title: DynaMorph: self-supervised learning of morphodynamic states of live cells

abstract: The cells shape and motion represent fundamental aspects of the cell identity, and can be highly predictive of the function and pathology. However, automated analysis of the morphodynamic states remains challenging for most cell types, especially primary human cells where genetic labeling may not be feasible. To enable automated and quantitative analysis of morphodynamic states, we developed DynaMorph - a computational framework that combines quantitative live cell imaging with self-supervised learning. To demonstrate the fidelity and robustness of this approach, we used DynaMorph to annotate morphodynamic states observed with label-free measurements of density and anisotropy of live microglia isolated from human brain tissue. These cells show complex behavior and have varied responses to disease-relevant stimuli. DynaMorph generates quantitative morphodynamic representations that can be used to evaluate the effects of disease-relevant perturbations. Using DynaMorph, we identify distinct morphodynamic states of microglia polarization and detect rare transition events between states. The methodologies presented here can facilitate automated discovery of functional states of diverse cellular systems.


title: Selection in males purges the mutation load on female fitness

abstract:
Theory predicts that the ability of selection and recombination to purge mutation load is enhanced if selection against deleterious genetic variants operates more strongly in males than females. However, direct empirical support for this tenet is limited, in part because traditional quantitative genetic approaches allow dominance and intermediate-frequency polymorphisms to obscure the effects of the many rare and partially recessive deleterious alleles that make up the main part of a populations mutation load. Here, we exposed the partially recessive genetic load of a population of Callosobruchus maculatus seed beetles via successive generations of inbreeding, and quantified its effects by measuring heterosis - the increase in fitness experienced when masking the effects of deleterious alleles by heterozygosity - in a fully factorial sex-specific diallel cross among 16 inbred strains. Competitive lifetime reproductive success (i.e. fitness) was measured in male and female outcrossed F1s as well as inbred parental  selfs, and we estimated the 4x4 male-female inbred-outbred genetic covariance matrix for fitness using Bayesian Markov chain Monte Carlo simulations of a custom-made general linear mixed effects model. We found that heterosis estimated independently in males and females was highly genetically correlated among strains, and that heterosis was strongly negatively genetically correlated to outbred male, but not female, fitness. This suggests that genetic variation for fitness in males, but not in females, reflects the amount of (partially) recessive deleterious alleles segregating at mutation-selection balance in this population. The populations mutation load therefore has greater potential to be purged via selection in males. These findings contribute to our understanding of the prevalence of sexual reproduction in nature and the maintenance of genetic variation in fitness-related traits.

Impact statementWhy do the large majority of eukaryotic species reproduce sexually if it means that females must spend half of their reproductive effort producing males, while males contribute few or no resources to offspring production themselves? In principle, a lineage of a mutant asexual female that simply clones herself into daughters would grow at twice the rate of her sexual competitors (all else equal). What prevents this from being the predominant mode of reproduction throughout eukaryotes? One hypothesis regards the role of males in facilitating the purging of deleterious mutations from the populations genome since very strong selection in males, unlike selection in females, can occur in many species without reductions in population offspring numbers. Due to the inherent difficulties of isolating this source of standing genetic variation for fitness, empirical evidence for this theory is mixed and limited to indirect evidence from manipulative experiments and experimental evolution studies. Here we demonstrate that recessive deleterious alleles in a population of the seed beetle, Callosobruchus maculatus, are selected against strongly in males but not females. Using a fully factorial diallel cross among 16 inbred strains, we measured the degree to which fitness in the outbred offspring of those crosses improved relative to their inbred parents. This measure is known as heterosis and offers an estimate of the relative amount of partially recessive deleterious alleles carried by a genetic strain. We then analyzed the relationship between the strains heterosis values and their additive genetic breeding values for fitness measured in males and females, revealing the extent to which segregating (partially recessive) deleterious alleles are selected against in males and females. We found that a strains heterosis value was strongly genetically correlated with its additive genetic breeding value for male fitness, but not female fitness. This suggests that mutations with deleterious effects on population growth rate due to their effects on females can be selected against (i.e. purged) more efficiently via their male siblings. This process would offer a benefit to sexual reproduction that may partly compensate for its costs, and therefore yields insight to the prevalence of sex in nature.

category: evolutionary biology


title: Two isoforms of the essential C. elegans Argonaute CSR-1 differentially regulate sperm and oocyte fertility

abstract: The C. elegans genome encodes nineteen functional Argonaute proteins that utilize 22G-RNAs, 26G-RNAs, miRNAs, or piRNAs to regulate their target transcripts. Only one Argonaute is essential under normal laboratory conditions: CSR-1. While CSR-1 has been studied widely, nearly all studies have overlooked the fact that the csr-1 locus encodes two isoforms. These isoforms differ by an additional 163 amino acids present in the N-terminus of CSR-1a. Using CRISPR-Cas9 genome editing to introduce GFP::3xFLAG into the long (CSR-1a) and short (CSR-1b) isoforms, we found that CSR-1a is expressed during spermatogenesis and in several somatic tissues, including the intestine. CSR-1b is expressed constitutively in the germline. small RNA sequencing of CSR-1 complexes shows that they interact with partly overlapping sets of 22G-RNAs. Phenotypic analyses reveal that the essential functions of csr-1 described in the literature coincide with CSR-1b, while CSR-1a plays tissue specific functions. During spermatogenesis, CSR-1a integrates into an sRNA regulatory network including ALG-3, ALG-4, and WAGO-10 that is necessary for fertility at 25{degrees}C. In the intestine, CSR-1a silences immunity and pathogen-responsive genes, and its loss results in improved survival from the pathogen Pseudomonas aeruginosa. Our findings functionally distinguish the CSR-1 isoforms and highlight the importance of studying each AGO isoform independently.

category: molecular biology


title: Identifying loci under selection via explicit demographic models

abstract: Adaptive genetic variation is a function of both selective and neutral forces. To accurately identify adaptive loci, it is thus critical to account for demographic history. Theory suggests that signatures of selection can be inferred using the coalescent, following the premise that genealogies of selected loci deviate from neutral expectations. Here, we build on this theory to develop an analytical framework to identify Loci under Selection via explicit Demographic models (LSD). Under this framework, signatures of selection are inferred through deviations in demographic parameters, rather than through summary statistics directly, and demographic history is accounted for explicitly. Leveraging on the property of demographic models to incorporate directionality, we show that LSD can provide information on the environment in which selection acts on a population. This can prove useful in elucidating the selective processes underlying local adaptation, by characterising genetic trade-offs and extending the concepts of antagonistic pleiotropy and conditional neutrality from ecological theory to practical application in genomic data. We implement LSD via Approximate Bayesian Computation and demonstrate, via simulations, that LSD has i) high power to identify selected loci across a large range of demographic-selection regimes, ii) outperforms commonly applied genome-scan methods under complex demographies, and iii) accurately infers the directionality of selection for identified candidates. Using the same simulations, we further characterise the behaviour of isolation-with-migration models conducive to the study of local adaptation under regimes of selection. Finally, we demonstrate an application of LSD by detecting loci and characterising genetic trade-offs underlying flower colour in Antirrhinum majus.


title: A minimal hepatocyte growth factor mimic acting as a powerful agonist of the MET receptor tyrosine kinase for regeneration of epithelial tissues and organs.

abstract: Hepatocyte Growth Factor/Scatter Factor (HGF/SF) and its cognate receptor MET play several essential roles in embryogenesis and regeneration in post-natal life of epithelial organs such as liver, kidney, lung, and pancreas, prompting a strong interest in harnessing HGF/SF-MET signalling for regeneration of epithelial organs after acute or chronic damage. The limited stability and tissue diffusion of native HGF/SF, however, which reflect the tightly controlled, local mechanism of action of the morphogen, have led to a major search for HGF/SF mimics for therapy. In this work, we describe the rational design, production and characterisation of K1K1, a novel minimal MET agonist consisting of two copies of the kringle 1 domain of HGF/SF placed in tandem. K1K1 is highly stable and displays biological activities equivalent or superior to native HGF/SF in a variety of in vitro assay systems and in a mouse model of liver disease. These data suggest that this engineered ligand may find wide applications in acute and chronic diseases of the liver and other epithelial organs dependent on MET activation.

category: bioengineering


title: Dimerization of kringle 1 domain from hepatocyte growth factor/scatter factor provides a potent minimal MET receptor agonist.


title: Regulation of immune receptor kinases plasma membrane nanoscale landscape by a plant peptide hormone and its receptors

abstract: Spatial partitioning is a propensity of biological systems orchestrating cell activities in space and time. The dynamic regulation of plasma membrane nano-environments has recently emerged as a key fundamental aspect of plant signaling, but the molecular components governing it are still mostly unclear. The receptor kinase FERONIA (FER) controls complex formation of the immune receptor kinase FLAGELLIN SENSING 2 (FLS2) with its co-receptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1), and this function is inhibited by the FER ligand RAPID ALKALANIZATION FACTOR 23 (RALF23). Here, we show that FER regulates the plasma membrane nanoscale organization of FLS2 and BAK1. Our study demonstrates that akin to FER, leucine-rich repeat (LRR) extensin (LRXs) proteins contribute to RALF23 responsiveness, regulate BAK1 nanoscale organization and immune signaling. Furthermore, RALF23 perception leads to rapid modulation of FLS2 and BAK1 nanoscale organization and its inhibitory activity on immune signaling relies on FER kinase activity. Our results suggest that perception of RALF peptides by FER and LRXs actively modulates the plasma membrane nanoscale landscape to regulate cell surface signaling by other receptor kinases.

category: plant biology


title: Neural representation of abstract task structure during generalization

abstract: Cognitive models in psychology and neuroscience widely assume that the human brain maintains an abstract representation of tasks. This assumption is fundamental to theories explaining how we learn quickly, think creatively, and act flexibly. However, neural evidence for a verifiably generative abstract task representation has been lacking. Here, we report an experimental paradigm that requires forming such a representation to act adaptively in novel conditions without feedback. Using functional magnetic resonance imaging, we observed that abstract task structure was represented within left mid-lateral prefrontal cortex, bilateral precuneus and inferior parietal cortex. These results provide support for the neural instantiation of the long-supposed abstract task representation in a setting where we can verify its influence. Such a representation can afford massive expansions of behavioral flexibility without additional experience, a vital characteristic of human cognition.

category: neuroscience


title: Motor and Sensory Cortical Processing of Neural Oscillatory Activities revealed by Human Swallowing using Intracranial Electrodes

abstract: Swallowing, a unique movement, is attributed to the indispensable orchestration of motor-output and sensory-input. We hypothesized that swallowing can illustrate differences between motor and sensory neural processing. Eight epileptic participants fitted with intracranial electrodes over the orofacial cortex were asked to swallow a water bolus. Mouth-opening and swallowing were treated as motor tasks, while water-injection as sensory tasks. Phase-amplitude coupling between lower frequency and high {gamma} (HG) band (75-150 Hz) was investigated. An  (10-16 Hz) -HG coupling appeared before motor-related HG power increase (burst), and a {theta} (5-9 Hz) -HG coupling appeared during sensory-related HG burst. The motor- and sensory-related HG amplitude were modulated at the trough of  oscillations and peak of {theta} oscillations, respectively. These contrasting results acquired from the orofacial cortex can help to fully elucidate the sensory-motor function in the brain.


title: ALG-2 interacting protein-X (Alix) is required for activity-dependent bulk endocytosis at brain synapses

abstract: In chemical synapses undergoing high frequency stimulation, vesicle components can be retrieved from the plasma membrane via a clathrin-independent process called activity dependent bulk endocytosis (ADBE). Alix (ALG-2 interacting protein X)/ PDCD6IP) is an adaptor protein binding to ESCRT and endophilin-A proteins which is required for clathrin-independent endocytosis in fibroblasts. Alix is expressed in neurons and concentrates at synapses during epileptic seizures. Here, we used cultured neurons to show that Alix is recruited to presynapses where it interacts with, and concentrates endophilin-A during conditions triggering ADBE. Using Alix knockout (ko) neurons we showed that this recruitment, which requires interaction with the calcium-binding protein ALG-2, is necessary for ABDE. We also found that presynaptic compartments of Alix ko hippocampi display subtle morphological defects compatible with flawed synaptic activity and plasticity detected electrophysiologically. Furthermore, mice lacking Alix in the forebrain undergo less seizures during kainate-induced status epilepticus and reduced propagation of the epileptiform activity. These results thus show that impairment of ADBE due to the lack of neuronal Alix alters synaptic recovery during physiological or pathological repeated stimulations.


title: MHC class IIa haplotypes derived by high throughput SNP screening in an isolated sheep population

abstract: Investigating the current evolutionary processes acting on a highly polymorphic gene region, such as the major histocompatibility complex (MHC), requires extensive population data for both genotypes and phenotypes. The MHC consists of several tightly linked loci with both allelic and gene content variation, making it challenging to genotype. Eight class IIa haplotypes have previously been identified in the Soay sheep (Ovis aries) of St. Kilda using Sanger sequencing and cloning, but no single locus is representative of all haplotypes. Here, we exploit the closed nature of the island population of Soay sheep and its limited haplotypic variation to identify a panel of SNPs that enable imputation of MHC haplotypes. We compared MHC class IIa haplotypes determined by Sanger sequence-based genotyping of 135 individuals to their SNP profiles generated using the Ovine Infinium HD BeadChip. A panel of 11 SNPs could reliably determine MHC diplotypes, and two additional SNPs within the DQA1 gene enabled detection of a recombinant haplotype affecting only the SNPs downstream of the expressed genes. The panel of 13 SNPs was genotyped in 5951 Soay sheep, of which 5349 passed quality control. Using the Soay sheep pedigree, we were able to trace the origin and inheritance of the recombinant SNP haplotype. This SNP-based method has enabled the rapid generation of locus-specific MHC genotypes for large numbers of Soay sheep. This volume of high-quality genotypes in a well-characterized population of free-living sheep will be valuable for investigating the mechanisms maintaining diversity at the MHC.


title: Imaging biomarkers for primary motor outcome after stroke - should we include information from beyond the primary motor system?

abstract: Hemiparesis is a common consequence of stroke to the primary motor system. Previous studies suggested that damage to additional brain areas might play a causal role in the occurrence and severity of hemiparesis and its recovery. Knowledge of these regions might be applied in the creation of imaging biomarkers for motor outcome prediction if lesion information from such areas carries predictive value. We assessed acute and chronic paresis of the upper limb in 102 patients with unilateral stroke. In a first experiment, the neural correlates of acute and chronic upper limb paresis were mapped by lesion behaviour mapping. Following the same approach, a lesion biomarker of corticospinal tract (CST) damage was mapped. This analysis served as an artificial control condition as the biomarker, by definition, is only causally related to damage of the CST. Mapping acute or chronic upper limb paresis implicated areas outside of the primary motor system. Likewise, mapping the CST lesion biomarker implicated several areas outside of the CST with high correspondence to areas associated with upper limb paresis. Damage to areas outside of the primary motor system thus might, to some degree, not play a causal role in hemiparesis. In a second experiment, we showed that lesion information from these areas outside of the primary motor system can be used to predict motor outcome. This was even the case for the CST lesion biomarker. Although the only causal source underlying the CST lesion biomarker was damage to the CST, lesion information that mainly included non-CST regions was able to predict the biomarker (non-significantly) better than information taken from only the CST itself. These findings suggest that simple theory-based biomarkers or qualitative rules to infer post-stroke outcome from imaging data might perform sub-optimally, as they do not consider the complexity of lesion data. Instead, high-dimensional models with data-driven feature selection strategies might be required.


title: Local Metabolism of Ethanol to Acetic Acid/Acetate in the Central Nucleus of Amygdala Elicits Sympathoexcitatory Responses through Activation of NMDAR in Sprague Dawley Rats

abstract:
AimBinge alcohol consumption elicits robust sympathoexcitation and excitatory neuronal output. However, the central mechanism that mediates these effects remains elusive. We investigated the effects of ethanol metabolism within the central nucleus of the amygdala (CeA) on sympathoexcitation, and elucidated the role of acetate in these excitatory responses.

MethodsIn vivo arterial blood pressure, heart rate and sympathetic nerve activity responses to CeA microinjected ethanol or acetate with appropriate inhibitors/antagonists were tracked. In vitro whole-cell electrophysiology recording responses to acetate in CeA neurons with axon projecting to the rostral ventrolateral medulla (CeA-RVLM) were investigated, and cytosolic calcium responses in primary neuronal cultures were quantified.

ResultsWe demonstrate that in Sprague Dawley rats, local brain metabolism of ethanol in the CeA to acetic acid/acetate elicits sympathoexcitatory responses in vivo through activation of NMDAR. Aldehyde dehydrogenase inhibition using cyanamide and NMDAR antagonism using AP5 or memantine blunted these effects. Whole-cell patch-clamp recordings in brain slices containing autonomic CeA-RVLM neurons revealed a dose-dependent increase in neuronal excitability in response to acetate. The NMDAR antagonists AP5 and memantine suppressed the acetate-induced increase in CeA-RVLM neuronal excitability, as well as the direct activation of NMDAR-mediated inward currents by acetate in brain slices. We observed that acetate increased cytosolic Ca2+ in a time-dependent manner in primary neuronal cell cultures. The acetate enhancement of calcium signaling was abolished by memantine.

ConclusionThese findings suggest that within the CeA, ethanol is sympathoexcitatory through local brain metabolism, which generates acetic acid/acetate leading to activation of NMDAR.

category: physiology


title: Crosstalk between chloroplast protein import and the SUMO system revealed through genetic and molecular investigation

abstract: The chloroplast proteome contains thousands of different proteins that are encoded by the nuclear genome. These proteins are imported into the chloroplast via the action of the TOC translocase and associated downstream systems. Our recent work has revealed that the stability of the TOC complex is dynamically regulated by the ubiquitin-dependent chloroplast-associated protein degradation (CHLORAD) pathway. Here, we demonstrate that the stability of the TOC complex is also regulated by the SUMO system. Arabidopsis mutants representing almost the entire SUMO conjugation pathway can partially suppress the phenotype of ppi1, a pale yellow mutant lacking the Toc33 protein. This suppression is linked to the increased stability of TOC proteins and improvements in chloroplast development. In addition, we demonstrate using molecular and biochemical experiments that the SUMO system directly targets TOC proteins. Thus, we have identified a regulatory link between the SUMO system and chloroplast protein import.

category: cell biology


title: Mycorrhizal symbiosis alleviates plant drought stress within and across plant generations via plasticity

abstract:
O_LIPhenotypic plasticity is essential for organisms to adapt to local ecological conditions. It is expected that mutualistic interactions, such as arbuscular mycorrhizal (AM) symbiosis, mediate plant phenotypic plasticity, although it is not clear to what extent this plasticity may be heritable (i.e., transgenerational plasticity).
C_LIO_LIWe tested for plant plasticity within- and across-generations in response to AM symbiosis and varying water availability in a full factorial experiment over two generations, using a genetically uniform line of a perennial apomictic herb, Taraxacum brevicorniculatum. We examined changes in phenotype, performance, and AM fungal colonization of the offspring throughout plant development.
C_LIO_LIAM symbiosis and water availability triggered phenotypic changes during the life cycle of plants. Additionally, both triggered adaptive transgenerational effects, especially detectable during the juvenile stage of the offspring. Water deficit and absence of AM fungi caused concordant plant phenotypic modifications towards a "stress-coping phenotype", both within- and across-generations. AM fungal colonization of offspring was also affected by the parental environment.
C_LIO_LIAM symbiosis can trigger within-generation and transgenerational plasticity in terms of functional traits related to resource-use acquisition and AM fungal colonization. Thus, transgenerational effects of mycorrhizal symbiosis are not limited to plant fitness, but also improve plants ability to cope with environmental stress.
C_LI

category: ecology


title: Arc1 and the microbiota together modulate growth and metabolic traits in Drosophila

abstract:
Perturbations to animal-associated microbial communities (the microbiota) have deleterious effects on various aspects of host fitness, but the molecular processes underlying these impacts are poorly understood. Here we identify a novel connection between the microbiota and the neuronal factor Arc1 that affects growth and metabolism in Drosophila. We find that Arc1 exhibits tissue-specific microbiota-dependent expression changes, and that germ-free flies bearing a null mutation of Arc1 exhibit delayed and stunted larval growth, along with a variety of molecular, cellular, and organismal traits indicative of metabolic dysregulation. Remarkably, we show that the majority of these phenotypes can be fully suppressed by mono-association with a single Acetobacter sp. isolate, through mechanisms involving both bacterial diet modification and live bacteria. Additionally, we provide evidence that Arc1 function in key neuroendocrine cells of the larval brain modulates growth and metabolic homeostasis under germ-free conditions. Our results reveal a novel role for Arc1 in modulating physiological responses to the microbial environment, and highlight how host-microbe interactions can profoundly impact the phenotypic consequences of genetic mutations in an animal host.

SUMMARYDrosophila Arc1 exhibits microbiota-dependent, tissue-specific differential expression and functionally interacts with a key Acetobacter sp. isolate to regulate developmental growth and metabolic traits.


title: rTASSEL: an R interface to TASSEL for association mapping of complex traits

abstract:
SummaryThe need for efficient tools and applications for analyzing genomic diversity is essential for any genetics research program. One such tool, TASSEL (Trait Analysis by aSSociation, Evolution and Linkage), provides many core methods for genomic analyses. Despite its efficiency, TASSEL has limited means to use scripting languages for reproducible research and interacting with other analytical tools. Here we present an R package rTASSEL, a front-end to connect to a variety of highly used TASSEL methods and analytical tools. The goal of this package is to create a unified scripting workflow that exploits the analytical prowess of TASSEL in conjunction with Rs popular data handling and parsing capabilities without ever having the user to switch between these two environments. By implementing this workflow, we can achieve performances ranging from approximately 2 to 20 times faster than other widely used R packages for various functionalities.

Availability and implementationrTASSEL is implemented in R using core TASSEL methods written in Java. The source code for rTASSEL can be found at https://bitbucket.org/bucklerlab/rtassel/src/master/. The source code for TASSEL can be found at https://bitbucket.org/tasseladmin/tassel-5-source/src/master/.

Supplemental informationThe rTASSEL user manual and tutorials are freely available at https://maize-genetics.github.io/rTASSEL/. Supplemental material for this manuscript regarding performance metrics can be found in the attached file.

category: bioinformatics


title: DreamAI: algorithm for the imputation of proteomics data

abstract: Deep proteomics profiling using labeled LC-MS/MS experiments has been proven to be powerful to study complex diseases. However, due to the dynamic nature of the discovery mass spectrometry, the generated data contain a substantial fraction of missing values. This poses great challenges for data analyses, as many tools, especially those for high dimensional data, cannot deal with missing values directly. To address this problem, the NCI-CPTAC Proteogenomics DREAM Challenge was carried out to develop effective imputation algorithms for labeled LC-MS/MS proteomics data through crowd learning. The final resulting algorithm, DreamAI, is based on an ensemble of six different imputation methods. The imputation accuracy of DreamAI, as measured by Pearson correlation, is about 15%-50% greater than existing tools among less abundant proteins, which are more vulnerable to be missed in proteomics data sets. This new tool notably enhances data analysis capabilities in proteomics research.


title: Predicting cancer prognosis and drug response from the tumor microbiome

abstract: Tumor gene expression is predictive of patient prognosis in some cancers. However, RNA- seq and whole genome sequencing data contain not only reads from host tumor and normal tissue, but also reads from the tumor microbiome, which can be used to infer the microbial abundances in each tumor. Here, we show that tumor microbial abundances, alone or in combination with tumor gene expression data, can predict cancer prognosis and drug response to some extent - microbial abundances are significantly less predictive of prognosis than gene expression, although remarkably, similarly as predictive of drug response, but in mostly different cancer-drug combinations. Thus, it appears possible to leverage existing sequencing technology, or develop new protocols, to obtain more non-redundant information about prognosis and drug response from RNA-seq and whole genome sequencing experiments than could be obtained from tumor gene expression or genomic data alone.

category: cancer biology


title: The role of Vitamin C in the energy supply of cells Hypothetical structure for energy transformation

abstract:
The present paper represents a hypothetical structure, the structure for energy transformation (SET), which might be responsible for the proper energy transformation steps leading to the continuous production of H+ and ATP in living cells. We predict that the electron flow is realized through the electron flow device (EFD). We suppose that there are several versions of the SET. Two of them are described below [Structure of Aerobic Glycolysis (SET-AG) and Structure of Oxidative Phosphorylation (SET-OP)]. The hypothesis is based on the atom properties of the protonated adenine molecule and the docking computations of molecular mechanics involved, suggesting that two ascorbate molecules may occupy the empty NADPH pocket, preferably binding to the adenine binding site. We hypothesize that the adenine originates from uric acid (UA), resulting in an ATP-UA-ADP-ATP-UA cycle. It would also mean that UA is one of the oxygen sources in aerobic glycolysis.

We also suppose that the EFD contains the well-known molecules of the Nicotinamide Adenine Dinucleotide (NAD) and Flavin Adenine Dinucleotide (FAD) supplemented with two additional UA-originated adenine molecules, two L-ascorbic acids, and two D-glucose molecules. Based on all this, we surmise that a tetra adenine octo phosphate ring (TAR) exists, in which the UA originated adenine molecules form a ring. The molecules are linked to each other through the N7-C2 and C8-N1 atoms of the adenine molecules by H2PO4e- molecules. The four N10 atoms of the adenine molecules bind one flavin, one nicotinamide, and two L-ascorbic acid molecules. Six D-glucose molecules complete one Unit of the structure. Both Fe-S and cytochrome clusters, as well as dehydrogenases, ensure the continuous operation of the Unit. The synchronized function of the three-stoke, three twin-cylinder engine results in continuous energy, ATP, and H+ production. Eukaryotic cells are equipped with the SET-AG and the SET-OP; thus, they can live in an anoxic and oxygenized environment. It is hoped that the SET concept developed here will help the better understanding the way of action regarding the cancer treatment with Vitamin C or glucose deprivation.

category: biochemistry


title: Topoisomerase 1 dependent R-loop deficiency drives accelerated replication and genomic instability

abstract: DNA replication is a complex process that is tightly regulated to ensure faithful genome duplication, and its perturbation leads to DNA damage and genomic instability. Replication stress is commonly associated with slow and stalled replication forks. Recently, accelerated replication has emerged as a non-canonical form of replication stress. However, the molecular basis underlying fork acceleration is largely unknown. Here we show that increased topoisomerase 1 (TOP1) expression induces aberrant replication fork acceleration and DNA damage by decreasing RNA-DNA hybrids (R-loops). Degradation of R-loops by overexpression of RNaseH1 also accelerates replication and generates DNA damage. Furthermore, upregulation of TOP1 by activation of the mutated HRAS oncogene leads to fork acceleration and DNA damage in pre-senescent cells. In these cells, restoration of TOP1 expression level or mild replication inhibition rescues the perturbed replication and reduces DNA damage. These findings highlight the importance of TOP1 equilibrium in the regulation of R-loop homeostasis to ensure faithful DNA replication and genome integrity.


title: Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification

abstract:
Genome-wide profiling of long-range interactions has revealed that the CCCTC-Binding factor (CTCF) often anchors chromatin loops and is enriched at boundaries of the so-called Topologically Associating Domains, which suggests that CTCF is essential in the 3D organization of chromatin. However, the systematic topological classification of pairwise CTCF-CTCF interactions has not been yet explored.

Here, we developed a computational pipeline able to classify all CTCF-CTCF pairs according to their chromatin interactions from Hi-C experiments. The interaction profiles of all CTCF-CTCF pairs were further structurally clustered using self-organizing feature maps and their functionality characterized by their epigenetic states. The resulting clusters were then input to a convolutional neural network aiming at the de novo detecting chromatin loops from Hi-C interaction matrices.

Our new method, called LOOPbit, is able to automatically detect significant interactions with a higher proportion of enhancer-promoter loops compared to any other callers. Our highly specific loop caller adds a new layer of detail to the link between chromatin structure and function.


title: Response of soil microbial communities to mixed forests of European beech and conifers: Variations with site conditions

abstract: Tree - soil interactions depend on environmental conditions. Planting trees may strongly impact microorganisms in particular at unfavorable site conditions, compromising the functioning of soil microorganisms. To understand the effects of tree species composition on soil microorganisms, we quantified structural and functional responses of soil microorganisms to forest types across environmental conditions using substrate-induced respiration and phospholipid fatty acid analyses. Five forest types were studied including pure stands of native European beech (Fagus sylvatica), range expanding Norway spruce (Picea abies), and non-native Douglas-fir (Pseudotsuga menziesii), as well as the two conifer - beech mixtures. We found that microbial functioning strongly depends on site conditions, in particular on soil nutrients. At nutrient-poor sites, soil microorganisms were more stressed in pure and mixed coniferous forests, especially in Douglas-fir, compared to beech forests. By contrast, microbial structure and functional indicators in beech forests varied little with site conditions, likely because beech provided high amounts of root-derived resources for microbial growth. Since soil microbial communities are sensitive to Douglas-fir, planting Douglas-fir may compromise ecosystem functioning in particular at nutrient-poor sites. Overall, root-derived resources are important for determining the structure and functioning of soil microbial communities, and soil microorganisms sensitively respond to plantations containing tree species that may differ in the provisioning of these resources.


title: Genome-wide association study and polygenic risk score analysis for hearing measures in children

abstract: An efficient auditory system contributes to cognitive and psychosocial development. A right ear advantage in hearing thresholds (HT) has been described in adults and atypical patterns of left/right hearing threshold asymmetry (HTA) have been described for psychiatric and neurodevelopmental conditions. Previous genome-wide association studies (GWAS) on HT have mainly been conducted in elderly participants whose hearing is more likely to be affected by external environmental factors. We analyzed HT and HTA in a children population cohort (ALSPAC, n = 6,743). Better hearing was associated with better cognitive performance and higher socioeconomic status (SES). At the group level, HTA suggested a left ear advantage (mean = -0.28 dB) that was mainly driven by females. SNP heritability for HT and HTA was 0.17 and 0.01, respectively (n = 5,344). Genetic correlation analysis confirmed associations between HT, reading ability, listening comprehension, and GCSE scores. GWAS for HT did not yield significant hits but polygenic risk score (PRS) analysis showed significant associations of higher educational attainment (EA, {beta} = -1564.72, p = .008) and risk for schizophrenia ({beta} = -241.14, p = .004) with lower HT, i.e. better hearing. In summary, we report new data supporting associations between hearing measures and cognitive abilities at the behavioral level. Genetic analysis suggests shared biological pathways between cognitive and sensory systems and provides evidence for a positive outcome of genetic risk for schizophrenia.

category: genetics


title: Isolation and Molecular Characterization of Pesticide Degrading Bacteria in Polluted Soil

abstract: Pesticides are the substances for preventing, destroying, repelling any pest. Due to bulk handling or accidental release, they are accumulated in soil which leads to occasional entry into ecosystem that shows lethal effect on living system. An enrichment culture technique was used to isolate bacterial strains from organophosphate soil degrading high concentration of the selected pesticides. Five pure bacterial cultures were isolated. All five isolates were characterized on the basis of molecular and biochemical features like biodegradation test and substrate specificity, phosphate solubilization and screened for pesticide residue, pH, and extraction of DNA, quantity and quality check and salt tolerance. The organophosphate isolates were also tested for quantitative production. The screening of pesticide tolerance was done at for fungicides and insecticides.


title: Inhibitors of L-type calcium channels show therapeutic potential for treating SARS-CoV-2 infections by preventing virus entry and spread

abstract: COVID-19 is caused by a novel coronavirus, severe acute respiratory syndrome coronavirus (CoV)-2 (SARS-CoV-2). The virus is responsible for an ongoing pandemic and concomitant public health crisis around the world. While vaccine development is proving to be highly successful, parallel drug development approaches are also critical in the response to SARS-CoV-2 and other emerging viruses. Coronaviruses require Ca2+ ions for host cell entry and we have previously shown that Ca2+ modulates the interaction of the viral fusion peptide with host cell membranes. In an attempt to accelerate drug development, we tested a panel of L-type calcium channel blocker (CCB) drugs currently developed for other conditions, to determine whether they would inhibit SARS-CoV-2 infection in cell culture. All the CCBs tested showed varying degrees of inhibition, with felodipine and nifedipine strongly limiting SARS-CoV-2 entry and infection in epithelial lung cells at concentrations where cell toxicity was minimal. Further studies with pseudo-typed particles displaying the SARS-CoV-2 spike protein suggested that inhibition occurs at the level of virus entry. Overall, our data suggest that certain CCBs have potential to treat SARS-CoV-2 infections and are worthy of further examination for possible treatment of COVID-19.

category: microbiology


title: Combination of high pressure treatment at 500 MPa and biopreservation with a Lactococcus lactis strain for lowering the bacterial growth during storage of diced cooked ham with reduced nitrite salt

abstract: We investigated the combined effects of biopreservation and high pressure treatment on bacterial communities of diced cooked ham prepared with diminished nitrite salt. First, bacterial communities of four commercial brands of dice cooked ham from local supermarkets, were characterised and stored frozen. Second, sterile diced cooked ham, prepared with reduced level of nitrite was inoculated with two different microbiota collected from the aforementioned commercial samples together with a nisin producing Lactococcus lactis protective strain able to recover from a 500 MPa high pressure treatment. Dices were then treated at 500 MPa for 5 minutes and bacterial dynamics was monitored during storage at 8{degrees}C. Depending on samples, ham microbiota were dominated by different Proteobacteria (Pseudomonas, Serratia, Psychrobacter, or Vibrio) or by Firmicutes (Latilactobacillus and Leuconostoc). Applied alone, none of the treatments stabilized durably the growth of hams microbiota. Nevertheless, the combination of biopreservation and high pressure treatment was efficient to reduce the growth of Proteobacteria spoilage species. However, this effect was dependent on the nature of the initial microbiota, showing that use of biopreservation and high pressure treatment as an alternative to nitrite reduction for ensuring cooked ham microbial safety merits attention but still requires improvement.


title: Regulation of poplar isoprenoid biosynthesis by methylerythritol phosphate and mevalonic acid pathways interactions

abstract: The isoprenoids found in plants are extremely important to survive with various human applications, such as flavoring, fragrance, dye, pharmaceuticals, and biomass used for biofuels. Methylerythritol phosphate (MEP) and mevalonic acid (MVA) pathways are critical in plants, responsible for isoprenoid biosynthesis. 1-deoxy-D-xylulose5-phosphate synthase (DXS) and 1-deoxy-D-xylulose5-phosphate reductoisomerase (DXR) catalyze the rate-limiting steps in the MEP pathway, while 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) catalyzes the rate-limiting step in the MVA pathway. Here, we showed while PtHMGR overexpressors (OEs) exhibited different MEP- and MVA-related gene expressions compared with non-transgenic poplars (NT), the PtDXR-OEs revealed upregulated MEP-related and downregulated MVA-related gene expressions. PtDXR and PtHMGR overexpressions caused changes in MVA-derived trans-zeatin-riboside, isopentenyl adenosine, castasterone, and 6-deoxocastasterone well as MEP-derived carotenoids and gibberellins. In PtHMGR-OEs, the accumulated geranyl diphosphate synthase (GPS) and geranyl pyrophosphate synthase (GPPS) transcript levels in the MEP pathway led to an accumulation of MEP-derived isoprenoids. In contrast, upregulation of farnesyl diphosphate synthase (FPS) expression in the MVA pathway contributed to increased levels of MVA-derived isoprenoids. In addition, PtHMGR-OEs increased MEP-related GPS and GPPS transcript levels, expanded MEP-derived isoprenoid levels, changed FPS transcript levels, and affected MVA-derived isoprenoid yields. These results demonstrate the contribution of MVA and MEP pathways regulating isoprenoid biosynthesis in poplars.


title: Isoprenoid biosynthesis regulation in poplars by methylerythritol phosphate and mevalonic acid pathways


title: Distinct networks coupled with parietal cortex for spatial representations inside and outside the visual field

abstract: Our mental representation of egocentric space is influenced by the disproportionate sensory perception of the body. Previous studies have focused on the neural architecture for egocentric representations within the visual field. However, the space representation underlying the body is still unclear. To address this problem, we applied both fMRI and MEG to a spatial-memory paradigm by using a virtual environment in which human participants remembered a target location left, right, or back relative to their own body. Both experiments showed larger involvement of the frontoparietal network in representing a retrieved target on the left/right side than on the back. Conversely, the medial temporal lobe (MTL)-parietal network was more involved in retrieving a target behind the participants. The MEG data showed preferential connectivity in the alpha-band frequency in both networks. These findings suggest that the parietal cortex may represent the entire space around the self-body by coordinating two distinct brain networks.


title: Selective targeting of non-centrosomal AURKA functions through use of a targeted protein degradation tool

abstract: Targeted protein degradation tools are becoming a new therapeutic modality, allowing small molecule ligands to be reformulated as heterobifunctional molecules (PROteolysis Targeting Chimeras, PROTACs) that recruit ubiquitin ligases to targets of interest, leading to ubiquitination and destruction of the targets. Several PROTACs against targets of clinical interest have been described, but detailed descriptions of the cell biology modulated by PROTACs are missing from the literature. Here we describe the functional characterization of a PROTAC derived from AURKA inhibitor MLN8237 (alisertib). We demonstrate efficient and specific destruction of both endogenous and overexpressed AURKA by Cereblon-directed PROTACs. At the subcellular level, we find differential targeting of AURKA on the mitotic spindle compared to centrosomes. The phenotypic consequences of PROTAC treatment are therefore distinct from those mediated by alisertib, and in mitotic cells differentially regulate centrosome- and chromatin-based microtubule spindle assembly pathways. In interphase cells PROTAC-mediated clearance of non-centrosomal AURKA modulates the cytoplasmic role played by AURKA in mitochondrial dynamics, whilst the centrosomal pool is refractory to PROTAC-mediated clearance. Our results point to differential sensitivity of subcellular pools of substrate, governed by substrate conformation or localization-dependent accessibility to PROTAC action, a phenomenon not previously described for this new class of degrader compounds.


title: Precise characterization of somatic structural variations and mobile element insertions from paired long-read sequencing data with nanomonsv

abstract: We introduce our novel software, nanomonsv, for detecting somatic structural variations (SVs) using tumor and matched control long-read sequencing data with a single-base resolution. Using paired long-read sequencing data from three cancer cell-lines and their matched lymphoblastoid lines, we demonstrate that our approach can identify not only somatic SVs that can be captured with short-read technologies but also novel ones especially those whose breakpoints are located in repeat regions. In addition, we have developed a workflow for classifying mobile element insertions while elucidating their in-depth properties such as 5' truncations, internal inversion as well as source sites in the case of LINE1 transductions. Finally, we identify complex SVs probably caused by replication mechanisms or telomere crisis by examining the co-occurrence of multiple somatic SVs in common supporting reads. In summary, our approaches applied to cancer long-read sequencing data can reveal various features of somatic SVs and will lead to further understanding of mutational processes and functional consequences of somatic SVs.


title: Neural state space alignment for magnitude generalization in humans and recurrent networks

abstract: A prerequisite for intelligent behaviour is to understand how stimuli are related and to generalise this knowledge across contexts. Generalisation can be challenging when relational patterns are shared across contexts but exist on different physical scales. Here, we studied neural representations in humans and recurrent neural networks performing a magnitude comparison task, for which it was advantageous to generalise concepts of "more" or "less" between contexts. Using multivariate analysis of human brain signals and of neural network hidden unit activity, we observed that both systems developed parallel neural "number lines" for each context. In both model systems, these number state spaces were aligned in a way that explicitly facilitated generalisation of relational concepts (more and less). These findings suggest a previously overlooked role for neural normalisation in supporting transfer of a simple form of abstract relational knowledge (magnitude) in humans and machine learning systems.


title: The prevalence of Angiostrongylus cantonensis in rodent hosts in China and several Asian countries: a systematic review and meta-analysis

abstract:
BackgroundAngiostrogylus cantonensis (A.cantonensis) is a zoonotic parasitic nematode, with a worldwide distribution, causing eosinophilic meningitis or meningoencephalitis in humans. Although the biology of A.cantonensis is relatively well known, little is understood about the transmission level in different zoogeographical regions, especially in Asia. Here, to evaluate the prevalence of A.cantonensis in rodent hosts in China and several Asian countries, we conducted a systematic review registered with PROSPERO (CRD42020161665).

MethodsRecords were selected systematically from 7 databases (Medline via to Pubmed, Web of science, Scopus, Google Scholar, CNKI, Wangfang, CBM). Forest plots and random-effects model were used to display pooled estimates. The Freeman-Tukey double arcsine transformation of R software was used to conduct meta-analysis and statistical significance was set at 0.05.

ResultsA total of 67 studies met the inclusion criteria and were included in the systematic review and meta-analysis. The pooled prevalence estimates of A.cantonensis infection in rodents was 0.1003 (95%CI: 0.0765, 0.1268). There was significant heterogeneity in reported outcomes (p<0.0001). So we considered that there was no publication bias in the included studies.

ConclusionThe A.cantonensis infection rate among rodent hosts was still high in Asia, particularly in China, especially in Rattus norvegicus, and thus comprehensive measures should be taken for rodent hosts control to avoid an angiostrongyliasis outbreak. Due to the wide distribution and movement of rodent hosts, people in all regions of China, even in other Asia area live at risk of an infection. Hence, the development of more reliable diagnostic tests will be key for an effective identification of cases as well as improved patient care. Consequently, further studies are required to updated strategies for controlling A.cantonensis infection among human population.

category: zoology


title: Robust Rhythmogenesis via Spike Timing Dependent Plasticity

abstract:
Rhythmic activity has been observed in numerous animal species ranging from insects to humans, and in relation to a wide range of cognitive tasks. Various experimental and theoretical studies have investigated rhythmic activity. The theoretical efforts have mainly been focused on the neuronal dynamics, under the assumption that network connectivity satisfies certain fine-tuning conditions required to generate oscillations. However, it remains unclear how this fine tuning is achieved.

Here we investigated the hypothesis that spike timing dependent plasticity (STDP) can provide the underlying mechanism for tuning synaptic connectivity to generate rhythmic activity. We addressed this question in a modeling study. We examined STDP dynamics in the framework of a network of excitatory and inhibitory neuronal populations that has been suggested to underlie the generation of oscillations in the gamma range. Mean field Fokker Planck equations for the synaptic weights dynamics are derived in the limit of slow learning. We drew on this approximation to determine which types of STDP rules drive the system to exhibit rhythmic activity, and demonstrate how the parameters that characterize the plasticity rule govern the rhythmic activity. Finally, we propose a novel mechanism that can ensure the robustness of self-developing processes, in general and for rhythmogenesis in particular.


title: Exclusion of the fittest predicts microbial community diversity in fluctuating environments

abstract: Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we still lack an intuition on how. Here, we build a mathematical model describing two microbial species living in an environment where substrate supplies randomly switch between abundant and scarce. We then vary the rate of switching as well as different properties of the interacting species, and measure the probability of the weaker species driving the stronger one extinct. We find that this probability increases with the strength of demographic noise under harsh conditions and peaks at either low, high, or intermediate switching rates depending on both species ability to withstand the harsh environment. This complex relationship shows why finding patterns between environmental fluctuations and diversity has historically been difficult. In parameter ranges where the fittest species was most likely to be excluded, however, the beta diversity in larger communities also peaked. In sum, how environmental fluctuations affect interactions between a few species pairs predicts their effect on the beta diversity of the whole community.


title: Portable real-time colorimetric LAMP-device for rapidquantitative detection of nucleic acids in crude samples

abstract: Loop-mediated isothermal amplification is known for its high sensitivity, specificity and tolerance to inhibiting-substances. We developed a device for performing real-time colorimetric LAMP combining the accuracy of lab-based quantitative molecular diagnosis with the simplicity of point-of-care testing. This handheld device employs a single reaction-pot for amplification and a mini-camera for detection. Competitive features are the rapid analysis (<30min), quantification over 9 log-units, crude sample-compatibility (saliva, tissue, swabs), low detection limit (<5copies/reaction), smartphone-operation and fast prototyping (3D-printing). The devices clinical utility is demonstrated in cancer-mutations and COVID-19 testing. Excellent performance includes: detection of 0.01% of BRAF-V600E-to-wild-type molecules; 97% sensitivity to SARS-CoV-2 RNA detection (89 samples); 83% (Ct<34), 98% (Ct<30) and 100% (Ct<25) to 163 nasopharyngeal-swabs; 100% specificity in all cases. The device high technology-readiness-level makes it a suitable platform for performing any colorimetric LAMP assay; moreover, its simple and inexpensive fabrication holds promise for fast deployment and application in global diagnostics.


title: Plasticity in astrocyte subpopulations regulates heroin relapse

abstract:
Opioid use disorder (OUD) produces detrimental personal and societal consequences. Astrocytes are a major cell group in the brain that receives little attention in mediating OUD. We determined how astrocytes and the astroglial glutamate transporter, GLT-1, in the nucleus accumbens core adapt and contribute to heroin seeking in rats. Seeking heroin, but not sucrose, produced two transient forms of plasticity in different astroglial subpopulations. Increased morphological proximity to synapses occurred in one subpopulation and increased extrasynaptic GLT-1 expression in another. Augmented synapse proximity by astroglia occurred selectively at D2-dopamine receptor expressing dendrites, while changes in GLT-1 were not neuron-subtype specific. Importantly, mRNA-antisense inhibition of either morphological or GLT-1 plasticity promoted cue-induced heroin seeking. We show that heroin cues induce two distinct forms of transient plasticity in separate astroglial subpopulations that dampen heroin relapse.

TEASERDifferent subpopulations of astrocytes engage with accumbens synapses to dampen heroin relapse.

category: animal behavior and cognition


title: Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing

abstract:
BackgroundMicrobial eukaryotes are found alongside bacteria and archaea in natural microbial systems, including host-associated microbiomes. While microbial eukaryotes are critical to these communities, they are challenging to study with shotgun sequencing techniques and are therefore often excluded.

ResultsHere we present EukDetect, a bioinformatics method to identify eukaryotes in shotgun metagenomic sequencing data. Our approach uses a database of 521,824 universal marker genes from 241 conserved gene families, which we curated from 3,713 fungal, protist, non-vertebrate metazoan, and non-streptophyte archaeplastid genomes and transcriptomes. EukDetect has a broad taxonomic coverage of microbial eukaryotes, performs well on low-abundance and closely related species, and is resilient against bacterial contamination in eukaryotic genomes. Using EukDetect, we describe the spatial distribution of eukaryotes along the human gastrointestinal tract, showing that fungi and protists are present in the lumen and mucosa throughout the large intestine. We discover that there is a succession of eukaryotes that colonize the human gut during the first years of life, mirroring patterns of developmental succession observed in gut bacteria. By comparing DNA and RNA sequencing of paired samples from human stool, we find that many eukaryotes continue active transcription after passage through the gut, though some do not, suggesting they are dormant or nonviable. We analyze metagenomic data from the Baltic Sea and find that eukaryotes differ across locations and salinity gradients. Finally, we observe eukaryotes in Arabidopsis leaf samples, many of which are not identifiable from public protein databases.

ConclusionsEukDetect provides an automated and reliable way to characterize eukaryotes in shotgun sequencing datasets from diverse microbiomes. We demonstrate that it enables discoveries that would be missed or clouded by false positives with standard shotgun sequence analysis. EukDetect will greatly advance our understanding of how microbial eukaryotes contribute to microbiomes.


title: Spatiotemporal dynamics between interictal epileptiform discharges and ripples during associative memory processing

abstract:
We describe the spatiotemporal course of cortical high-gamma activity (HGA), hippocampal ripple activity and interictal epileptiform discharges (IEDs) during an associative memory task in 15 epilepsy patients undergoing invasive electroencephalography. Successful encoding trials manifested significantly greater HGA in hippocampus and frontal regions. Successful cued recall trials manifested sustained HGA in hippocampus compared to failed responses. Hippocampal ripple rates were greater during successful encoding and retrieval trials. IEDs during encoding were associated with 15% decreased odds of remembering in hippocampus (95% CI 6-23%). Hippocampal IEDs during retrieval predicted 25% decreased odds of remembering (15-33%). Odds of remembering were reduced by 25-52% if IEDs occurred during the 500-2000 ms window of encoding or by 41% during retrieval. During encoding and retrieval, hippocampal IEDs were followed by a transient decrease in ripple rate. We hypothesize that IEDs impair associative memory in a regionally and temporally specific manner by decreasing physiologic hippocampal ripples necessary for effective encoding and recall. Because dynamic memory impairment arises from pathological IED events competing with physiological ripples, IEDs represent a promising therapeutic target for memory remediation in patients with epilepsy.

SummaryHippocampal interictal epileptiform discharges in hippocampus acutely impair declarative memory, potentially by hijacking physiological processes essential for encoding and recall.


title: Single-cell analysis reveals cellular heterogeneity and molecular determinants of hypothalamic leptin-receptor cells

abstract: Hypothalamic nuclei which regulate homeostatic functions express leptin receptor (LepR), the primary target of the satiety hormone leptin. Single-cell RNA sequencing (scRNA-seq) has facilitated the discovery of a variety of hypothalamic cell types. However, low abundance of LepR transcripts prevented further characterization of LepR cells. Therefore, we perform scRNA-seq on isolated LepR cells and identify eight neuronal clusters, including three uncharacterized Trh-expressing populations as well as 17 non-neuronal populations including tanycytes, oligodendrocytes and endothelial cells. Food restriction had a major impact on Agrp neurons and changed the expression of obesity-associated genes. Multiple cell clusters were enriched for GWAS signals of obesity. We further explored changes in the gene regulatory landscape of LepR cell types. We thus reveal the molecular signature of distinct populations with diverse neurochemical profiles, which will aid efforts to illuminate the multi-functional nature of leptins action in the hypothalamus.


title: Non-synaptic interactions between olfactory receptor neurons, a possible key feature of odor processing in flies

abstract:
When flies explore their environment, they encounter odors in complex, highly intermittent plumes. To navigate a plume and, for example, find food, they must solve several challenges, including reliably identifying mixtures of odorants and their intensities, and discriminating odorant mixtures emanating from a single source from odorants emitted from separate sources and just mixing in the air. Lateral inhibition in the antennal lobe is commonly understood to help solving these challenges. With a computational model of the Drosophila olfactory system, we analyze the utility of an alternative mechanism for solving them: Non-synaptic ("ephaptic") interactions (NSIs) between olfactory receptor neurons that are stereotypically co-housed in the same sensilla.

We found that NSIs improve mixture ratio detection and plume structure sensing and they do so more efficiently than the traditionally considered mechanism of lateral inhibition in the antennal lobe. However, we also found that NSIs decrease the dynamic range of co-housed ORNs, especially when they have similar sensitivity to an odorant. These results shed light, from a functional perspective, on the role of NSIs, which are normally avoided between neurons, for instance by myelination.

Author summaryMyelin is important to isolate neurons and avoid disruptive electrical interference between them; it can be found in almost any neural assembly. However, there are a few exceptions to this rule and it remains unclear why. One particularly interesting case is the electrical interaction between olfactory sensory neurons co-housed in the sensilla of insects. Here, we created a computational model of the early stages of the Drosophila olfactory system and observed that the electrical interference between olfactory receptor neurons can be a useful trait that can help flies, and other insects, to navigate the complex plumes of odorants in their natural environment.

With the model we were able to shed new light on the trade-off of adopting this mechanism: We found that the non-synaptic interactions (NSIs) improve both the identification of the concentration ratio in mixtures of odorants and the discrimination of odorant mixtures emanating from a single source from odorants emitted from separate sources - both highly advantageous. However, they also decrease the dynamic range of the olfactory sensory neurons - a clear disadvantage.


title: HTSeqQC: A Flexible and One-Step Quality Control Software for High-throughput Sequence Data Analysis

abstract: Use of high-throughput sequencing (HTS) has become indispensable in life science research. Raw HTS data contains several sequencing artifacts, and as a first step it is imperative to remove the artifacts for reliable downstream bioinformatics analysis. Although there are multiple stand-alone tools available that can perform the various quality control steps separately, availability of an integrated tool that can allow one-step, automated quality control analysis of HTS datasets will significantly enhance handling large number of samples parallelly. Here, we developed HTSQualC, a stand-alone, flexible, and easy-to-use software for one-step quality control analysis of raw HTS data. HTSQualC can evaluate HTS data quality and perform filtering and trimming analysis in a single run. We evaluated the performance of HTSQualC for conducting batch analysis of HTS datasets with 322 samples with an average [~]1M (paired end) sequence reads per sample. HTSQualC accomplished the QC analysis in [~]3 hours in distributed mode and [~]31 hours in shared mode, thus underscoring its utility and robust performance. In addition to command-line execution, we integrated HTSQualC into the free, open-source, CyVerse cyberinfrastructure resource as a GUI interface, for wider access to experimental biologists who have limited computational resources and/or programming abilities.


title: HTSQualC is a Flexible and One-Step Quality Control Software for High-throughput Sequencing Data Analysis


title: Retinal optic flow during natural locomotion

abstract: We examine the structure of visual motion on the retina during natural locomotion in real world environments. Natural locomotion generates a rhythmic translation and rotation profile of the head in space, which means that visually specified heading varies throughout the gait cycle. This presents a challenge if optic flow is to be used to control heading towards a goal. The complex, phasic head movements that occur through the gait cycle create a highly unstable pattern of flow relative to the head. In contrast, vestibular-ocular-reflex mediated fixation simplifies patterns of optic flow on the retinae, resulting in regular features that may be valuable for the control of locomotion. In particular, the sign and magnitude of foveal curl in retinal flow fields specifies the bodys trajectory relative to the fixation point. In addition, the peak in the divergence of the retinal flow field specifies the walkers instantaneous overground velocity/momentum vector in retinotopic coordinates. Assuming that walkers can determine the body position relative to fixation, this time-varying retinotopic cue for the bodys momentum could provide a visual control signal for foot placement over complex terrain. In contrast, the temporal variation of heading is large enough to be problematic for use in steering towards a goal. Consideration of optic flow in the context of natural locomotion therefore suggests a re-evaluation of the role of optic flow in the visual control of locomotion.


title: A reference tissue atlas for the human kidney

abstract: AO_SCPLOWBSTRACTC_SCPLOWKidney Precision Medicine Project (KPMP) is building a spatially-specified human tissue atlas at the single-cell resolution with molecular details of the kidney in health and disease. Here, we describe the construction of an integrated reference tissue map of cells, pathways and genes using unaffected regions of nephrectomy tissues and undiseased human biopsies from 55 subjects. We use single-cell and -nucleus transcriptomics, subsegmental laser microdissection bulk transcriptomics and proteomics, near-single-cell proteomics, 3-D nondestructive and CODEX imaging, and spatial metabolomics data to hierarchically identify genes, pathways and cells. Integrated data from these different technologies coherently describe cell types/subtypes within different nephron segments and interstitium. These spatial profiles identify cell-level functional organization of the kidney tissue as indicative of their physiological functions and map different cell subtypes to genes, proteins, metabolites and pathways. Comparison of transcellular sodium reabsorption along the nephron to levels of mRNAs encoding the different sodium transporter genes indicate that mRNA levels are largely congruent with physiological activity.This reference atlas provides an initial framework for molecular classification of kidney disease when multiple molecular mechanisms underlie convergent clinical phenotypes.


title: The essential role of Dnmt1 in gametogenesis in the large milkweed bug Oncopeltus fasciatus

abstract: Given the importance of DNA methylation in protection of the genome against transposable elements and transcriptional regulation in other taxonomic groups, the diversity in both levels and patterns of DNA methylation in the insects raises questions about its function and evolution. We show that the maintenance DNA methyltransferase, DNMT1, affects meiosis and is essential to fertility in milkweed bugs, Oncopeltus fasciatus, while DNA methylation is not required in somatic cells. Our results support the hypothesis that Dnmt1 is required for the transition of germ cells to gametes in O. fasciatus and that this function is conserved in male and female gametogenesis. They further suggest that DNMT1 has a function independent of DNA methylation in germ cells. Our results raise the question of how a gene so critical in fitness across multiple insect species can have diverged widely across the insect tree of life.


title: A hacked kitchen scale for quantification of grip strength in rodents

abstract:
Assessment of neuromuscular function is critical for understanding pathophysiological changes related to motor system dysfunction in many rodent disease models. Among methods used for quantification of grip performance in rodents, gauge-based grip strength meters provide the most reliable results, however, such instruments are unaffordable by many laboratories. Here we demonstrate how to build a rodent grip strength apparatus from scratch using a digital kitchen scale, an empty cage, and a microcontroller, with both hardware and software being completely open-source to enable maximal modularity and flexibility of the instrument in concordance with the principles of open-source bioinstrumentation. Furthermore, we test the griPASTA system for assessment of increased muscular rigidity in the proof-of-concept experiment in the rat model of Parkinsons disease induced by intrastriatal administration of 6-hydroxydopamine (6-OHDA). Finally, the importance of bioinstrumental customization is demonstrated by utilizing griPASTA for assessment of trial speed from initial-to-maximal deflection time segments and controlling for its potential confounding effects on the grip strength.

Significance StatementNeuromuscular function analyzed by grip strength performance tests is an integral part of motor system neuroscience and neurotoxicology. Strain gauge-based grip strength meters provide the most reliable results, however, commercial solutions are unaffordable by many. Consequently, cheap semi-quantitative tests are often used at the expense of precision and reliability. We propose griPASTA - a simple and robust open-source grip strength platform made from an ordinary kitchen scale. griPASTA could improve the quality and reproducibility of grip strength experiments by enabling researchers to obtain quantitative grip strength data in high resolution using a highly customizable platform.


title: Balancing selection maintains hyper-divergent haplotypes in C. elegans

abstract: Across diverse taxa, selfing species have evolved independently from outcrossing species thousands of times. The transition from outcrossing to selfing significantly decreases the effective population size, effective recombination rate, and heterozygosity within a species. These changes lead to a reduction in genetic diversity, and therefore adaptive potential, by intensifying the effects of random genetic drift and linked selection. Within the nematode genus Caenorhabditis, selfing has evolved at least three times and all three species, including in the model organism Caenorhabditis elegans, show substantially reduced genetic diversity relative to outcrossing species. Selfing and outcrossing Caenorhabditis species are often found in the same niches, but we still do not know how selfing species with limited genetic diversity can adapt to these environments. Here, we examine the whole-genome sequences from 609 wild C. elegans strains isolated worldwide and show that genetic variation is concentrated in punctuated hyper-divergent regions that cover 20% of the C. elegans reference genome. These regions are enriched in environmental response genes that mediate sensory perception, pathogen response, and xenobiotic stress response. Population genomic evidence suggests that genetic diversity in these regions has been maintained by long-term balancing selection. Using long-read genome assemblies for 15 wild strains, we show that hyper-divergent haplotypes contain unique sets of genes and show levels of divergence comparable to levels found between Caenorhabditis species that diverged millions of years ago. These results provide an example for how species can avoid the evolutionary "dead end" associated with selfing.


title: Retinoic acid rewires the adrenergic core regulatory circuitry of neuroblastoma

abstract: Neuroblastoma cell identity depends on a core regulatory circuit (CRC) of transcription factors that collaborate with MYCN to drive the oncogenic gene expression program. For neuroblastomas dependent on the adrenergic CRC, treatment with retinoids can inhibit cell growth and induce differentiation. Here we show that when MYCN-amplified neuroblastomas cells are treated with retinoic acid, histone H3K27 acetylation and methylation become redistributed to decommission super-enhancers driving the expression of PHOX2B and GATA3, together with the activation of new super-enhancers that drive high levels of MEIS1 and SOX4 expression. These findings indicate that treatment with retinoids can reprogram the enhancer landscape, resulting in downregulation of MYCN expression, while establishing a new retino-sympathetic CRC that causes proliferative arrest and sympathetic differentiation. Thus, we provide mechanisms that account for the beneficial effects of retinoids in high-risk neuroblastoma and explain the rapid downregulation of expression of MYCN despite massive levels of amplification of this gene.


title: An atlas of lamina-associated chromatin across twelve human cell types revealsan intermediate chromatin subtype

abstract: Association of chromatin with lamin proteins at the nuclear periphery has emerged as a potential mechanism to coordinate cell type-specific gene expression and maintain cellular identity via gene silencing. Unlike many histone modifications and chromatin-associated proteins, lamin-associated domains (LADs) have yet to be mapped genome-wide in a diverse panel of human cell types, which has limited our understanding of the role peripheral chromatin plays in development and disease. To address this gap, we mapped LAMIN B1 (LB1) across twelve human cell types encompassing pluripotent stem cells, intermediate progenitors, and differentiated cells from all three germ layers. Integrative analyses of this atlas of peripheral chromatin with publicly available genomic data, as well as gene expression and repressive histone maps generated for this study, revealed that in all twelve cellular contexts lamin-associated chromatin is organized into at least two subtypes defined by differences in LB1 occupancy, gene expression, chromatin accessibility, transposable elements, replication timing, and radial positioning. Most genes gain or lose LB1 occupancy consistent with their cell type along developmental trajectories; however, we also identified examples where the enhancer, but not the gene body and promoter, change LAD state. Imaging of fluorescently labeled DNA in single cells validated these transitions and showed intermediate radial positioning of LADs that are gene dense, relatively accessible, and dynamic across development. This atlas represents the largest resource to date for peripheral chromatin organization studies.

category: developmental biology


title: Shape Dimensionality Metrics for Landmark Data

abstract:
This paper is concerned with rank deficiency in phenotypic covariance matrices: first to establish it is a problem by measuring it, and then proposing methods to treat for it. Significant rank deficiency can mislead current measures of whole-shape phenotypic integration, because they rely on eigenvalues of the covariance matrix, and highly rank deficient matrices will have a large percentage of meaningless eigenvalues. This paper has three goals. The first is to examine a typical geometric morphometric data set and establish that its covariance matrix is rank deficient. We employ the concept of information, or Shannon, entropy to demonstrate that a sample of dire wolf jaws is highly rank deficient. The different sources of rank deficiency are identified, and include the Generalized Procrustes analysis itself, use of the correlation matrix, insufficient sample size, and phenotypic covariance. Only the last of these is of biological interest.

Our second goal is to examine a test case where a change in integration is known, allowing us to document how rank deficiency affects two measures of whole shape integration (eigenvalue standard deviation and standardized generalized variance). This test case utilizes the dire wolf data set from Part 1, and introduces another population that is 5000 years older. Modularity models are generated and tested for both populations, showing that one population is more integrated than the other. We demonstrate that eigenvalue variance characterizes the integration change incorrectly, while the standardized generalized variance lacks sensitivity. Both metrics are impacted by the inclusion of many small eigenvalues arising from rank deficiency of the covariance matrix. We propose a modification of the standardized generalized variance, again based on information entropy, that considers only the eigenvalues carrying non-redundant information. We demonstrate that this metric is successful in identifying the integration change in the test case.

The third goal of this paper is to generalize the new metric to the case of arbitrary sample size. This is done by normalizing the new metric to the amount of information present in a permuted covariance matrix. We term the resulting metric the  relative dispersion, and it is sample size corrected. As a proof of concept we us the new metric to compare the dire wolf data set from the first part of this paper to a third data set comprising jaws of Smilodon fatalis. We demonstrate that the Smilodon jaw is much more integrated than the dire wolf jaw. Finally, this information entropy-based measures of integration allows comparison of whole shape integration in dense semilandmark environments, allowing characterization of the information content of any given shape, a quantity we term  latent dispersion.


title: On Rank Deficiency in Phenotypic Covariance


title: Characterization of a novel amastin-like surface protein (ALSP) of Leishmania donovani, a probable lipase

abstract: In the current study, a novel putative protein of Leishmania donovani, amastin-like surface protein (ALSP) has been characterized. The gene was cloned in a bacterial system and the protein was overexpressed. A polyclonal antibody was developed against the protein, which detected a 10 kDa band in the L. donovani amastigote. ALSP mRNA was detected in L. donovani amastigote, which was not expressed in the promastigote. ALSP mRNA was not expressed in either morphological forms of Leishmania major. MALDI-TOF confirmed the molecular weight of ALSP as 10 kDa. I-TASSER predicted the function of ALSP as a lipase, which was confirmed by preliminary in-vitro experiments using amastigotes of L. donovani. ALSP has GAS amino acid sequences, which might act as the active site for its lipase activity. The selective expression of ALSP in amastigotes probably makes it important in virulence mechanisms such as survival in the phagolysosome and modulation of its membrane and other metabolic functions, necessary for parasite survival in the human host. ALSP can act as a peptide vaccine target and maybe detected in the peripheral blood or urine as a molecular biomarker of active disease in visceral leishmaniasis.


title: Phenotypic plasticity underlies local invasion and distant metastasis in colon cancer

abstract: Phenotypic plasticity represents the most relevant hallmark of the carcinoma cell as it bestows it with the capacity of transiently altering its morphologic and functional features while en route to the metastatic site. However, the study of phenotypic plasticity is hindered by the rarity of these events within primary lesions and by the lack of experimental models. Here, we identified a subpopulation of phenotypic plastic colon cancer cells: EpCAMlo cells are motile, invasive, chemo-resistant, and highly metastatic. EpCAMlo bulk and single-cell RNAseq analysis indicated 1. enhanced Wnt/{beta}-catenin signaling, 2. a broad spectrum of degrees of EMT activation including hybrid E/M states (partial EMT) with highly plastic features, and 3. high correlation with the CMS4 subtype, accounting for colon cancer cases with poor prognosis and a pronounced stromal component. Of note, a signature of genes specifically expressed in EpCAMlo cancer cells is highly predictive of overall survival in tumors other than CMS4, thus highlighting the relevance of quasi-mesenchymal tumor cells across the spectrum of colon cancers. Enhanced Wnt and the downstream EMT activation represent key events in eliciting phenotypic plasticity along the invasive front of primary colon carcinomas. Distinct sets of epithelial and mesenchymal genes define transcriptional trajectories through which state transitions arise. pEMT cells, often earmarked by the extracellular matrix glycoprotein SPARC together with nuclear ZEB1 and {beta}-catenin along the invasive front of primary colon carcinomas, are predicted to represent the origin of these (de)differentiation routes through biologically-distinct cellular states, and to underlie the phenotypic plasticity of colon cancer cells.


title: Decreasing arousal modulates perceptual decision-making

abstract:
The ability to make decisions based on external information, prior knowledge and evidence, is a crucial aspect of cognition and may determine the success and survival of an organism. Despite extensive work on decision-making mechanisms/models, understanding the effects of alertness on neural and cognitive processes remain limited. Here we use electroencephalography and behavioural modelling to characterise cognitive and neural dynamics of perceptual decision-making in awake/low alertness periods in humans (14 male, 18 female) and characterise the compensatory mechanisms as alertness decreases. Well-rested human participants, changing between full-wakefulness and low alertness, performed an auditory tone-localisation task and its behavioural dynamics was quantified with psychophysics, signal detection theory and drift-diffusion modelling, revealing slower reaction times, inattention to the left side of space, and a lower rate of evidence accumulation in periods of low alertness. Unconstrained multivariate pattern analysis (decoding) showed a ~280ms delayed onset driven by low alertness of the neural signatures differentiating between left and right decision, with a spatial reconfiguration from centro-parietal to lateral frontal regions 150-360ms. To understand the neural compensatory mechanisms with decreasing alertness, we connected the evidence-accumulation behavioural parameter to the neural activity, showing in the early periods (125-325ms) a shift in the associated patterns from right parietal regions in awake, to right fronto-parietal during low alertness. This change in the neurobehavioural dynamics for central accumulation related cognitive processes define a clear reconfiguration of the brain networks regions and dynamics needed for the implementation of decision-making, revealing mechanisms of resilience of cognition when challenged by decreased alertness.

Significance statementMost living organisms make multiple daily decisions and these require a degree of evidence from both the environment and the internal milieu. Such decisions are usually studied under sequential sampling models and involve making a behavioural choice based on sensory encoding, central accumulation, and motor implementation processes. Since there is little research on how decreasing alertness affects such cognitive processes, this study has looked at the cognitive and neural dynamics of perceptual decision-making in people while fully awake and in drowsy periods. Using computational modelling of behaviour and neural dynamics on human participants performing an auditory tone-localisation task, we reveal how low alertness modulates evidence accumulation related processes and its corresponding compensatory neural signatures.


title: Decreasing alertness modulates perceptual decision-making


title: Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster

abstract:
As part of ongoing studies with clinically relevant Klebsiella spp., we characterized the genomes of three clinical GES-5-positive ST138 strains originally identified as Klebsiella oxytoca. blaOXY gene, average nucleotide identity and phylogenetic analyses showed the strains to be Klebsiella michiganensis. Affiliation of the strains to ST138 led us to demonstrate that the current multi-locus sequence typing scheme for K. oxytoca can be used to speciate members of this genetically diverse complex of bacteria. The strains encoded the kleboxymycin biosynthetic gene cluster (BGC), previously only found in K. oxytoca strains and one strain of Klebsiella grimontii. The finding of this BGC, associated with antibiotic-associated haemorrhagic colitis, in K. michiganensis led us to carry out a wide-ranging study to determine the prevalence of this BGC in Klebsiella spp. Of 7,170 publicly available Klebsiella genome sequences screened, 88 encoded the kleboxymycin BGC. All BGC-positive strains belonged to the K. oxytoca complex, with strains of four (K. oxytoca, K. pasteurii, K. grimontii, K. michiganensis) of the six species of the complex found to encode the complete BGC. In addition to being found in K. grimontii strains isolated from preterm infants, the BGC was found in K. oxytoca and K. michiganensis metagenome-assembled genomes recovered from neonates. Detection of the kleboxymycin BGC across the K. oxytoca complex may be of clinical relevance and this cluster should be included in databases characterizing virulence factors, in addition to those characterizing BGCs.

IMPACT STATEMENTMembers of the Klebsiella oxytoca complex are difficult to speciate using phenotypic and chemotaxonomic methods. Consequently, many genomes deposited in public databases are misclassified as K. oxytoca. Here we demonstrate that the current multi-locus sequence typing (MLST) system for the complex can be used to accurately speciate many strains, which will be of use to clinical laboratories in resource-limited settings which rely on the MLST scheme for typing and epidemiological tracking of isolates. In addition, extended analyses of the genomes of Klebsiella spp. have revealed the kleboxymycin biosynthetic gene cluster (BGC) is restricted to species of the Klebsiella oxytoca complex (K. oxytoca, K. michiganensis, K. pasteurii and K. grimontii). Species- and/or gene-specific differences in the clusters sequences may be relevant to virulence of K. oxytoca and related species. The finding of the kleboxymycin BGC in the preterm infant gut microbiota may have implications for disease presentation in a subset of neonates.


title: Hierarchized phosphotarget binding by the seven human 14-3-3 isoforms

abstract: The seven human 14-3-3 isoforms, highly similar yet encoded by distinct genes, are among the top 1% highest-expressed human proteins. 14-3-3 proteins recognize phosphorylated motifs within numerous human or viral proteins. We analyzed by crystallography, fluorescence polarization, mutagenesis and fusicoccin-mediated modulation the structural basis and druggability of 14-3-3 binding to four E6 oncoproteins of tumorigenic HPV. The seven isoforms bound variant and mutated phospho-motifs of E6 and unrelated protein RSK1 with different affinities, albeit following an ordered ranking profile with conserved relative KD ratios. Remarkably, 14-3-3 isoforms obey the same hierarchy when binding to most of their established targets, nicely supported by a recent proteome-wide human complexome map. This knowledge allows predicting the proportions of 14-3-3 isoforms engaged with phosphoproteins in various tissues. Notwithstanding their individual functions, cellular concentrations of 14-3-3 may be collectively adjusted to buffer the strongest phosphorylation outbursts, explaining their expression variations in different tissues and tumors.


title: Population genomics reveals molecular determinants of specialization to tomato in the polyphagous fungal pathogen Botrytis cinerea

abstract: Many fungal plant pathogens encompass multiple populations specialized on different plant species. Understanding the factors underlying pathogen adaptation to their hosts is a major challenge of evolutionary microbiology, and it should help preventing the emergence of new specialized pathogens on novel hosts. Previous studies have shown that French populations of the grey mould pathogen Botrytis cinerea parasitizing tomato and grapevine are differentiated from each other, and have higher aggressiveness on their host-of-origin than on other hosts, indicating some degree of host specialization in this polyphagous pathogen. Here, we aimed at identifying the genomic features underlying the specialization of B. cinerea populations to tomato and grapevine. Based on whole genome sequences of 32 isolates, we confirmed the subdivision of B. cinerea pathogens into two genetic clusters on grapevine and another, single cluster on tomato. Levels of genetic variation in the different clusters were similar, suggesting that the tomato-specific cluster has not recently emerged following a bottleneck. Using genome scans for selective sweeps and divergent selection, tests of positive selection based on polymorphism and divergence at synonymous and non-synonymous sites and analyses of presence/absence variation, we identified several candidate genes that represent possible determinants of host specialization in the tomato-associated population. This work deepens our understanding of the genomic changes underlying the specialization of fungal pathogen populations.


title: A two-phase model of skin epidermal stratification: lessons from centrosomes

abstract: The development of complex stratified epithelial barriers in mammals is initiated from single-layered epithelia. How stratification is initiated and fueled are still open questions. Previous studies on skin epidermal stratification suggested a central role for perpendicular/asymmetric cell division orientation of the basal keratinocyte progenitors. Here, we use centrosomes, that organize the mitotic spindle, to test whether cell division orientation and stratification are linked. Genetically ablating centrosomes from the developing epidermis led to the activation of the p53-, 53BP1- and USP28-dependent mitotic surveillance pathway causing a thinner epidermis and hair follicle arrest. The centrosome/p53-double mutant keratinocyte progenitors significantly altered their division orientation in the later stages without majorly affecting epidermal differentiation. Together with time-lapse imaging and tissue growth dynamics measurements, the data suggested that the first and major phase of epidermal stratification is boosted by high proliferation rates of the basal and suprabasal transit-amplifying cells as well as cell delamination, whereas the second phase maybe uncoupled from the division orientation of the basal progenitors. The data provide insights for tissue homeostasis and hyperproliferative diseases that may recapitulate developmental programs.


title: Maintenance of mitochondrial integrity in midbrain dopaminergic neurons governed by a conserved developmental transcription factor

abstract: The degeneration of dopaminergic (DA) neurons in the substantia nigra is a hallmark of Parkinsons disease (PD). Dysregulation of developmental transcription factors is implicated in dopaminergic neurodegeneration, but the underlying molecular mechanisms remain largely unknown. Drosophila Fer2 is a prime example of a developmental transcription factor required for the birth and maintenance of midbrain DA neurons. Using an approach combining ChIP-seq, RNA-seq, and genetic epistasis experiments with PD-linked genes, here we demonstrate that Fer2 controls a transcriptional network to maintain mitochondrial structure and function, and thus confers dopaminergic neuroprotection against genetic and oxidative insults. We further show that conditional ablation of Nato3, a mouse homolog of Fer2, in differentiated DA neurons results in locomotor impairments and mitochondrial abnormality in aged mice. Our results reveal the essential and conserved role of Fer2 homologs in the mitochondrial maintenance of midbrain DA neurons, opening new perspectives for modelling and treating PD.


title: DLX5/6 GABAergic expression affects social vocalization: implications for human evolution

abstract:
DLX5 and DLX6 are two closely related transcription factors involved in brain development and in GABAergic differentiation. The DLX5/6 locus is regulated by FoxP2, a gene involved in language evolution and has been associated to neurodevelopmental disorders and mental retardation. Targeted inactivation of Dlx5/6 in mouse GABAergic neurons (Dlx5/6VgatCre mice) results in behavioural and metabolic phenotypes notably increasing lifespan by 33%.

Here, we show that Dlx5/6VgatCre mice present a hyper-vocalization and hyper-socialization phenotype. While only 7% of control mice emitted more than 700 vocalizations/10min, 30% and 56% of heterozygous or homozygous Dlx5/6VgatCre mice emitted more than 700 and up to 1400 calls/10min with a higher proportion of complex and modulated calls. Hyper-vocalizing animals were more sociable: the time spent in dynamic interactions with an unknown visitor was more than doubled compared to low-vocalizing individuals.

The characters affected by Dlx5/6 in the mouse (sociability, vocalization, skull and brain shape...) overlap those affected in the "domestication syndrome". We therefore explored the possibility that DLX5/6 played a role in human evolution and "self-domestication" comparing DLX5/6 genomic regions from Neanderthal and modern humans. We identify an introgressed Neanderthal haplotype (DLX5/6-N-Haplotype) present in 12.6% of European individuals that covers DLX5/6 coding and regulatory sequences. The DLX5/6-N-Haplotype includes the binding site for GTF2I, a gene associated to Williams-Beuren syndrome, a hyper-sociability and hyper-vocalization neurodevelopmental disorder. The DLX5/6-N-Haplotype is significantly underrepresented in semi-supercentenarians (>105y of age), a well-established human model of healthy ageing and longevity, suggesting their involvement in the co-evolution of longevity, sociability and speech.


title: What the Phage: A scalable workflow for the identification and analysis of phage sequences

abstract: Phages are among the most abundant and diverse biological entities on earth. Phage prediction from sequence data is a crucial first step to understanding their impact on the environment. A variety of bacteriophage prediction tools have been developed over the years. They differ in algorithmic approach, results, and ease of use. We, therefore, developed "What the Phage" (WtP), an easy-to-use and parallel multitool approach for phage prediction combined with an annotation and classification downstream strategy, thus, supporting the users decision-making process by summarizing the results of the different prediction tools in charts and tables. WtP is reproducible and scales to thousands of datasets through a workflow manager (Nextflow). WtP is freely available under a GPL-3.0 license (https://github.com/replikation/What_the_Phage).


title: Effect of Cholesterol vs. Ergosterol on DPPC Bilayer Properties: Insights from Atomistic Simulations

abstract: Sterols have been ascribed a major role in the organization of biological membranes, in particular for the formation of liquid ordered domains in complex lipid mixtures. Here, we employed molecular dynamics simulations to compare the effects of cholesterol and ergosterol as the major sterol of mammalian and fungal cells, respectively, on binary mixtures with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) as a proxy for saturated lipids. In agreement with previous work, we observe that the addition of sterol molecules modifies the order of DPPC both in the gel phase and in the liquid phase. When disentangling the overall tilt angle and the structure of the tail imposed by trans/gauche configurations of torsion angles in the tail, respectively, a more detailed picture of the impact of sterols can be formulated, revealing, e.g., an approximate temperature-concentration superposition ranging from the liquid to the gel phase. Furthermore, a new quantitative measure to identify the presence of collective sterol effects is discussed. Moreover, when comparing both types of sterols, addition of cholesterol has a noticeably stronger impact on phospholipid properties than of ergosterol. The observed differences can be attributed to higher planarity of the cholesterol ring system. This planarity combined with an inherent asymmetry in its molecular interactions leads to better alignment and hence stronger interaction with saturated acyl chains. Our results suggest that the high order demonstrated for ergosterol in fungal plasma membranes must therefore be generated via additional mechanisms.

category: biophysics