title: Does deterministic coexistence theory matter in a finite world?

abstract: Contemporary studies of species coexistence are underpinned by deterministic models that assume that competing species have continuous (i.e. non-integer) densities, live in infinitely large landscapes, and coexist over infinite time horizons. By contrast, in nature species are composed of discrete individuals subject to demographic stochasticity, and occur in habitats of finite size where extinctions occur in finite time. One consequence of these discrepancies is that metrics of species coexistence derived from deterministic theory may be unreliable predictors of the duration of species coexistence in nature. These coexistence metrics include invasion growth rates and niche and fitness differences, which are now commonly applied in theoretical and empirical studies of species coexistence. Here we test the efficacy of deterministic coexistence metrics on the duration of species coexistence in a finite world. We introduce new theoretical and computational methods to estimate coexistence times in stochastic counterparts of classic deterministic models of competition. Importantly, we parameterized this model using experimental field data for 90 pairwise combinations of 18 species of annual plants, allowing us to derive biologically-informed estimates of coexistence times for a natural system. Strikingly, we find that for species expected to deterministically coexist, habitat sizes containing only tens of individuals have predicted coexistence times of greater than 1, 000 years. We also find that invasion growth rates explain 60% of the variation in intrinsic coexistence times, reinforcing their general usefulness in studies of coexistence. However, only by integrating information on both invasion growth rates and species equilibrium population sizes could most (> 99%) of the variation in species coexistence times be explained. This integration is achieved with demographically uncoupled single species models solely determined by the invasion growth rates and equilibrium population sizes. Moreover, because of a complex relationship between niche overlap/fitness differences and equilibrium population sizes, increasing niche overlap and increasing fitness differences did not always result in decreasing coexistence times as deterministic theory would predict. Nevertheless, our results tend to support the informed use of deterministic theory for understanding the duration of species coexistence, while highlighting the need to incorporate information on species equilibrium population sizes in addition to invasion growth rates.


title: Splicing motifs are organized within global structural scaffold of a pre-mRNA

abstract: The specific recognition of splice signals at or near exon-intron junctions is not explained by their weak conservation and instead is postulated to require a multitude of features embedded in the pre-mRNA strand. We explored the possibility of three-dimensional structural scaffold of AdML - a model pre-mRNA substrate - guiding early spliceosomal components to the splice signal sequences. We find that mutations in the non-cognate splice signal sequences impede recruitment of early spliceosomal components due to disruption of the global structure of the pre-mRNA. We further find that the pre-mRNA segments potentially interacting with the early spliceosomal component U1 snRNP are distributed across the intron, that there is a spatial proximity of 5' and 3' splice sites within the pre-mRNA scaffold, and that an interplay exists between the structural scaffold and splicing regulatory elements in recruiting early spliceosomal components. These results suggest that early spliceosomal components can recognize a three-dimensional structural scaffold beyond the short splice signal sequences, and that in our model pre-mRNA, this scaffold is formed across the intron involving the major splice signals. This provides a conceptual basis to analyze the contribution of recognizable three-dimensional structural scaffolds to the splicing code across the mammalian transcriptome.

category: biochemistry


title: Discovery of a pre-mRNA structural scaffold as a contributor to the mammalian splicing code


title: Manipulation of the unfolded protein response: a pharmacological strategy against coronavirus infection

abstract:
Coronavirus infection induces the unfolded protein response (UPR), a cellular signalling pathway composed of three branches, triggered by unfolded proteins in the endoplasmic reticulum (ER) due to high ER load. We have used RNA sequencing and ribosome profiling to investigate holistically the transcriptional and translational response to cellular infection by murine hepatitis virus (MHV), often used as a model for the Betacoronavirus genus to which the recently emerged SARS-CoV-2 also belongs. We found the UPR to be amongst the most significantly up-regulated pathways in response to MHV infection. To confirm and extend these observations, we show experimentally the induction of all three branches of the UPR in both MHV- and SARS-CoV-2-infected cells. Over-expression of the SARS-CoV-2 ORF8 or S proteins alone is itself sufficient to induce the UPR. Remarkably, pharmacological inhibition of the UPR greatly reduced the replication of both MHV and SARS-CoV-2, revealing the importance of this pathway for successful coronavirus replication. This was particularly striking when both IRE1 and ATF6 branches of the UPR were inhibited, reducing SARS-CoV-2 virion release [~]1,000-fold. Together, these data highlight the UPR as a promising antiviral target to combat coronavirus infection.

Author SummarySARS-CoV-2 is the novel coronavirus responsible for the COVID-19 pandemic which has resulted in over 100 million cases since the end of 2019. Most people infected with the virus will experience mild to moderate respiratory illness and recover without any special treatment. However, older people, and those with underlying medical problems like chronic respiratory disease are more likely to develop a serious illness. So far, more than 2 million people have died of COVID-19. Unfortunately, there is no specific medication for this viral disease.

In order to produce viral proteins and to replicate their genetic information, all coronaviruses use a cellular structure known as the endoplasmic reticulum or ER. However, the massive production and modification of viral proteins stresses the ER and this activates a compensatory cellular response that tries to reduce ER protein levels. This is termed the unfolded protein response or UPR. We believe that coronaviruses take advantage of the activation of the UPR to enhance their replication.

The UPR is also activated in some types of cancer and neurodegenerative disorders and UPR inhibitor drugs have been developed to tackle these diseases. In this work, we have tested some of these compounds in human lung cells infected with SARS-CoV-2 and found that virus production was reduced 1000-fold in human lung cells.

category: microbiology


title: Dissecting indirect genetic effects from peers in laboratory mice

abstract:
The phenotype of one individual can be affected not only by the individuals own genotypes (direct genetic effects, DGE) but also by genotypes of interacting partners (indirect genetic effects, IGE). IGE have been detected using polygenic models in multiple species, including laboratory mice and humans. However, the underlying mechanisms remain largely unknown. Genome-wide association studies of IGE (igeGWAS) can point to IGE genes, but have not yet been applied to non-familial IGE arising from "peers" and affecting biomedical phenotypes. In addition, the extent to which igeGWAS will identify loci not identified by dgeGWAS remains an open question. Finally, findings from igeGWAS have not been confirmed by experimental manipulation.

We leveraged a dataset of 170 behavioural, physiological and morphological phenotypes measured in 1,812 genetically heterogeneous laboratory mice to study IGE arising between same-sex, adult, unrelated laboratory mice housed in the same cage. We developed methods for igeGWAS in this context and identified 24 significant IGE loci for 17 phenotypes (FDR < 10%). There was no overlap between IGE loci and DGE loci for the same phenotype, which was consistent with the moderate genetic correlations between DGE and IGE for the same phenotype estimated using polygenic models. Finally, we fine-mapped seven significant IGE loci to individual genes and confirmed, in an experiment with a knockout model, that Epha4 gives rise to IGE on stress-coping strategy and wound healing.

Our results demonstrate the potential for igeGWAS to identify IGE genes and shed some light into the mechanisms of peer influence.

category: genetics


title: Spatial distribution of private gene mutations in clear cell renal cell carcinoma

abstract: Intra-tumour heterogeneity is the molecular hallmark of renal cancer, and the molecular tumour composition determines the treatment outcome of renal cancer patients. In renal cancer tumourigenesis, in general, different tumour clones evolve over time. We analysed intra-tumour heterogeneity and subclonal mutation patterns in 178 tumour samples obtained from 89 clear cell renal cell carcinoma patients. In an initial discovery phase, whole-exome and transcriptome sequencing data from paired tumour biopsies from 16 ccRCC patients were used to design a gene panel for follow-up analysis. In this second phase, 826 selected genes were targeted at deep coverage in an extended cohort of 89 patients for a detailed analysis of tumour heterogeneity. On average, we found 22 mutations per patient. Pairwise comparison of the two biopsies from the same tumour revealed that on average 62% of the mutations in a patient were detected in one of the two samples. In addition to commonly mutated genes (VHL, PBRM1, SETD2 and BAP1), frequent subclonal mutations with low variant allele frequency (<10%) were observed in TP53 and in mucin coding genes MUC6, MUC16, and MUC3A. Of the 89 ccRCC tumours, 87 (~98%) harboured private mutations, occurring in only one of the paired tumour samples. Clonally exclusive pathway pairs were identified using the WES data set from 16 ccRCC patients. Our findings imply that shared and private mutations significantly contribute to the complexity of differential gene expression and pathway interaction, and might explain clonal evolution of different molecular renal cancer subgroups. Multi-regional sequencing is central for the identification of subclones within ccRCC.

category: cancer biology


title: DsbA is a redox-switchable mechanical chaperone

abstract: DsbA is a ubiquitous bacterial oxidoreductase that associates with substrates during and after translocation, yet its involvement in protein folding and translocation remains an open question. Here we demonstrate a redox-controlled chaperone activity of DsbA, on both cysteine-containing and cysteine-free substrate, using a magnetic tweezers-based single molecule force spectroscopy that enables independent measurements of oxidoreductase activity and chaperone behavior. Interestingly we found, this chaperone activity is tuned by the oxidation state of DsbA; oxidized DsbA is a strong promoter of folding, but the effect is weakened by reduction of the catalytic CXXC motif. We further localize the chaperone binding site of DsbA using a seven-residue peptide which effectively blocks the chaperone activity. We calculated that DsbA assisted folding of proteins in the periplasm generates enough mechanical work to decrease the ATP consumption needed for periplasmic translocation by up to 33%. In turn, pharmacologic inhibition of this chaperone activity may open up a new class of anti-virulence agents.

category: biophysics


title: A constraints-based theory of senescence: imbalance of epigenetic and non-epigenetic information in histone crosstalk

abstract: Cellular aging has been progressively elucidated by science. However, the fundamental cause of senescence--i.e., why organisms age at the multicellular-individual level--remains unclear. A recent theory of individuated multicellularity describes the emergence and growth of crucial information content for cell differentiation. This information is mostly conveyed in the non-epigenetic (i.e., transcription uncorrelated) histone crosstalk near transcription start sites. According to this theory, the non-epigenetic content emerges and grows at the expense of the information capacity for epigenetic content. If this "reassignment" of information capacity continues after adulthood, it may explain the senescence phenomenon. Here, I present a novel, falsifiable theory describing an uninterrupted growth of capacity for non-epigenetic information at the expense of that for epigenetic information not only during ontogeny but also throughout adulthood. As a byproduct, this continuous "reassignment" of capacity effectively creates an information imbalance in histone crosstalk, which in turn overregulates transcriptional levels. This overregulation is to be understood as transcriptional levels becoming more and more accurate but also less and less precise with respect to the needs of the multicellular individual--up to the point of dysfunctionality. This epigenetic/non-epigenetic information imbalance is proposed to be the primary reason why individuated multicellular organisms senesce.

category: developmental biology


title: A constraints-based theory of the primary cause of senescence: imbalance of epigenetic and non-epigenetic information in histone crosstalk


title: Cargo-Loading of Misfolded Proteins into Extracellular Vesicles: The CSPα-EV Export Pathway

abstract: Extracellular vesicles (EVs) are secreted vesicles of diverse size and cargo that are implicated in the cell-to-cell transmission of disease-causing-proteins in several neurodegenerative diseases. Mutant huntingtin, the disease-causing entity in Huntingtons disease, has an expanded polyglutamine track at the N terminus that causes the protein to misfold and form toxic intracellular aggregates. In Huntingtons disease, mutant huntingtin aggregates are transferred between cells by an unknown route. We have previously identified a cellular pathway that is responsible for the export of mutant huntingtin via extracellular vesicles, given the heterogeneity of EVs, here we examine the specific EVs involved. In this work we expressed a form of polyglutamine expanded huntingtin (GFP-tagged 72Qhuntingtinexon1) in cells to assess the EVs involved in cellular export. We demonstrate that the molecular chaperone, cysteine string protein (CSP; DnaJC5), mediates export of disease-causing-polyglutamine-expanded huntingtin cargo via two distinct vesicle populations of 180-240nm and 15-30m. In doing so, our data links the molecular chaperone, CSP, and the packaging of pathogenic misfolded huntingtin into two separate extracellular vesicles pathways.

category: neuroscience


title: Structurally Constrained Effective Brain Connectivity

abstract:
The relationship between structure and function is of interest in many research fields involving the study of complex biological processes. In neuroscience in particular, the fusion of structural and functional data can help understanding the underlying principles of the operational networks in the brain. To address this issue, this paper proposes a constrained autoregressive model leading to a representation of "effective" connectivity that can be used to better understand how the structure modulates the function. Or simply, it can be used to find novel biomarkers characterizing groups of subjects. In practice, an initial structural connectivity representation is re-weighted to explain the functional co-activations. This is obtained by minimizing the reconstruction error of an autoregressive model constrained by the structural connectivity prior. The model has been designed to also include indirect connections, allowing to split direct and indirect components in the functional connectivity, and it can be used with raw and deconvoluted BOLD signal.

The derived representation of dependencies was compared to the well known dynamic causal model, giving results closer to known ground-truth. Further evaluation of the proposed effective network was performed on two typical tasks. In a first experiment the direct functional dependencies were tested on a community detection problem, where the brain was partitioned using the effective networks across multiple subjects. In a second experiment the model was validated in a case-control task, which aimed at differentiating healthy subjects from individuals with autism spectrum disorder. Results showed that using effective connectivity leads to clusters better describing the functional interactions in the community detection task, while maintaining the original structural organization, and obtaining a better discrimination in the case-control classification task.

HighlightsO_LIA method to combine structural and functional connectivity by using autoregressive model is proposed.
C_LIO_LIThe autoregressive model is constrained by structural connectivity defining coefficients for Granger causality.
C_LIO_LIThe usefulness of the generated effective connections is tested on simulations, ground-truth default mode network experiments, a classification and clustering task.
C_LIO_LIThe method can be used for direct and indirect connections, and with raw and deconvoluted BOLD signal.
C_LI


title: Characterization of Animal Movement Patterns using Information Theory: a Primer

abstract:
Understanding the movement patterns of animals across different spatio-temporal scales, conditions, habitats and contexts is becoming increasingly important for addressing a series of questions in animal behaviour studies, such as mapping migration routes, evaluating resource use, modelling epidemic spreading in a population, developing strategies for animal conservation as well as understanding several emerging patterns related to feeding, growth and reproduction. In recent times, information theory has been successfully applied in several fields of science, in particular for understanding the dynamics of complex systems and characterizing adaptive social systems, such as dynamics of entities as individuals and as part of groups.

In this paper, we describe a series of non-parametric information-theoretic measures that can be used to derive new insights about animal behaviour with a specific focus on movement patterns, namely Shannon entropy, Mutual information, Kullback-Leibler divergence and Kolmogorov complexity. In particular, we believe that the metrics presented in this paper can be used to formulate new hypotheses that can be verified potentially through a set of different observations and be complementary to existing techniques. We show how these measures can be used to characterize the movement patterns of several animals across different habitats and scales. Specifically, we show the effectiveness in using Shannon entropy to characterize the movement of sheep with Batten disease, mutual information to measure association in pigeons, Kullback-Leibler divergence to study the flights of Turkey vulture, and Kolmogorov complexity to find similarities in the movement patterns of animals across different scales and habitats. Finally, we discuss the limitations of these methods and we outline the challenges in this research area.

category: ecology


title: Sperm morphology differences associated with pig fertility

abstract: Artificial insemination is routine in commercial pig breeding, and as such, the use of high-quality semen samples is imperative. Here, we have developed a novel, semi-automated, software-based approach to assess pig sperm nucleus morphology in greater detail than was previously possible. This analysis identified subtle morphological differences between samples assessed by the industry as normal and those assessed as abnormal. 50 normal and 50 abnormal samples that were initially categorised using manual assessment to industry standards, were investigated using this new method, with at least 200 fixed stained sperm heads analysed in each case. Differences in sperm nuclear morphology were observed between normal and abnormal samples; specifically, normal samples were associated with higher mean nuclear area, a consequence of a greater head width and a lower variability between sperm heads. This novel, unbiased and fast analysis method demonstrates a significant difference in sperm head morphology between normal and abnormal pig sperm and has the potential to be further developed to be used as a tool for sperm morphology assessment both in the pig breeding industry and potentially in human assisted reproductive technologies.


title: Direct programming of human mammary self-organised organoids by miR-106a-3p

abstract: Organoids development relies on the self-organizing properties of adult stem cells to create structures which recapitulate the architecture, functionality, and genetic signature observed in original tissues. Little is known about of the exact nature of the intrinsic cell properties at the origin of organoid generation, and of the signaling pathways governing their differentiation. Herein, we carried out a functional microRNA screen to identify miRNAs at the origin of organoid generation from human epithelial cell culture. We uncover miR-106a-3p that initiates and promotes organoids. This miRNA acts as a master inducer of the expression of the three core pluripotency transcription factors (NANOG, OCT4 and SOX2) through the regulation of a set of 10 genes, and thus strengthening the reprogramming and cell differentiation of human epithelial cells into organoids. These data demonstrate that organoids can be directly generated from human epithelial cells by only one miRNA: miR-106a-3p. Hence, we appear to have identified a new determinant of organoid identity, which plays a role in reprogramming, cell differentiation and tissue engineering.

category: cell biology


title: Polymer brush bilayers at thermal equilibrium: A density functional theory approach

abstract:
By means of the density functional theory (DFT) framework, the longstanding problem of the polymer brush bilayers at thermal equilibrium is studied. The calculated density profiles reveal that the brushes balance compression and interpenetration when they come into contact. The equation of state of the polymer brush bilayers is obtained and it represents scaling of the pressure with molecular parameters and distance between substrates.

SIGNIFICANCEThe results of this study may shed light in our understanding of some severe Musloskeletal diseases which degrade the synovium. The significance of this study lays on the fact that the molecular structure is investigated through fundamental physical laws. So, this study bridges between theoretical biological physics and medicine.


title: Empirical single-cell tracking and cell-fate simulation reveal dual roles of p53 in tumor suppression

abstract: The tumor suppressor p53 regulates various stress responses via increasing its cellular levels. The lowest p53 levels occur in unstressed cells; however, the functions of these low levels remains unclear. To investigate the functions, we used empirical single-cell tracking of p53-expressing (Control) cells and cells in which p53 expression was silenced by RNA interference (p53 RNAi). Here we show that p53 RNAi cells underwent more frequent cell death and cell fusion, which further induced multipolar cell division to generate aneuploid progeny. Those results suggest that the low levels of p53 in unstressed cells indeed have a role in suppressing the induction of cell death and the formation of aneuploid cells. We further investigated the impact of p53 silencing by developing an algorithm to simulate the fates of individual cells. Simulation of the fate of aneuploid cells revealed that these cells could propagate to create an aneuploid cell population. In addition, the simulation also revealed that more frequent induction of cell death in p53 RNAi cells under unstressed conditions conferred a growth disadvantage compared with Control cells, resulting in faster expansion of Control cells compared with p53 RNAi cells, leading to Control cells predominating in mixed cell populations. In contrast, growth of Control cells, but not p53 RNAi cells, was suppressed when the damage response was induced, allowing p53 RNAi cells to gain a growth advantage over Control cells. These results suggest that, although p53 could suppress the formation of aneuploid cells, which could have a role in tumorigenesis, it could also allow the expansion of cells lacking p53 expression when the damage response is induced. p53 may thus play a role in both the suppression and the promotion of malignant cell formation during tumorigenesis.


title: Identification and design of vinyl sulfone inhibitors against Cryptopain1-a cysteine protease from cryptosporidiosis-causing Cryptosporidium parvum

abstract: Cryptosporidiosis, a disease marked by diarrhea in adults and stunted growth in children, is associated with the unicellular protozoan pathogen Cryptosporidium; often the species parvum. Cryptopain-1, a cysteine protease characterized in the genome of Cryptosporidium parvum, had been earlier shown to be inhibited by a vinyl sulfone compound called K11777 (or K-777). Cysteine proteases have long been established as valid drug targets, which can be covalently and selectively inhibited by vinyl sulfones. This computational study was initiated to identify purchasable vinyl sulfone compounds, which could possibly inhibit cryptopain-1 with higher efficacy than K11777. Docking simulations screened a number of such possibly better inhibitors. The work was furthered to probe the enzymatic pocket of cryptopain-1, through in-silico mutations, to derive a map of receptor-ligand interactions in the docked complexes. The idea was to provide crucial clues to aid the design of inhibitors, which would be able to bind the protease well by making favorable interactions with important residues of the enzyme. The analyses dictated placement of ligands towards the front of the enzymatic cleft, and disfavored interactions deep within. The S1 and S2 subsites of the enzyme preferred to remain occupied by polar ligand subgroups. Reasonably distanced ring systems and polar backbones of ligands were desired across the cleft. Large as well as inflexible subgroups were not tolerated. Double ringed systems such as substituted napthalene, especially in S1, were exceptions though. The S2 subsite, which is typically a specificity determinant in papain (C1) family cysteine proteases such as cathepsin L-like cryptopain-1, can possibly accommodate polar and hydrophobic ligand subgroups alike.

category: bioinformatics


title: Spatial RNA sequencing identifies robust markers of vulnerable and resistant human midbrain dopamine neurons and their expression in Parkinson's Disease

abstract: Defining transcriptional profiles of substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) dopamine neurons is critical to understanding their differential vulnerability in Parkinsons Disease (PD). Here, we determine transcriptomes of human SNc and VTA dopamine neurons using LCM-seq on a large sample cohort. We apply a bootstrapping strategy as sample input to DESeq2 and identify 33 stably differentially expressed genes (DEGs) between these two subpopulations. We also compute a minimal sample size for identification of stable DEGs, which highlights why previous reported profiles from small sample sizes display extensive variability. Network analysis reveal gene interactions unique to each subpopulation and highlight differences in regulation of mitochondrial stability, apoptosis, neuronal survival, cytoskeleton regulation, extracellular matrix modulation and well as synapse integrity, which could explain the relative resilience of VTA dopamine neurons. Analysis of PD tissues showed that while identified stable DEGs can distinguish the subpopulations also in disease, the SNc markers SLIT1 and ATP2A3 were downregulated and thus appears to be biomarkers of disease. In summary, our study identifies human SNc and VTA marker profiles, which will be instrumental for studies aiming to modulate dopamine neuron resilience and to validate cell identity of stem cell-derived dopamine neurons.


title: Dissociating Language and Thought in Human Reasoning

abstract: What is the relationship between natural language and complex thought? In the context of complex reasoning, there are two main views. Under the first, language is central to the syntax-like combinatorial operations necessary for complex reasoning. Under the second, these operations are independent of the mechanisms of natural language. We used noninvasive neuromodulation, in the form of continuous theta burst stimulation, to transiently inhibit Brocas area, a region associated in prior research with parsing the syntactic relations of natural language, and dorsomesial frontal cortex, a region previously described as core for logical reasoning. The dissociative hypothesis of language and deductive reasoning predicts an interaction between stimulated areas and tested functions, which we observed. Transient inhibition of Brocas area significantly disrupted linguistic processing without affecting deductive reasoning. The reverse pattern was seen for transient inhibition of dorsomesial frontal cortex, albeit not reaching significance. These results are evidence for the independence of abstract complex reasoning from natural language in the adult brain.


title: Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in Drosophila

abstract: To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched in large chromosomal inversions and we find a broad concordance between seasonal and spatial allele frequency change. The direction of allele frequency change at seasonally variable polymorphisms can be predicted by weather conditions in the weeks prior to sampling, linking the environment and the genomic response to selection. Our results suggest that fluctuating selection is an important evolutionary force affecting patterns of genetic variation in Drosophila.

category: evolutionary biology


title: 3D Reconstruction of Bird Flight Using a Single Video Camera

abstract: Video cameras are finding increasing use in the study and analysis of bird flight over short ranges. However, reconstruction of flight trajectories in three dimensions typically requires the use of multiple cameras and elaborate calibration procedures. We present an alternative approach that uses a single video camera and a simple calibration procedure for the reconstruction of such trajectories. The technique combines prior knowledge of the wingspan of the bird with a camera calibration procedure that needs to be used only once in the lifetime of the system. The system delivers the exact 3D coordinates of the position of the bird at the time of every full wing extension and uses interpolated height estimates to compute the 3D positions of the bird in the video frames between successive wing extensions. The system is inexpensive, compact and portable, and can be easily deployed in the laboratory as well as the field.

category: animal behavior and cognition


title: 3D Reconstruction of Bird Flight Trajectories Using a Single Video Camera


title: The interspecific fungal hybrid Verticillium longisporum displays sub-genome-specific gene expression

abstract:
Hybridization is an important evolutionary mechanism that can enable organisms to adapt to environmental challenges. It has previously been shown that the fungal allodiploid species Verticillium longisporum, causal agent of Verticillium stem striping in rape seed, has originated from at least three independent hybridization events between two haploid Verticillium species. To reveal the impact of genome duplication as a consequence of the hybridization, we studied the genome and transcriptome dynamics upon two independent V. longisporum hybridization events, represented by the hybrid lineages "A1/D1" and "A1/D3". We show that the V. longisporum genomes are characterized by extensive chromosomal rearrangements, including between parental chromosomal sets. V. longisporum hybrids display signs of evolutionary dynamics that are typically associated with the aftermath of allodiploidization, such as haploidization and a more relaxed gene evolution. Expression patterns of the two sub-genomes within the two hybrid lineages are more similar than those of the shared A1 parent between the two lineages, showing that expression patterns of the parental genomes homogenized within a lineage. However, as genes that display differential parental expression in planta do not typically display the same pattern in vitro, we conclude that sub-genome-specific responses occur in both lineages. Overall, our study uncovers the genomic and transcriptomic plasticity during evolution of the filamentous fungal hybrid V. longisporum and illustrate its adaptive potential.

ImportanceVerticillium is a genus of plant-associated fungi that include a handful of plant pathogens that collectively affect a wide range of hosts. On several occasions, haploid Verticillium species hybridized into the stable allodiploid species Verticillium longisporum, which is, in contrast to haploid Verticillium species, a Brassicaceae specialist. Here, we studied the evolutionary genome and transcriptome dynamics of V. longisporum and the impact of the hybridization. V. longisporum genomes display a mosaic structure due do genomic rearrangements between the parental chromosome sets. Similar to other allopolyploid hybrids, V. longisporum displays an ongoing loss of heterozygosity and a more relaxed gene evolution. Also, differential parental gene expression is observed, with an enrichment for genes that encode secreted proteins. Intriguingly, the majority of these genes displays sub-genome-specific responses under differential growth conditions. In conclusion, hybridization has incited the genomic and transcriptomic plasticity that enables adaptation to environmental changes in a parental allele-specific fashion.


title: Ecological Network assembly: how the regional meta web influence local food webs

abstract:
O_LILocal food webs result from a sequence of colonisations and extinctions by species from the regional pool or metaweb, i.e., the assembly process. Assembly is theorised to be a selective process: whether or not certain species or network structures can persist is partly determined by local processes including habitat filtering and dynamical constraints. Consequently, local food web structure should reflect these processes.
C_LIO_LIThe goal of this study was to test evidence for these selective processes by comparing the structural properties of real food webs to the expected distribution given the metaweb. We were particularly interested in ecological dynamics; if the network properties commonly associated with dynamical stability are indeed the result of stability constraints, then they should deviate from expectation in the direction predicted by theory.
C_LIO_LITo create a null expectation, we used the novel approach of randomly assembling model webs by drawing species and interactions from the empirical metaweb. The assembly model permitted colonisation and extinction, and required a consumer species to have at least one prey, but had no habitat type nor population dynamical constraints. Three data sets were used: (1) the marine Antarctic metaweb, with 2 local food-webs; (2) the 50 lakes of the Adirondacks; and (3) the arthropod community from Florida Keys classic defaunation experiment.
C_LIO_LIContrary to our expectations, we found that there were almost no differences between empirical webs and those resulting from the null assembly model. Few empirical food webs showed significant differences with network properties, motif representations and topological roles. Network properties associated with stability did not deviate from expectation in the direction predicted by theory.
C_LIO_LIOur results suggest that -- for the commonly used metrics we considered -- local food web structure is not strongly influenced by dynamical nor habitat restrictions. Instead, the structure is inherited from the metaweb. This suggests that the network properties typically attributed as causes or consequences of ecological stability are instead a by-product of the assembly process (i.e., spandrels), and may potentially be too coarse to detect the true signal of dynamical constraint.
C_LI


title: Network Reconstruction from Perturbation Time Course Data

abstract: Networks underlie much of biology from subcellular to ecological scales. Yet, understanding what experimental data are needed and how to use them for unambiguously identifying the structure of even small networks remains a broad challenge. Here, we integrate a dynamic least squares framework into established modular response analysis (DL-MRA), that specifies sufficient experimental perturbation time course data to robustly infer arbitrary two and three node networks. DL-MRA considers important network properties that current methods often struggle to capture: (i) edge sign and directionality; (ii) cycles with feedback or feedforward loops including self-regulation; (iii) dynamic network behavior; (iv) edges external to the network; and (v) robust performance with experimental noise. We evaluate the performance of and the extent to which the approach applies to cell state transition networks, intracellular signaling networks, and gene regulatory networks. Although signaling networks are often an application of network reconstruction methods, the results suggest that only under quite restricted conditions can they be robustly inferred. For gene regulatory networks, the results suggest that incomplete knockdown is often more informative than full knockout perturbation, which may change experimental strategies for gene regulatory network reconstruction. Overall, the results give a rational basis to experimental data requirements for network reconstruction and can be applied to any such problem where perturbation time course experiments are possible.

category: systems biology


title: Network Inference from Perturbation Time Course Data


title: Rapid adaptation of endocytosis, exocytosis and eisosomes after an acute increase in membrane tension in yeast cells

abstract: During clathrin-mediated endocytosis in eukaryotes, actin assembly is required to overcome large membrane tension and turgor pressure. However, the molecular mechanisms by which the actin machinery adapts to varying membrane tension remain unknown. In addition, how cells reduce their membrane tension when they are challenged by hypotonic shocks remains unclear. We used quantitative microscopy to demonstrate that cells rapidly reduce their membrane tension using three parallel mechanisms. In addition to using their cell wall for mechanical protection, yeast cells disassemble eisosomes to buffer moderate changes in membrane tension on a minute time scale. Meanwhile, a temporary reduction of the rate of endocytosis for 2 to 6 minutes, and an increase in the rate of exocytosis for at least 5 minutes allow cells to add large pools of membrane to the plasma membrane. We built on these results to submit the cells to abrupt increases in membrane tension and determine that the endocytic actin machinery of fission yeast cells rapidly adapts to perform clathrin-mediated endocytosis. Our study sheds light on the tight connection between membrane tension regulation, endocytosis and exocytosis.


title: Evolutionary forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens

abstract:
Experimental evolution with microbes is often highly repeatable under identical conditions, suggesting the possibility to predict short-term evolution. However, it is not clear to what degree evolutionary forecasts can be extended to related species in non-identical environments, which would allow testing of general predictive models and fundamental biological assumptions. To develop an extended model system for evolutionary forecasting, we used previous data and models of the genotype-to-phenotype map from the wrinkly spreader system in Pseudomonas fluorescens SBW25 to make predictions of evolutionary outcomes on different biological levels for Pseudomonas protegens Pf-5. In addition to sequence divergence (78% amino acid and 81% nucleotide identity) for the genes targeted by mutations, these species also differ in the inability of Pf-5 to make cellulose, which is the main structural basis for the adaptive phenotype in SBW25. The experimental conditions were also changed compared to the SBW25 system to test the robustness of forecasts to environmental variation. Forty-three mutants with increased ability to colonize the air-liquid interface were isolated, and the majority had reduced motility and was partly dependent on the pel exopolysaccharide as a structural component. Most (38/43) mutations are expected to disrupt negative regulation of the same three diguanylate cyclases as in SBW25, with a smaller number of mutations in promoter regions, including that of an uncharacterized polysaccharide operon. A mathematical model developed for SBW25 predicted the order of the three main pathways and the genes targeted by mutations, but differences in fitness between mutants and mutational biases also appear to influence outcomes. Mutated regions in proteins could be predicted in most cases (16/22), but parallelism at the nucleotide level was low and mutational hot spots were not conserved. This study demonstrates the potential of short-term evolutionary forecasting in experimental populations and provides testable predictions for evolutionary outcomes in other Pseudomonas species.

Author SummaryBiological evolution is often repeatable in the short-term suggesting the possibility of forecasting and controlling evolutionary outcomes. In addition to its fundamental importance for biology, evolutionary processes are at the core of several major societal problems, including infectious diseases, cancer and adaptation to climate change. Experimental evolution allows study of evolutionary processes in real time and seems like an ideal way to test the predictability of evolution and our ability to make forecasts. However, lack of model systems where forecasts can be extended to other species evolving under different conditions has prevented studies that first predict evolutionary outcomes followed by direct testing. We showed that a well-characterized bacterial experimental evolution system, based on biofilm formation by Pseudomonas fluorescens at the surface of static growth tubes, can be extended to the related species Pseudomonas protegens. We tested evolutionary forecasts experimentally and showed that mutations mainly appear in the predicted genes resulting in similar phenotypes. We also identified factors that we cannot yet predict, such as variation in mutation rates and differences in fitness. Finally, we make forecasts for other Pseudomonas species to be tested in future experiments.


title: KChIP4a selectively controls mesolimbic dopamine neuron inhibitory integration and learning from negative prediction errors

abstract:
Midbrain dopamine (DA) neurons are essential for multiple behaviors. DA neurons that project to different regions also have unique biophysical properties, and it is thought that this diversity reflects specializations to particular computational functions. If this is true, there should be specific genetic determinants of this heterogeneity whose manipulation would lead to circumscribed impacts on behavior. We test this general hypothesis by homing in on one particular mechanism using a new transgenic model and a combination of molecular, electrophysiological, computational, and behavioral approaches. We demonstrate that KChIP4a, a singular Kv4 {beta}-subunit splice variant, determines the long hyperpolarization-rebound delays observed in nucleus accumbens core-projecting DA neurons, that this biophysical switch controls the efficacy of inhibitory inputs to pause firing and, congruently, selectively regulates learning from negative prediction errors. Our results reveal a highly specialized gene-to-behavior mechanistic chain within the DA system, illuminating how cellular diversity shapes information processing in this key neuronal population.

Graphical abstract

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title: A pragmatic approach to make theoretical syntheses in ecology

abstract: Theoretical syntheses have the role of describing and guiding knowledge generation, and are usually done by enunciating the conceptual bases that guide research in a given field. In fields that develop axiomatically, the conceptual basis can be easily identified in the set of axioms guiding model building. However, ecology does not develop axiomatically but rather pragmatically, i.e., ecologists do not build models based on a predefined set of assumptions (axioms). They rather resort to any information that seems useful to learn about ecological phenomena. Therefore, a theoretical synthesis in ecology cannot rely on the enunciation of axioms; instead, it requires identifying what information and knowledge ecologists use (i.e., what they decide is useful to learn). Here we present an approach for producing theoretical syntheses based on the information/knowledge most frequently used to learn about the world. The approach consists of (i) defining a phenomenon of interest; (ii) defining a collective of scientists studying the phenomenon; (iii) surveying the scientific studies about the phenomenon published by this collective; (iv) identifying the most relevant publications used in these studies; (v) identifying how the studies refer to the most relevant publications; (vi) synthesizing what is being used by this collective to learn about the phenomenon. We implemented the approach in a case study on the phenomenon of ecological succession, defining the collective as the scientists currently studying succession. We identified three propositions that synthesize the views of the defined collective about succession. The theoretical synthesis revealed that there is no clear division between "classical" and "contemporary" succession models, and that neutral models are being used to explain successional patterns alongside with models based on niche assumptions.By implementing the pragmatic approach in a case study, we show that it can be successfully used to produce syntheses describing the conceptual bases of a field, which have the potential to guide knowledge generation. As such, these syntheses fulfil the roles ascribed to scientific theories in the epistemological literature.


title: Microbial adaptation to venom is common in snakes and spiders

abstract:
Animal venoms are considered sterile sources of antimicrobial compounds with strong membrane disrupting activity against multi-drug resistant bacteria. However, bite wound infections are common in developing nations. Investigating the oral and venom microbiome of five snake and two spider species, we evidence viable microorganisms potentially unique to venom for black-necked spitting cobras (Naja nigricollis). Among these are two venom-resistant novel sequence types of Enterococcus faecalis; the genome sequence data of these isolates feature an additional 45 genes, nearly half of which improve membrane integrity. Our findings challenge the dogma of venom sterility and indicate an increased primary infection risk in the clinical management of venomous animal bite wounds.

One Sentence SummaryIndependent bacterial colonization of cobra venom drives acquisition of genes antagonistic to venom antimicrobial peptides.


title: The Goldilocks Effect: Female geladas in mid-sized groups have higher fitness

abstract: The cost-benefit ratio of group-living is thought to vary with group size: individuals in "optimally-sized" groups should have higher fitness than individuals in groups that are either too large or too small. However, the relationship between group size and individual fitness has been difficult to establish for long-lived species where the number of groups studied is typically quite low. Here we present evidence for optimal group size that maximizes female fitness in a population of geladas (Theropithecus gelada). Drawing on 14 years of demographic data, we found that females in small groups experienced the highest death rates, while females in mid-sized units exhibited the highest reproductive performance. This group-size effect on female reproductive performance was largely explained by variation in infant mortality (and, in particular, by infanticide from immigrant males) but not by variation in reproductive rates. Taken together, females in mid-sized units are projected to attain optimal fitness due to conspecific infanticide and, potentially, predation. Our findings provide insight into how and why group size shapes fitness in long-lived species.


title: Joint inference of species histories and gene flow

abstract: When populations become isolated, members of these populations can diverge genetically over time. This leads to genetic differences between these populations that increase over time if the isolation persists. This process can be counteracted by gene flow, i.e. when genes are exchanged between populations. In order to study the speciation processes when gene flow is present, isolation-with-migration methods have been developed. These methods typically assume that the ranked topology of the species history is already known. However, this is often not the case and the species tree is therefore of interest itself. For the inference of species trees, it is in turn often necessary to assume that there is no gene flow between co-existing species. This assumption, however, can lead to wrongly inferred speciation times and species tree topologies. We here introduce a new method that allows inference of the species tree while explicitly modelling the flow of genes between coexisting species. By using Markov chain Monte Carlo sampling, we co-infer the species tree alongside evolutionary parameters of interest. By using simulations, we show that our newly introduced approach is able to reliably infer the species trees and parameters of the isolation-with-migration model from genetic sequence data. We then use this approach to infer the species history of the mosquitoes from the Anopheles gambiae species complex. Accounting for gene flow when inferring the species history suggests a slightly different speciation order and gene flow than previously suggested.


title: 5' Modifications Improve Potency and Efficacy of DNA Donors for Precision Genome Editing

abstract: Nuclease-directed genome editing is a powerful tool for investigating physiology and has great promise as a therapeutic approach to correct mutations that cause disease. In its most precise form, genome editing can use cellular homology-directed repair (HDR) pathways to insert information from an exogenously supplied DNA repair template (donor) directly into a targeted genomic location. Unfortunately, particularly for long insertions, toxicity and delivery considerations associated with repair template DNA can limit HDR efficacy. Here, we explore chemical modifications to both double-stranded and single-stranded DNA-repair templates. We describe 5'-terminal modifications, including in its simplest form the incorporation of triethylene glycol (TEG) moieties, that consistently increase the frequency of precision editing in the germlines of three animal models (Caenorhabditis elegans, zebrafish, mice) and in cultured human cells.

category: molecular biology


title: Structure-aware M. tuberculosis functional annotation uncloaks resistance, metabolic, and virulence genes

abstract:
Accurate and timely functional genome annotation is essential for translating basic pathogen research into clinically impactful advances. Here, through literature curation and structure-function inference, we systematically update the functional genome annotation of Mycobacterium tuberculosis virulent type strain H37Rv. First, we systematically curated annotations for 589 genes from 662 publications, including 282 gene products absent from leading databases. Second, we modeled 1,711 under-annotated proteins and developed a semi-automated pipeline that captured shared function between 400 protein models and structural matches of known function on protein data bank, including drug efflux proteins, metabolic enzymes, and virulence factors. In aggregate, these structure- and literature-derived annotations update 940/1,725 under-annotated H37Rv genes and generate hundreds of functional hypotheses. Retrospectively applying the annotation to a recent whole-genome transposon mutant screen provided missing function for 48% (13/27) of under-annotated genes altering antibiotic efficacy and 33% (23/69) required for persistence during mouse TB infection. Prospective application of the protein models enabled us to functionally interpret novel laboratory generated Pyrazinamide-resistant (PZA) mutants of unknown function, which implicated the emerging Coenzyme A depletion model of PZA action in the mutants PZA resistance. Our findings demonstrate the functional insight gained by integrating structural modeling and systematic literature curation, even for widely studied microorganisms. Functional annotations and protein structure models are available at https://tuberculosis.sdsu.edu/H37Rv in human- and machine-readable formats.

IMPORTANCEMycobacterium tuberculosis, the primary causative agent of tuberculosis, kills more humans than any other infectious bacteria. Yet 40% of its genome is functionally uncharacterized, leaving much about the genetic basis of its resistance to antibiotics, capacity to withstand host immunity, and basic metabolism yet undiscovered. Irregular literature curation for functional annotation contributes to this gap. We systematically curated functions from literature and structural similarity for over half of poorly characterized genes, expanding the functionally annotated Mycobacterium tuberculosis proteome. Applying this updated annotation to recent in vivo functional screens added functional information to dozens of clinically pertinent proteins described as having unknown function. Integrating the annotations with a prospective functional screen identified new mutants resistant to a first-line TB drug supporting an emerging hypothesis for its mode of action. These improvements in functional interpretation of clinically informative studies underscores the translational value of this functional knowledge. Structure-derived annotations identify hundreds of high-confidence candidates for mechanisms of antibiotic resistance, virulence factors, and basic metabolism; other functions key in clinical and basic tuberculosis research. More broadly, it provides a systematic framework for improving prokaryotic reference annotations.

category: genomics


title: Distracting Linguistic Information Impairs Neural Tracking of Attended Speech

abstract: Listening to speech is difficult in noisy environments, and is even harder when the interfering noise consists of intelligible speech as compared to unintelligible sounds. This suggests that the competing linguistic information interferes with the neural processing of target speech. Interference could either arise from a degradation of the neural representation of the target speech, or from increased representation of distracting speech that enters in competition with the target speech. We tested these alternative hypotheses using magnetoencephalography (MEG) while participants listened to a target clear speech in the presence of distracting noise-vocoded speech. Crucially, the distractors were initially unintelligible but became more intelligible after a short training session. Results showed that the comprehension of the target speech was poorer after training than before training. The neural tracking of target speech in the delta range (1-4 Hz) reduced in strength in the presence of a more intelligible distractor. In contrast, the neural tracking of distracting signals was not significantly modulated by intelligibility. These results suggest that the presence of distracting speech signals degrades the linguistic representation of target speech carried by delta oscillations.


title: Extracellular histones, a new class of inhibitory molecules of CNS axonal regeneration

abstract:
Axonal regeneration in the mature CNS is limited by extracellular inhibitory factors. Triple knockout mice lacking the major myelin-associated inhibitors do not display spontaneous regeneration after injury, indicating the presence of other inhibitors. Searching for such inhibitors we have detected elevated levels of histone H3 in human cerebrospinal fluid (CSF) 24 hours after spinal cord injury. Following dorsal column lesions in mice and optic nerve crushes in rats, elevated levels of extracellular histone H3 were detected at the injury site. Similar to myelin-associated inhibitors, these extracellular histones induced growth cone collapse and inhibited neurite outgrowth. Histones mediate inhibition through the transcription factor YB-1 and Toll-like receptor 2, and these effects are independent of the Nogo receptor. Histone-mediated inhibition can be reversed by the addition of activated protein C (APC) in vitro, and APC treatment promotes axonal regeneration in the crushed optic nerve in vivo. These findings identify extracellular histones as a new class of nerve regeneration-inhibiting molecules within the injured CNS.

One sentence summaryProteins typically associated with chromatin structure play an unexpected role in limiting axonal regeneration after injury.


title: Dispensing a synthetic green leaf volatile to two plant species in a common garden differentially alters physiological responses and herbivory

abstract: Herbivore-induced plant volatile (HIPV)-mediated eavesdropping by plants is a well-documented, inducible phenomenon that has practical agronomic applications for enhancing plant defense and pest management. However, as with any inducible phenomenon, responding to volatile cues may incur physiological and ecological costs that limit plant productivity. In a common garden experiment, we tested the hypothesis that exposure to a single HIPV would decrease herbivore damage at the cost of reduced plant growth and reproduction. Lima bean (Phaseolus lunatus) and pepper (Capsicum annuum) plants were exposed to a persistent, low-dose ([~]10ng/hour) of the green leaf volatile cis-3-hexenyl acetate (z3HAC), which is an HIPV and damage-associated volatile. z3HAC-treated pepper plants were shorter, had less aboveground and belowground biomass, and produced fewer flowers and fruits relative to controls while z3HAC-treated lima bean plants were taller and produced more leaves and flowers than did controls. Natural herbivory was reduced in z3HAC-exposed lima bean plants, but not in pepper. Cyanogenic potential, a putative direct defense mechanism in lima bean, was lower in young z3HAC-exposed leaves, suggesting a growth-defense tradeoff from z3HAC exposure alone. Plant species-specific responses to an identical volatile cue have important implications for agronomic costs and benefits of volatile-mediated inter-plant communication under field conditions.


title: The taxonomic and functional biogeographies of phytoplankton and zooplankton communities across boreal lakes

abstract: AO_SCPLOWBSTRACTC_SCPLOWStrong trophic interactions link primary producers (phytoplankton) and consumers (zooplankton) in lakes. However, the influence of such interactions on the biogeographical distribution of the taxa and functional traits of planktonic organisms in lakes has never been explicitly tested. To better understand the spatial distribution of these two major aquatic groups, we related composition across boreal lakes (104 for zooplankton and 48 for phytoplankton) in relation to a common suite of environmental and spatial factors. We then directly tested the degree of coupling in their taxonomic and functional distributions across the subset of common lakes. Although phytoplankton composition responded mainly to properties related to water quality while zooplankton composition responded more strongly to lake morphometry, we found significant coupling between their spatial distributions at taxonomic and functional levels based on a Procrustes test. This coupling was not significant after removing the effect of environmental drivers (water quality and morphometry) on the spatial distributions of the two groups. This result suggests that top-down and bottom-up effects (e.g. nutrient concentration and predation) drove trophic interactions at the landscape level. We also found a significant effect of dispersal limitation on the distribution of taxa, which could explain why coupling was stronger for taxa than for traits at the scale of this study, with a turnover of species observed between regions, but no trait turnover. Our results indicate that landscape pelagic food web responses to anthropogenic changes in ecosystem parameters should be driven by a combination of top-down and bottom-factors for taxonomic composition, but with a relative resilience in functional trait composition of lake communities.


title: Predicting subclinical psychotic-like experiences on a continuum using machine learning

abstract:
Previous studies applying machine learning methods to psychosis have primarily been concerned with the binary classification of chronic schizophrenia patients and healthy controls. The aim of this study was to use electroencephalographic (EEG) data and pattern recognition to predict subclinical psychotic-like experiences on a continuum between these two extremes in otherwise healthy people. We applied two different approaches to an auditory oddball regularity learning task obtained from N = 73 participants:

O_LIA feature extraction and selection routine incorporating behavioural measures, event-related potential components and effective connectivity parameters;
C_LIO_LIRegularisation of spatiotemporal maps of event-related potentials.
C_LI

Using the latter approach, optimal performance was achieved using the response to frequent, predictable sounds. Features within the P50 and P200 time windows had the greatest contribution toward lower Prodromal Questionnaire (PQ) scores and the N100 time window contributed most to higher PQ scores. As a proof-of-concept, these findings demonstrate that EEG data alone are predictive of individual psychotic-like experiences in healthy people. Our findings are in keeping with the mounting evidence for altered sensory responses in schizophrenia, as well as the notion that psychosis may exist on a continuum expanding into the non-clinical population.


title: Individuals with ventromedial frontal damage have more unstable but still fundamentally transitive preferences

abstract: The ventromedial frontal lobes (VMF) are important for decision-making, but the precise causal role of the VMF in the decision process has not yet fully been established. Previous studies have suggested that individuals with VMF damage violate transitivity, a hallmark axiom of rational decisions. However, these prior studies cannot properly distinguish whether individuals with VMF damage are truly prone to choosing irrationally from whether their preferences are simply more variable. We had individuals with focal VMF damage, individuals with other frontal damage, and healthy controls make repeated choices across three categories - artwork, chocolate bar brands, and gambles. Using sophisticated tests of transitivity, we find that, without exception, individuals with VMF damage make rational decisions consistent with transitive preferences, even though they exhibit greater variability in their preferences. That is, the VMF is necessary for having strong and reliable preferences, but not for being a rational decision maker. VMF damage affects the noisiness with which value is assessed, but not the consistency with which value is sought.


title: De Novo Mutational Signature Discovery in Tumor Genomes using SparseSignatures

abstract:
Cancer is the result of mutagenic processes that can be inferred from tumor genomes by analyzing rate spectra of point mutations, or "mutational signatures". Here we present SparseSignatures, a novel framework to extract signatures from somatic point mutation data. Our approach incorporates a user-specified background signature, employs regularization to reduce noise in non-background signatures, uses cross-validation to identify the number of signatures, and is scalable to large datasets. We show that SparseSignatures outperforms current state-of-the-art methods on simulated data using a variety of standard metrics. We then apply SparseSignatures to whole genome sequences of pancreatic and breast tumors, discovering well-differentiated signatures that are linked to known mutagenic mechanisms and are strongly associated with patient clinical features.

Authors SummaryCancer is a genetic disease, occurring as a result of mutagenic processes causing DNA somatic mutations in genes controlling cellular growth and division. These somatic mutations arise from processes such as defective DNA repair and environmental mutagens, which massively increase the rate of somatic variants. As a result, due to the specificity of molecular lesions caused by such processes, and the specific repair mechanisms deployed by the cell to mitigate the damage, mutagenic processes generate characteristic point mutation rate spectra which are called mutational signatures. These signatures can indicate which mutagenic processes are active in a tumor, reveal biological differences between cancer subtypes, and may be useful markers for therapeutic response. Here, we develop SparseSignatures, a novel framework for mutational signature discovery capable of both identifying the active signatures in a dataset of point mutations and calculating their exposure values, i.e., the number of mutations originating from each signature in each patient. We show that our approach outperforms current state-of-the-art methods on simulated data using a variety of standard metrics and then apply SparseSignatures to whole genome sequences of pancreatic and breast tumors, discovering well-differentiated signatures that are linked to known mutagenic mechanisms.


title: GranatumX: A community engaging, modularized and flexible software environment for single-cell analysis

abstract: We present GranatumX, a next-generation software environment for single-cell data analysis. GranatumX is inspired by the interactive web tool Granatum. It enables biologists to access the latest single-cell bioinformatics methods in a web-based graphical environment. It also offers software developers the opportunity to rapidly promote their own tools with others in customizable pipelines. The architecture of GranatumX allows for easy inclusion of plugin modules, named Gboxes, that wrap around bioinformatics tools written in various programming languages and on various platforms. GranatumX can be run on the cloud or private servers and generate reproducible results. It is a community-engaging, flexible, and evolving software ecosystem for scRNA-Seq analysis, connecting developers with bench scientists. GranatumX is freely accessible at http://garmiregroup.org/granatumx/app.


title: GranatumX: A community engaging, modularized and flexible webtool for single-cell analysis


title: High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur).

abstract:
The Src homology-2 domain containing phosphatase SHP2 is a critical regulator of signal transduction, being implicated in cell growth and differentiation. Activating mutations cause developmental disorders and act as oncogenic drivers in hematologic cancers. SHP2 is activated by phosphopeptide binding to the N-SH2 domain, triggering the release of N-SH2 from the catalytic PTP domain. Based on early crystallographic data, it has been widely accepted that opening of the binding cleft of N-SH2 serves as the key "allosteric switch" driving SHP2 activation. To test the putative coupling between binding cleft opening and SHP2 activation as assumed by the "allosteric switch" model, we critically reviewed structural data of SHP2 and we used extensive molecular dynamics (MD) simulation and free energy calculations of isolated N-SH2 in solution, SHP2 in solution, and SHP2 in a crystal environment. Our results demonstrate that the binding cleft in N-SH2 is constitutively flexible and open in solution, and that a closed cleft found in certain structures is a consequence of crystal contacts. The degree of opening of the binding cleft has only a negligible effect on the free energy of SHP2 activation. Instead, SHP2 activation is greatly favored by the opening of the central {beta}- sheet of N-SH2. We conclude that opening of the N-SH2 binding cleft is not the key allosteric switch triggering SHP2 activation.

Significance StatementSHP2 is a multi-domain protein, playing an important role in up-regulating cellular processes such as cell survival, proliferation, and programmed cell death. SHP2 mutations cause developmental disorders and were found in many cancer types, including neuroblastoma, breast cancer, and leukemia. In healthy cells, SHP2 mainly takes an autoinhibited, inactive form, and SHP2 is activated upon binding of phosphopeptides to the N-SH2 domain. For the past two decades, the widening of the binding cleft upon peptide binding has been considered as the key event driving SHP2 activation. Here, by analyzing crystallographic data and molecular simulations, we demonstrate that the binding cleft in N-SH2 is, instead, already open and accessible in solution, and its degree of opening does not influence SHP2 activation.


title: Eye movements during text reading align with the rate of speech production

abstract: Across languages, the speech signal is characterized by a predominant modulation of the amplitude spectrum between about 4.3-5.5Hz, reflecting the production and processing of linguistic information chunks (syllables, words) every [~]200ms. Interestingly, [~]200ms is also the typical duration of eye fixations during reading. Prompted by this observation, we demonstrate that German readers sample written text at [~]5Hz. A subsequent meta-analysis with 142 studies from 14 languages replicates this result, but also shows that sampling frequencies vary across languages between 3.9Hz and 5.2Hz, and that this variation systematically depends on the complexity of the writing systems (character-based vs. alphabetic systems, orthographic transparency). Finally, we demonstrate empirically a positive correlation between speech spectrum and eye-movement sampling in low-skilled readers. Based on this convergent evidence, we propose that during reading, our brains linguistic processing systems imprint a preferred processing rate, i.e., the rate of spoken language production and perception, onto the oculomotor system.


title: Basal ganglia and cortical control of thalamic rebound spikes

abstract: Movement-related decreases in firing rate have been observed in basal ganglia output neurons. They may transmit motor signals to the thalamus, but the effect of these firing rate decreases on downstream neurons in the motor thalamus is not known. One possibility is that they lead to thalamic post-inhibitory rebound spikes. However, it has also been argued that the physiological conditions permitting rebound spiking are pathological, and primarily present in Parkinsons disease. As in Parkinsons disease neural activity becomes pathologically correlated, we investigated the impact of correlations in basal ganglia output on the transmission of motor signals using a Hodgkin-Huxley model of thalamocortical neurons. We found that such correlations disrupt the transmission of motor signals via rebound spikes by decreasing the signal-to-noise ratio and increasing the trial-to-trial variability. We further examined the role of sensory responses in basal ganglia output neurons and the effect of cortical excitation of motor thalamus in modulating rebound spiking. Interestingly, both could either promote or suppress the generation of rebound spikes depending on their timing relative to the motor signal. Finally, we determined parameter regimes, such as levels of excitation, under which rebound spiking is feasible in the model, and confirmed that the conditions for rebound spiking are primarily given in pathological regimes. However, we also identified specific conditions in the model that would allow rebound spiking to occur in healthy animals in a small subset of thalamic neurons. Overall, our model provides novel insights into differences between normal and pathological transmission of motor signals.


title: Reduction in CD11c+ microglia correlates with clinical progression in chronic experimental autoimmune demyelination

abstract: Multiple sclerosis (MS) is a chronic autoimmune demyelinating disease with high variability of clinical symptoms. In most cases MS appears as a relapsing-remitting disease course that at a later stage transitions into irreversible progressive decline of neurologic function. The mechanisms underlying MS progression remain poorly understood. Experimental autoimmune encephalomyelitis (EAE) is an animal model of MS. Here we demonstrate that mice that develop mild EAE after immunization with myelin oligodendrocyte glycoprotein 35-55 are prone to undergo clinical progression around 30 days after EAE induction. EAE progression was associated with reduction in CD11c+ microglia and dispersed coalescent parenchymal infiltration. We found sex-dependent differences mediated by p38 signaling, a key regulator of inflammation. Selective reduction of CD11c+ microglia in female mice with CD11c-promoter driven p38 knockout (KO) correlated with increased rate of EAE progression. In protected animals, we found CD11c+ microglia forming contacts with astrocyte processes at the glia limitans and immune cells retained within perivascular spaces. Together, our study provides evidence on the protective role of CD11c+ microglia in controlling CNS immune cell parenchymal infiltration in autoimmune demyelination.


title: Dimerisation of APOBEC1 is dispensable for its RNA/DNA editing activity and modulates its availability

abstract:
The AID/APOBECs are DNA/RNA deaminases whose mutagenic activity has been linked to cancer. Among them, APOBEC1 physiologically partakes into a complex that edits a CAA codon into UAA Stop codon in the transcript of Apolipoprotein B (APOB), a protein crucial in the transport of lipids in the blood. Catalytically inactive mutants of APOBEC1 have a dominant negative effect on its activity, as they compete for the targeting of the APOB mRNA. Here we titrate APOBEC1-mediated editing in presence of catalytically inactive chimeras and mutants of APOBEC1, and we show that APOBEC1 inability to dimerise is the main determinant for its activity. This property is especially evident in an APOBEC1 mutant (L173A G227A) with increased activity on RNA despite decreased self-interaction. Moreover, dimerisation protects APOBEC1 from degradation and regulates its availability. Considering APOBEC1 capability to target DNA, we demonstrate that increased availability of the protein due to dimerisation leads to increase in the DNA damage induced by APOBEC1. These findings demonstrate that dimerisation, a property common to other APOBECs targeting DNA, might represent another layer in the regulation of this editing enzyme.

BULLET POINTSO_LIAPOBEC1 inability to dimerise is the main determinant for its activity.
C_LIO_LIDimerisation protects APOBEC1 from degradation and regulates its availability.
C_LIO_LIAlterations in the balance between monomeric and dimeric APOBEC1 increase DNA damage.
C_LI


title: Diversity and composition of cave methanotrophic communities

abstract:
Methane oxidizing bacteria (methanotrophs) are a ubiquitous group of microorganisms that represent a major sink for the greenhouse gas methane (CH4). Recent studies have demonstrated that methanotrophs are abundant and contribute to CH4 dynamics in caves. However, very little is known about what controls the distribution and abundance of methanotrophs in subterranean ecosystems. Here, we report a survey of sediments collected from >20 caves in North America to elucidate the factors shaping cave methanotroph communities. Using 16S rRNA sequencing, we recovered methanotrophs from nearly all (98 %) of the samples, including cave sites where CH4 concentrations were at or below detection limits ([≤] 0.3 ppmv). We identified a core microbiome among caves that was dominated by members of the USC-{gamma} clade, which are recognized as high-affinity methanotrophs. Although methanotrophs were associated with local-scale mineralogy, their community composition did not systematically vary between the entrances and interior of caves, where CH4 concentrations varied. However, we did detect a decay in compositional similarity of methanotrophic community composition with geographic distance. This biogeographic pattern is consistent with dispersal limitation perhaps due to the insular nature of cave ecosystems. Last, the relative abundance of methanotrophs was positively correlated with cave-air CH4 concentrations--suggesting that these microorganisms contribute to CH4 flux in subterranean ecosystems.

IMPORTANCERecent observations have shown that the atmospheric greenhouse gas methane (CH4) is consumed by microorganisms (methanotrophs) in caves at rates comparable to CH4 oxidation in surface soils. Caves are abundant in karst landscapes that comprise 14 % of Earths land surface area, and therefore may be acting as a substantial CH4 sink. A detailed ecological understanding of the forces that shape methanotrophic communities in caves is lacking. We sampled cave sediments to better understand the community composition and structure of cave methanotrophs. Our results show that the members of the USC-{gamma} clade are dominant in cave communities, that the relative abundance of methanotrophs was positively correlated with CH4 concentrations in cave air, and that methanotroph relative abundance was correlated with local scale mineralogy of soils.


title: Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies

abstract:
Sprague Dawley (SD) rats are among the most widely used outbred laboratory rat populations. Despite this, the genetic characteristics of SD rats have not been clearly described, and SD rats are rarely used for experiments aimed at exploring genotype-phenotype relationships. In order to use SD rats to perform a genome-wide association study (GWAS), we collected behavioral data from 4,625 SD rats that were predominantly obtained from two commercial vendors, Charles River Laboratories and Harlan Sprague Dawley Inc. Using double-digest genotyping-by-sequencing (ddGBS), we obtained dense, high-quality genotypes at 291,438 SNPs across 4,061 rats. This genetic data allowed us to characterize the variation present in Charles River vs. Harlan SD rats. We found that the two populations are highly diverged (FST > 0.4). Furthermore, even for rats obtained from the same vendor, there was strong population structure across breeding facilities and even between rooms at the same facility. We performed multiple separate GWAS by fitting a linear mixed model that accounted population structure and using meta-analysis to jointly analyze all cohorts. Our study examined Pavlovian conditioned approach (PavCA) behavior, which assesses the propensity for rats to attribute incentive salience to reward-associated cues. We identified 46 significant associations for the various metrics used to define PavCA. The surprising degree of population structure among SD rats from different sources has important implications for their use in both genetic and non-genetic studies.

Author SummaryOutbred Sprague Dawley rats are among the most commonly used rats for neuroscience, physiology and pharmacological research; in the year 2020, 4,188 publications contained the keyword "Sprague Dawley". Rats identified as "Sprague Dawley" are sold by several commercial vendors, including Charles River Laboratories and Harlan Sprague Dawley Inc. (now Envigo). Despite their widespread use, little is known about the genetic diversity of SD. We genotyped more than 4,000 SD rats, which we used for a genome-wide association study (GWAS) and to characterize genetic differences between SD rats from Charles River Laboratories and Harlan. Our analysis revealed extensive population structure both between and within vendors. The GWAS for Pavlovian conditioned approach (PavCA) identified a number of genome-wide significant loci for that complex behavioral trait. Our results demonstrate that, despite sharing an identical name, SD rats that are obtained from different vendors are very different. Future studies should carefully define the exact source of SD rats being used and may exploit their genetic diversity for genetic studies of complex traits.


title: Nuclear envelope budding is a response to cellular stress

abstract:
Nuclear envelope budding (NEB) is a recently discovered alternative pathway for nucleocytoplasmic communication distinct from the movement of material through the nuclear pore complex. Through quantitative electron microscopy and tomography, we demonstrate how NEB is evolutionarily conserved from early protists to human cells. In the yeast Saccharomyces cerevisiae, NEB events occur with higher frequency during heat shock, upon exposure to arsenite or hydrogen peroxide, and when the proteasome is inhibited. Yeast cells treated with azetidine-2-carboxylic acid, a proline analogue that induces protein misfolding, display the most dramatic increase in NEB, suggesting a causal link to protein quality control. This link was further supported by both localization of ubiquitin and Hsp104 to protein aggregates and NEB events, and the evolution of these structures during heat shock. We hypothesize that NEB is part of normal cellular physiology in a vast range of species and that in S. cerevisiae NEB comprises a stress response aiding the transport of protein aggregates across the nuclear envelope.

Significance StatementA defining feature of eukaryotes is the nuclear envelope, a double lipid bilayer that serves to isolate and protect the cells genetic material. Transport of large molecules over this barrier is believed to occur almost exclusively via the nuclear pores. However, herpes virions and mega ribonucleoproteins (megaRNPs) use an alternative means of transport - via nuclear envelope budding (NEB). Here, we show NEB is a ubiquitous eukaryotic phenomenon and increases when exposed to various forms of cellular stress. NEB frequency was maximal when the cell was challenged with a drug that induces protein misfolding, indicating this transport pathway plays a role in protein quality control. These results imply that NEB is an underappreciated yet potentiallyfundamental means of nuclear transport.


title: Tension suppresses Aurora B kinase-triggered release of reconstituted kinetochore-microtubule attachments

abstract: Chromosome segregation requires kinetochores to attach to microtubules from opposite spindle poles. Proper attachments come under tension and are stabilized, but defective attachments lacking tension are released, giving another chance for correct attachments to form. This error correction process requires the Aurora B kinase, which phosphorylates kinetochores to destabilize microtubule attachments. However, the mechanism by which Aurora B can distinguish kinetochore tension remains unclear because it is difficult to detect kinase-triggered detachment and manipulate kinetochore tension in vivo. To address these challenges, we developed an optical trapping-based flow assay with soluble Aurora B and reconstituted kinetochore-microtubule attachments. Strikingly, we found that tension on these attachments suppressed their Aurora B-triggered release, suggesting that tension-dependent changes in the conformation of kinetochores can regulate Aurora B activity or its outcome. Our work uncovers the basis for a key mechano-regulatory event that ensures accurate segregation and may inform studies of other mechanically regulated enzymes.


title: Human cortical dynamics during full-body heading changes

abstract: The retrosplenial complex (RSC) plays a crucial role in spatial orientation by computing heading direction and translating between distinct spatial reference frames based on multi-sensory information. While invasive studies allow investigating heading computation in moving animals, established non-invasive analyses of human brain dynamics are restricted to stationary setups. To investigate the role of the RSC in heading computation of actively moving humans, we used a Mobile Brain/Body Imaging approach synchronizing electroencephalography with motion capture and virtual reality. Data from physically rotating participants were contrasted with rotations based only on visual flow. During physical rotation, varying rotation velocities were accompanied by pronounced wide frequency band synchronization in RSC, the parietal and occipital cortices. In contrast, the visual flow rotation condition was associated with pronounced alpha band desynchronization, replicating previous findings in desktop navigation studies, and notably absent during physical rotation. These results suggest an involvement of the human RSC in heading computation based on visual, vestibular, and proprioceptive input and implicate revisiting traditional findings of alpha desynchronization in areas of the navigation network during spatial orientation in movement-restricted participants.


title: Paternal knockdown of tRNA (cytosine-5-)-methyltransferase (Dnmt2) increases offspring susceptibility to infection in flour beetles

abstract: Intergenerational effects from fathers to offspring are increasingly reported from diverse organisms, but the underlying mechanisms remain speculative. Paternal trans-generational immune priming (TGIP) was demonstrated in the red flour beetle Tribolium castaneum: non-infectious bacterial exposure of fathers protects their offspring against an infectious challenge for at least two generations. Epigenetic processes, such as cytosine methylation of nucleic acids, have been proposed to enable transfer of information from fathers to offspring. Here we studied a potential role in TGIP of the Dnmt2 gene (renamed as Trdmt1 in humans), which encodes a highly conserved enzyme that methylates different RNAs, including specific cytosines of a set of tRNAs. Dnmt2 has previously been reported to be involved in intergenerational epigenetic inheritance in mice and protection against viruses in fruit flies. We first studied gene expression and found that Dnmt2 is expressed in various life history stages and tissues of T. castaneum, with high expression in the reproductive organs. RNAi-mediated knockdown of Dnmt2 in fathers was systemic, slowed down offspring larval development and increased mortality of the adult offspring upon bacterial infection. However, these effects were independent of bacterial exposure of the fathers. In conclusion, our results point towards a role of Dnmt2 for paternal effects, while elucidation of the mechanisms behind paternal TGIP needs further studies.


title: Paternal knockdown of tRNA (cytosine-5-)-methyltransferase (Dnmt2) increases offspring susceptibility to infection in red flour beetles


title: An epi-evolutionary model to predict spore-producing pathogens adaptation to quantitative resistance in heterogeneous environments

abstract: We model the evolutionary epidemiology of spore-producing plant pathogens in heterogeneous environments sown with several cultivars carrying quantitative resistances. The model explicitly tracks the infection-age structure and genetic composition of the pathogen population. Each strain is characterized by pathogenicity traits describing its infection efficiency and a time-varying sporulation curve taking into account lesion ageing. We first derive a general expression of the basic reproduction number [R]0 for fungal pathogens in heterogeneous environments. We show that evolutionary attractors of the model coincide with local maxima of [R]0 only if the infection efficiency is the same on all host types. We then study how three basic resistance characteristics (pathogenicity trait targeted, resistance effectiveness, and adaptation cost) in interaction with the deployment strategy (proportion of fields sown with a resistant cultivar) (i) lead to pathogen diversification at equilibrium and (ii) shape the transient dynamics from evolutionary and epidemiological perspectives. We show that quantitative resistance impacting only the sporulation curve will always lead to a monomorphic population, while dimorphism (i.e. pathogen diversification) can occur with resistance altering infection efficiency, notably with high adaptation cost and proportion of R cultivar. Accordingly, the choice of quantitative resistance genes operated by plant breeders is a driver of pathogen diversification. From an evolutionary perspective, the emergence time of the evolutionary attractor best adapted to the R cultivar tends to be shorter when the resistance impacts infection efficiency than when it impacts sporulation. In contrast, from an epidemiological perspective, the epidemiological control is always higher when the resistance impacts infection efficiency. This highlights the difficulty of defining deployment strategies of quantitative resistance maximising at the same time epidemiological and evolutionary outcomes.


title: Subcutaneous neurotrophin-3 infusion induces corticospinal neuroplasticity and improvements in dexterity and walking in elderly rats after large cortical stroke

abstract: There is an urgent need for a therapy which reverses disability after stroke when initiated in a time frame suitable for the majority of new victims. Neurotrophin-3 (NT3) is a growth factor made by muscle spindles and skin which is required for the survival, development and function of locomotor circuits involving afferents from muscle and skin that mediate proprioception and tactile sensation. Its level declines in muscle and other tissues postnatally. We show that levels of NT-3 in the bloodstream were low in humans with ischemia stroke relative to young healthy controls. Accordingly, we set out to determine whether subcutaneous delivery of NT3 improves sensorimotor recovery after stroke in elderly rats. We show that one-month-long subcutaneous infusion of NT3 protein induces sensorimotor recovery after cortical stroke in elderly rats. Specifically, in a randomised, blinded pre-clinical trial, we show improved dexterity, walking and sensory function in rats following cortical ischemic stroke when treatment with NT3 is initiated 24 hours after stroke. Importantly, NT-3 was given in a clinically feasible time frame via this straightforward route. MRI and histology showed that recovery was not due to neuroprotection, as expected given the delayed treatment. Rather, anterograde tracing showed that corticospinal axons from the less-affected hemisphere sprouted in the spinal cord from cervical levels 2 to 8. Importantly, Phase I and II clinical trials by others show that repeated, subcutaneously administered high doses of recombinant NT-3 are safe and well tolerated in humans with other conditions. This paves the way for NT-3 as a therapy for stroke.


title: Ratio-based sensing of two transcription factors regulates the transit to differentiation

abstract: Cell state transitions are usually thought to be triggered by changes in the absolute concentrations of relevant transcription factors. In the Drosophila eye, the transcription factor Yan maintains cells in a progenitor state by repressing gene expression, while the Pointed transcription factor activates gene expression programs that promote photoreceptor specification. In this study we investigate how retinal cell state transitions are resolved by quantifying the expression dynamics of Yan and Pointed proteins. Despite extensive cell-to-cell variation in absolute concentrations of Yan and Pointed, progenitor cells maintain a relatively constant ratio of Pointed-to-Yan protein. A sustained change in the Pointed-to-Yan ratio accompanies the transition to photoreceptor fates. Genetic perturbations that disrupt the ratio produce photoreceptor specification defects, suggesting that transitions depend upon a sustained change in the ratio. A model based on the statistical physics of protein-DNA binding illustrates how ratiometric sensing could produce the changes in gene expression that underlie these cell state transitions. We propose that ratiometric control mechanisms facilitate regulation of developmental transitions by multiple transcription factors, and thereby make the transitions robust to fluctuations in absolute protein levels.


title: Pink Cedar (Acrocarpus fraxinifolius): its prophylactic role against APAP induced organs toxicity in rats and its antiviral activity against Herpes simplex virus type 1

abstract: The possible protective effects of methanolic extract Acrocarpus fraxinifolius leaves (MEAFL) were assessed against the APAP-induced organ toxicity in male rats. Also, the content of polyphenols extracted from AFL was studied, and their relationship with antioxidant activity was investigated. MEAFL was tested for cytotoxicity on Vero cell line, with reference to IC50, and other non-toxic concentrations of all the extracts. The antiviral activity against HSV1 for all non-toxic concentrations of the extract was determined using plaque reduction assay. It was found that MEAFL showed a reduction of serum hepatic and renal cellular toxicity and cellular lipid peroxidation, as well as enhanced cellular antioxidant. Also, our results revealed that the inhibitory activity of the virus was dose dependent on the polyphenol content of the examined extract. The MIC for the MEAFL extract was determined as well as the EC50 and SI. Calculated SI showed promising value for the MEAFL, and hence can be used as therapeutic medication for HSV1. To study other possible mode of action, Vero cells were treated with the examined extracts before, during, and after virus infection to give an insight on the interference of the extract in each step in the virus life cycle. In conclusion, MEAFL showed a remarkable antioxidant effect against APAP induced organs toxicity. Also, examined extracts exhibited the antiviral activity against HSV1.

category: physiology


title: Dual brain cortical calcium imaging reveals social interaction-specific wide-spread correlated cortical activity in mice.

abstract: We employ cortical mesoscale calcium-imaging to observe brain activity in two head-fixed mice in a staged social touch-like interaction. Using a rail system, mice are brought together to a distance where macrovibrissae of each mouse make contact. Cortical signals were recorded from both mice simultaneously before, during, and after the social contact period. When the mice were together, we observed bouts of mutual whisking and cross-mouse correlated cortical activity in the vibrissae cortex. This correlated activity was specific to individual interactions as the correlations fell in trial-shuffled mouse pairs. Whisk-related global GCAMP6s signals were greater in cagemate pairs during the together period. The effects of social interaction extend outside of regions associated with mutual touch and had global synchronizing effects on cortical activity. We present an open-source platform to investigate the neurobiology of social interaction by including mechanical drawings, protocols, and software necessary for others to extend this work.


title: RegTools: Integrated analysis of genomic and transcriptomic data for the discovery of splicing variants in cancer

abstract: Somatic mutations in non-coding regions of the genome and even exonic mutations may have unidentified non-coding consequences which are often overlooked in analysis workflows. Here we present RegTools (www.regtools.org), a free, open-source software package designed to integrate analysis of somatic variant calls from genomic data with splice junctions extracted from transcriptomic data to efficiently identify variants that may cause aberrant splicing in tumors. RegTools was applied to over 9,000 tumor samples with both tumor DNA and RNA sequence data. We discovered 235,778 events where a variant significantly increased the splicing of a particular junction, across 158,200 unique variants and 131,212 unique junctions. To further characterize these somatic variants and their associated splice isoforms, we annotated them with the Variant Effect Predictor (VEP), SpliceAI, and Genotype-Tissue Expression (GTEx) junction counts and compared our results to other tools that integrate genomic and transcriptomic data. While variants associated with certain types of alternative splicing events can be identified by the aforementioned tools, the unbiased nature of Regtools has allowed us to identify novel splice variants, including previously unreported patterns of splicing disruption in cancer drivers, such as TP53, CDKN2A, and B2M, and genes not previously reported that could represent novel driver events, such RNF145.