title: EFFECTS OF LAND-USE INTENSIFICATION AND ENVIRONMENTAL STRESSORS ON INTRASPECIFIC FUNCTIONAL TRAITS VARIABILITY IN BUMBLEBEES

abstract:
The way urbanization shapes the intraspecific variation of pollinator functional traits is little understood. However, this topic is relevant for investigating ecosystem services and pollinator health. Here, we studied how urbanization affects the functional traits of workers in two bumblebee species (Bombus terrestris and B. pascuorum) sampled in 37 sites along a gradient of urbanization in North Italy (an area of 1800 km2 including the metropolitan context of Milan and other surrounding capital districts). Namely, we investigated the role played by land-use composition, configuration, temperature, flower resource abundance, and air pollutants on the variation of traits related to flight performance (i.e., body size, wing shape and size fluctuating asymmetry). These traits are relevant because they are commonly used as indicators of stress during insect development. The functional traits of the two bumblebees responded idiosyncratically to urbanization. Urban temperatures were associated with smaller wing sizes in B. pascuorum and with more accentuated fluctuating asymmetry of wing size in B. terrestris. Moreover, flower abundance correlated with bigger wings in B. terrestris and with less asymmetric wing sizes in B. pascuorum. Other traits did not vary significantly and other urban variables played minor effects. These patterns highlight that environmental stressors linked to urbanization negatively impact traits related to flight performance and development stability of these species with possible consequences on the pollination service they provide.

Overall, this study found species-specific variation patterns in syntopic taxa, expanding our understanding about the effects of anthropic disturbance in shaping relevant functional traits of pollinator model species.


title: Effect of urbanization and its environmental stressors on the intraspecific variation of flight functional traits in two bumblebee species

category: ecology


title: Experimental sexual selection reveals rapid divergence in male and female reproductive transcriptomes and their interactions

abstract: Postcopulatory interactions between the sexes in internally fertilizing species elicits both sexual conflict and sexual selection. Macroevolutionary and comparative studies have linked these processes to rapid transcriptomic evolution in sex-specific tissues and substantial transcriptomic postmating responses in females, patterns of which are altered when mating between reproductively isolated species. Here we test multiple predictions arising from sexual selection and conflict theory about the evolution of sex-specific and tissue-specific gene expression and the postmating response at the microevolutionary level. Following over 150 generations of experimental evolution under either reduced (enforced monogamy) or elevated (polyandry) sexual selection in Drosophila pseudoobscura, we found a substantial effect of sexual selection treatment on transcriptomic divergence in virgin male and female reproductive tissues (testes, male accessory glands, the female reproductive tract and ovaries). Sexual selection treatment also had a dominant effect on the postmating response, particularly in the female reproductive tract - the main arena for sexual conflict - compared to ovaries. This affect was asymmetric with monandry females typically showing more postmating responses than polyandry females, with enriched gene functions varying across treatments. The evolutionary history of the male partner had a larger effect on the postmating response of monandry females, but females from both sexual selection treatments showed unique patterns of gene expression and gene function when mating with males from the alternate treatment. Our microevolutionary results mostly confirm comparative macroevolutionary predictions on the role of sexual selection on transcriptomic divergence and altered gene regulation arising from divergent coevolutionary trajectories between sexual selection treatments.

category: evolutionary biology


title: Experimental sexual selection reveals rapid evolutionary divergence in sex-specific transcriptomes and their interactions following mating


title: Whole-genome analysis of de novo and polymorphic retrotransposon insertions in Autism Spectrum Disorder

abstract: Retrotransposons are dynamic forces in evolutionary genomics and have been implicated as causes of Mendelian disease and hereditary cancer, but their role in Autism Spectrum Disorder (ASD) has never been systematically defined. Here, we report 86,154 polymorphic retrotransposon insertions including >60% not previously reported and 158 de novo retrotransposition events identified in whole genome sequencing (WGS) data of 2,288 families with ASD from the Simons Simplex Collection (SSC). As expected, the overall burden of de novo events was similar between ASD individuals and unaffected siblings, with 1 de novo insertion per 29, 104, and 192 births for Alu, L1, and SVA respectively, and 1 de novo insertion per 20 births total, while the location of transposon insertions differed between ASD and unaffected individuals. ASD cases showed more de novo L1 insertions than expected in ASD genes, and we also found de novo intronic retrotransposition events in known syndromic ASD genes in affected individuals but not in controls. Additionally, we observed exonic insertions in genes with a high probability of being loss-of-function intolerant, including a likely causative exonic insertion in CSDE1, only in ASD individuals. Although de novo retrotransposition occurs less frequently than single nucleotide and copy number variants, these findings suggest a modest, but important, impact of intronic and exonic retrotransposition mutations in ASD and highlight the utility of developing specific bioinformatic tools for high-throughput detection of transposable element insertions.

category: genetics


title: Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii

abstract: In most eukaryotes, subtelomeres are dynamic genomic regions populated by multi-copy sequences of different origins, which can promote segmental duplications and chromosomal rearrangements. However, their repetitive nature has complicated the efforts to sequence them, analyze their structure and infer how they evolved. Here, we use recent and forthcoming genome assemblies of Chlamydomonas reinhardtii based on long-read sequencing to comprehensively describe the subtelomere architecture of the 17 chromosomes of this model unicellular green alga. We identify three main repeated elements present at subtelomeres, which we call Sultan, Subtile and Suber, alongside three chromosome extremities with ribosomal DNA as the only identified component of their subtelomeres. The most common architecture, present in 27 out of 34 subtelomeres, is an array of 1 to 46 tandem copies of Sultan elements adjacent to the telomere and followed by a transcribed centromere-proximal Spacer sequence, a G-rich microsatellite and a region rich in transposable elements. Sequence similarity analyses suggest that Sultan elements underwent segmental duplications within each subtelomere and rearranged between subtelomeres at a much lower frequency. Comparison of genomic sequences of three laboratory strains and a wild isolate of C. reinhardtii shows that the overall subtelomeric architecture was already present in their last common ancestor, although subtelomeric rearrangements are on-going at the species level. Analysis of other green algae reveals the presence of species-specific repeated elements, highly conserved across subtelomeres and unrelated to the Sultan element, but with a subtelomere structure similar to C. reinhardtii. Overall, our work uncovers the complexity and evolution of subtelomere architecture in green algae.

category: genomics


title: DIAmeter: Matching peptides to data-independent acquisition mass spectrometry data

abstract: Tandem mass spectrometry data acquired using data independent acquisition (DIA) is challenging to interpret because the data exhibits complex structure along both the mass-to-charge (m/z) and time axes. The most common approach to analyzing this type of data makes use of a library of previously observed DIA data patterns (a "spectral library"), but this approach is expensive because the libraries do not typically generalize well across laboratories. Here we propose DIAmeter, a search engine that detects peptides in DIA data using only a peptide sequence database. Unlike other library-free DIA analysis methods, DIAmeter supports data generated using both wide and narrow isolation windows, can readily detect peptides containing post-translational modifications, can analyze data from a variety of instrument platforms, and is capable of detecting peptides even in the absence of detectable signal in the survey (MS1) scan.

category: bioinformatics


title: Lateral electric field inhibits gel-to-fluid transition in lipid bilayers

abstract: We report evidence of lateral electric field-induced changes in the phase transition temperatures of lipid bilayers. Our atomic scale molecular dynamics simulations show that lateral electric field increases the melting temperature of DPPC, POPC and POPE bilayers. Remarkably, this shift in melting temperature is only induced by lateral electric field, and not normal electric field. This mechanism could provide new mechanistic insights into lipid-lipid and lipid-protein interactions in the presence of endogenous and exogenous electric fields.

category: biophysics


title: Proton egress pathway during the S1 to S2 transition of the Oxygen Evolving Complex ofPhotosystem II

abstract: Photosystem II uses water as the ultimate electron source of the photosynthetic electron transfer chain. Water is oxidized to dioxygen at the Oxygen Evolving Complex (OEC), a Mn4CaO5 inorganic core embedded in the lumenal side of PSII. Water-filled channels are thought to bring in substrate water molecules to the OEC, remove the substrate protons to the lumen, and may transport the product oxygen. Three water-filled channels, denoted large, narrow, and broad, that extend from the OEC towards the aqueous surface more than 15 [A] away are seen. However, the actual mechanisms of water supply to the OEC, the removal of protons to the lumen and diffusion of oxygen away from the OEC have yet to be established. Here, we combine Molecular Dynamics (MD), Multi Conformation Continuum Electrostatics (MCCE) and Network Analysis to compare and contrast the three potential proton transfer paths during the S1 to S2 transition of the OEC. Hydrogen bond network analysis shows that the three channels are highly interconnected with similar energetics for hydronium as calculated for all paths near the OEC. The channels diverge as they approach the lumen, with the water chain in the broad channel better interconnected that in the narrow and large channels, where disruptions in the network are observed at about 10 [A] from the OEC. In addition, the barrier for hydronium translocation is lower in the broad channel, suggesting that a proton from the OEC could access the paths near the OEC, and likely exit to the lumen via the broad channel, passing through PsbO.


title: Metformin protects against insulin resistance induced by high uric acid in cardiomyocytes via AMPK signaling pathways in vitro and in vivo

abstract: High uric acid (HUA) is associated with insulin resistance and abnormal glucose metabolism in cardiomyocytes. Metformin is a recognized agonist of AMP-activated protein kinase (AMPK) and an antidiabetic drug widely used for type 2 diabetes. It can play a cardioprotective role in many pathways. We investigated whether metformin protects against HUA-induced insulin resistance and abnormal glucose metabolism in cardiomyocytes. We exposed primary cardiomyocytes to HUA, and cellular glucose uptake was quantified by measuring the uptake of 2-NBDG, a fluorescent glucose analog, after insulin excitation. Treatment with metformin (10 mol/L) protected against HUA-inhibited glucose uptake induced by insulin in primary cardiomyocytes, as shown by fluorescence microscopy and flow cytometry analysis. HUA directly inhibited the phosphorylation of Akt and the translocation of glucose transporter type 4 (GLUT4) induced by insulin, which was blocked by metformin. Metformin promoted phosphorylation of AMPK, renewed HUA-inhibited glucose uptake induced by insulin and protected against insulin resistance in cardiomyocytes. As a result of these effects, in a mouse model of acute hyperuricemia, metformin improved insulin tolerance and glucose tolerance, accompanied by increased AMPK phosphorylation, Akt phosphorylation and translocation of GLUT4 in myocardial tissues. As expected, AICAR, another AMPK activator, had equivalent effects to metformin, demonstrating the important role of AMPK activation in protecting against insulin resistance induced by HUA in cardiomyocytes. Metformin protects against insulin resistance induced by HUA in cardiomyocytes and improves insulin tolerance and glucose tolerance in an acute hyperuricemic mouse model, along with the activation of AMPK. Consequently, metformin may be an important potential new treatment strategy for hyperuricemia-related cardiovascular disease.

category: pharmacology and toxicology


title: Gypenosides modulate NCX calcium flux, insulin secretion and cytoprotection in BRIN-BD11 pancreatic β-cells

abstract: Gypenosides are saponins extracted from the plant Gynostemma pentaphyllum, suggested to have antidiabetic and anti-obesity potential. However, its mechanism of action is not fully understood. The present study aimed to investigate the cytoprotective and insulin stimulatory effects of gypenosides using the rat BRIN-BD11 {beta}-cell line. Gypenosides provided a significant cytoprotective effect against palmitate-, peroxide- and cytokine-induced cytotoxicity, with upregulation of antioxidant genes Nrf2, Cat, Sod1, and Gpx1. Acutely, gypenosides enhanced intracellular calcium ([Ca2+]i) and insulin secretion in a dose-dependent manner. The presence of the sodium/calcium exchanger (NCX) reverse mode inhibitor SN-6 blocked the gypenosides mediated increase in [Ca2+]I but not the insulin secretion. These findings indicate that gypenosides may enhance [Ca2+]i by activating the reverse mode of NCX channels and a possible calcium-independent mechanism involved in their insulin secretion. Gypenosides also upregulate the antioxidant gene expression and protect against oxidative stress and lipotoxicity, providing the rationale for their observed antidiabetic actions.


title: An artificial self-assembling nanocompartment for organising metabolic pathways in yeast

abstract: Metabolic pathways are commonly organised by sequestration into discrete cellular compartments. Compartments prevent unfavourable interactions with other pathways and provide local environments conducive to the activity of encapsulated enzymes. Such compartments are also useful synthetic biology tools for examining enzyme/pathway behaviour and for metabolic engineering. Here, we expand the intracellular compartmentalisation toolbox for budding yeast (Saccharomyces cerevisiae) with engineered Murine polyomavirus virus-like particles (MPyV VLPs). The MPyV system has two components: VP1 which self-assembles into the compartment shell; and a short anchor, VP2C, which mediates cargo protein encapsulation via binding to the inner surface of the VP1 shell. Destabilised GFP fused to VP2C was specifically sorted into VLPs and thereby protected from host-mediated degradation. In order to access metabolites of native and engineered yeast metabolism, VLP-based nanocompartments were directed to assemble in the cytosol by removal of the VP1 nuclear localisation signal. To demonstrate their ability to function as a metabolic compartment, MPyV VLPs were used to encapsulate myo-inositol oxygenase (MIOX), an unstable and rate-limiting enzyme in D-glucaric acid biosynthesis. Strains with encapsulated MIOX produced ~20% more D-glucaric acid compared to controls expressing  free MIOX - despite accumulating dramatically less expressed protein - and also grew to higher cell densities. These effects were linked to enzyme stabilisation and mitigation of cellular toxicity by the engineered compartment. This is the first demonstration in yeast of an artificial biocatalytic compartment that can participate in a metabolic pathway and establishes the MPyV platform as a promising synthetic biology tool for yeast engineering.

category: synthetic biology


title: Metabolic flux partitioning between the TCA cycle and glyoxylate shunt combined with a reversible methyl citrate cycle provide nutritional flexibility for Mycobacterium tuberculosis

abstract:
The utilisation of multiple host-derived carbon substrates is required by Mycobacterium tuberculosis (Mtb) to successfully sustain a tuberculosis infection thereby identifying the Mtb specific metabolic pathways and enzymes required for carbon co-metabolism as potential drug targets. Metabolic flux represents the final integrative outcome of many different levels of cellular regulation that contribute to the flow of metabolites through the metabolic network. It is therefore critical that we have an in-depth understanding of the rewiring of metabolic fluxes in different conditions. Here, we employed 13C-metabolic flux analysis using stable isotope tracers (13C and 2H) and lipid fingerprinting to investigate the metabolic network of Mtb growing slowly on physiologically relevant carbon sources in a steady state chemostat. We demonstrate that Mtb is able to efficiently co-metabolise combinations of either cholesterol or glycerol along with C2 generating carbon substrates. The uniform assimilation of the carbon sources by Mtb throughout the network indicated no compartmentalization of metabolism in these conditions however there were substrate specific differences in metabolic fluxes. This work identified that partitioning of flux between the TCA cycle and the glyoxylate shunt combined with a reversible methyl citrate cycle as the critical metabolic nodes which underlie the nutritional flexibility of Mtb. These findings provide new insights into the metabolic architecture that affords adaptability of Mtb to divergent carbon substrates.

ImportanceEach year more than 1 million people die of tuberculosis (TB). Many more are infected but successfully diagnosed and treated with antibiotics, however antibiotic-resistant TB isolates are becoming ever more prevalent and so novel therapies are urgently needed that can effectively kill the causative agent. Mtb specific metabolic pathways have been identified as an important drug target in TB. However the apparent metabolic plasticity of this pathogen presents a major obstacle to efficient targeting of Mtb specific vulnerabilities and therefore it is critical to define the metabolic fluxes that Mtb utilises in different conditions. Here, we used 13C-metabolic flux analysis to measure the metabolic fluxes that Mtb uses whilst growing on potential in vivo nutrients. Our analysis identified selective use of the metabolic network that included the TCA cycle, glyoxylate shunt and methyl citrate cycle. The metabolic flux phenotypes determined in this study improves our understanding about the co-metabolism of multiple carbon substrates by Mtb identifying a reversible methyl citrate cycle and the glyoxylate shunt as the critical metabolic nodes which underlie the nutritional flexibility of Mtb.

category: systems biology


title: Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks of Mycobacterium tuberculosis

abstract: The ability of Mycobacterium tuberculosis (Mtb) to adopt heterogeneous physiological states, underlies its success in evading the immune system and tolerating antibiotic killing. Drug tolerant phenotypes are a major reason why the tuberculosis (TB) mortality rate is so high, with over 1.8 million deaths annually. To develop new TB therapeutics that better treat the infection (faster and more completely), a systems-level approach is needed to reveal the complexity of network-based adaptations of Mtb. Here, we report a new predictive model called PRIME (Phenotype of Regulatory influences Integrated with Metabolism and Environment) to uncover environment-specific vulnerabilities within the regulatory and metabolic networks of Mtb. Through extensive performance evaluations using genome-wide fitness screens, we demonstrate that PRIME makes mechanistically accurate predictions of context-specific vulnerabilities within the integrated regulatory and metabolic networks of Mtb, accurately rank-ordering targets for potentiating treatment with frontline drugs.


title: Four new species of Cichlidogyrus (Platyhelminthes, Monogenea, Dactylogyridae) from Lake Victoria haplochromine cichlid fishes, with the redescription of C. bifurcatus and C. longipenis

abstract:
African cichlids are model systems for evolutionary studies and for host-parasite interactions, because of their adaptive radiations and because they harbour many species of monogenean parasites with high host-specificity. Here, we sampled five locations in southern Lake Victoria, the youngest of the African Great Lakes. We surveyed gillinfecting monogeneans from 18 cichlid species belonging to the Lake Victoria radiation superflock and two cichlid species representing two older and distantly related lineages. We found one species of Gyrodactylus (Gyrodactylidae, Monogenea), Gyrodactylus sturmbaueri Vanhove, Snoeks, Volckaert & Huyse, 2011, and seven species of Cichlidogyrus (Dactylogyridae, Monogenea). Four species are herein described: Cichlidogyrus pseudodossoui n. sp., C. nyanza n. sp., C. furu n. sp., C. vetusmolendarius n. sp.. Another species is reported but not formally described (because of few specimens and morphological similarity with C. furu n. sp.). Two other species are redescribed: Cichlidogyrus bifurcatus Paperna, 1960 and C. longipenis Paperna & Thurston, 1969. Our results confirm that the monogenean fauna of Victorian littoral cichlids displays lower species richness and lower host-specificity than that of Lake Tanganyika littoral cichlids. In C. furu n. sp., hooks V are clearly longer than the other hooks, highlighting the need to re-evaluate the current classification system of haptoral configurations that considers hook pairs III-VII as rather uniform. Some morphological features of C. bifurcatus, C. longipenis and C. nyanza n. sp. suggest that these are closely related to other congeners that infect haplochromines. We also found morphological indications that representatives of Cichlidogyrus colonised Lake Victoria haplochromines or their ancestors at least twice, which is in line with the Lake Victoria superflock being colonized by two cichlid tribes (Haplochromini and Oreochromini).

DisclaimerThis preprint is disclaimed for purposes of Zoological Nomenclature in accordance with the International Code of Zoological Nomenclature, Fourth Edition Articles 8.2 and 8.3 (ICZN 1999). No new names or nomenclatural changes are available from statements in this preprint.

Resume - Quatre especes nouvelles de Cichlidogyrus (Platyhelminthes, Monogenea, Dactylogyridae) parasites dhaplochromine (Cichlidae) du lac Victoria, avec la redescription de C. bifurcatus and C. longipenisA cause des radiations adaptatives quils ont subies, les cichlides africain sont des systemes modeles pour etudier levolution, mais aussi les relations hotes/parasites, car ils hebergent de nombreuses especes de Monogenes parasites qui presentent une specificite etroite vis-a-vis de leurs hotes. Dans ce travail, nous avons echantillonne cinq localites dans le Sud du lac Victoria, le plus jeune des grands lacs dAfrique de lEst. Nous avons examine les Monogenes presents sur les branchies de 18 especes de Cichlides appartenant a la radiation adaptative << superflock >> du lac Victoria et de deux especes representant deux lignees anciennes et non etroitement apparentees. Nous avons trouve une espece de Gyrodactylus (Gyrodactylidae, Monogenea), Gyrodactylus sturmbaueri Vanhove, Snoeks, Volckaert & Huyse, 2011 et sept especes de Cichlidogyrus (Dactylogyridae, Monogenea). Quatre especes nouvelles sont decrites dans le present travail : Cichlidogyrus pseudodossoui n. sp., C. nyanza n. sp., C. furu n. sp., C. vetusmolendarius n. sp.. Une est signalee mais non decrite formellement (trop peux dindividus recueillis, morphologiquement proche de C. furu n. sp.). Deux autres sont redecrites : Cichlidogyrus bifurcatus Paperna, 1960 and C. longipenis Paperna & Thurston, 1969. Nos resultats confirment que la faune des Monogenes des Cichlides du lac Victoria fait preuve dune richesse specifique et dune specificite moins importante que celle du lac Tanganyika. Chez C. furu n. sp. la paire de crochet V etant nettement plus longue que les autres, il faudra reconsiderer le systeme de classification actuel des types de hapteurs chez les Cichlidogyrus, qui considere que tous les crochets (III a VII) ont la meme taille. Quelques caracteristiques morphologiques de C. bifurcatus, C. longipenis et C. nyanza n. sp. pourraient etre la preuve dune ascendance commune avec des congeneres presents chez dautres Haplochromines. De meme, certains caracteres indiqueraient que des representants des Cichlidogyrus ont colonise les Haplochromines du lac Victoria, ou leurs ancetres, au moins a deux reprises, ce qui est coherent avec une colonisation du lac par deux lignees de cichlides distinctes (Haplochromini and Oreochromini).

category: zoology


title: Natural IgA and TNFRSF13B polymorphism: a double edged sword fueling balancing selection

abstract: TNFRSF13B encodes the "transmembrane-activator and CAML-interactor" (TACI) receptor, which drives plasma cell differentiation. Although TNFRSF13B supports host defense, dominant-negative TNFRSF13B alleles are common in humans and other species and only rarely associate with disease. We reasoned the high frequency of disruptive TNFRSF13B alleles reflects balancing selection, the loss of function conferring advantage in some settings. Testing that concept, we asked whether and how a common human dominant negative variant, TNFRSF13B A181E, imparts resistance to enteric pathogens. Mice engineered to express mono-allelic or bi-allelic A144E variants of tnrsf13B, corresponding to A181E exhibited striking resistance to pathogenicity and transmission of C. rodentium, a murine pathogen that models enterohemorrhagic E. coli, and resistance was principally owed to deficiency of natural IgA in the intestine. In wild type mice with gut IgA and in mutant mice fed IgA, binding of Ig induces expression of LEE encoded virulence genes, which confer pathogenicity and transmission. C. rodentium and probably some other enteric organisms thus appropriated binding of otherwise protective antibodies to signal induction of the virulence program and the high prevalence of TNFRSF13B dominant negative variants thus reflects balancing selection.

category: immunology


title: Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions

abstract: Genetic effects on gene expression and splicing can be modulated by cellular and environmental factors; yet interactions between genotypes, cell type and treatment have not been comprehensively studied together. We used an induced pluripotent stem cell system to study multiple cell types derived from the same individuals and exposed them to a large panel of treatments. Cellular responses involved different genes and pathways for gene expression and splicing processes, and were also highly variable across cell types and treatments. For thousands of genes, we identified variable allelic expression across contexts, and characterized different types of gene-environment interactions. Many of these GxE genes are associated with complex traits. We characterized promoter functional and evolutionary features that distinguish genes with elevated allelic imbalance mean and variance. More than 47% of the genes with dynamic regulatory interactions were missed by GTEx, but we identified them using a suitable allelic imbalance study design. This indicates the importance of exploring multiple treatments to reveal previously unrecognized regulatory loci that may be important for disease.


title: Family dynamics reveal that female house mice preferentially breed in their maternal community

abstract:
Whether females breed in their natal group is an important factor in the evolution of extended families in animal sociality. Breeding in natal groups comes with clear costs and benefits, depending on size of the group and presence of older relatives, including mothers. Studying individual decisions about whether to stay or leave can provide insight into the mechanisms and trade-offs governing the formation and structure of family groups. We investigated the family dynamics of a large population of free-ranging commensal house mice. Using dynamic community detection on long term datasets, we determined which females first bred in their natal group. We then looked at how this influenced breeding success. We found most females (77%) exhibited strong philopatry, breeding in their natal groups. Whether a female bred elsewhere was only predictable when natal groups were extremely small and related or large and unrelated. Despite this preference, breeding elsewhere made no difference in how quickly and successfully a female bred. However, presence of their mother did lead females to breed sooner when born during high breeding activity, when competition over reproduction is high. Based on these results, potential loss of fitness does not seem to be the main driver of philopatry in female house mice. The effect of the presence of mothers may indicate retaining prior social connections is an important benefit of breeding in the natal group. Mothers providing benefits also suggests lack of conflict between generations, which is likely an important attribute in the development of extended family groups.

Lay summaryWhether animals breed in the group they are born in influences how they form extended family groups. Whether females stay will depend on properties such as presence of older relatives, including mothers. Using long-term wild mouse data, we track groups and which group females bred in. Most stayed, but leaving didnt reduce breeding success. Presence of mother, who generally stayed, did lead to earlier breeding. This might be a key advantage to remaining to breed.

category: animal behavior and cognition


title: Dendritic domain-specific sampling of long-range axons shapes feedforward and feedback connectivity of L5 neurons

abstract: Feedforward and feedback pathways interact in specific dendritic domains to enable cognitive functions such as predictive processing and learning. Based on axonal projections, hierarchically lower areas are thought to form synapses primarily on dendrites in middle cortical layers, while higher-order areas are posited to target dendrites in layer 1 and in deep layers. However, the extent to which functional synapses form in regions of axo-dendritic overlap has not been extensively studied. Here, we use viral tracing in the secondary visual cortex of mice to map brain-wide inputs to thick-tufted layer 5 pyramidal neurons. Furthermore, we provide a comprehensive map of input locations through subcellular optogenetic circuit mapping. We show that input pathways target distinct dendritic domains with far greater specificity than appears from their axonal branching, often deviating substantially from the canonical patterns. Common assumptions regarding the dendrite-level interaction of feedforward and feedback inputs may thus need revisiting.

category: neuroscience


title: Cortical Processing of Arithmetic and Simple Sentences in an Auditory Attention Task

abstract:
Cortical processing of arithmetic and of language rely on both shared and task-specific neural mechanisms, which should also be dissociable from the particular sensory modality used to probe them. Here, spoken arithmetical and non-mathematical statements were employed to investigate neural processing of arithmetic, compared to general language processing, in an attention-modulated cocktail party paradigm. Magnetoencephalography (MEG) data was recorded from 22 subjects listening to audio mixtures of spoken sentences and arithmetic equations while selectively attending to one of the two speech streams. Short sentences and simple equations were presented diotically at fixed and distinct word/symbol and sentence/equation rates. Critically, this allowed neural responses to acoustics, words, and symbols to be dissociated from responses to sentences and equations. Indeed, the simultaneous neural processing of the acoustics of words and symbols was observed in auditory cortex for both streams. Neural responses to sentences and equations, however, was predominantly to the attended stream, and originated primarily from left temporal, and parietal areas, respectively. Additionally, these neural responses were correlated with behavioral performance in a deviant detection task. Source-localized Temporal Response Functions revealed distinct cortical dynamics of responses to sentences in left temporal areas and equations in bilateral temporal, parietal and motor areas. Finally, the target of attention could be decoded from MEG responses, especially in left superior parietal areas. In short, the neural responses to arithmetic and language are especially well segregated during the cocktail party paradigm, and the correlation with behavior suggests that they may be linked to successful comprehension or calculation.

Significance StatementNeural processing of arithmetic relies on dedicated, modality independent cortical networks that are distinct from those underlying language processing. Using a simultaneous cocktail party listening paradigm, we found that these separate networks segregate naturally when listeners selectively attend to one type over the other. Time-locked activity in the left temporal lobe was observed for responses to both spoken sentences and equations, but the latter additionally showed bilateral parietal activity consistent with arithmetic processing. Critically, these responses were modulated by selective attention and correlated with task behavior, consistent with reflecting high-level processing for speech comprehension or correct calculations. The response dynamics show task-related differences that were used to reliably decode the attentional target of sentences or equations.


title: Innate visual attraction in wood ants is a hardwired behaviour seen across different motivational and ecological contexts

abstract: Ants are expert navigators combing innate and learnt navigational strategies. Whereas we know that the ants feeding state segregates visual navigational memories in ants navigating along a learnt route, it is an open question if the motivational state also affects the ants innate visual preferences. Wood ant foragers show an innate attraction to conspicuous visual cues. These foragers inhabit cluttered woodland habitat and feed on honeydew from aphids on trees, hence, the attraction to  tree-like objects might be an ecologically relevant behaviour that is tailored to the wood ants foraging ecology. Foragers from other ant species with different foraging ecologies show very different innate attractions. We investigated here the innate visual response of wood ant foragers with different motivational states, i.e. unfed or fed, as well as males that have a short life span and show no foraging activity. Our results show that ants from all three groups orient towards a prominent visual cue, i.e. the wood ants innate visual attraction is not context dependent, but a hardwired behaviour seen across different motivational and ecological contexts.


title: DeepRank: A deep learning framework for data mining 3D protein-protein interfaces

abstract:
Three-dimensional (3D) structures of protein complexes provide fundamental information to decipher biological processes at the molecular scale. The vast amount of experimentally and computationally resolved protein-protein interfaces (PPIs) offers the possibility of training deep learning models to aid the predictions of their biological relevance.

We present here DeepRank, a general, configurable deep learning framework for data mining PPIs using 3D convolutional neural networks (CNNs). DeepRank maps features of PPIs onto 3D grids and trains a user-specified CNN on these 3D grids. DeepRank allows for efficient training of 3D CNNs with data sets containing millions of PPIs and supports both classification and regression.

We demonstrate the performance of DeepRank on two distinct challenges: The classification of biological versus crystallographic PPIs, and the ranking of docking models. For both problems DeepRank is competitive or outperforms state-of-the-art methods, demonstrating the versatility of the framework for research in structural biology.


title: Neptune: An environment for the delivery of genomic medicine

abstract:
PurposeGenomic medicine holds great promise for improving healthcare, but integrating searchable and actionable genetic data into electronic health records remains a challenge. Here, we describe Neptune, a system for managing the interaction between a clinical laboratory and an electronic health record system.

MethodsWe developed Neptune and applied it to two clinical sequencing projects that required report customization, variant reanalysis and EHR integration.

ResultsNeptune enabled the analysis of data for generation of and delivery to EHR systems of over 15,000 clinical genomic reports. These projects demanded customizable clinical reports that contained a variety of genetic data types including SNVs, CNVs, pharmacogenomics and polygenic risk scores. Two variant reanalysis activities were also supported, highlighting this important workflow.

ConclusionsMethods are needed for delivering structured genetic data to EHRs. This need extends beyond developing data formats to providing infrastructure that manages the reporting process itself. Neptune was successfully applied on two high-throughput clinical sequencing projects to build and deliver clinical reports to EHR systems. The software is open and available at https://gitlab.com/bcm-hgsc/neptune.


title: MDM-TASK-web: A web platform for protein dynamic residue networks and modal analysis

abstract:
MDM-TASK-web is the web server for the MD-TASK and MODE-TASK software suites. It simplifies the set-up required to perform and visualize results from dynamic residue network analysis, perturbation-response scanning, dynamic cross-correlation, essential dynamics and normal mode analysis. In a nutshell, the server gives access to updated versions of the tool suites, and offers new functionalities and integrated 2D/3D visualization. An embedded work-flow, integrated documentation and visualization tools shortens the number of steps to follow, starting from calculations to result visualization. The web server (available at https://mdmtaskweb.rubi.ru.ac.za/) is powered by Django and a MySQL database, and is compatible with all major web browsers. All scripts implemented in the web platform are freely available at https://github.com/RUBi-ZA/MD-TASK/tree/mdm-task-web and https://github.com/RUBi-ZA/MODE-TASK/tree/mdm-task-web.

HighlightsO_LIMDM-TASK-web is the web server for highly utilized MD-TASK and MODE-TASK with updates
C_LIO_LIEight residue network centrality metrics are available to analyze static and dynamic proteins
C_LIO_LINovel comparative essential dynamics is established to compare independent MD simulations
C_LIO_LICommunication propensity tool to evaluate residue communication efficiency is implemented.
C_LIO_LINormal mode analysis from static and protein MD simulations is provided
C_LI


title: MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics


abstract: Secondary metabolites (SMs) are a vast group of compounds with different structures and properties. Humankind uses SMs as drugs, food additives, dyes, and as monomers for novel plastics. In many cases, the biosynthesis of SMs is catalysed by enzymes whose corresponding genes are co-localized in the genome in biosynthetic gene clusters (BGCs). Notably, BGCs may contain so-called gap genes, that are not involved in the biosynthesis of the SM. Current genome mining tools can identify BGCs but they have problems with distinguishing essential genes from gap genes and defining the borders of a BGC. This can and must be done by expensive, laborious, and time-consuming comparative genomic approaches or co-expression analyses. In this study, we developed a novel tool that allows automated identification of essential genes in a BGC based solely on genomic data. The Functional Order (FunOrder) tool - Identification of essential biosynthetic genes through computational molecular co-evolution - searches for co-evolutionary linked genes in the BGCs. In light of the growing number of genomic data available, this will contribute to the studies of BGCs in native hosts and facilitate heterologous expression in other organisms with the aim of the discovery of novel SMs, including antibiotics and other pharmaceuticals.


title: DeepFrag: An Open-Source Browser App for Deep-Learning Lead Optimization

abstract: 1Lead optimization, a critical step in early-stage drug discovery, involves making chemical modifications to a small-molecule ligand to improve its drug-like properties (e.g., binding affinity). We recently developed DeepFrag, a deep-learning model capable of recommending such modifications. Though a powerful hypothesis-generating tool, DeepFrag is currently implemented in Python and so requires a certain degree of computational expertise. To encourage broader adoption, we have created the DeepFrag browser app, which provides a user-friendly graphical user interface that runs the DeepFrag model in users web browsers. The browser app does not require users to upload their molecular structures to a third-party server, nor does it require the separate installation of any third-party software. We are hopeful that the app will be a useful tool for both researchers and students. It can be accessed free of charge, without requiring registration, at http://durrantlab.com/deepfrag. The source code is also available at http://git.durrantlab.com/jdurrant/deepfrag-app, released under the terms of the open-source Apache License, Version 2.0.


title: Trial-by-trial modulation of express visuomotor responses induced by symbolic or barely detectable cues

abstract:
Human cerebral cortex can produce visuomotor responses that are modulated by contextual and task-specific constraints. However, the distributed cortical network for visuomotor transformations limits the minimal response time of that pathway. Notably, humans can generate express visuomotor responses that are inflexibly tuned to the target location and occur 80-120ms from stimulus presentation (stimulus-locked responses, SLRs). This suggests a subcortical pathway for visuomotor transformations involving the superior colliculus and its downstream reticulo-spinal projections. Here we investigated whether cognitive expectations can modulate the SLR. In one experiment, we recorded surface EMG from shoulder muscles as participants reached toward a visual target whose location was unpredictable in control conditions, and partially predictable in cue conditions by extrapolating a symbolic cue (75% validity). Valid symbolic cues led to faster and larger SLRs than control conditions; invalid symbolic cues produced slower and smaller SLRs than control conditions. This is consistent with a cortical top-down modulation of the putative subcortical SLR-network. In a second experiment, we presented high-contrast targets in isolation (control) or ~24ms after low-contrast stimuli, which could appear at the same (valid cue) or opposite (invalid cue) location as the target, and with equal probability (50% cue validity). We observed faster SLRs than control with the valid low-contrast cues, whereas the invalid cues led to the opposite results. These findings may reflect exogenous priming mechanisms of the SLR network, potentially evolving subcortically via the superior colliculus. Overall, our results support both top-down and bottom-up modulations of the putative subcortical SLR network in humans.

NEW & NOTEWORTHYExpress visuomotor responses in humans appear to reflect subcortical sensorimotor transformation of visual inputs, potentially conveyed via the tecto-reticulo-spinal pathway. Here we show that the express responses are influenced both by symbolic and barely detectable spatial cues about stimulus location. The symbolic cue-induced effects suggest cortical top-down modulation of the putative subcortical visuomotor network. The effects of barely detectable cues may reflect exogenous priming mechanisms of the tecto-reticulo-spinal pathway.


title: Small size of recorded neuronal structures confines the accuracy in direct axonal voltage measurements

abstract: Patch-clamp instruments including amplifier circuits and pipettes affect the recorded voltage signals. We hypothesized that realistic and complete in silico representation of recording instruments together with detailed morphology and biophysics of small recorded structures will precisely reveal signal distortions and provides a tool that predicts native signals from distorted voltage recordings. Therefore, we built a model that was verified by small axonal recordings. The model accurately recreated actual action potential measurements with typical recording artefacts and predicted the native electrical behavior. The simulations verified that recording instruments substantially filter voltage recordings. Moreover, we revealed that instrumentation directly interferes with local signal generation depending on the size of the recorded structures, which complicates the interpretation of recordings from smaller structures, such as axons. However, our model offers a straightforward approach that predicts the native waveforms of fast voltage signals and the underlying conductances even from the smallest neuronal structures.


title: Fat and carbohydrate interact to potentiate food reward in healthy weight but not in overweight or obesity

abstract: Prior work suggests that actual, but not estimated, energy density drives the reinforcing value of food [1,2] and that energy from fat and carbohydrate can interact to potentiate reward [2]. Here we sought to replicate these findings in an American sample and to determine if the effects are influenced by body mass index (BMI). Thirty participants with healthy weight (HW; BMI 21.92 {+/-} 1.77; M {+/-} SD) and 30 participants with overweight/obesity (OW/OB; BMI 29.42 {+/-} 4.44) rated pictures of common American snacks in 120-kcal portions for liking, familiarity, frequency of consumption, expected satiety, healthiness, energy content, energy density, and price. Participants then completed an auction task where they bid for the opportunity to consume each food. Snacks contained either primarily carbohydrate, primarily fat, or roughly equal portions of fat and carbohydrate (combo). Replicating prior work, we found that participants with HW bid the most for combo foods in linear mixed model analyses. This effect was not observed among individuals with OW/OB. Additionally, in contrast with previous reports [1,2], our linear regression analyses revealed a negative relationship between the actual energy density of the snacks and bid amount that was mediated by food price. Our findings support altered macronutrient reinforcement in obesity and highlight potential influences of the food environment on the regulation of food reward.


title: Characterization of cognitive-motor function in women who have experienced intimate partner violence-related brain injury

abstract: Intimate partner violence (IPV) affects at least 1 in 3 women worldwide and up to 92% report symptoms consistent with brain injury (BI). Although a handful of studies have examined different aspects of brain structure and function in this population, none has characterized potential deficits in cognitive-motor function. This knowledge gap was addressed in the current study by having participants who had experienced IPV complete the bimanual Object Hit & Avoid (OHA) task on a Kinarm End-Point Lab. BI load, as assessed by the Brain Injury Severity Assessment (BISA) tool as well as measures of comorbidities (PTSD, anxiety, depression, substance use, history of abuse) were also collected. Results demonstrated BI load accounted for a significant amount of variability in the number of targets hit and average hand speed. PTSD, anxiety, and depression also contributed significantly to the variability in these measures as well as to the number and proportion of distractor hits, and the object processing rate. Taken together, these findings suggest IPV-related BI, as well as comorbid PTSD, anxiety, and depression, disrupt the processing required to quickly and accurately hit targets while avoiding distractors. This pattern of results reflects the complex interaction between the physical injuries induced by the episodes of IPV and the resulting impacts these experiences have on mental health.


title: Multi-Tissue Multi-Compartment models of diffusion MRI

abstract: State-of-the-art multi-compartment microstructural models of diffusion MRI (dMRI) in the human brain have limited capability to model multiple tissues at the same time. In particular, the available techniques that allow this multi-tissue modelling are based on multi-TE acquisitions. In this work we propose a novel multi-tissue formulation of classical multi-compartment models that relies on more common single-TE acquisitions and can be employed in the analysis of previously acquired datasets. We show how modelling multiple tissues provides a new interpretation of the concepts of signal fraction and volume fraction in the context of multi-compartment modelling. The software that allows to inspect single-TE diffusion MRI data with multi-tissue multi-compartment models is included in the publicly available Dmipy Python package.


title: Just-in-time: gaze guidance behavior while action planning and execution in VR

abstract:
AO_SCPLOWBSTRACTC_SCPLOWEye movements in the natural environment have primarily been studied for over-learned activities such as tea-making, sandwich-making, and hand-washing, which have a fixed sequence of actions associated with them. These studies indicate an interplay of low-level cognitive schemas that facilitate task completion. However, it is unclear if this strategy is also in play when the task is novel and a sequence of actions must be planned. Here, to study attention mechanisms, we recorded gaze and body movements in a naturalistic sorting task. In a virtual environment, subjects moved objects on a life-size shelf to achieve a given order. To study the action planning and execution related gaze guidance behavior we also controlled the complexity of the tasks, i.e. the objects were to be sorted based on a single or two different object features. We show that subjects are close to optimal while performing the easy tasks and are more sub-optimal while performing the more complex tasks. Fixations aligned with action onset showed gaze is tightly coupled with the action sequence and less so with task complexity. Task complexity elicited differences at specific time points where oculomotor behavior could be categorized into searching, guiding, checking fixations. Task complexity also affected the scan-paths on the task-relevant regions of interest during action planning and execution where subjects exhibit a greater search and action monitoring behavior in more complex tasks. Furthermore, task complexity also affected the timing of first fixations on the task-relevant regions of interest for action planning but not for action execution. Finally, the scan paths and the temporal sequence of first fixations suggest a just-in-time strategy of gaze allocation. Based on the spatio-temporal features of gaze control, we can conclude that eye movements during novel tasks correspond closely to low-level cognitive schemas that support the production and execution of actions.

Author SummaryEye movements in the natural environment have primarily been studied for over-learned and habitual everyday activities (tea-making, sandwich-making, hand-washing) which have a fixed sequence of actions associated with them. These studies typically categorize eye movements related to low level action plans of locating the object of interest, directing the body or hand to the object, and monitoring the action execution. In this study, we were interested in generalizing these task-oriented eye movements for novel tasks that are not associated with an inherent action sequence. To that end, we asked subjects to sort objects based on object features on a life-size shelf in a virtual environment as we recorded their eye and body movements. We then analyzed gaze features relative to the action onset i.e. when the hand made contact with an object. By only studying the sequence of fixations based on past, current and next actions, we aimed to elucidate the general characteristics of gaze behavior relative to action planning and execution and independent of object identity. With our analysis, we could categorize fixations into searching, guiding, monitoring fixations in a data-driven manner. Based on the spatio-temporal features of gaze control, we can conclude that novel tasks predominantly elicit eye movements corresponding to low-level action plans that support the production and execution of actions.


title: Low-level Action Schemas Support Gaze Guidance Behavior for Action Planning and Execution in Novel Tasks


title: Chronic nicotine increases midbrain dopamine neuron activity and biases individual strategies towards reduced exploration in a foraging task.

abstract: Long-term exposure to nicotine alters brain circuits and induces profound changes in decision-making strategies, affecting behaviors both related and unrelated to drug seeking and consumption. Using an intracranial self-stimulation reward-based foraging task, we investigated the impact of chronic nicotine on the trade-off between exploitation and exploration, and the role of ventral tegmental area (VTA) dopamine (DA) neuron activity in decision-making unrelated to nicotine-seeking. Model-based and archetypal analysis revealed a substantial inter-individual variability in decision-making strategies, with mice passively exposed to chronic nicotine visiting more frequently options associated with higher reward probability and therefore shifting toward a more exploitative profile compared to non-exposed animals. We then mimicked the effect of chronic nicotine on the tonic activity of VTA DA neurons using optogenetics, and found that photo-stimulated mice had a behavioral phenotype very close to that of mice exposed to nicotine, suggesting that the dopaminergic control of the exploration/exploitation balance is altered under nicotine exposure. Our results thus reveal a key role of tonic midbrain DA in the exploration/exploitation trade-off and highlight a potential mechanism by which nicotine affects decision-making.


title: Defensive freezing and its relation to approach-avoidance decision-making under threat

abstract: Successful responding to acutely threatening situations requires adequate approach-avoidance decisions. However, it is unclear how threat-induced states-like freezing-related bradycardia-impact the weighing of the potential outcomes of such value-based decisions. Insight into the underlying computations is essential, not only to improve our models of decision-making but also to improve interventions for maladaptive decisions, for instance in anxiety patients and first-responders who frequently have to make decisions under acute threat. Forty-two participants made passive and active approach-avoidance decisions under threat-of-shock when confronted with mixed outcome-prospects (i.e., varying money and shock amounts). Choice behavior was best predicted by a model including individual action-tendencies and bradycardia, beyond the subjective value of the outcome. Moreover, threat-related bradycardia interacted with subjective value, depending on the action-context (i.e., passive vs. active). Specifically, in action-contexts incongruent with participants intrinsic action-tendencies, strong freezers showed diminished effects of subjective value on choice. These findings illustrate the relevance of testing approach-avoidance decisions in relatively ecologically valid conditions of acute and primarily reinforced threat. These mechanistic insights into approach-avoidance conflict-resolution may inspire biofeedback-related techniques to optimize decision-making under threat. Critically, the findings demonstrate the relevance of incorporating internal psychophysiological states and external action-contexts into models of approach-avoidance decision-making.


title: Agri-environment nectar chemistry suppresses parasite social epidemiology in an important pollinator

abstract: Emergent infectious diseases are a principal driver of biodiversity loss globally. The population and range declines of a suite of North American bumblebees, a group of important pollinators, have been linked to emergent infection with the microsporidian Nosema bombi. Previous work has shown that phytochemicals in pollen and nectar can negatively impact parasites in individual bumblebees, but how this relates to social epidemiology and by extension whether plants can be effectively used as disease management strategies remains unexplored. Here we show that caffeine, identified in the nectar of Sainfoin, a constituent of agri-environment schemes, significantly reduced N. bombi infection intensity in individual bumblebees and, for the first time, that such effects impact social epidemiology, with colonies reared from wild caught queens having lower prevalence and intensity of infection. Furthermore, infection prevalence was lower in foraging bumblebees from these colonies, suggesting a likely reduction in population-level transmission. Our results demonstrate that phytochemicals can impact pollinator disease epidemiology and that planting strategies, which increase floral abundance to support biodiversity could be co-opted as disease management strategies.


title: Modeling Vertical Migrations of Zooplankton Based on Maximizing Fitness

abstract:
The purpose of the work is to calculate the evolutionarily stable strategy of zooplankton diel vertical migrations from known data of the environment using principles of evolutionary optimality and selection.

At the first stage of the research, the fitness function is identified using artificial neural network technologies. The training sample is formed based on empirical observations. It includes pairwise comparison results of the selective advantages of a certain set of species. Key parameters of each strategy are calculated: energy gain from ingested food, metabolic losses, energy costs on movement, population losses from predation and unfavorable living conditions. The problem of finding coefficients of the fitness function is reduced to a classification problem. The single-layer neural network is built to solve this problem. The use of this technology allows one to construct the fitness function in the form of a linear convolution of key parameters with identified coefficients.

At the second stage, an evolutionarily stable strategy of the zooplankton behavior is found by maximizing the identified fitness function. The maximization problem is solved using optimal control methods. A feature of this work is the use of piecewise linear approximations of environmental factors: the distribution of food and predator depending on the depth. As a result of the study, mathematical and software tools have been created for modeling and analyzing the hereditary behavior of living organisms in an aquatic ecosystem. Mathematical modeling of diel vertical migrations of zooplankton in Saanich Bay has been carried out.


title: Functional and comparative genome analysis reveals clade-specific genome innovations in the killer fungus Candida auris

abstract: The thermotolerant multidrug-resistant ascomycete Candida auris rapidly emerged since 2009 and simultaneously evolved in different geographical zones worldwide, causing superficial as well as systemic infections. The molecular events that orchestrated this sudden emergence of the killer fungus remain mostly elusive. Here, we identify centromeres in C. auris and related species, using a combined approach of chromatin immunoprecipitation and comparative genomic analyses. We find that C. auris and multiple other species in the Clavispora/Candida clade shared a conserved small regional centromere landscape lacking pericentromeres. Further, a centromere inactivation event led to karyotypic alterations in this species complex. Inter-species genome analysis identified several structural chromosomal changes around centromeres. In addition, centromeres are found to be rapidly evolving loci among the different geographical clades of the same species of C. auris. Finally, we reveal an evolutionary trajectory of the unique karyotype associated with clade 2 that consists of the drug susceptible isolates of C. auris.


title: SFARI Genes and where to find them; classification modelling to identify genes associated with Autism Spectrum Disorder from RNA-seq data

abstract:
MotivationAutism spectrum disorder (ASD) has a strong, yet heterogeneous, genetic component. Among the various methods that are being developed to help reveal the underlying molecular aetiology of the disease, one that is gaining popularity is the combination of gene expression and clinical genetic data. For ASD, the SFARI-gene database comprises lists of curated genes in which presumed causative mutations have been identified in patients. In order to predict novel candidate SFARI-genes we built classification models combining differential gene expression data for ASD patients and unaffected individuals with a genes status in the SFARI-gene list.

ResultsSFARI-genes were not found to be significantly associated with differential gene expression patterns, nor were they enriched in gene co-expression network modules that had a strong correlation with ASD diagnosis. However, network analysis and machine learning models that incorporate information from the whole gene co-expression network were able to predict novel candidate genes that share features of existing SFARI genes and have support for roles in ASD in the literature. We found a statistically significant bias related to the absolute level of gene expression for existing SFARI genes and their scores. It is essential that this bias be taken into account when studies interpret ASD gene expression data at gene, module and whole-network levels.

AvailabilitySource code is available from GitHub (https://doi.org/10.5281/zenodo.4463693) and the accompanying data from The University of Edinburgh DataStore (https://doi.org/10.7488/ds/2980)

Contactian.simpson@ed.ac.uk


title: Rest-fMRI Based Comparison Study between Autism Spectrum Disorder and Typically Control Using Graph Frequency Bands

abstract: Graph signal processing is a subset of signal processing enabling the analysis of functional magnetic resonance imaging (fMRI) data in brain topological domain. One of the most important and highly interested tool of GSP is graph Fourier transform (GFT) by which brain signals can be analyzed in different graph frequency bands. In this paper, the resting-state fMRI (rfMRI) data is analyzed using GFT tool in order to discover new knowledge about the autism spectrum disorder (ASD) and find features discriminating between ASD and typically control (TC) subjects. For ASD group, the signal concentration in both low and high frequency bands is decreased by increasing the age in most of the brain well-known networks. The ASD in comparison to TC shows less intention for changing the signal concentration level when the level is very low or very high. In graph low frequency band, increasing the age is along with increasing the segregation and integration of brain ROIs respectively for ASD and TC. Also, in this band, the brain ROIs integration of ASD is more than TC. By increasing the age, the auditory network of ASD subjects shows increasing segregation and integration in graph low and high frequency bands, respectively. The reduced segregation of default mode network in ASD is happened in graph middle and higher frequency bands. The functional connectivity analysis between low and high frequency signals shows that some of the high frequency ROIs have connections with all low frequency ROIs so that the most of these connections are dramatically and significantly different between ASD and TC. By analyzing the local vertex frequency spectrum (LVFS) of ASD and TC at different states, it is seen these groups show contradictory behaviors with respect to each other in brain default mode network in two states. The results of different scenarios at different graph frequency bands demonstrate that using functional and structural data together can provide powerful tool for recognizing the ASD or even other brain disorders.

category: bioengineering


title: Expected 10-anonymity of HyperLogLog sketches for federated queries of clinical data repositories

abstract:
MotivationThe rapid growth in of electronic medical records provide immense potential to researchers, but are often silo-ed at separate hospitals. As a result, federated networks have arisen, which allow simultaneously querying medical databases at a group of connected institutions. The most basic such query is the aggregate count--e.g. How many patients have diabetes? However, depending on the protocol used to estimate that total, there is always a trade-off in the accuracy of the estimate against the risk of leaking confidential data. Prior work has shown that it is possible to empirically control that trade-off by using the HyperLogLog (HLL) probabilistic sketch.

ResultsIn this article, we prove complementary theoretical bounds on the k-anonymity privacy risk of using HLL sketches, as well as exhibit code to efficiently compute those bounds.

Availabilityhttps://github.com/tzyRachel/K-anonymity-Expectation

Contactywyu@math.toronto.edu

Supplementary informationN/A


title: PATO: Pangenome Analysis Toolkit

abstract:
MotivationComparative genomics is a growing field but one that will be eventually overtaken by sample size studies and the increase of available genomes in public databases. We present the Pangenome Analysis Toolkit (PATO) designed to simultaneously analyze thousands of genomes using a desktop computer. The tool performs common tasks of pangenome analysis such as core-genome definition and accessory genome properties and includes new features that help characterize population structure, annotate pathogenic features and create gene sharedness networks. PATO has been developed in R to integrate with the large set of tools available for genetic, phylogenetic and statistical analysis in this environment.

ResultsPATO can perform the most demanding bioinformatic analyses in minutes with an accuracy comparable to state-of-the-art software but 20-30x times faster. PATO also integrates all the necessary functions for the complete analysis of the most common objectives in microbiology studies. Lastly, PATO includes the necessary tools for visualizing the results and can be integrated with other analytical packages available in R.

AvailabilityThe source code for PATO is freely available at https://github.com/irycisBioinfo/PATO under the GPLv3 license.

Contactval.fernandez@salud.madrid.org

Supplementary informationSupplementary data are available at Bioinformatics online


title: Morphological Metrics of Magnetic Resonance Imaging of Glioblastoma as Biomarkers of Prognosis

abstract: Morphological characteristics have been linked to outcomes across a variety of cancers. Lacunarity is a quantitative morphological measure of how shapes fill space while fractal dimension is a morphological measure of the complexity of pixel arrangement. Glioblastoma is the most aggressive primary brain tumor with a short expected survival given the current standard-of-care treatment. Due to the sensitive location of the tumor, there is a heavy reliance on imaging to assess the state of the disease in the clinic. In this project, we computed lacunarity and fractal dimension values for glioblastoma-induced abnormalities on gadolinium-enhanced T1-weighted magnetic resonance imaging (T1Gd MRI) as well as T2-weighted (T2) and fluid-attenuated inversion recovery (FLAIR) MRIs. In our patient cohort (n=402), we aim to connect these morphological metrics calculated on pretreatment MRI with the survival of patients with GBM. We calculated lacunarity and fractal dimension across all MRI slices on necrotic regions (n=390) and abnormalities on T1Gd MRI (n=402), as well as on enhancing abnormalities present on T2/FLAIR MRI (n=257). We also explored the relationship between these metrics and age at diagnosis, as well as abnormality volume. We found statistically significant relationships to outcome across all three imaging subtypes, with the shape of T2/FLAIR abnormalities showing the strongest relationship with overall survival. The link between morphological and survival metrics could be driven by underlying biological phenomena, tumor location or microenvironmental factors that should be further explored.


title: GraphUnzip: unzipping assembly graphs with long reads and Hi-C

abstract: Long reads and Hi-C have revolutionized the field of genome assembly as they have made highly continuous assemblies accessible for challenging genomes. As haploid chromosome-level assemblies are now commonly achieved for all types of organisms, phasing assemblies has become the new frontier for genome reconstruction. Several tools have already been released using long reads and/or Hi-C to phase assemblies, but they all start from a linear sequence, and are ill-suited for non-model organisms with high levels of heterozygosity. We present GraphUnzip, a fast, memory-efficient and accurate tool to unzip assembly graphs into their constituent haplotypes using long reads and/or Hi-C data. As GraphUnzip only connects sequences in the assembly graph that already had a potential link based on overlaps, it yields high-quality gap-less supercontigs. To demonstrate the efficiency of GraphUnzip, we tested it on a simulated diploid Escherichia coli genome, and on two real datasets for the genomes of the rotifer Adineta vaga and the potato Solanum tuberosum. In all cases, GraphUnzip yielded highly continuous phased assemblies.


title: A Mixture Model Incorporating Individual Heterogeneity in Human Lifetimes

abstract: Analysis of some extensive individual-record data using a demographically informed model suggests constructing a general population model in which the lifetime of a person, beyond a certain threshold age, follows an extreme value distribution with a finite upper bound, and with that upper bound randomized over the population. The resulting population model incorporates heterogeneity in life-lengths, with lifetimes being finite individually, but with extremely long lifespans having negligible probability. Our findings are compared in detail with those of related studies in the literature, and used to reconcile contradictions between previous studies of extreme longevity. While being consistent with currently reported analyses of human lifetimes, we nevertheless differ with those who conclude in favour of unbounded human lifetimes.


title: Separated and overlapping neural coding of face and body identity

abstract: Recognising a persons identity often relies on face and body information, and is tolerant to changes in low-level visual input (e.g. viewpoint changes). Previous studies have suggested that face identity is disentangled from low-level visual input in the anterior face-responsive regions. It remains unclear which regions disentangle body identity from variations in viewpoint, and whether face and body identity are encoded separately or combined into a coherent person identity representation. We trained participants to recognize three identities, and then recorded their brain activity using fMRI while they viewed face and body images of the three identities from different viewpoints. Participants task was to respond to either the stimulus identity or viewpoint. We found consistent decoding of body identity across viewpoint in the fusiform body area, right anterior temporal cortex, middle frontal gyrus and right insula. This finding demonstrates a similar function of fusiform and anterior temporal cortex for bodies as has previously been shown for faces, suggesting these regions may play a general role in extracting high-level identity information. Moreover, we could decode identity across neural activity evoked by faces and bodies in the early visual cortex, right inferior occipital cortex, right parahippocampal cortex and right superior parietal cortex, revealing a distributed network that encodes person identity abstractly. Lastly, identity decoding was consistently better when participants attended to identity, indicating that attention to identity enhances its neural representation. These results offer new insights into how the brain develops an abstract neural coding of person identity, shared by faces and bodies.


title: Aperiodic measures of neural excitability are associated with anticorrelated hemodynamic networks at rest: a combined EEG-fMRI study

abstract:
The hallmark of resting EEG spectra are distinct rhythms emerging from a broadband, aperiodic background. This aperiodic neural signature accounts for most of total EEG power, although its significance and relation to functional neuroanatomy remains obscure. We hypothesized that aperiodic EEG reflects a significant metabolic expenditure and therefore might be associated with the default mode network while at rest. During eyes-open, resting-state recordings of simultaneous EEG-fMRI, we find that aperiodic and periodic components of EEG power are only minimally associated with activity in the default mode network. However, a whole-brain analysis identifies increases in aperiodic power correlated with hemodynamic activity in an auditory-salience-cerebellar network, and decreases in aperiodic power are correlated with hemodynamic activity in prefrontal regions. Desynchronization in residual alpha and beta power is associated with visual and sensorimotor hemodynamic activity, respectively. These findings suggest that resting-state EEG signals acquired in an fMRI scanner reflect a balance of top-down and bottom-up stimulus processing, even in the absence of an explicit task.

HIGHLIGHTSO_LIPeriodic and aperiodic EEG parameters associated with distinct resting-state networks
C_LIO_LIIncreases in aperiodic power associated with an auditory-salience-cerebellar network
C_LIO_LIDecreases in aperiodic power associated with prefrontal regions
C_LIO_LIGlobal neural excitability may reflect stimulus processing or arousal attributable to the uniqueness of the resting-state MR-scanner environment
C_LI


title: Sense of Agency for Mental Actions: Insights from a Belief-Based Action-Effect Paradigm

abstract: A substantial body of research in the past few decades has converged on the idea that the so-called "sense of agency", the feeling of being in control of our own actions, arises from the integration of multiple sources of information at different levels. In this study, we investigated whether a measurable sense of agency can be detected for mental actions, without the contribution of motor components. We used a fake action-effect paradigm, where participants were led to think that a motor action or a particular thought could trigger a sound. Results showed that the high-level sense of agency, measured through explicit reports, was of comparable strength for motor and mental actions. The  intentional binding effect, a phenomenon typically associated with the experience of agency, was also observed for both motor and mental actions, with the only exception of short action-effect delays. Furthermore, a consistent relationship between explicit reports of agency and intentional binding was found. Taken together, our results provide novel insights into the specific role of intentional cues in instantiating a sense of agency, even in the absence of motor signals. These results may have important implications for future brain-computer interfaces as well as for the study of pathological disruptions of agency.


title: Non cell-autonomous effect of astrocytes on cerebral cavernous malformations

abstract: Cerebral cavernous malformations (CCMs) are common neurovascular lesions caused by loss-of-function mutations in one of three genes, including KRIT1 (CCM1), CCM2, and PDCD10 (CCM3), and generally regarded as an endothelial cell-autonomous disease. Here we report that proliferative astrocytes play a critical role in CCM pathogenesis by serving as a major source of VEGF during CCM lesion formation. An increase in astrocyte VEGF synthesis is driven by endothelial nitric oxide (NO) generated as a consequence of KLF2 and KLF4-dependent elevation of eNOS in CCM endothelium. The increased brain endothelial production of NO stabilizes HIF-1 in astrocytes, resulting in increased VEGF production and expression of a "hypoxic" program under normoxic conditions. We show that the upregulation of cyclooxygenase-2 (COX-2), a direct HIF-1 target gene and a known component of the hypoxic program, contributes to the development of CCM lesions because the administration of a COX-2 inhibitor significantly prevents progression of CCM lesions. Thus, non-cell-autonomous crosstalk between CCM endothelium and astrocytes propels vascular lesion development, and components of the hypoxic program represent potential therapeutic targets for CCMs.


title: Individual structural MRI abnormality indexes are associated with molecular,histological and cognitive indicators for frontal glioma patients

abstract: Although every glioma patient varies in tumor size, location, histological grade and molecular biomarkers, structural abnormalities are commonly conducted in a group-level, leading to the miss of individual structural atrophy. In this study, we introduced an individual-level structural abnormality detection method for glioma patients and proposed several novel abnormality indexes to depict the individual atrophy pattern. Forty-five glioma patients in frontal lobe and fifty-two age-matched healthy controls participated in the study. All patients underwent neurocognitive test and molecular examinations, including 1p/19q co-deletion, isocitrate dehydrogenase (IDH) mutation, telomerase reverse transcriptase (TERT) promoter mutation and O6-methylguanine-DNA methyltransferase (MGMT) promotor methylation. Individual structural abnormality maps for every glioma patient were calculated from the preoperative T1 images, and the individual abnormality index were further computed and explored the associations with clinical indicators. The results manifested that: 1. Every glioma patient show unique atrophy pattern; 2. Glioma patients also share consistent atrophy regions; 3. The atrophy pattern is influenced by some molecular biomarkers. Our study provides an effective way to access the individual structural abnormalities in glioma patients, and displays great potentials in individualized precision medicine for glioma patients.


title: Probing individual-level structural atrophy in frontal glioma patients


title: Small Intestinal Resident Eosinophils Maintain Gut Homeostasis Following Microbial Colonisation

abstract:
Intestinal homeostasis following postnatal microbial colonization requires the coordination of multiple processes including the activation of immune cells, cell-cell communication, the controlled deposition of extracellular matrix, and epithelial cell turnover and differentiation. The intestine harbors the largest frequency of resident eosinophils of all homeostatic organs, yet the functional significance of eosinophil recruitment to this organ has long remained enigmatic. Eosinophils are equipped to both respond to, and modify, their local tissue environment and thus are able to regulate the adaption of tissues to environmental changes. We report a critical role for eosinophils in regulating villous structure, barrier integrity and motility in the small intestine. Notably, the microbiota was identified as a key driver of small intestinal eosinophil activation and function. Collectively our findings demonstrate a critical role for eosinophils in facilitating mutualistic interactions between host and microbiota and provide a rationale for the functional significance of their early life recruitment in the small intestine.

HIGHLIGHTSO_LIThe microbiota is a critical regulator of eosinophil activation and turnover
C_LIO_LIEosinophils uphold intestinal barrier integrity following microbial colonization
C_LIO_LILoss of eosinophils at steady-state results in increased villous blunting and altered intestinal motility
C_LI


title: piRNAs Coordinate poly(UG) Tailing to Prevent Aberrant and Permanent Gene Silencing

abstract: Noncoding RNAs have emerged as mediators of transgenerational epigenetic inheritance (TEI) in a number of organisms. A robust example of RNA-directed TEI is the inheritance of gene silencing states following RNA interference (RNAi) in the metazoan C. elegans. During RNAi inheritance, gene silencing is transmitted by a self-perpetuating cascade of siRNA-directed poly(UG) tailing of mRNA fragments (pUGylation), followed by siRNA synthesis from poly(UG)-tailed mRNA templates (termed pUG RNA/siRNA cycling). Despite the self-perpetuating nature of pUG RNA/siRNA cycling, RNAi inheritance is finite, suggesting that systems likely exist to prevent permanent RNAi-triggered gene silencing. Here we show that, in the absence of Piwi-interacting RNAs (piRNAs), an animal-specific class of small noncoding RNA, RNAi-based gene silencing can become essentially permanent, lasting at near 100% penetrance for more than five years and hundreds of generations. This permanent gene silencing is mediated by perpetual activation of the pUG RNA/siRNA TEI pathway. Further, we find that piRNAs coordinate endogenous RNAi pathways to prevent germline-expressed genes, which are not normally subjected to TEI, from entering a state of permanent and irreversible epigenetic silencing also mediated by perpetual activation of pUG RNA/siRNA cycling. Together, our results show that one function of C. elegans piRNAs is to insulate germline-expressed genes from aberrant and runaway inactivation by the pUG RNA/siRNA epigenetic inheritance system.


title: A genome-wide screen in the mouse liver reveals sex-specific and cell non-autonomous regulation of cell fitness

abstract: Our ability to understand and modulate mammalian physiology and disease requires knowing how all genes contribute to any given phenotype in the organism. Genome-wide screening using CRISPR-Cas9 has emerged as a powerful method for the genetic dissection of cellular processes1,2, but the need to stably deliver single guide RNAs to millions of cells has restricted its implementation to ex vivo systems. These ex vivo systems cannot reproduce all of the cellular phenotypes observed in vivo nor can they recapitulate all of the factors that influence these phenotypes. There thus remains a pressing need for high-throughput functional genomics in a living organism. Here, we establish accessible genome-wide screening in the mouse liver and use this approach to uncover the complete regulation of cellular fitness in a living organism. We discover novel sex-specific and cell non-autonomous regulation of cell growth and viability. In particular, we find that the class I major histocompatibility complex is essential for preventing immune-mediated clearance of hepatocytes. Our approach provides the first comprehensive picture of cell fitness in a living organism and highlights the importance of investigating cellular phenomena in their native context. Our screening method is robust, scalable, and easily adapted to examine diverse cellular processes using any CRISPR application. We have hereby established a foundation for high-throughput functional genomics in a living mammal, enabling unprecedented insight into mammalian physiology and disease.


title: Is energetics or competition a stronger driver of male smallmouth bass seasonal reproductive timing?

abstract: Intraspecific competitive ability is often associated with body size and has been shown to influence reproductive timing in many species. However, energetic constraints provide an alternative explanation for size-related differences of reproductive timing. In temperate fishes that experience a winter starvation period, for instance, a negative allometric relationship between body size and winter energy loss might explain why larger males spawn earlier in a season than smaller males, especially in fishes that exhibit paternal care, which is energetically costly and limits parental foraging opportunities. Male smallmouth bass, Micropterus dolomieu, defend nesting territories in which they care for offspring over an extended period. In northern populations, males rely on energy reserves over a winter starvation period and in spring must recoup energy losses before initiating reproduction, making them ideal systems in which to study contributions of competition and energetic allometry on differences of reproductive timing. Here, we harness data on parental male M. dolomieu from a 10-year study and show that larger males required fewer degree days-a measure of thermal energy experienced-in spring before they spawned each year and that the time of peak seasonal reproduction in the population was negatively related to the number of degree days accumulated before reproduction started. Furthermore, we found that growth of individual males between seasons better predicted changes in timing of reproduction than changes in size relative to competitors. Together, these results suggest that timing of reproduction in this population is more strongly influenced by energetic constraints than size-based competition amongst males.


title: Larval zebrafish display dynamic learning of aversive stimuli in a constant visual surrounding

abstract: Balancing exploration and anti-predation are fundamental to the fitness and survival of all animal species from early life stages. How these basic survival instincts drive learning remains poorly understood. Here, employing a light/dark preference paradigm with well-controlled luminance history and constant visual surrounding in larval zebrafish, we analyzed intra- and inter-trial dynamics for two behavioral components, dark avoidance and center avoidance. We uncover that larval zebrafish display short-term learning of dark avoidance with initial sensitization followed by habituation; they also exhibit long-term learning that is sensitive to trial interval length. We further show that such stereotyped learning patterns is stimulus specific, as they are not observed for center avoidance. Finally, we demonstrate at individual levels that long-term learning is under homeostatic control. Together, our work has established a novel paradigm to understand learning, uncovered sequential sensitization and habituation, and demonstrated stimulus specificity, individuality, as well as dynamicity in learning.


title: A Facile and Rapid Route to Self-Digitization of Samples into a High Density Microwell Array for Digital Bioassays

abstract: Digital bioassays are powerful methods to detect rare analytes from complex mixtures and study the temporal processes of individual entities within biological systems. In digital bioassays, a crucial first step is the discretization of samples into a large number of identical independent partitions. Here, we developed a rapid and facile sample partitioning method for versatile digital bioassays. This method is based on a detachable self-digitization (DSD) chip which couples a reversible assembly configuration and a predegassing-based self-pumping mechanism to achieve an easy, fast and large-scale sample partitioning. The DSD chip consists of a channel layer used for loading sample and a microwell layer used for holding the sample partitions. Benefitting from its detachability, the chip avoids a lengthy oil flushing process used to remove the excess sample in loading channels and can compartmentalize a sample into more than 100,000 wells of picoliter volume with densities up to 14,000 wells/cm2 in less than 30 s. We also demonstrated the utility of the proposed method by applying it to digital PCR and digital microbial assays.


title: Manipulation of stimulus waveform and frequency permits targeted fiber activation during vagus nerve stimulation in 2 rodent species

abstract: Afferent and efferent vagal fibers mediate bidirectional communication between the brain and visceral organs. Small, unmyelinated C-afferents constitute the majority of vagal fibers, play critical roles in numerous interoceptive circuits and autonomic reflexes in health and disease and may contribute to the efficacy and safety of vagus nerve stimulation (VNS). Selective engagement of C-afferents with electrical stimuli has not been feasible, due to the default fiber recruitment order: larger fibers first, smaller fibers last. Here, we determine and optimize an electrical stimulus that selectively engages vagal C-afferents. Intermittent KHz-frequency electrical stimulation (KES) activates motor and, preferentially, sensory vagal neurons in the brainstem. During KES, asynchronous activity of C-afferents increases, while that of larger fibers remains largely unchanged. In parallel, KES effectively blocks excitability of larger fibers while moderately suppressing excitability of C-afferents. By compiling selectivity indices in individual animals, we find that optimal KES parameters for C-afferents are >5KHz frequency and 7-10 times engagement threshold (xT) intensity in rats, 15-25xT in mice. These effects can be explained in computational models by how sodium channel responses to KES are shaped by axonal size and myelin. Our results indicate that selective engagement of vagal C-afferents is attainable by intermittent KES.


title: Stimulus manipulations permit activation of fiber subpopulations in the mouse and rat vagus


title: Intermittent KHz-frequency electrical stimulation selectively engages small unmyelinated vagal afferents


title: Improving sequence-based modeling of protein families using secondary structure quality assessment

abstract:
MotivationModeling of protein family sequence distribution from homologous sequence data recently received considerable attention, in particular for structure and function predictions, as well as for protein design. In particular, Direct Coupling Analysis, a method to infer effective pairwise interactions between residues, was shown to capture important structural constraints and to successfully generate functional protein sequences. Building on this and other graphical models, we introduce a new framework to assess the quality of the secondary structures of the generated sequences with respect to reference structures for the family.

ResultsWe introduce two scoring functions characterizing the likeliness of the secondary structure of a protein sequence to match a reference structure, called Dot Product and Pattern Matching. We test these scores on published experimental protein mutagenesis and design dataset, and show improvement in the detection of non-functional sequences. We also show that use of these scores help rejecting non-functional sequences generated by graphical models (Restricted Boltzmann Machines) learned from homologous sequence alignments.

AvailabilitySupplementary Materials, Data and Code available at https://github.com/CyrilMa/ssqa.

Contactcyril.malbranke@ens.fr

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title: dSCOPE: a software to detect sequences critical for liquid-liquid phase separation

abstract: Membrane based cells are the fundamental structure and function units of organisms, while evidences were increasing that liquid-liquid phase separation (LLPS) is associated with the formation of membraneless organelles, such as P-bodies, nucleoli and stress granules. Many studies have been undertaken to explore the functions of protein phase separation, but these studies lacked an effective tool to identify the sequence segments that critical for LLPS (SCOPEs). In this study, we presented a novel software called dSCOPE (http://dscope.omicsbio.info) to predict the SCOPEs. To develop the predictor, we curated experimentally identified sequence segments that can drive LLPS from published literature. Then sliding sequence window based physiological, biochemical, structural and coding features were integrated by random forest algorithm to perform prediction. Through rigorous evaluation, dSCOPE was demonstrated to achieve satisfactory performance. Furthermore, large-scale analysis of human proteome based on dSCOPE showed that the predicted SCOPEs enriched various protein post-translational modifications and cancer mutations, and the proteins which contain predicted SCOPEs enriched critical cellular signaling pathways. Taken together, dSCOPE precisely predicted the protein sequence segments critical for LLPS, with various helpful information visualized in the webserver to facilitate LLPS related research.


title: Attention is all you need for general-purpose protein structure embedding

abstract: General-purpose protein structure embedding can be used for many important protein biology tasks, such as protein design, drug design and binding affinity prediction. Recent researches have shown that attention-based encoder layers are more suitable to learn high-level features. Based on this key observation, we treat low-level representation learning and high-level representation learning separately, and propose a two-level general-purpose protein structure embedding neural network, called ContactLib-ATT. On the local embedding level, a simple yet meaningful hydrogen-bond representation is learned. On the global embedding level, attention-based encoder layers are employed for global representation learning. In our experiments, ContactLib-ATT achieves a SCOP superfamily classification accuracy of 82.4% (i.e., 6.7% higher than state-of-the-art method) on the SCOP40 2.07 dataset. Moreover, ContactLib-ATT is demonstrated to successfully simulate a structure-based search engine for remote homologous proteins, and our top-10 candidate list contains at least one remote homolog with a probability of 91.9%. Source codes: https://github.com/xfcui/contactlib.


title: Hydrogen bonds meet self-attention: all you need for general-purpose protein structure embedding


title: Super-delta2: An Enhanced Differential Expression Analysis Procedure for Multi-Group Comparisons of RNA-seq Data

abstract:
BackgroundWe developed super-delta2, a differential gene expression analysis pipeline designed for multi-group comparisons for RNA-seq data. It includes a customized one-way ANOVA F-test and a post-hoc test for pairwise group comparisons; both are designed to work with a multivariate normalization procedure to reduce technical noise. It also includes a trimming procedure with bias-correction to obtain robust and approximately unbiased summary statistics used in these tests. We demonstrated the asymptotic applicability of super-delta2 to log-transformed read counts in RNA-seq data by large sample theory based on Negative Binomial Poisson (NBP) distribution.

ResultsWe compared super-delta2 with three commonly used RNA-seq data analysis methods: limma/voom, edgeR, and DESeq2 using both simulated and real datasets. In all three simulation settings, super-delta2 not only achieved the best overall statistical power, but also was the only method that controlled type I error at the nominal level. When applied to a breast cancer dataset to identify differential expression pattern associated with multiple pathologic stages, super-delta2 selected more enriched pathways than other methods, which are directly linked to the underlying biological condition (breast cancer).

ConclusionsBy incorporating trimming and bias-correction in the normalization step, super-delta2 was able to achieve tight control of type I error. Because the hypothesis tests are based on asymptotic normal approximation of the NBP distribution, super-delta2 does not require computationally expensive iterative optimization procedures used by methods such as edgeR and DESeq2, which occasionally have convergence issues.


title: In silico assessment of missense point mutations on human cathelicidin LL-37

abstract: Cathelicidin antimicrobial peptides are a diverse family of cationic amphipathic peptides with multiple activities. In humans, cathelicidin LL-37 is one of the main host defense peptides with a remarkable medical and biotechnological potential. Deregulation of LL-37 expression has been associated with inflammatory diseases. However the effects of point mutations driven by single nucleotide polymorphisms (SNPs) on LL-37 are unknown. Here we applied an array of computational tools to investigate the effects of such mutations on LL-37 structure and activity. Due to the fact that, on cathelicidins, the prodomain is more conserved than the mature peptide, the SNP effect predictions were biased and, overall, resulted in neutral effects; and due to the slight changes in physicochemical properties, the antimicrobial predictions indicated the maintenance of such activity. Nonetheless, six out of eleven mutations altered the positive net charge, which in turn could result in less active LL-37 variants. Molecular dynamics data indicated that R07Q and N30Y mutations altered the LL-37 structure. In addition to these ones, the G03A, R07P, R07W and L31P mutations altered the helix dipole, which could also alter the antimicrobial activity. Our results indicated despite the mutations did not alter the residues from LL-37 active core, they could influence the antimicrobial activity and consequently, could be involved in inflammatory diseases.