrates. We thus elucidate the mechanisms that drive sex-induced differences in pluripotent cells with implications for gender medicine in the context of induced pluripotent stem cell based therapies.

category: genetics


title: Mutagenic effectiveness and efficiency of gamma rays and sodium azide in M2 generation of Cowpea

abstract: Legumes play a pivotal role in combating the chronic hunger and malnutrition in the developing nations and are also ideal crops to achieve global food and nutrition security. In the era of climate change, erratic rainfalls, depleting arable land and water resource, feeding the rapidly growing population is a challenging task. Like most other pulses, cowpea is a self pollinated, nutritious, versatile and widely adapted grain legume, but harbor a little accessible genetic variability. Lack of sufficient genetic variability and small size of flowers, traditional plant breeding methods are not enough to meet the demands of improvement of cowpea. Hence, induced mutagenesis was employed to induce significant genetic variability across a range of agro-economical traits in two cowpea varieties Gomati VU-89 and Pusa- 578 from M1 to M4 generations. The success of induced mutagenesis largely depends on the selection of appropriate mutagen, its dose, effectiveness and efficiency. Hence present study was conduct to assess the effectiveness and efficiency of single and combined doses of sodium azide and gamma rays to set an appropriate protocol for induced mutagenesis experimentation in cowpea.

category: plant biology


title: Visualizing protein-protein interactions in plants by rapamycin-dependent delocalization

abstract: Identifying protein-protein interactions (PPI) is crucial for understanding biological processes. Many PPI tools are available, yet only some function within the context of a plant cell. Narrowing down even further, only a few tools allow complex multi-protein interactions to be visualized. Here, we present a conditional in vivo PPI tool for plant research that meets these criteria. Knocksideways in plants (KSP) is based on the ability of rapamycin to alter the localization of a bait protein and its interactors via the heterodimerization of FKBP and FRB domains. KSP is inherently free from many limitations of other PPI systems. This in vivo tool does not require spatial proximity of the bait and prey fluorophores and it is compatible with a broad range of fluorophores. KSP is also a conditional tool and therefore the visualization of the proteins in the absence of rapamycin acts as an internal control. We used KSP to confirm previously identified interactions in Nicotiana benthamiana leaf epidermal cells. Furthermore, the scripts that we generated allow the interactions to be quantified at high throughput. Finally, we demonstrate that KSP can easily be used to visualize complex multi-protein interactions. KSP is therefore a versatile tool with unique characteristics and applications that complements other plant PPI methods.

category: cell biology


title: Oscillatory and aperiodic neural activity jointly predict language learning

abstract: Memory formation involves the synchronous firing of neurons in task-relevant networks, with recent models postulating that a decrease in low frequency oscillatory activity underlies successful memory encoding and retrieval. However, to date, this relationship has been investigated primarily with face and image stimuli; considerably less is known about the oscillatory correlates of complex rule learning, as in language. Further, recent work has shown that non-oscillatory (1/f) activity is functionally relevant to cognition, yet its interaction with oscillatory activity during complex rule learning remains unknown. Using spectral decomposition and power-law exponent estimation of human EEG data (17 females, 18 males), we show for the first time that 1/f and oscillatory activity jointly influence the learning of word order rules of a miniature artificial language system. Flexible word order rules were associated with a steeper 1/f slope, while fixed word order rules were associated with a shallower slope. We also show that increased theta and alpha power predicts fixed relative to flexible word order rule learning and behavioural performance. Together, these results suggest that 1/f activity plays an important role in higher-order cognition, including language processing, and that grammar learning is modulated by different word order permutations, which manifest in distinct oscillatory profiles.


title: Causal relationship between the right auditory cortex and speech-evoked envelope-following response: Evidence from combined tDCS and EEG

abstract: Speech-evoked envelope-following response (EFR) reflects brain encoding of speech periodicity that serves as a biomarker for pitch and speech perception and various auditory and language disorders. While EFR is thought to originate from the subcortex, recent research illustrated a right-hemispheric cortical contribution to EFR. However, it is unclear whether this contribution is causal. This study aimed to establish this causality by combining transcranial direct current stimulation (tDCS) and measurement of EFR (pre- and post-tDCS) via scalp-recorded electroencephalography (EEG). We applied tDCS over the left and right auditory cortices in right-handed normal-hearing participants and examined whether altering cortical excitability via tDCS causes changes in EFR during monaural listening to speech syllables. We showed significant changes in EFR magnitude when tDCS was applied over the right auditory cortex compared to sham stimulation for the listening ear contralateral to the stimulation site. No such effect was found when tDCS was applied over the left auditory cortex. Crucially, we further observed a hemispheric laterality where after-effect was significantly greater for tDCS applied over the right than the left auditory cortex in the contralateral ear condition. Our finding thus provides the first evidence that validates the causal relationship between the right auditory cortex and EFR.


title: Long-read sequencing to interrogate strain-level variation among adherent-invasive Escherichia coli isolated from human intestinal tissue

abstract: Adherent-invasive Escherichia coli (AIEC) is a pathovar linked to inflammatory bowel diseases (IBD), especially Crohns disease, and colorectal cancer. AIEC are genetically diverse, and in the absence of a universal molecular signature, are defined by in vitro functional attributes. The relative ability of difference AIEC strains to colonize, persist, and induce inflammation in an IBD-susceptible host is unresolved. To evaluate strain-level variation among tissue-associated E. coli in the intestines, we develop a long-read sequencing approach to identify AIEC by strain that excludes host DNA. We use this approach to distinguish genetically similar strains and assess their fitness in colonizing the intestine. Here we have assembled complete genomes using long-read nanopore sequencing for a model AIEC strain, NC101, and seven strains isolated from the intestinal mucosa of Crohns disease and non-Crohns tissues. We show these strains can colonize the intestine of IBD susceptible mice and induce inflammatory cytokines from cultured macrophages. We demonstrate that these strains can be quantified and distinguished in the presence of 99.5% mammalian DNA and from within a fecal population. Analysis of global genomic structure and specific sequence variation within the ribosomal RNA operon provides a framework for efficiently tracking strain-level variation of closely-related E. coli and likely other commensal/pathogenic bacteria impacting intestinal inflammation in experimental settings and IBD patients.

category: genomics


title: Massively parallel encapsulation of single cells with structured microparticles and secretion-based flow sorting

abstract: Techniques to analyze and sort single cells based on functional outputs, such as secreted products, have the potential to transform our understanding of cellular biology, as well as accelerate the development of next generation cell and antibody therapies. However, secreted molecules rapidly diffuse away from cells, and analysis of these products requires specialized equipment and expertise to compartmentalize individual cells and capture their secretions. Herein we demonstrate the use of suspendable microcontainers to sort single viable cells based on their secreted products at high-throughput using only commonly accessible laboratory infrastructure. Our microparticles act as solid supports which facilitate cell attachment, partition uniform aqueous compartments, and capture secreted proteins. Using this platform, we demonstrate high-throughput screening of stably- and transiently-transfected producer cells based on relative IgG production as well as screening of B lymphocytes and hybridomas based on antigen-specific antibody production using commercially available flow sorters. Leveraging the high-speed sorting capabilities of standard sorters, we sorted >1,000,000 events in less than an hour. The reported microparticles can be easily stored, and distributed as a consumable reagent amongst researchers, democratizing access to high-throughput functional cell screening.


title: Dopamine pathway characterization during the reproductive mode switch in the pea aphid

abstract: Aphids are major pests of most of the crops worldwide. Such a success is largely explained by the remarkable plasticity of their reproductive mode. They reproduce efficiently by viviparous parthenogenesis during spring and summer generating important damage on crops. At the end of the summer, viviparous parthenogenetic females perceive the photoperiod shortening and transduce this signal to their embryos that change their reproductive fate to produce sexual individuals: oviparous females and males. After mating, those females lay cold-resistant eggs. Earlier studies showed that some transcripts coding for key components of dopamine pathway were regulated between long days and short days conditions suggesting that dopamine might be involved in the transduction of seasonal cues prior to reproductive mode switch. In this study, we aimed at going deeper into the characterization of the expression dynamics of this pathway but also in the analysis of its functional role in this context in the pea aphid Acyrthosiphon pisum. We first analysed the level of expression of ten genes of this pathway in embryos and larval heads of aphids reared under long days (asexual producers) or short days (sexual producers) conditions. We then performed in situ hybridization experiments to localize in embryos the ddc and pale transcripts that are coding for two key enzymes in dopamine synthesis. Finally, Using CRISPR-Cas9 mutagenesis in eggs produced after the mating of sexual individuals, we targeted the ddc gene. We could observe strong melanization defaults in ddc mutated eggs, which confidently mimicked the Drosophila ddc phenotype. Nevertheless, such a lethal phenotype did not allow us to validate the involvement of dopamine as a signaling pathway necessary to trigger the reproductive mode switch in embryos.

category: developmental biology


title: Heat treatment functionalizes hepatocyte-like cells derived from human embryonic stem cells.

abstract:
Hepatocyte-like cells derived from human pluripotent stem cells (hPSC-HLCs) offer an alternative to primary hepatocytes commonly used for drug screenings and toxicological tests. Although tremendous efforts have been made to facilitate hepatic functions of hPSC-HLCs using growth factors and chemicals, these cells have not yet reached hepatic functions comparable to hepatocytes in vivo. Therefore, there exists a critical need to use an alternative trigger to facilitate hepatic functions in hPSC-HLCs. We noted that human liver temperature (around 39{degrees}C) is higher than normal human body temperature (around 36.5{degrees}C), yet hepatocytes are generally cultured at 37{degrees}C in-vitro. Here we showed that hepatic functions of hPSC-HLCs would be facilitated under physiological liver temperatures. We identified the optimal temperature by treating HLCs derived from H9 human embryonic stem cells (hESC-HLCs) at 39{degrees}C and 42{degrees}C. 42{degrees}C-treatment caused significantly greater cell death compared to 39{degrees}C. We also confirmed the increases of hepatic functions, such as secretion of albumin, cytochrome P450 3A4 (CYP3A4) activities, and collagen productions, without severe cell damages. To elucidate the underlying mechanisms of heat-induced hepatic functions, RNA-seq was to identify gene expression signatures due to 39{degrees}C-treated hESC-HLCs. This study also showed the possible mechanisms of heat-induced hepatic function via glucocorticoid receptor pathway and molecular chaperons. In combination with existing hepatic differentiation protocols, the method proposed here may further improve hepatic functions for hPSCs, and lead to the realization of drug discovery efforts and drug toxicological tests.

Significance statementHepatocyte-like cells derived from human pluripotent stem cells (hPSC-HLCs) offer an alternative to primary hepatocytes commonly used for drug screenings and toxicological tests. We noted that human liver temperature (around 39{degrees}C) is higher than normal human body temperature (around 36.5{degrees}C), affecting the in-vitro hepatic functions of hPSC-HLCs, such as metabolic activities. Here we showed that hepatic functions of hPSC-HLCs, albumin secretion, CYP3A4 activities, and collagen production would be facilitated under physiological liver temperatures at 39{degrees}C, without severe cell damages. RNA-seq was used to elucidate the underlying mechanisms of heat-induced hepatic functions. This study also showed the possible mechanisms of heat-induced hepatic function via glucocorticoid receptor pathway and molecular chaperons.


title: Assortative mate choice and epistatic mating-trait architecture induce complex movement of the crow hybrid zone

abstract: Hybrid zones provide a window into the evolutionary processes governing species divergence. While the role of postzygotic isolation has been extensively characterized in the context of hybrid zones, the contribution of prezygotic isolation is less well explored. Here, we investigate the effects of assortative mate choice, the underlying preference function and mating-trait architecture, and the strength of sexual selection on hybrid zone dynamics. We explore this question by means of a mathematical model parameterized with phenotype and genotype data from the hybrid zone between all-black carrion and grey-coated hooded crows. The best-fit model resulted in narrow clines for two mating-trait loci coding for colour phenotype maintained by a moderate degree of assortative mating. Epistasis between the two loci induced hybrid-zone movement in favor of alleles conveying dark plumage followed by a shift in the opposite direction favouring grey-coated phenotypes [~]1,200 generations after secondary contact. Unlinked neutral loci diffused near-unimpeded across the zone. These results were generally robust to the choice of matching rule (self-referencing or parental imprinting) and effects of genetic drift. Overall, this study illustrates under which conditions assortative mating can maintain steep clines in mating-trait loci without generalizing to genome-wide reproductive isolation. It further emphasizes the importance of mating-trait architecture for spatio-temporal hybrid-zone dynamics.


title: Contributions of the four essential entry glycoproteins to HSV-1 tropism and the selection of entry routes.

abstract:
Herpes Simplex viruses (HSV-1 and HSV-2) encode up to 16 envelope proteins, four of which are essential for entry. However, whether these four proteins alone are sufficient to dictate the broad cellular tropism of HSV-1 and the selection of different cell-type dependent entry routes is unknown. To begin addressing this, we previously pseudotyped VSV, lacking its native glycoprotein G, with only the four essential entry glycoproteins of HSV-1: gB, gH, gL, and gD. This novel VSV{Delta}G-BHLD pseudotype recapitulated several important features of HSV-1 entry: the requirement for gB, gH, gL, gD, a cellular receptor, and sensitivity to anti-gB and anti-gH/gL neutralizing antibodies. However, due to the use of a single cell type in that study, the tropism of the VSV{Delta}G-BHLD pseudotype was not investigated. Here, we show that the cellular tropism of the pseudotype is severely limited compared to wild-type HSV-1 and that its entry pathways differ from the native HSV-1 entry pathways. To test the hypothesis that other HSV-1 envelope proteins may contribute to HSV-1 tropism, we generated a derivative pseudotype containing the HSV-1 glycoprotein gC (VSV{Delta}G-BHLD-gC) and observed a gC-dependent increase in entry efficiency in two cell types. We propose that the pseudotyping platform developed here has the potential to uncover functional contributions of HSV-1 envelope proteins to entry in a gain-of-function manner.

ImportanceHerpes simplex viruses (HSV-1 and HSV-2) contain up to 16 different proteins in their envelopes. Four of these, glycoproteins gB, gD, gH, and gL, are termed essential with regard to entry whereas the rest are typically referred to as non-essential based on the entry phenotypes of the respective single genetic deletions. However, the single-gene deletion approach, which relies on robust loss-of-function phenotypes, may be confounded by functional redundancies among the many HSV-1 envelope proteins. We have developed a pseudotyping platform, in which the essential four entry glycoproteins are isolated from the rest, which can be added back individually for systematic gain-of-function entry experiments. Here, we show the utility of this platform for dissecting the contributions of HSV envelope proteins, both the essential four and the remaining dozen (using gC as an example), to HSV entry.


title: Coevolutionary dynamics of genetic traits and their long-term extended effects under non-random interactions

abstract: Organisms continuously modify their living conditions via extended genetic effects on their envi-ronment, microbiome, and in some species culture. These effects can impact the fitness of current but also future conspecifics due to non-genetic transmission via ecological or cultural inheritance. In this case, selection on a gene with extended effects depends on the degree to which current and future genetic relatives are exposed to modified conditions. Here, we detail the selection gradient on a quantitative trait with extended effects in a patch-structured population, when gene flow between patches is limited and ecological inheritance within patches can be biased towards offspring. Such a situation is relevant to understand evolutionary driven changes in individual condition that can be preferentially transmitted from parent to offspring, such as cellular state, micro-environments (e.g., nests), pathogens, microbiome, or culture. Our analysis quantifies how the interaction between limited gene flow and biased ecological inheritance influences the joint evolutionary dynamics of traits together with the conditions they modify, helping understand adaptation via non-genetic modifications. As an illustration, we apply our analysis to a gene-culture coevolution scenario in which genetically-determined learning strategies coevolve with adaptive knowledge. In particular, we show that when social learning is synergistic, selection can favour strategies that generate remarkable levels of knowledge under intermediate levels of both vertical cultural transmission and limited dispersal. More broadly, our theory yields insights into the interplay between genetic and non-genetic inheritance, with implications for how organisms evolve to transform their environments.


title: Conditional repeatability and the variance explained by reaction norm variation in random slope models

abstract: Individuals differ in average phenotypes and in sensitivity to environmental variation. Such context-sensitivity can be modelled as random-slope variation. Random-slope variation implies that the proportion of between-individual variation varies across the range of a covariate (environment/context/time/age) and has thus been called  conditional repeatability. We propose to put conditional repeatabilities in perspective of the total phenotypic variance and suggest a way of standardization using the random-slope coefficient of determination [Formula]. Furthermore, we illustrate that the marginalized repeatability Rmar averaged across an environmental gradient offers a biologically relevant description of between-individual variation. We provide simple equations for calculating key descriptors of conditional repeatabilities, clarify the difference between random-intercept variation and average between-individual variation and make recommendations for comprehensive reporting. While we introduce the concept with individual variation in mind, the framework is equally applicable to other type of between-group/cluster variation that varies across some (environmental) gradient.

category: animal behavior and cognition


title: Filamentous Bacteriophage Delay Healing of Pseudomonas-Infected Wounds

abstract: We have identified a novel role for filamentous bacteriophage in the delayed healing associated with chronic Pseudomonas aeruginosa (Pa) wound infections. Pf phage delays wound re-epithelialization in the absence of live Pa, indicative that Pf effects on wound healing are independent of Pa pathogenesis. Pf phage directly inhibits autocrine signaling of CXCL1 (KC) to impede keratinocyte migration and wound re-epithelization. In agreement with these studies, a prospective cohort study of 36 human patients with chronic Pa wound infections revealed that wounds infected with Pf positive strains of Pa took longer to heal and were more likely to increase in size compared to wounds infected with Pf negative strains. Together, these data implicate Pf phage in the delayed wound healing associated with Pa infection through direct manipulation of mammalian target cells. We propose that Pf phage may have potential as a biomarker and therapeutic target in delayed wound healing.


title: Automated Annotation of Cell Identities in Dense Cellular Images

abstract: Although identifying cell names in dense image stacks is critical in analyzing functional whole-brain data enabling comparison across experiments, unbiased identification is very difficult, and relies heavily on researchers experiences. Here we present a probabilistic-graphical-model framework, CRF_ID, based on Conditional Random Fields, for unbiased and automated cell identification. CRF_ID focuses on maximizing intrinsic similarity between shapes. Compared to existing methods, CRF_ID achieves higher accuracy on simulated and ground-truth experimental datasets, and better robustness against challenging noise conditions common in experimental data. CRF_ID can further boost accuracy by building atlases from annotated data in highly computationally efficient manner, and by easily adding new features (e.g. from new strains). We demonstrate cell annotation in C. elegans images across strains, animal orientations, and tasks including gene-expression localization, multi-cellular and whole-brain functional imaging experiments. Together, these successes demonstrate that unbiased cell annotation can facilitate biological discovery, and this approach may be valuable to annotation tasks for other systems.


title: Glucose-dependent activation, activity, and deactivation of beta cell networks in acute mouse pancreas tissue slices

abstract: Many details of glucose-stimulated intracellular calcium changes in beta cells during activation, activity and deactivation, as well as their concentration-dependence, remain to be described. Classical physiological experiments indicated that in islets functional differences between individual cells are largely attenuated, but recent findings suggest considerable intercellular heterogeneity, with some cells possibly coordinating the collective responses. To address the above with an emphasis on heterogeneity and describing the relations between classical physiological and functional network properties, we performed functional multicellular calcium imaging in mouse pancreas tissue slices over a wide range of glucose concentrations. During activation, delays to activation of cells and first responder-any cell delays shortened, and the sizes of simultaneously responding clusters increased with increasing glucose. Exactly the opposite characterized deactivation. The frequency of fast calcium oscillations during activity increased with increasing glucose up to 12 mM glucose, beyond which oscillation duration became longer, resulting in a homogenous increase in active time. In terms of functional connectivity, islets progressed from a very segregated network to a single large functional unit with increasing glucose. A comparison between classical physiological and network parameters revealed that the first-responders during activation had longer active times during plateau and the most active cells during the plateau tended to deactivate later. Cells with the most functional connections tended to activate sooner, have longer active times, and deactivate later. Our findings provide a common ground for recent differing views on beta cell heterogeneity and an important baseline for future studies of stimulus-secretion and intercellular coupling.

category: physiology


title: Molecular mechanism of the pH-dependent calcium affinity in langerin

abstract: The C-type lectin receptor langerin plays a vital role in the mammalian defense against invading pathogens. Its function hinges on the affinity to its co-factor Ca2+ which in turn is regulated by the pH. We studied the structural consequences of protonating the allosteric pH-sensor histidine H294 by molecular dynamics simulations (total simulation time: about 120 {micro}s) and Markov models. We discovered a mechanism in which the signal that the pH has dropped is transferred to the Ca2+-binding site without transferring the initial proton. Instead, protonation of H294 unlocks a conformation in which a protonated lysine side-chain forms a hydrogen bond with a Ca2+-coordinating aspartic acid. This destabilizes Ca2+ in the binding pocket, which we probed by steered molecular dynamics. After Ca2+-release, the proton is likely transferred to the aspartic acid and stabilized by a dyad with a nearby glutamic acid, triggering a conformational transition and thus preventing Ca2+-rebinding.

category: molecular biology


title: The 16S microbiota of Budu, the Malaysian fermented anchovy sauce

abstract: Budu is a Malaysian fermented anchovy sauce produced by immersing small fishes into a brine solution for 6 to 18 months. Fermentation of the anchovy sauce is contributed partly by microbial enzymes, but little is known about the microbial community in Budu. Therefore, a better understanding of the Budu microbiome is necessary to better control the quality, consistency and safety of the product. In this study, we collected 60 samples from twenty bottles of Budu produced by seven different manufacturers. We analyzed their microbiota based on V3-V4 16S rRNA amplicon sequencing at the time of opening the bottle as well as 3- and 7-months post-opening. Tetragenococcus was the dominant genus in many samples, reaching a maximum proportion of 98.62%, but was found in low abundance, or absent, in other samples. When Budu samples were not dominated by a dominant taxa, we observed a wider genera diversity such as Staphylococcus, Acinetobacter, Halanaerobium and Bacillus. While the taxonomic composition was relatively stable across sampling periods, samples from two brands showed a sudden increase in relative abundance of the genus Chromobacterium in the 7th month. Based on prediction of metagenome functions, non-Tetragenococcus-dominated samples were predicted to have enriched functional pathways related to amino acid metabolism and purine metabolism compared to Tetragenococcus-dominated microbiome; these two pathways are fundamental fermented quality and health attributes of fish sauce. Within the non-Tetragenococcus-dominated group, contributions towards amino acid metabolism and purine metabolism were biased towards the dominant taxa when species evenness is low, while in samples with higher species evenness, the contributions towards the two pathways were predicted to be evenly distributed between taxa.


title: Age-related trajectories of DNA methylation network markers: a parenclitic network approach to a family-based cohort of patients with Down Syndrome

abstract: Despite the cause of Down Syndrome (DS) is well established, the underlying molecular mechanisms that contribute to the syndrome and to the phenotype of accelerated ageing remain largely unknown. DNA methylation profiles are largely altered in DS but it remains unclear how different methylation regions and probes are structured into a network of interactions. We develop and generalize the Parenclitic Networks approach that enables to find correlations between distant CpG probes (and not pronounced as stand-alone biomarkers) and quantifies hidden network changes in DNA methylation. DS and a family-based cohort (including healthy siblings and mothers of persons with DS) is used as a case study. Following this approach, we constructed parenclitic networks and obtained different signatures informative for (i) the differences between individuals with DS from healthy individuals; (ii) differences between young and old healthy individuals and determining the place of DS individuals on this scale; (iii) differences between DS individuals from their age-matched siblings, and (iv) the difference between DS and the adult population (their mothers). Conducted Gene Ontology analysis showed that the CpG network approach is more powerful than the single CpG approach in identifying biological processes related to DS phenotype, like those involved in central nervous system, skeletal muscles, disorders in carbohydrate metabolism, cardiopathology, and oncogenes. Our open-source software implementation is accessible to all researchers. The software includes a complete workflow to construct Parenclitic Networks with any machine learning algorithm as a kernel to build edges. We anticipate a broad applicability of the approach to other diseases.


title: A Generalized Robust Allele-based Genetic Association Test

abstract: The allele-based association test, comparing allele frequency difference between case and control groups, is locally most powerful. However, application of the classical allelic test is limited in practice, because the method is sensitive to the Hardy-Weinberg equilibrium (HWE) assumption, not applicable to continuous traits, and not easy to account for covariate effect or sample correlation. To develop a generalized robust allelic test, we propose a new allele-based regression model with individual allele as the response variable. We show that the score test statistic derived from this robust and unifying regression framework contains a correction factor that explicitly adjusts for potential departure from HWE, and encompasses the classical allelic test as a special case. When the trait of interest is continuous, the corresponding allelic test evaluates a weighted difference between individual-level allele frequency estimate and sample estimate where the weight is proportional to an individuals trait value, and the test remains valid under Y - dependent sampling. Finally, the proposed allele-based method can analyze multiple (continuous or binary) phenotypes simultaneously and multi-allelic genetic markers, while accounting for covariate effect, sample correlation and population heterogeneity. To support our analytical findings, we provide empirical evidence from both simulation and application studies.


title: TrkB agonist antibody delivery to the brain using a TfR1 specific BBB shuttle provides neuroprotection in a mouse model of Parkinson's Disease

abstract: Single domain shark antibodies that bind to the transferrin receptor 1 (TfR1) on brain endothelial cells can be used to shuttle antibodies and other cargos across the blood brain barrier (BBB). We have fused one of these (TXB4) to differing regions of TrkB and TrkC neurotrophin receptor agonist antibodies (AAb) and determined the effect on agonist activity, brain accumulation and engagement with neurons in the mouse brain following systemic administration. The TXB4-TrkB and TXB4-TrkC fusion proteins retain agonist activity at their respective neurotrophin receptors and in contrast to their parental AAb they rapidly accumulate in the brain reaching nM levels following a single IV injection. Following SC administration, the most active TrkB fusion protein, TXB4-TrkB1, associates with and activates ERK1/2 signalling in TrkB positive cells in the cortex and tyrosine hydroxylase (TH) positive dopaminergic neurons in the substantia nigra pars compacta (SNc). When tested in the 6-hydroxydopamine (6-OHDA) mouse model of Parkinsons disease (PD) TXB4-TrkB1, but not the parental TrkB AAb or a TXB4-TrkC1 fusion protein, completely prevented the 6-OHDA induced death of TH positive neurons in the SNc. In conclusion, the fusion of the TXB4 TfR1 binding module allows a TrkB AAb to reach neuroprotective concentrations in the brain parenchyma following systemic administration.


title: A single domain shark antibody targeting the transferrin receptor 1 delivers a TrkB agonist antibody across the blood brain barrier to provide full neuroprotection in a mouse model of Parkinson's Disease


title: A Combined Evidence Approach to Prioritize Nipah Virus Inhibitors

abstract: Nipah Virus (NiV) came into limelight due to an outbreak in Kerala, India. NiV causes severe disease and death in people with over 75% case fatality rate. It is a public health concern and has the potential to become a global pandemic. Lack of treatment has forced the containment methods to be restricted to isolation and surveillance. WHOs  R&D Blueprint list of priority diseases (2018) indicates that there is an urgent need for accelerated research & development for addressing NiV. In the quest for druglike NiV inhibitors (NVIs) a thorough literature search followed by systematic data curation was conducted. Rigorous data analysis was done with curated NVIs for prioritizing druglike compounds. For the same, more than 1800 descriptors of NVIs were computed and comparative analysis was performed with the FDA approved small molecules and antivirals. These compounds were further evaluated through PAINS filter to study their toxicity profile. Simultaneously, compounds were also prioritized based on the robustness of the assays through which they were identified. Our efforts lead to the creation of a well-curated structured knowledgebase of 182 NVIs with 98 small molecule inhibitors. The reported IC50/EC50 values for some of these inhibitors are in the nanomolar range - as low as 0.47 nM. In order to prioritize these inhibitors, we performed several tests and applied filters to identify drug-like non-toxic compounds. Of 98, a few compounds passed DruLito & PAINS filters exhibiting drug-like properties and were also prioritized in an independent screen based only the assay robustness. The NVIs have diverse structural features and offer a wide spectrum of ways in which they can be developed further as druglike molecules. We report a knowledgebase for furthering the development of NVIs. The platform has a diverse set of 98 NVIs of which a few have been prioritized based on a combined evidence strategy. The platform has the provision to submit new inhibitors as and when reported by the community for further enhancement of NiV inhibitor landscape.


title: ZIP9 is a Druggable Determinant of Sex Differences in Melanoma

abstract:
Melanoma and most other cancers occur more frequently, and have worse prognosis, in males compared with females. Though sex steroids are thought to be involved, classical androgen and estrogen receptors are not detectable in most melanomas. Here we show that testosterone promotes melanoma proliferation by activating ZIP9 (SLC39A9), a zinc transporter that is not intentionally targeted by available therapeutics, but is widely expressed in human melanoma. This testosterone activity requires zinc influx, MAPK activation and YAP1 nuclear translocation. We demonstrate that FDA approved inhibitors of the classical androgen receptor also inhibit ZIP9, and thereby antagonize the pro-tumorigenic effects of testosterone in melanoma. In male mice, androgen receptor inhibitors suppressed growth of ZIP9-expressing melanomas, but had no effect on isogenic melanomas lacking ZIP9, nor on melanomas in females. These data suggest that ZIP9 might be effectively targeted in melanoma and other cancers by repurposing androgen receptor inhibitors that are currently approved only for prostate cancer.

SignificanceMelanoma outcomes are worse in males than in females. Some of this difference is driven by testosterone signaling through ZIP9, a nonclassical testosterone receptor. Drugs that target AR can be repurposed to block ZIP9, and inhibit melanoma in males.

category: cancer biology


title: Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle

abstract:
Selection on complex traits can rapidly drive evolution, especially in stressful environments. This polygenic selection does not leave intense sweep signatures on the genome, rather many loci experience small allele frequency shifts, resulting in large cumulative phenotypic changes. Directional selection and local adaptation are actively changing populations; but, identifying loci underlying polygenic or environmental selection has been difficult. We use genomic data on tens of thousands of cattle from three populations, distributed over time and landscapes, in linear mixed models with novel dependent variables to map signatures of selection on complex traits and local adaptation. We identify 207 genomic loci associated with an animals birth date, representing ongoing selection for monogenic and polygenic traits. Additionally, hundreds of additional loci are associated with continuous and discrete environments, providing evidence for local adaptation. These candidate loci highlight the nervous systems possible role in local adaptation. While advanced technologies have increased the rate of directional selection in cattle, it has likely been at the expense of historically generated local adaptation, which is especially problematic in changing climates. When applied to large, diverse cattle datasets, these selection mapping methods provide an insight into how selection on complex traits continually shapes the genome. Further, by understanding the genomic loci implicated in adaptation, may help us breed more adapted and efficient cattle and begin understanding the basis for mammalian adaptation, especially in changing climates. These selection mapping approaches help clarify selective forces and loci in evolutionary, model, and agricultural contexts.

Author SummaryInterest in mapping the impacts of selection and local adaptation on the genome is increasing due to the novel stressors presented by climate change. Until now, approaches have largely focused on mapping "sweeps" on large-effect loci. Highly powered datasets that are both temporally and geographically distributed have not existed. Recently, large numbers of beef cattle have been genotyped across the United States, including influential individuals with cryopreserved semen. This has created multiple powerful datasets distributed over time and landscapes. Here, we map the recent effects of selection and local adaptation in three cattle populations. The results provide insight into the biology of mammalian adaptation and generate useful tools for selecting and breeding better-adapted cattle for a changing environment.


title: Synchronised oscillations in growing cell populations are explained by demographic noise

abstract:
Understanding synchrony in growing populations is important for applications as diverse as epidemiology and cancer treatment. Recent experiments employing fluorescent reporters in melanoma cell lines have uncovered growing subpopulations exhibiting sustained oscillations, with nearby cells appearing to synchronise their cycles. In this study we demonstrate that the behaviour observed is consistent with long-lasting transient phenomenon initiated, and amplified by the finite-sample effects and demographic noise. We present a novel mathematical analysis of a multi-stage model of cell growth which accurately reproduces the synchronised oscillations. As part of the analysis, we elucidate the transient and asymptotic phases of the dynamics and derive an analytical formula to quantify the effect of demographic noise in the appearance of the oscillations. The implications of these findings are broad, such as providing insight into experimental protocols that are used to study the growth of asynchronous populations and, in particular, those investigations relating to anti-cancer drug discovery.

Statement of SignificanceRecent experiments have reported strong evidence of periodic oscillations in the proportion of young and old melanoma cells. The biological mechanism generating this synchronisation and the potential impact that can have on commonly used experimental protocols is still unclear. Here we studied a population of melanoma cells for which we found oscillations in the proportions of cells in each phase of the cell cycle. We demonstrate that these observations may be triggered by intrinsic demographic noise alone, rather than any active synchronisation mechanism requiring cell-cell communication. Our findings may have implications for typical experimental protocols which aim to produce asynchronous cell populations.


title: Architecture and assembly dynamics of the essential mitochondrial TIM chaperone systems

abstract: The mitochondrial Tim chaperones are responsible for the transport of membrane proteins across the inter-membrane space to the inner and outer mitochondrial membranes. TIM9{middle dot}10, a hexameric 70 kDa protein complex formed by 3 copies of Tim9 and Tim10, guides its clients across the aqueous compartment. The TIM9{middle dot}10{middle dot}12 complex is the anchor point at the inner-membrane insertase complex TIM22. The subunit composition of the TIM9{middle dot}10{middle dot}12 complex remains debated. Joint NMR, small-angle X-ray scattering and MD simulation data allow us to derive a structural model of the TIM9{middle dot}10{middle dot}12 assembly, which has a 2:3:1 stoichiometry (Tim9:Tim10:Tim12). We find that both TIM9{middle dot}10 and TIM9{middle dot}10{middle dot}12 hexamers are in a dynamic equilibrium with their constituent subunits, exchanging on a minutes time scale. Residue-resolved NMR data establish that the subunits exhibit large conformational dynamics: when the conserved cysteines of the CX3C-Xn-CX3C motifs are formed, short marginally stable -helices are formed, and these are fully stabilized only upon formation of the mature hexameric chaperone. We propose that the continuous subunit exchange is a means of mitochondria to control their level of inter-membrane space chaperones, and thus rapidly adapt to the cellular state.

category: biophysics


title: Human and macaque pairs employ different coordination strategies in a dyadic decision game with face-to-face action visibility

abstract:
Interactions of group-living primates range from cooperation to competition. Many corresponding real-world decisions critically depend on observing partners actions. In classical game theory studies, however, agents act without knowing the partners choices. To overcome these limitations, we developed a setup where two agents engage face-to-face in cooperative or competitive tasks on a shared transparent touchscreen display ("transparent games"), ensuring mutual action visibility. We compared human and macaque pairs in a transparent version of the coordination game "Bach-or-Stravinsky", which entails the conflict about which of the two individually-preferred coordinated options to choose. Most human pairs developed coordinated behavior and adopted dynamic turn-taking to equalize the payoffs. All macaque pairs also converged on coordination, but in simpler, static ways. Remarkably, two animals that underwent training with a human confederate learned to coordinate dynamically, exhibiting turn-taking driven by temporal competition. The observed choices were captured by modeling the probability to see the others action before ones own movement. Such competitive turn-taking is unlike the prosocial turn-taking in humans, who equally often initiated switches to and from their preferred option. Our results show that dynamic coordination is not restricted to humans, but it can be subserved by different social attitudes, and emphasize the importance of action visibility in studies of the emergence and maintenance of coordinated behavior.

TeaserIn real-time transparent interactions, both species show dynamic coordination, but macaques compete while humans strive for fairness by taking turns.


title: Dynamic changes in tRNA modifications and abundance during T-cell activation

abstract:
The tRNA pool determines the efficiency, throughput, and accuracy of translation. Previous studies have identified dynamic changes in the tRNA supply and mRNA demand during cancerous proliferation. Yet, dynamic changes may occur also during physiologically normal proliferation, and these are less characterized. We examined the tRNA and mRNA pools of T-cells during their vigorous proliferation and differentiation upon triggering their antigen receptor. We observe a global signature of switch in demand for codons at the early proliferation phase of the response, accompanied by corresponding changes in tRNA expression levels. In the later phase, upon differentiation, the response of the tRNA pool is relaxed back to basal level, potentially restraining excessive proliferation. Sequencing of tRNAs allowed us to also evaluate their diverse base-modifications. We found that two types of tRNA modifications, wybutosine and ms2t6A, are reduced dramatically during T-cell activation. These modifications occur in the anti-codon loops of two tRNAs that decode "slippery codons", that are prone to ribosomal frameshifting. Attenuation of these frameshift-protective modifications is expected to increase the potential for proteome-wide frameshifting during T-cell proliferation. Indeed, human cell lines deleted of a wybutosine writer showed increased ribosomal frameshifting, as detected with a HIV gag-pol frameshifting site reporter. These results may explain HIVs specific tropism towards proliferating T-Cells since it requires ribosomal frameshift exactly on the corresponding codon for infection. The changes in tRNA expression and modifications uncover a new layer of translation regulation during T-cell proliferation and exposes a potential trade-off between cellular growth and translation fidelity.

Significance statementThe tRNA pool decodes genetic information during translation. As such, it is subject to intricate physiological regulation in all species, across different physiological conditions. Here we show for the first time a program that governs the tRNA pool and its interaction with the transcriptome upon a physiological cellular proliferation- T-cells activation. We found that upon antigenic activation of T-cells, their tRNA and mRNA pools undergo coordinated and complementary changes, which are relaxed when cells reduce back their proliferation rate and differentiate into memory cells. We found a reduction in two particular tRNA modifications that have a role in governing translation fidelity and frameshift prevention. This exposes a vulnerability in activated T-cells that may be utilized by HIV for its replication.

ClassificationBIOLOGICAL SCIENCES; cell biology


title: Cropping systems impact changes in soil fungal, but not prokaryote, alpha-diversity and community composition stability over a growing season in a long-term field trial.

abstract: Crop harvest followed by a fallow period can act as a disturbance on soil microbial communities. Cropping systems intended to improve alpha-diversity of communities may also confer increased compositional stability during succeeding growing seasons. Over a single growing season in a long-term (18 year) agricultural field experiment incorporating conventional (CON), conservation (CA), organic (ORG) and integrated (INT) cropping systems, temporal changes in prokaryote, fungal and arbuscular mycorrhizal fungi (AMF) communities were investigated overwinter, during crop growth and at harvest. While certain prokaryote phyla were influenced by cropping system (e.g. Acidobacteria), the community as a whole was primarily driven by temporal changes over the growing season as distinct overwinter and crop-associated communities, with the same trend observed regardless of cropping system. Species- rich prokaryote communities were most stable over the growing season. Cropping system exerted a greater effect on fungal communities, with alpha-diversity highest and temporal changes most stable under CA. CON was particularly detrimental for alpha-diversity in AMF communities, with AMF alpha-diversity and stability improved under all other cropping systems. Practices that promoted alpha-diversity tended to also increase the similarity and temporal stability of soil fungal (and AMF) communities during a growing season, while prokaryote communities were largely insensitive to management.


title: Hippocampal-medial prefrontal event segmentation and integration contribute to episodic memory formation

abstract: How do we encode our continuous life experiences for later retrieval? Theories of event segmentation and integration suggest that the hippocampus binds separately represented events into an ordered narrative. Using a functional Magnetic Resonance Imaging (fMRI) movie watching-recall dataset, we quantified two types of neural similarities (i.e., activation pattern similarity and within-region voxel-based connectivity pattern similarity) between separate events during movie watching and related them to subsequent retrieval of events as well as retrieval of sequential order. We demonstrated that compared to forgotten events, successfully remembered events were associated with distinct activation patterns in the hippocampus and medial prefrontal cortex. By contrast, similar connectivity patterns between events were associated with memory formation and were also relevant for retaining events in the correct order. We applied the same approaches to an independent movie watching fMRI dataset as validation and highlighted again the role of hippocampal activation pattern and connectivity pattern in memory formation. We propose that distinct activation patterns represent neural segmentation of events while similar connectivity patterns encode context information, and therefore integrate events into a narrative. Our results provide novel evidence for the role of hippocampal-medial prefrontal event segmentation and integration in episodic memory formation of real-life experience.


title: Evolutionary Pressures and Codon Bias in Low Complexity Regions of Plasmodia Parasites

abstract: One of the most debated topics in Evolutionary Biology concerns Low Complexity Regions of P. falciparum, the causative agent of the most virulent and deadly form of human malaria. In this work, we analysed the proteome of 22 plasmodium species including P. falciparum. SEG predicts that proteins containing Low Complexity Regions turn out to be longer than those which are predicted to be completely complex (without Low Complexity Regions). Moreover, using some well-known bioinformatics tools such as the Effective Number of Codons, the Pr2 and a new index that we have called SPI, we have noticed how proteins that embed Low Complexity Regions are under lower selective pressure than those that do not present this type of locus. By applying the Relative Synonymous Codon Usage and other tools developed ad hoc for this study, we note, instead, how the Low Complexity Regions appear to have a non-neutral codon bias with respect to the host proteins.

category: bioinformatics


title: From work stress to disease: A computational model

abstract: In modern society, work stress is highly prevalent. Problematically, work stress can cause disease. To help understand the causal relationship between work stress and disease, we present a computational model of this relationship. That is, drawing from allostatic load theory, we captured the link between work stress and disease in a set of mathematical formulas. With simulation studies, we then examined our models ability to reproduce key findings from previous empirical research. Specifically, results from Study 1 suggested that our model could accurately reproduce established findings on daily fluctuations in cortisol levels (both on the group level and the individual level). Results from Study 2 suggested that our model could accurately reproduce established findings on the relationship between work stress and cardiovascular disease. Finally, results from Study 3 yielded new predictions about the relationship between workweek configurations (i.e., how working hours are distributed over days) and the subsequent development of disease. Together, our studies suggest a new, computational approach to studying the causal link between work stress and disease. We suggest that this approach is fruitful, as it aids the development of falsifiable theory, and as it opens up new ways of generating predictions about why and when work stress is (un)healthy.


title: Morphognostic honey bees communicating nectar location through dance movements

abstract: AO_SCPLOWBSTRACTC_SCPLOWHoney bees are social insects that forage for flower nectar cooperatively. When an individual forager discovers a flower patch rich in nectar, it returns to the hive and performs a "waggle dance" in the vicinity of other bees that consists of movements communicating the direction and distance to the nectar source. The dance recruits "witnessing" bees to fly to the location of the nectar to retrieve it, thus cooperatively exploiting the environment. Replicating such complex animal behavior is a step forward on the path to artificial intelligence. This project simulates the bee foraging behavior in a cellular automaton using the Morphognosis machine learning model. The model features hierarchical spatial and temporal contexts that output motor responses from sensory inputs. Given a set of bee foraging and dancing exemplars, and exposing only the external input-output of these behaviors to the Morphognosis learning algorithm, a hive of artificial bees can be generated that forage as their biological counterparts do. A comparison of Morphognosis foraging performance with that of an artificial recurrent neural network is also presented.


title: Functional Organization of the Maternal and Paternal Human 4D Nucleome

abstract: Every human somatic cell inherits a maternal and a paternal genome, which work together to give rise to cellular phenotypes. However, the allele-specific relationship between gene expression and genome structure through the cell cycle is largely unknown. By integrating haplotype-resolved genome-wide chromosome conformation capture, mature and nascent mRNA, and protein binding data, we investigate this relationship both globally and locally. We introduce the maternal and paternal 4D Nucleome, enabling detailed analysis of the mechanisms and dynamics of genome structure and gene function for diploid organisms. Our analyses find significant coordination between allelic expression biases and local genome conformation, and notably absent expression bias in universally essential cell cycle and glycolysis genes. We propose a model in which coordinated biallelic expression reflects prioritized preservation of essential gene sets.


title: V367F mutation in SARS-CoV-2 spike RBD emerging during the early transmission phase enhances viral infectivity through increased human ACE2 receptor binding affinity

abstract:
The current global pandemic of COVID-19 is caused by a novel coronavirus SARS-CoV-2. The SARS-CoV-2 spike protein receptor-binding domain (RBD) is the critical determinant of viral tropism and infectivity. To investigate whether naturally occurring mutations in the RBD during the early transmission phase have altered the receptor binding affinity and infectivity, firstly we analyzed in silico the binding dynamics between mutated SARS-CoV-2 RBDs and the human ACE2 receptor. Among 32,123 genomes of SARS-CoV-2 isolates (January through March, 2020), 302 non-synonymous RBD mutants were identified and clustered into 96 mutant types. The six dominant mutations were analyzed applying molecular dynamics simulations. The mutant type V367F continuously circulating worldwide displayed higher binding affinity to human ACE2 due to the enhanced structural stabilization of the RBD beta-sheet scaffold. The increased infectivity of V367 mutants was further validated by performing receptor-ligand binding ELISA, surface plasmon resonance, and pseudotyped virus assays. Genome phylogenetic analysis of V367F mutants showed that during the early transmission phase, most V367F mutants clustered more closely with the SARS-CoV-2 prototype strain than the dual-mutation variants (V367F + D614G) which emerged later and formed a distinct sub-cluster. The analysis of critical RBD mutations provides further insights into the evolutionary trajectory of SARS-CoV-2 under negative selection pressure and supports the continuing surveillance of spike mutations to aid in the development of new COVID-19 drugs and vaccines.

ImportanceA novel coronavirus SARS-CoV-2 has caused the pandemic of COVID-19. The origin of SARS-CoV-2 was associated with zoonotic infections. The spike protein receptor-binding domain (RBD) is identified as the critical determinant of viral tropism and infectivity. Thus, whether the mutations in the RBD of the circulating SARS-CoV-2 isolates have altered the receptor binding affinity and caused them more infectious, should be paid more attentions to. Given that SARS-CoV-2 is a novel coronavirus, the significance of our research is in identifying and validating the RBD mutant types emerging during the early transmission phase that have increased human ACE2 receptor binding affinity and infectivity. The RBD mutation analysis provides insights into SARS-CoV-2 evolution. The continuous surveillance of RBD mutations with increased human ACE2 affinity in human or other animals is important and necessary, particularly when the direct correlation between the virus variations and vaccine effectiveness is underdetermined during the sustained COVID-19 pandemic.


title: pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods

abstract:
SummaryVariability in datasets is not only the product of biological processes: they are also the product of technical biases. ComBat is one of the most widely used tool for correcting those technical biases, called batch effects, in microarray expression data.

In this technical note, we present a new Python implementation of ComBat. While the mathematical framework is strictly the same, we show here that our implementation: (i) has similar results in terms of batch effects correction; (ii) is as fast or faster than the R implementation of ComBat and; (iii) offers new tools for the bioinformatics community to participate in its development.

Availability and ImplementationpyComBat is implemented in the Python language and is available under GPL-3.0 (https://www.gnu.org/licenses/gpl-3.0.en.html) license at https://github.com/epigenelabs/pyComBat and https://pypi.org/project/combat/.

Contactakpeli@epigenelabs.com


title: Target deconvolution using in vitro evolution in haploid human cells

abstract: BackgroundIn vitro evolution and whole genome analysis has proven to be a powerful method for studying the mechanism of action of small molecules in many haploid microbes but has generally not been applied to human cell lines in part because their diploid state complicates the identification of variants that confer drug resistance. To determine if haploid human cell could be used in MOA studies, we evolved resistance to five different anticancer drugs (doxorubicin, gemcitabine, etoposide, topotecan, and paclitaxel) using a near-haploid cell line (HAP1) and then analyzed the genomes of the drug resistant clones, developing a bioinformatic pipeline that involved filtering for high frequency alleles predicted to change protein sequence, or alleles which appeared in the same gene for multiple independent selections with the same compound. Applying the filter to sequences from 28 drug resistant clones identified a set of 21 genes which was strongly enriched for known resistance genes or known drug targets (TOP1, TOP2A, DCK, WDR33, SLCO3A1). In addition, some lines carried structural variants that encompassed additional known resistance genes (ABCB1, WWOX and RRM1). Gene expression knockdown and knockout experiments of 10 validation targets showed a high degree of specificity and accuracy in our calls and demonstrates that the same drug resistance mechanisms found in diverse clinical samples can be evolved, discovered and studied in an isogenic background.


title: Polymorphic SNPs, short tandem repeats and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains

abstract: Mouse substrains are an invaluable model for understanding disease. We compared C57BL/6J, which is the most commonly used inbred mouse strain, with 8 C57BL/6 and 5 C57BL/10 closely related inbred substrains. Whole genome sequencing and RNA-sequencing analysis yielded 352,631 SNPs, 109,096 INDELs, 150,344 short tandem repeats (STRs), 3,425 structural variants (SVs) and 2,826 differentially expressed genes (DEGenes) among these 14 strains. 312,981 SNPs (89%) distinguished the B6 and B10 lineages. These SNPs were clustered into 28 short segments that are likely due to introgressed haplotypes rather than new mutations. Outside of these introgressed regions, we identified 53 SVs, protein-truncating SNPs and frameshifting INDELs that were associated with DEGenes. Our results can be used for both forward and reverse genetic approaches, and illustrate how introgression and mutational processes give rise to differences among these widely used inbred substrains.


title: Sox2 controls neural stem cell self-renewal through a Fos-centered gene regulatory network

abstract:
The Sox2 transcription factor is necessary for the long-term self-renewal of neural stem cells (NSC). Its mechanism of action is still poorly defined. To identify molecules regulated by Sox2, and acting in mouse NSC maintenance, we transduced, into Sox2-deleted NSC, genes whose expression is strongly downregulated following Sox2 loss (Fos, Jun, Egr2), individually or in combination. Fos alone rescued long-term proliferation, as shown by in vitro cell growth and clonal analysis. Further, pharmacological inhibition of the FOS/JUN AP1 complex binding to its targets, decreased cell proliferation and expression of the putative target Suppressor of cytokine signaling 3 (Socs3). Additionally, Fos requirement for efficient long-term proliferation was demonstrated by the reduction of NSC clones capable of long-term expansion following CRISPR/Cas9-mediated Fos inactivation. Previous work showed that the Socs3 gene is strongly downregulated following Sox2 deletion, and its reexpression by lentiviral transduction rescues long-term NSC proliferation. Fos appears to be an upstream regulator of Socs3, possibly together with Jun and Egr2; indeed, Sox2 reexpression in Sox2-deleted NSC progressively activates both Fos and Socs3 expression; in turn, Fos transduction activates Socs3 expression. Based on available SOX2 ChIPseq and ChIA-PET data, we propose a model whereby Sox2 is a direct activator of both Socs3 and Fos, as well as possibly Jun and Egr2; further, we provide direct evidence for FOS and JUN binding on Socs3 promoter, suggesting direct transcriptional regulation. These results provide the basis for developing a model of a network of interactions, regulating critical effectors of NSC proliferation and long-term maintenance.

Significance statementProliferation and maintenance of NSC are essential during normal brain development, and, postnatally, for the maintenance of hippocampal function and memory until advanced age. Little is known about the molecular mechanisms that maintain the critical aspects of NSC biology (quiescence and proliferation) in postnatal age. Our work provides a methodology, transduction of genes deregulated following Sox2 deletion, that allows to test many candidate genes for their ability to sustain NSC proliferation. In principle, this may have interesting implications for identifying targets for pharmacological manipulations.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/995621v2_ufig1.gif" ALT="Figure 1">
View larger version (49K):
org.highwire.dtl.DTLVardef@e9241forg.highwire.dtl.DTLVardef@4276deorg.highwire.dtl.DTLVardef@18a2058org.highwire.dtl.DTLVardef@151b2d2_HPS_FORMAT_FIGEXP  M_FIG C_FIG


title: Anaerobic sulfur oxidation underlies adaptation of a chemosynthetic symbiont to oxic-anoxic interfaces

abstract:
Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by monocultures of thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. However, nothing is known about how these variations affect their physiology or metabolism. Here, by applying omics, Raman microspectroscopy and stable isotope labelling, we investigated the effect of oxygen on Candidatus Thiosymbion oneisti. Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation were upregulated in oxic conditions, together with genes involved in organic carbon assimilation, polyhydroxyalkanoate (PHA) biosynthesis, nitrogen fixation and urea utilization. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand its deleterious effects, and the symbiont appeared to proliferate less. Based on its physiological response to oxygen, we propose that Ca. T. oneisti may exploit anaerobic sulfur oxidation coupled to denitrification to proliferate in anoxic sand. However, the ectosymbiont would still profit from the oxygen available in superficial sand, as the energy-efficient aerobic respiration would facilitate carbon and nitrogen assimilation by the ectosymbiont.

IMPORTANCEChemoautotrophic endosymbionts are famous for exploiting sulfur oxidization to feed marine organisms with fixed carbon. However, the physiology of thiotrophic bacteria thriving on the surface of animals (ectosymbionts) is less understood. One long standing hypothesis posits that attachment to animals that migrate between reduced and oxic environments would boost sulfur oxidation, as the ectosymbionts would alternatively access sulfide and oxygen, the most favorable electron acceptor. Here, we investigated the effect of oxygen on the physiology of Candidatus Thiosymbion oneisti, a Gammaproteobacterium which lives attached to marine nematodes inhabiting shallow water sand. Surprisingly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions. Furthermore, under anoxia, the ectosymbiont appeared to be less stressed and to proliferate more. We propose that animal-mediated access to oxygen, rather than enhancing sulfur oxidation, would facilitate assimilation of carbon and nitrogen by the ectosymbiont.


title: Brain network motifs are markers of loss and recovery of consciousness

abstract: Motifs are patterns of inter-connections between nodes of a network, and have been investigated as building blocks of directed networks. This study explored the re-organization of 3-node motifs during loss and recovery of consciousness. Nine healthy subjects underwent a 3-hour anesthetic protocol while 128-channel electroencephalography (EEG) was recorded. In the alpha (8-13 Hz) band, five-minute epochs of EEG were extracted for: baseline; induction; unconscious; 30-, 10- and 5-minutes pre-recovery of responsiveness; 30- and 180-minutes post-recovery of responsiveness. We constructed a functional brain network using the weighted and directed phase lag index, on which we calculated the frequency and topology of 3-node motifs. Three motifs (motifs 1, 2 and 5) were significantly present across participants and epochs, when compared to random networks (p<0.05). The topology of motifs 1 and 5 changed significantly between responsive and unresponsive epochs (p<0.01). Motif 1 was constituted by long-range chain-like connections, while motif 5 was constituted by short-range, loop-like connections. Our results suggest that anesthetic-induced unconsciousness is associated with a topological re-organization of network motifs. As motif topological re-organization may precede (motif 5) or accompany (motif 1) the return of responsiveness, motifs could contribute to the understanding of the neural correlates of consciousness.

category: neuroscience


title: Cortical Depth-Dependent Modeling of Visual Hemodynamic Responses

abstract: A physiologically based three-dimensional (3D) hemodynamic model is used to predict the experimentally observed blood oxygen level dependent (BOLD) responses versus the cortical depth induced by visual stimuli. Prior 2D approximations are relaxed in order to analyze 3D blood flow dynamics as a function of cortical depth. Comparison of the predictions with experimental data for typical stimuli demonstrates that the full 3D model matches at least as well as previous approaches while requiring significantly fewer assumptions and model parameters (e.g., there is no more need to define depth-specific parameter values for spatial spreading, peak amplitude, and hemodynamic velocity).


title: Causal evidence for a cerebellar role in prefrontal-hippocampal interaction in spatial working memory decision-making

abstract: Spatial working memory (SWM) is a cognitive skill supporting survival-relevant behaviors, such as optimizing foraging behavior by remembering recent routes and visited sites. It is known that SWM decision-making in rodents requires the medial prefrontal cortex (mPFC) and dorsal hippocampus. The decision process in SWM tasks carries a specific electrophysiological signature of a brief, decision-related increase in neuronal communication in the form of an increase in the coherence of neuronal theta oscillations (4-12 Hz) between the mPFC and dorsal hippocampus, a finding we replicated here during spontaneous exploration of a plus maze in freely moving mice. We further evaluated SWM decision-related coherence changes within frequency bands above theta. Decision-related coherence increases occurred in seven frequency bands between 4 and 200 Hz and decision-outcome related differences in coherence modulation occurred within the beta and gamma frequency bands and in higher frequency oscillations up to 130 Hz. With recent evidence that Purkinje cells in the cerebellar lobulus simplex (LS) represent information about the phase and phase differences of gamma oscillations in the mPFC and dorsal hippocampus, we hypothesized that LS might be involved in the modulation of mPFC-hippocampal gamma coherence. We show that optical stimulation of LS significantly impairs SWM performance and decision-related mPFC-dCA1 coherence modulation, providing causal evidence for an involvement of cerebellar LS in SWM decision making at the behavioral and neuronal level. Our findings suggest that the cerebellum might contribute to SWM decision-making by optimizing the decision-related modulation of mPFC-dCA1 coherence.


title: Temporal context actively shapes EEG signatures of time perception

abstract:
Our subjective perception of time is optimized to temporal regularities in the environment. This is illustrated by the central tendency effect: when estimating a range of intervals, short intervals are overestimated whereas long intervals are underestimated to reduce the overall estimation error. Most models of interval timing ascribe this effect to the weighting of the current interval with previous memory traces after the interval has been perceived. Alternatively, the perception of the duration could already be flexibly tuned to its temporal context. We investigated this hypothesis using an interval reproduction task in which human participants (both sexes) reproduced a shorter and longer interval range. As expected, reproductions were biased towards the subjective mean of each presented range. EEG analyses showed that temporal context indeed affected neural dynamics during the perception phase. Specifically, longer previous durations decreased CNV and P2 amplitude and increased beta power. In addition, multivariate pattern analysis showed that it is possible to decode context from the transient EEG signal quickly after both onset and offset of the perception phase. Together, these results suggest that temporal context creates dynamic expectations which actively affect the perception of duration.

Significance StatementThe subjective sense of duration does not arise in isolation, but is informed by previous experiences. This is demonstrated by abundant evidence showing that the production of duration estimates is biased towards previously experienced time intervals. However, it is yet unknown whether this temporal context actively affects perception or only asserts its influence in later, post-perceptual stages as proposed by most current formal models of this task. Using an interval reproduction task, we show that EEG signatures flexibly adapt to the temporal context during perceptual encoding. Furthermore, interval history can be decoded from the transient EEG signal even when the current duration was identical. Thus, our results demonstrate that context actively influences perception.