title: Cerebro-cerebellar networks facilitate learning through feedback decoupling

abstract: Behavioural feedback is critical for learning in the cerebral cortex. However, such feedback is often not readily available. How the cerebral cortex learns efficiently despite the sparse nature of feedback remains unclear. Inspired by recent deep learning algorithms, we introduce a systems-level computational model of cerebro-cerebellar interactions. In this model a cerebral recurrent network receives feedback predictions from a cerebellar network, thereby decoupling learning in cerebral networks from future feedback. When trained in a simple sensorimotor task the model shows faster learning and reduced dysmetria-like behaviours, in line with the widely observed functional impact of the cerebellum. Next, we demonstrate that these results generalise to more complex motor and cognitive tasks. Finally, the model makes several experimentally testable predictions regarding (1) cerebro-cerebellar task-specific representations over learning, (2) task-specific benefits of cerebellar predictions and (3) the differential impact of cerebellar and inferior olive lesions. Overall, our work offers a theoretical framework of cerebro-cerebellar networks as feedback decoupling machines.


title: Sex-specific regulation of binge drinking and affective behaviors by subcortical serotonin 5HT2c receptors

abstract: Serotonin 5HT2c receptors have been implicated in the pathophysiology of both mood disorders and substance use disorders, but the precise cells and circuits mediating the effects on behavior have yet to be identified. In this study, we employed anatomical tracing, in-vivo fiber photometry with both calcium and serotonin sensors, electrophysiology, chemogenetics, and genetic manipulations of the 5HT2c receptor to identify two populations of neurons expressing serotonin 5HT2c receptors, one in the lateral habenula and one in the bed nucleus of the stria terminalis, that sex-specifically co-regulate affective behaviors and are modulated by binge alcohol consumption. These findings may have implications for the development of sex-specific treatments for mood disorders and substance use disorders targeting the brains serotonin system.

category: neuroscience


title: Campylobacter jejuni induces differentiation of human neutrophils to the CD16hi/CD62Llo subtype which possess cancer promoting activities

abstract: The discovery of neutrophil subtypes has expanded what is known about neutrophil functions, yet there is still much to learn about the role of these subtypes during bacterial infection. We investigated whether Campylobacter jejuni induced differentiation of human neutrophils into the hypersegmented, CD16hi/CD62Llo subtype. In addition, we investigated whether C. jejuni-dependent differentiation of this neutrophil subtype induced cancer promoting activities of human T cells and colonocytes, which were observed in other studies of hypersegmented, CD16hi/CD62Llo neutrophils. We found that C. jejuni causes a significant shift in human neutrophil populations to the hypersegmented, CD16hi/CD62Llo subtype and that those populations exhibit delayed apoptosis, elevated arginase-1 expression, and increased reactive oxygen species production. Furthermore, incubation of C. jejuni-infected neutrophils with human T cells resulted in decreased expression of the {zeta}-chain of the T cell receptor (TCR{zeta}), which was restored upon supplementation with exogenous L-arginine. In addition, incubation of C. jejuni-infected neutrophils with human colonocytes resulted in increased HIF-1 stabilization and NF-{kappa}B activation in those colonocytes, which may result in the upregulation of pro-tumorigenic genes. This response, coupled with the ability of C. jejuni-infected neutrophils to suppress TCR{zeta} expression in T cells, could result in the promotion of colorectal tumorigenesis during infection with C. jejuni.

category: microbiology


title: Tardigrade community microbiomes in North American orchards include putative endosymbionts and plant pathogens

abstract: The microbiome of tardigrades, a phylum of microscopic animals best known for their ability to survive extreme conditions, is poorly studied worldwide and completely unknown in North America. An improved understanding of tardigrade-associated bacteria is particularly important because tardigrades have been shown to act as vectors of the plant pathogen Xanthomonas campestris in the laboratory. However, the potential role of tardigrades as reservoirs and vectors of phytopathogens has not been investigated further. This study analyzed the microbiota of tardigrades from six apple orchards in central Iowa, USA, and is the first analysis of the microbiota of North American tardigrades. It is also the first ever study of the tardigrade microbiome in an agricultural setting. We utilized 16S rRNA gene amplicon sequencing to characterize the tardigrade community microbiome across four contrasts: location, substrate type (moss or lichen), collection year, and tardigrades versus their substrate. Alpha diversity of the tardigrade community microbiome differed significantly by location and year of collection but not by substrate type. Our work also corroborated earlier findings, demonstrating that tardigrades harbor a distinct microbiota from their environment. We also identified tardigrade-associated taxa that belong to genera known to contain phytopathogens (Pseudomonas, Ralstonia, and the Pantoea/Erwinia complex). Finally, we observed members of the genera Rickettsia and Wolbachia in the tardigrade microbiome; because these are obligate intracellular genera, we consider these taxa to be putative endosymbionts of tardigrades. These results suggest the presence of putative endosymbionts and phytopathogens in the microbiota of wild tardigrades in North America.


title: A single nucleotide polymorphism determines constitutive versus inducible type VI secretion in Vibrio cholerae

abstract: Vibrio cholerae is a well-studied human pathogen that is also a common inhabitant of marine habitats. In both environments, the bacterium is subject to interbacterial competition. A molecular nanomachine that is often involved in such competitive behavior is the type VI secretion system (T6SS). Interestingly and in contrast to non-pandemic or environmental isolates, the T6SS of the O1 El Tor clade of V. cholerae, which is responsible for the ongoing 7th pandemic, is largely silent under standard conditions. Instead, these strains induce their full T6SS capacity only under specific conditions such as growth on chitinous surfaces (signaled through TfoX and QstR) or when the cells encounter low intracellular c-di-GMP levels (TfoY-driven). In this study, we identified a single nucleotide polymorphism (SNP) within an intergenic region of the major T6SS gene cluster of V. cholerae that determines the T6SS status of the cell. We show that SNP conversion is sufficient to induce T6SS production in numerous pandemic strains, while the converse approach renders non-pandemic/environmental V. cholerae strains T6SS-silent. We further demonstrate that SNP-dependent T6SS production occurs independently of the known T6SS regulators TfoX, QstR, and TfoY. Finally, we identify a putative promoter region adjacent to the identified SNP that is required for all forms of T6SS regulation.


title: Strong interactions between highly-dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin

abstract:
BackgroundInteractions between topologically associating domains (TADs), and between the nuclear envelope (NE) and lamina-associated domains (LADs) are expected to shape various aspects of 3D chromatin structure and dynamics at the level of the entire nucleus; however, a full quantitative picture is still lacking. Relevant genome-wide experiments that may provide statistically significant conclusions remain difficult.

ResultsWe have developed a coarse-grained dynamic model of the Drosophila melanogaster nucleus at TAD ([~]100 kb) resolution that explicitly accounts for four distinct epigenetic classes of TADs and describes time evolution of the chromatin over the entire interphase. Best agreement with experiment is achieved when the simulation includes an entire biological system - an ensemble of complete nuclei, corresponding to the experimentally observed set of mutual arrangements of chromosomes, properly weighted according to experiment. The model is validated against multiple experiments, including those that describe changes in chromatin induced by lamin depletion.

Predicted positioning of LADs at the NE is highly dynamic (mobile) - the same LAD can attach, detach, and re-attach itself to the NE multiple times during interphase. The average probability of a LAD to be found at the NE varies by an order of magnitude, determined by the highly variable local density of nearby LADs along the genome. The distribution of LADs along the genome has a strong effect on the average radial positioning of individual TADs, playing a notable role in maintaining a non-random average global structure of chromatin.

Predicted sensitivity of fruit fly chromatin structure to the balance between TAD-TAD and LAD-NE interactions, also observed previously in models of mammalian chromosomes, suggests conservation of this principle of chromatin organisation across species of higher eukaryotes. Reduction of LAD-NE affinity weakly affects local chromatin structure, as seen in the model-derived Hi-C maps, however, its wild-type strength substantially reduces sensitivity of the chromatin density distribution to variations in the strength of TAD-TAD interactions.

ConclusionsA dynamical model of the entire 3D fruit fly genome makes multiple genome-wide predictions of biological interest. We conjecture that one important role of LADs and their attractive interactions with the NE is to create the average global chromatin structure and stabilize it against inevitable cell-to-cell variations of TAD-TAD interactions.

category: molecular biology


title: Haplotype-aware modeling of cis-regulatory effects highlights the gaps remaining in eQTL data

abstract: Expression Quantitative Trait Loci (eQTLs) are critical to understanding the mechanisms underlying disease-associated genomic loci. Nearly all protein-coding genes in the human genome have been associated with one or more eQTLs. Here we introduce a multi-variant generalization of allelic Fold Change (aFC), aFC-n, to enable accurate quantification of the cis-regulatory effects in genes with multiple conditionally independent eQTLs. Applying aFC-n to 458,465 eQTLs in the Genotype-Tissue Expression (GTEx) project data, we demonstrate significant improvement in accuracy over the current tools for estimating the eQTL effect size and predicting genetically regulated gene expression. We characterize some of the empirical properties of the eQTL data and use this framework to assess the current state of eQTL data in terms of characterizing cis-regulatory landscape in individual genomes. Notably, we show that 77.4% of the genes with an allelic imbalance in a sample show 0.5 log2 fold or more of residual imbalance after accounting for the eQTL data underlining the remaining gap in characterizing regulatory landscape in individual genomes. We further contrast this gap across tissue types, and ancestry backgrounds to identify its correlates and guide future studies.

category: genetics


title: Nematodes can survive in a suspended form of life for indefinite time

abstract: When environmental conditions are unfavorable, such as the complete absence of water or oxygen, high temperature, freezing or extreme salinity, some organisms can enter suspended animation (cryptobiosis)1. This reversible transition is preceded by execution of complex genetic and biochemical programs (preconditioning)2,3,4. Under laboratory conditions, however, animals have only been maintained in a viable cryptobiotic state for a short time. Here we show that desiccation followed by freezing allows C. elegans dauer larvae to retain full viability over very long periods (around 500 days). Consistent with this finding, recently nematode individuals have been reanimated from the Siberian permafrost5, that according to precise radiocarbon dating shows that they remained in cryptobiosis since the late Pleistocene, for about 46,000 years. Phylogenomic inference based on our high-quality genome assembly and morphological analysis demonstrate that these nematodes belong to a novel parthenogenetic species, which we named Panagrolaimus kolymaensis. Genome analysis revealed that the core of the molecular toolkit for cryptobiosis in P. kolymaensis and C. elegans is orthologous. To survive desiccation and freezing under laboratory conditions these two species display similar biochemical responses. Thus, nematodes possess extraordinarily robust adaptive mechanisms that potentially allow them to remain in suspended animation over geological time scales.

category: genomics


title: Extending Bayesian Elo-rating to quantify dominance hierarchy steepness

abstract: The steepness of dominance hierarchies provides information about the degree of competition within animal social groups and is thus an important concept in socioecology. The currently most widely-used metrics to quantify steepness are based on Davids scores (DS) derived from dominance interaction networks. One serious drawback of these DS-based metrics is that they are biased, i.e., network density systematically decreases steepness values. Here, we provide a novel approach to estimate steepness based on Elo-ratings, implemented in a Bayesian framework (STEER: Steepness estimation with Elo-rating). Our new metric has two key advantages. First, STEER is unbiased, precise and more robust to data density than DS-based steepness. Second, it provides explicit probability distributions of the estimated steepness coefficient, which allows uncertainty assessment. In addition, it relies on the same underlying concept and is on the same scale as the original measure, and thus allows comparison to existing published results. We evaluate and validate performance of STEER by means of experimentation on empirical and artificial data sets and compare its performance to that of several other steepness estimators. Our results suggest that STEER provides a considerable improvement over existing methods to estimate dominance hierarchy steepness. We provide an R package EloSteepness to calculate the new steepness measure, and also show an example of using steepness in a comparative analysis.

category: animal behavior and cognition


title: Extending Bayesian Elo-rating to quantify the steepness of dominance hierarchies


title: Cryo-EM structure of RNA-induced tau fibrils reveals a small C-terminal core that may nucleate fibril formation

abstract:
In neurodegenerative diseases including Alzheimers and ALS, proteins that bind RNA are found in aggregated forms in autopsied brains. Evidence suggests that RNA aids nucleation of these pathological aggregates; however, the mechanism has not been investigated at the level of atomic structure. Here we present the 3.4 [A] resolution structure of fibrils of full-length recombinant tau protein in the presence of RNA, determined by electron cryo-microscopy (cryoEM). The structure reveals the familiar in-register cross-{beta} amyloid scaffold, but with a small fibril core spanning residues Glu391 to Ala426, a region disordered in the fuzzy coat in all previously studied tau polymorphs. RNA is bound on the fibril surface to the positively charged residues Arg406 and His407 and runs parallel to the fibril axis. The fibrils dissolve when RNAse is added, showing that RNA is necessary for fibril integrity. While this structure cannot exist simultaneously with the tau fibril structures extracted from patients brains, it could conceivably account for the nucleating effects of RNA cofactors followed by remodeling as fibrils mature.

Significance statementApplication of cryoEM has greatly expanded our understanding of atomic structures of mature pathological amyloid fibrils, but little is known at the molecular level of the initiation of fibril formation. RNA has been shown to be one cofactor for formation of fibrils of tau protein, and is known also to bind to other proteins, including TDP-43, FUS, and HNRNPA2, which form pathological inclusions. Our cryoEM structure of recombinant tau protein with RNA reveals a 36 residue, C-terminal fibril core bound to RNA which runs parallel to the fibril axis. We speculate that this structure could represent an early step in the formation of tau fibrils.

category: biophysics


title: Water-Only Look-Locker Inversion recovery (WOLLI) T1 mapping

abstract:
PurposeModified Look-Locker Inversion recovery (MOLLI) and Shortened MOLLI (ShMOLLI) T1 values can deviate substantially from the water T1 in voxels containing large amounts of water and fat. We introduce Water-Only Look-Locker Inversion recovery (WOLLI) to map water T1 in tissue containing fat.

TheoryWOLLI comprises adiabatic water-selective inversion and several balanced steady-state free precession (bSSFP) readouts, followed immediately by adiabatic fat-selective inversion and bSSFP readout(s). Data are fitted pixel-wise and an adapted Deichmann-Haase saturation-correction gives the water T1.

MethodsWe compared two WOLLI protocols (WOLLI-w7f1 and WOLLI-w7f2f1), ShMOLLI and single-voxel spectroscopy at 3T in: simulations, fat/water phantoms, and 12 subjects livers.

ResultsIn simulations with 0-40% fat fraction, T1 varied by: <0.5% (WOLLI-w7f1), <12% (WOLLI-w7f2f1), and >100% (MOLLI). In phantoms, the accuracy of the methods (i.e. worst-case T1w difference vs spectroscopy) was: WOLLI-w7f1 (best, maximum difference of 10.2%), WOLLI-w7f2f1 (max. 10.5%), and ShMOLLI (max. 81.5%). In the liver, the root-mean-squared deviations vs spectroscopy were: 374ms (WOLLI-w7f1), 645ms (WOLLI-w7f2f1), and 700ms (ShMOLLI).

ConclusionCompared to ShMOLLI, WOLLI is less influenced by fat, but more by B0-inhomogeneity. WOLLI was a clear improvement in phantoms but less so in vivo. WOLLI may be suited to scan organs with high fat content such as the liver.


title: Molecular markers of mechanosensation in glycinergic neurons in the avian lumbosacral spinal cord

abstract: Birds are exceptionally adept at controlling their body position. For example, they can coordinate rapid movements of their body while stabilizing their head. Intriguingly, this ability may rely in part on a mechanosensory organ in the avian lower spinal cord called the lumbosacral organ (LSO). However, molecular mechanotransduction mechanisms have not been identified in the avian spinal cord. Here, we report the presence of glycinergic neurons in the LSO that exhibit immunoreactivity for myosin7a and epsin, molecules essential for function and maintenance of hair cells in the inner ear. Specifically, we find glycinergic cell bodies near the central canal and processes that extend laterally to the accessory lobes and spinal ligaments. These LSO neurons are reminiscent of glycinergic neurons in a recently-described lateral spinal proprioceptive organ in zebrafish that detects spinal bending. The avian LSO, however, is located inside a series of fused vertebrae called the synsacrum, which constrains spinal bending. We suggest the LSO may be a modification and elaboration of a pre-existing mechanosensory spinal network in vertebrates. A mechanistic understanding of its function may be an important clue to understanding the evolution and development of avian locomotion.


title: CRY-BARs: Versatile light-gated molecular tools for the remodeling of membrane architectures

abstract: BAR (Bin, Amphiphysin and Rvs) protein domains are responsible for the generation of membrane curvature and represent a critical mechanical component of cellular functions. Thus, BAR domains have great potential as components of membrane-remodeling tools for cell biologists. In this work, we describe the design and implementation of a family of versatile light-gated I-BAR domain containing tools ( CRY-BARs) with applications in the remodeling of membrane architectures and the control of cellular dynamics. By taking advantage of the intrinsic membrane binding propensity of the I-BAR domain, CRY-BARs can be used for spatial and temporal control of cellular processes that require induction of membrane protrusions. Using cell lines and primary neuron cultures, we demonstrate that the CRY-BAR optogenetic tool reports membrane dynamic changes associated with cellular activity. Moreover, we provide evidence that Ezrin acts as a relay between the plasma membrane and the actin cytoskeleton and therefore is an important mediator of switch function. Overall, CRY-BARs hold promise as a useful addition to the optogenetic toolkit to study membrane remodeling in live cells.

category: cell biology


title: Single-cell Transcriptome and Accessible Chromatin Dynamics During Endocrine Pancreas Development

abstract: Delineating gene regulatory networks that orchestrate cell-type specification is an ongoing challenge for developmental biology studies. Single-cell analyses offer opportunities to address these challenges and accelerate discovery of rare cell lineage relationships and mechanisms underlying hierarchical lineage decisions. Here, we describe the molecular analysis of pancreatic endocrine cell differentiation using single-cell gene expression, chromatin accessibility assays coupled to genetic labeling and cell sorting. We uncover transcription factor networks that delineate {beta}-, - and{delta} -cell lineages. Through genomic footprint analysis we identify transcription factor-regulatory DNA interactions governing pancreatic cell development at unprecedented resolution. Our analysis suggests that the transcription factor Neurog3 may act as a pioneer transcription factor to specify the pancreatic endocrine lineage. These findings could improve protocols to generate replacement endocrine cells from renewable sources, like stem cells, for diabetes therapy.

category: developmental biology


title: From microbes to mammals: pond biodiversity homogenization across different land-use types in an agricultural landscape

abstract: Local biodiversity patterns are expected to strongly reflect variation in topography, land use, dispersal boundaries, nutrient supplies, contaminant spread, management practices and other anthropogenic influences. In contrast, studies focusing on specific taxa revealed a biodiversity homogenization effect in areas subjected to long-term intensive industrial agriculture. We investigated whether land use affects biodiversity and metacommunity structure in 67 kettle holes (KH) representing small aquatic islands embedded in the patchwork matrix of a largely agricultural landscape comprising grassland, forest, and arable fields. These KH, similar to millions of standing water bodies of glacial origin, spread across northern Europe, Asia, and North America, are physico-chemically diverse, differ in the degree of coupling with their surroundings. We assessed biodiversity patterns of eukaryotes, Bacteria and Archaea in relation to environmental features of the KH, using deep-amplicon-sequencing of eDNA. First, we asked whether deep sequencing of eDNA provides a representative picture of KH biodiversity across the three domains of life. Second, we investigated if and to what extent KH biodiversity is influenced by the surrounding land-use. Our data shows that deep eDNA amplicon sequencing is useful for in-depth assessments of cross-domain biodiversity comprising both micro- and macro-organisms, but, has limitations with respect to single-taxa conservation studies. Using this broad method, we show that sediment eDNA, integrating several years to decades, depicts the history of agricultural land-use intensification. The latter, coupled with landscape wide nutrient enrichment (including by atmospheric deposition), groundwater connectivity between KH and organismal movement in the tight network of ponds, resulted in a biodiversity homogenization in the KH water, levelling off todays detectable differences in KH biodiversity between land-use types.

category: ecology


title: Dynamic changes to signal allocation rules in response to variable social environments in house mice

abstract: Male house mice use metabolically costly urine marks in intrasexual competition and mate attraction. Given the high costs of signaling and the depletable nature of urine reserves, males should dynamically modulate signal allocation as the social landscape is updated with new information. We investigate which aspects of male urine marking behavior are static or dynamic in light of changing social environments. To do this, we use thermal imaging to capture spatiotemporal data of urine deposition decisions. This novel method reveals fine-scale variation in urinary motor patterns in response to competition and social odors. Males demonstrate striking winner-loser effects in both the total allocation effort and temporal dynamics of scent marking. We find that competitive experience primes key temporal features of signal allocation and modulates responses to familiar and unfamiliar male scents. Males adjust their signaling effort, mark latency, and scent mark rhythm, depending on the scent identities present in the environment. Winners dramatically increase marking effort toward unfamiliar compared to familiar male scent, consistent with a  dear enemy effect. Losers, in contrast, greatly reduce marking to unfamiliar scent but increase marking effort to the scent of their familiar rival, consistent with a  nasty neighbor effect. Counter to the high lability of many features, the initial signal investment pattern influences allocation decisions days later, revealing the possibility of alternative scent mark strategies among competitive males. Thus, different features of urine mark signal allocation vary in responsiveness to fluctuating social landscapes, suggesting there are multiple distinct behavioral modules underlying marking behavior.


title: Endogenous pancreatic microRNAs differentially target the Delta, Omicron, and Wuhan SARS-CoV-2 genomes to upregulate the Diabetes-associated genes

abstract: The SARS-CoV-2 viral genome is mutating and evolving into new variations, including the recently discovered Delta and Omicron. In this study, we used and evaluated our notion of differential targeting of SARS-CoV-2 variant genomes by microRNAs (miRNAs) of the infected human pancreas. We found that even with UTR mutations, the Delta, Omicron, and original Wuhan variations genomes would be differentially targeted by the host pancreas cells native miRNAs in the same way. The miRNAs show a difference in Minimal Free Energy (MFE) with the different viral variants genomes; however, they would still be responsible for the upregulation of the diabetes-associated genes.


title: A role for heritable transcriptomic variation in maize adaptation to temperate environments

abstract: Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments. We generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core processes such as cell division, chromosome organization and cytoskeleton organization showed lower heritability of gene expression. While genes involved in anti-oxidation activity exhibited higher expression heritability. An expression genome-wide association study (eGWAS) identified 19,602 expression quantitative trait loci (eQTLs) associated with the expression of 11,444 genes. A GWAS for alternative splicing identified 49,897 splicing QTLs (sQTLs) for 7,614 genes. Rare allele burden within genomic intervals with trans-eQTLs correlated with extremes of expression in target genes as previously reported for cis-eQTLs. Genes harboring both cis-eQTLs and cis-sQTLs in linkage disequilibrium were disproportionately likely to encode transcription factors or were annotated as responding to one or more stresses. Independent component analysis of gene expression data identified loci regulating co-expression modules involved in phytohormone pathways, cell wall biosynthesis, lipid metabolism and stress response. Several genes involved in cell proliferation, flower development, DNA replication and gene silencing showed lower gene expression variation explained by genetic factors between temperate and tropical maize lines. A GWAS of 27 previously published phenotypes identified several candidate genes overlapping with genomic intervals showing signatures of selection during adaptation to temperate environments. Our results illustrate how maize transcriptional regulatory networks enable changes in transcriptional regulation to adapt to temperate regions.

category: bioinformatics


title: A study of thermally-induced sex reversal in casque-headed lizards

abstract: Non-avian reptiles, unlike mammals and birds, have undergone numerous sex determination turnovers. For example, casque-headed lizards replaced the ancestral XY system shared across pleurodonts with a new pair of XY chromosomes. However, the evolutionary forces that triggered this transition have remained unclear. An interesting evolutionary hypothesis suggests that species with intermediate states, with sex chromosomes but also thermal-induced sex reversal at specific incubation temperatures, could be more susceptible to sex determination turnovers. We contrasted genotypic data (presence/absence of the Y chromosome) against the histology of gonads of embryos from stages 35-37 incubated at various temperatures, including typical male-producing (26{degrees}C) and female-producing (32{degrees}C) temperatures. We observed perfect concordance between genotype and phenotype at all temperatures. However, analysis of transcriptomic data from embryos incubated at 26{degrees}C and 32{degrees}C identified transcript variants of the chromatin modifiers JARID2 and KDM6B that have been linked to temperature-dependent sex determination in other reptiles. Besides, our work reports for the first time to our knowledge the histology of gonads, including morphological changes, from stages 35-37 of development in the Corytophanidae family. We also observed that all embryos developed hemipenes, suggesting sex-linked developmental heterochrony.Our work tested the validity of a mixed sex determination system in the Corytophanidae family. We showed that XY chromosomes are dominant, however, our work supports the hypothesis of a conserved transcriptional response to incubation temperatures across non-avian reptiles that could be the reminiscence of an ancestral sex determination system.


title: Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence

abstract: Tumours evolve as heterogeneous populations of cells, which may be distinguished by different genomic aberrations. The resulting intra-tumour heterogeneity plays an important role in cancer patient relapse and treatment failure, so that obtaining a clear understanding of each patients tumour composition and evolutionary history is key for personalised therapies. Single-cell sequencing now provides the possibility to resolve tumour heterogeneity at the highest resolution of individual tumour cells, but brings with it challenges related to the particular noise profiles of the sequencing protocols as well as the uncertainty of the underlying evolutionary process. By modelling the noise processes and allowing mutations to be lost or to reoccur during tumour evolution, we present a method to jointly call mutations in each cell, reconstruct the phylogenetic relationship between cells, and determine the locations of mutational losses and recurrences. Our Bayesian approach allows us to accurately call mutations as well as to quantify our certainty in such predictions. We show the advantages of allowing mutational loss or recurrence with simulated data and present its application to tumour single-cell sequencing data.


title: Identification of 121 variants of honey bee Vitellogenin protein sequences with structural differences at functional sites

abstract: Proteins are under selection to maintain central functions and to accommodate needs that arise in ever-changing environments. The positive selection and neutral drift that preserve functions result in a diversity of protein variants. The amount of diversity differs between proteins: multifunctional or disease-related proteins tend to have fewer variants than proteins involved in some aspects of immunity. Our work focuses on the extensively studied protein Vitellogenin (Vg), which in honey bees (Apis mellifera) is multifunctional and highly expressed and plays roles in immunity. Yet, almost nothing is known about the natural variation in the coding sequences of this protein or how amino acid-altering variants might impact structure-function relationships. Here, we map out allelic variation in honey bee Vg using biological samples from 15 countries. The successful barcoded amplicon Nanopore sequencing of 543 bees revealed 121 protein variants, indicating a high level of diversity in Vg. We find that the distribution of non-synonymous single nucleotide polymorphisms (nsSNPs) differs between protein regions with different functions; domains involved in DNA and protein-protein interactions contain fewer nsSNPs than the proteins lipid binding cavities. We outline how the central functions of the protein can be maintained in different variants and how the variation pattern may inform about selection from pathogens and nutrition.

category: biochemistry


title: An optimized method for the isolation of urinary extracellular vesicles for molecular phenotyping: detection of biomarkers for radiation exposure

abstract:
BackgroundUrinary extracellular vesicles (EVs) are a source of biomarkers with broad potential applications across clinical research, including monitoring radiation exposure. A key limitation to their implementation is minimal standardization in EV isolation and analytical analysis methods. Further, most urinary EV isolation protocols necessitate large volumes of sample. This study aimed to compare and optimize isolation and analytical methods for EVs from small volumes of urine.

Methods3 EV isolation methods were compared: ultracentrifugation, magnetic bead-based, and size-exclusion chromatography from 0.5 mL or 1 mL of rat and human urine. EV yield and mass spectrometry signals (Q-ToF and Triple Quad) were evaluated from each method. Metabolomic profiling was performed on EVs isolated from the urine of rats exposed to ionizing radiation 1-, 14-, 30- or 90-days post-exposure, and human urine from patients receiving thoracic radiotherapy for the treatment of lung cancer pre- and post-treatment.

ResultsSize-exclusion chromatography is the preferred method for EV isolation from 0.5 mL of urine. Mass spectrometry-based metabolomic analyses of EV cargo identified biochemical changes induced by radiation, including altered nucleotide, folate, and lipid metabolism. We have provided standard operating procedures for implementation of these methods in other laboratories.

ConclusionsWe demonstrate that EVs can be isolated from small volumes of urine and analytically investigated for their biochemical contents to detect radiation induced metabolomic changes. These findings lay a groundwork to develop future methods to monitor response to radiotherapy and can be extended to an array of molecular phenotyping studies aimed at characterizing EV cargo.

category: cancer biology


title: Does a single exposure to social defeat render rats more vulnerable to chemically induced colitis than brief inescapable foot-shocks?

abstract: All social species are to different degrees exposed to stressors being physical or social environmental, which may affect health and well-being. Stressful and traumatic situations have direct effect on immune responses that may underlie susceptibility of developing somatic illness. In animal research, different types of stressors have been investigated in studying the effect on bowel disorders, some stressor being more or less of environmental origin. We aimed therefore to explore whether a more natural stressor would differ from a stressor of more unnatural characteristics on dextran sulphate sodium (DSS) induced colitis in adult rats. Specifically, if social stress within a single social defeat (SD) paradigm would be a more potent stressor than brief inescapable foot-shocks (IFS) in causing elevated faecal granulocyte marker protein (GMP), crypt- and inflammation score in colon tissue. Three groups of male Wistar rats were used; socially defeated rats; inescapable foot-shock rats; and comparison rats. Main findings showed no difference between the groups on GMP levels, however, there was a significant difference on inflammation and crypt score for the distal part of colon, detected through histology, where socially defeated rats were more susceptible. A single SD seems to be more adverse for these animals, but further studies are recommended to validate a broader range of different outcomes comparing two such different rodent stress models.

category: physiology


title: Decline in Environmental Quality and Spatial Dynamics of New City Area Development Metropolitan Mamminasata, South Sulawesi, Indonesia

abstract: AbstractsThe expansion of urban areas towards the development of new urban areas has an impact on changes in land use, socio-economic dynamics and a decrease in environmental quality. This study aims to analyze land use change as a determinant of environmental degradation and the spatial dynamics of metropolitan urban areas, the effect of land use change, housing development, infrastructure development, and land reclamation on the environmental degradation of the new city area, and control strategies environmental pollution and sustainable development of the new city area. This study uses a quantitative-qualitative concurrent triangulation design approach. Elaboration of data through observation, in-depth interviews, surveys, and documentation is used to describe the socio-economic community, and the decline in the environmental quality of new city area development in relation to the spatial dynamics of metropolitan urban areas. The results of the study show that the intensity of land use change coupled with an increase in socio-economic activities in the development of new city areas is positively associated with a decrease in environmental quality and segregation towards the spatial dynamics of metropolitan urban areas. Changes in land use, housing development, infrastructure development, and land reclamation simultaneously affect environmental quality degradation with a coefficient of determination of 64.96%. This study recommends strategies for controlling environmental pollution and sustainable development of new city areas for the needs of formulating urban development policies for Mamminasata Metropolitan South Sulawesi, Indonesia.


title: Lactate Signaling Mediated by AMD3100 Ameliorates Astrocyte Pathology and Remyelination Without Additional Extension of SOD1G93A Mice' Life-Span

abstract:
BackgroundAmyotrophic lateral sclerosis (ALS) is characterized by the progressive degeneration of motor neurons accompanied by the accumulation of the morphologically and functionally altered glial cells. Reactive astrocytes and microglia secrete pro-inflammatory mediators and contribute to disease progression. Notably, oligodendrocyte functions are disrupted in ALS, including trophic support, myelination, and oligodendrocyte differentiation. ALS patients and mutant SOD1 mice models display reduced levels of myelin basic protein (MBP) and monocarboxylate transporter 1 (MCT1) contributing to impairment of oligodendrocyte function. Lactate, an active metabolite capable of moving into or out of cells, acts as a signaling molecule, transported exclusively by monocarboxylate transporters (MCTs). We showed previously, that AMD3100 increases the lactate transporter MCT1 in an animal models of Alzheimers disease (AD) and ALS.

Methods and ResultsAMD3100 is a reversible antagonist of CXCR4, and therefore inhibits the CXCR4/CXCL12 axis. AMD3100 was shown to have beneficial effects on extension of SOD1G93A mice life-span and enabling migration of hematopoietic stem cells (HSPCs) from bone marrow to periphery. The low content of lactate and transporters in SOD1G93A mice model led us to propose a combined treatment with AMD3100 and exogeneous L-lactate.

ConclusionsThe combined treatment attenuated neuroinflammation and remyelination but did not have a significant extension of SOD1G93A mice life-span compared with AMD3100 treatment alone.


title: Inner membrane complex proteomics reveals a palmitoylation cascade regulating intraerythrocytic development of malaria parasite

abstract: Malaria is caused by infection of the erythrocytes by the parasites Plasmodium. Inside the erythrocytes, the parasites multiply via schizogony, an unconventional cell division mode. The Inner Membrane Complex (IMC), an organelle located beneath the parasite plasma membrane, serving as the platform for protein anchorage, is essential for schizogony. So far, complete repertoire of IMC proteins and their localization determinants remain unclear. Here we used biotin ligase (TurboID)-based proximity labelling to compile the proteome of the schizont IMC of rodent malaria parasite Plasmodium yoelii. In total, 300 TurboID-interacting proteins were identified. 19 of the 22 selected candidates were confirmed to localize in the IMC, indicating good reliability. In light of the existing palmitome of Plasmodium falciparum, 83 proteins of the P. yoelii IMC proteome are potentially palmitoylated. We further identified DHHC2 as the major resident palmitoyl-acyl-transferase of the IMC. Depletion of DHHC2 led to defective schizont segmentation and growth arrest both in vitro and in vivo. DHHC2 was found to palmitoylate two critical IMC proteins CDPK1 and GAP45 for their IMC localization. In summary, this study reports an inventory of new IMC proteins and demonstrates a central role of DHHC2 in governing IMC localization of proteins during the schizont development.


title: A nucleation barrier spring-loads the CBM signalosome for binary activation

abstract: Immune cells activate in a binary, switch-like fashion that involves proteins polymerizing into large complexes known as signalosomes. The switch-like nature of signalosome formation has been proposed to result from large energy barriers to polymer nucleation. Whether such nucleation barriers indeed drive binary immune responses has not yet been shown. Here, we employed an in-cell biophysical approach to dissect the assembly mechanism of the CARD-BCL10-MALT1 (CBM) signalosome, a key determinant of transcription factor NF-{kappa}B activation in both innate and adaptive immunity. We found that the adaptor protein BCL10 encodes an intrinsic nucleation barrier, and that this barrier has been conserved from cnidaria to humans. Using optogenetic tools and a single-cell transcriptional reporter of NF-{kappa}B activity, we further revealed that endogenous human BCL10 is supersaturated even in unstimulated cells, indicating that the nucleation barrier operationally stores energy for subsequent activation. We found that upon stimulation, BCL10 nucleation by CARD9 multimers triggers self-templated polymerization that saturates NF-{kappa}B activation to produce a binary response. Pathogenic mutants of CARD9 that cause human immunodeficiencies eliminated nucleating activity. Conversely, a hyperactive cancer-causing mutation in BCL10 increased its spontaneous nucleation. Our results indicate that unassembled CBM signalosome components function analogously to a spring-loaded mousetrap, constitutively poised to activate NF-{kappa}B through irrevocable polymerization. This finding may inform our understanding of the root causes and progressive nature of pathogenic and age-associated inflammation.


title: A novel genomic DNA library preparation method with low GC bias

abstract: The amount of input DNA available to prepare next-generation sequencing (NGS) libraries is often limited, which can lead to GC content bias and enrichment of specific genomic regions with currently available protocols. In this study, we used breath capture technology to incorporate sequencing adapters into DNA to develop a novel cost-effective protocol for the preparation of genomic DNA libraries. We performed a benchmarking experiment comparing our protocol with common commercially available kits for genomic DNA library preparation with input DNA amount in the range of 1 to 50 ng. Our protocol can generate high-quality genomic sequence data with a marked improvement in coverage breadth and low GC bias, in contrast to standard protocols. Further, our protocol reduces sample handling time and reagent costs, and requires comparatively fewer enzymatic steps relative to other protocols, making it suitable for a range of genomics applications.


title: Deep learning of Protein Sequence Design of Protein-protein Interactions

abstract:
MotivationAs more data of experimentally determined protein structures is becoming available, data-driven models to describe protein sequence-structure relationship become more feasible. Within this space, the amino acid sequence design of protein-protein interactions has still been a rather challenging sub-problem with very low success rates - yet it is central for the most biological processes.

ResultsWe developed an attention-based deep learning model inspired by algorithms used for image-caption assignments for sequence design of peptides or protein fragments. These interaction fragments are derived from and represent core parts of protein-protein interfaces. Our trained model allows the one-sided design of a given protein fragment which can be applicable for the redesign of protein-interfaces or the de novo design of new interactions fragments. Here we demonstrate its potential by recapitulating naturally occurring protein-protein interactions including antibody-antigen complexes. The designed interfaces capture essential native interactions with high prediction accuracy and have native-like binding affinities. It further does not need precise backbone location, making it an attractive tool for working with de novo design of protein-protein interactions.

AvailabilityThe source code of the method is available at https://github.com/strauchlab/iNNterfaceDesign

Supplementary informationSupplementary data are available at Bioinformatics online.


title: Mucins form a nanoscale material barrier against immune cell attack

abstract: The cancer cell glycocalyx serves as a major line of defense against immune surveillance. However, how specific physical properties of the glycocalyx contribute to immune evasion and how these properties are regulated are not well understood. Here, we uncover how the surface density, glycosylation, and crosslinking of cancer-associated mucins contribute to the nanoscale material thickness of the glycocalyx, and further analyze the effect of the glycocalyx thickness on resistance to effector cell attack. Natural Killer (NK) cell-mediated cytotoxicity exhibits a near perfect inverse correlation with the glycocalyx thickness of target cells regardless of the specific glycan structures present. NK cells expressing a chimeric antigen receptor (CAR) have an enhanced ability to breach the glycocalyx and kill target cells. Equipping the NK cell surface with a mucin-digesting enzyme also improves killing with a performance enhancement that rivals or exceeds CARs in some cases. Together, our results provide new considerations for improving cancer immunotherapies.


title: PPRD: a comprehensive online database for expression analysis of ~45,000 plant public RNA-Seq libraries

abstract: High-throughput RNA-sequencing (RNA-seq) has become the most popular technology for profiling gene expression in the last decade due to its low cost and high coverage. As a result, the number of RNA-seq libraries from the plant community has been increasing exponentially in recent years. For major crops, such as maize, rice, soybean, wheat, and cotton, the plant community has collected a total of ~45,000 libraries by 2021. To take full advantage of the bigdata of RNA-seq libraries, an effort to integrate all publicly available libraries via a uniformed processing pipeline and curate them into an easy-to-use searchable database is urgently needed. To address this challenge, here we present a comprehensive web-based platform, Plant Public RNA-seq Database (PPRD, http://ipf.sustech.edu.cn/pub/plantrna/). PPRD consists of a large number of RNA-seq libraries of maize (11,726), rice (19,664), soybean (4,085), wheat (5,816), and cotton (3,483) from Gene Expression Omnibus (GEO), Sequence Read Archive (SRA), European Nucleotide Archive (ENA), and DNA Data Bank of Japan (DDBJ) databases.

category: plant biology


title: Direct DNA sequencing of "Candidatus Liberibacter asiaticus" from Diaphorina citri, the Asian citrus psyllid, and its implications for citrus greening disease management

abstract: The Asian citrus psyllid, Diaphorina citri is an invasive insect 1 and a vector of Candidatus Liberibacter asiaticus (CLas), a bacterium whose growth in Citrus species results in citrus greening disease 2,3. Methods to enrich and sequence CLas from D. citri often rely on biased genome amplification 4 and nevertheless contain significant quantities of host DNA 5,6. To overcome these hurdles, we developed a simple pre-treatment DNase and filtration (hereafter PDF) protocol to directly sequence CLas and the complete, primarily uncultivable, microbiome from D. citri adults. The PDF protocol yielded CLas abundances upwards of 60% and enabled detection of 156 genetic variants in these strains compared to progenitor strains in Florida, which included prophage encoding regions with key functions in CLas pathogenesis, putative antibiotic resistance loci, and a single secreted effector. These variants suggest laboratory propagation of CLas may result in different phenotypic trajectories among laboratories, and may confound CLas physiology or therapeutic design and evaluation if these differences remain undocumented. Finally, we obtained genetic signatures affiliated with Citrus nuclear and organellar genomes, entomopathogenic fungal mitochondria, and commensal bacteria from laboratory-reared and field-collected D. citri adults. Hence, the PDF protocol can inform agricultural management strategies related to pathogen evolution 7, insect microbiome surveillance 8, antibiotic resistance screening 9, and gut content analysis 10.


title: Reduction in cardiolipin reduces expression of creatine transporter-1 and creatine transport in hBMEC/D3 human brain microvessel endothelial cells

abstract:
BackgroundCardiolipin (CL) is the signature phospholipid of mitochondria and regulates a plethora of cellular functions including mitochondrial energy production. There is little knowledge of how CL regulates uptake and membrane transport processes in mammalian cells. Endothelial cells of the blood brain barrier (BBB) play a vital role in uptake of metabolites into the brain and are enriched in mitochondria compared with peripheral endothelial cells. We examined how deficiency in BBB endothelial CL regulates the expression of selected drug and metabolite transporters and their function.

MethodsCardiolipin synthase-1 (hCLS1) was knocked down in a human brain microvessel endothelial cell line, hBMEC/D3, by Lipofectamine(R) transfection with hCLS1 siRNA and CL levels, CL synthase activity and the mRNA expression of selected blood brain barrier drug and metabolite transporters examined. Mock transfected hBMEC/D3 cells served as controls. The incorporation of [14C]creatine and [14C]oleate into hBMEC/D3 cells was determined as a measure of solute metabolite transport and protein expression of the creatine transporter determined.

ResultsKnockdown of the CL biosynthetic enzyme hCLS1 in hBMEC/D3 reduced CL and CL synthase activity and the mRNA expression of creatine transporter-1, p-glycoprotein and breast cancer resistance protein compared to controls. In contrast, mRNA expression of ATP binding cassette subfamily C members-1, -3, multidrug resistance-associated protein-4 variants 1, -2, and fatty acid transport protein-1 were unaltered. Although ATP production was unaltered by hCLS1 knockdown, incorporation of [14C]creatine into hBMEC/D3 cells was reduced compared to controls. The reduction in [14C]creatine incorporation was associated with a reduction in creatine transporter-1 protein expression. In contrast, incorporation of [14C]oleic acid into hBMEC/D3 cells and the mRNA expression of fatty acid transport protein-1 was unaltered by knockdown of hCLS1 compared to controls.

ConclusionKnockdown of hCLS1 in hBMEC/D3, with a corresponding reduction in CL, results in alteration in expression of specific solute membrane transporters.


title: Antibodies to native gluten arise from cross-reactive B cells with implications for epitope spreading in celiac disease

abstract: Antibodies to deamidated gluten peptides are accurate diagnostic markers of celiac disease (CeD). However, antibody binding to all possible gluten epitopes has not previously been investigated. To map antibody reactivity in detail and to understand the connection between disease-relevant B-cell and T-cell epitopes, we took advantage of a high-density peptide array for assessment of serum antibody specificity in CeD across the wheat gluten proteome. We confirm the importance of peptide deamidation for antibody binding, and we show that the response is remarkably focused on the known epitope QPEQPFP (where E results from deamidation of Q). In addition, we describe a new epitope in native (non-deamidated) gluten, QQPEQII (where E is gene encoded), which was associated with both B-cell and T-cell reactivity. By generating monoclonal antibodies from peptide-binding gut plasma cells of CeD patients, we show that antibodies to this native gluten epitope are cross-reactive with the major deamidated epitope due to recognition of the shared PEQ motif. Hence, antibodies to native gluten appear to arise from cross-reactive B cells that are generated as a side effect of the immune response to deamidated gluten. Since cross-reactive B cells could present peptides to different gluten-specific T cells, we suspect that such B cells can play a role in epitope spreading by engaging T cells with multiple specificities.

category: immunology


title: Evolution of β-lactamase mediated cefiderocol resistance

abstract:
Cefiderocol is a novel siderophore {beta}-lactam with improved hydrolytic stability toward {beta}-lactamases, including carbapenemases, achieved by combining structural moieties of two clinically efficient cephalosporins, ceftazidime and cefepime. Consequently, cefiderocol represents a treatment alternative for infections caused by multi-drug resistant Gram-negatives. Using directed evolution on a wide variety of different {beta}-lactamases, such as KPC-2 and CTX-M-15 (Ambler class A), NDM-1 (class B), CMY-2 (class C) and OXA-48 (class D), we studied the role of cefiderocol during {beta}-lactamase-mediated resistance development. First, we investigated how the expression of different {beta}-lactamases causes changes in cefiderocol susceptibility. In a low-copy number vector, we found that OXA-48 and KPC-2 conferred non or marginal decreases in cefiderocol susceptibility, respectively. On the contrary, CMY-2, CTX-M-15 and NDM-1 substantially decreased cefiderocol susceptibility by 16-, 8- and 32-fold, respectively. Second, we determined the evolutionary potential of these enzymes to adapt to increasing concentrations of cefiderocol. Our data show that with the acquisition of only 1 to 2 mutations, all {beta}-lactamases were evolvable to further cefiderocol resistance by 2- (NDM-1, CTX-M-15), 4- (CMY-2), 8- (OXA-48) and 16-fold (KPC-2). Cefiderocol resistance development was often associated with collateral susceptibility changes including increased resistance to ceftazidime and ceftazidime-avibactam as well as functional trade-offs against different {beta}-lactam drugs. Taken together, contemporary {beta}-lactamases of all Ambler classes can potentially contribute to cefiderocol resistance development and can acquire mutations allowing them to adapt to increasing cefiderocol concentration. At the same time, resistance development caused clinically important cross-resistance, especially against ceftazidime combinations.

SummaryDespite the reported higher stability of cefiderocol against {beta}-lactamase hydrolysis, we show that the expression of {beta}-lactamases from different Ambler classes significantly contributes to cefiderocol resistance and that these enzymes have the evolutionary potential to evolve towards increasing cefiderocol concentrations.


title: Interaction with TopBP1 mediates human papillomavirus 16 E2 plasmid segregation/retention function and stability during the viral life cycle

abstract:
Human papillomavirus 16 (HPV16) E2 is a DNA binding protein that regulates transcription, replication and potentially, segregation of the HPV16 genome during the viral life cycle. In the segregation model, E2 simultaneously binds to viral and host chromatin, acting as a bridge to ensure that viral genomes reside in daughter nuclei following cell division. The host chromatin receptor for E2 mediating this function is unknown. Recently, we demonstrated that CK2 phosphorylation of E2 on serine 23 (S23) is required for interaction with TopBP1, and that this interaction promotes E2 and TopBP1 recruitment to mitotic chromatin. Here, we demonstrate that in U2OS and N/Tert-1 cells expressing wild type E2 and a non-TopBP1 binding mutant (S23A, serine 23 mutated to alanine), interaction with TopBP1 is essential for E2 recruitment of plasmids to mitotic chromatin. Using a novel quantitative segregation assay, we demonstrate that interaction with TopBP1 is required for E2 plasmid segregation. The interaction of E2 with TopBP1 promotes increased levels of E2 protein during mitosis in U2OS and N/Tert-1 cells, as well as in human foreskin keratinocytes immortalized by the HPV16 genome. Additionally, interaction with TopBP1 is required for expression of the E2 protein during the viral life cycle. Overall, our results demonstrate that E2 has plasmid segregation activity, and that the E2-TopBP1 interaction is essential for this E2 function and for E2 expression during the viral life cycle.

ImportanceHPV16 causes 3-4% of all human cancers. During the viral life cycle, it is proposed that the viral genome is actively segregated into daughter nuclei, ensuring viral replication in the subsequent S phase. The E2 protein potentially bridges the viral and host genomes during mitosis to mediate segregation of the circular viral plasmid. Here, we demonstrate that E2 has the ability to mediate plasmid segregation, and that this function is dependent upon interaction with the host protein TopBP1. Additionally, we demonstrate that the E2-TopBP1 interaction promotes enhanced E2 expression during mitosis which likely promotes the plasmid segregation function of E2. Overall, our results present a mechanism of how HPV16 can segregate its viral genome during an active infection, a critical aspect of the viral life cycle.


title: The genome sequence of Hirschfeldia incana, a species with high photosynthetic light-use efficiency

abstract: Photosynthesis is a biophysical and biochemical process that plays a key role in sustaining plant and human life, being the first step in the production of energy-rich molecules and oxygen in the biosphere. Improving the photosynthetic capacity of agricultural crops is highly desirable to increase their yields. While the core mechanisms of photosynthesis are highly conserved, certainly in higher plants, plants that can maintain a high photosynthetic light-use efficiency at high irradiance are exceptional and may be useful to understand and improve high irradiance photosynthesis of crops. One such exceptional species is Hirschfeldia incana, a member of the well-studied Brassicaceae family that is easy to grow under standard laboratory conditions, providing an excellent resource for studying the genetic and physiological basis of this trait. Here, we present a reference assembly of H. incana and affirm its high photosynthetic efficiency relative to the Brassicaceae species Brassica rapa, Brassica nigra, and Arabidopsis thaliana. We estimate that it diverged from B. rapa and B. nigra 10-11 million years ago and that its genome has diversified from that of the latter two species through large chromosomal rearrangements, species-specific transposon activity, and differential retention of duplicated genes. Genes present at copy numbers different from B. rapa and B. nigra include those involved in photosynthesis and/or abiotic stress, which may mediate the high photosynthetic efficiency of H. incana. We expect the reference assembly of H. incana to be a valuable genomic resource for identifying ways to enhance photosynthetic rates in crop species.


title: Sparse spike trains and the limitations of rate codes underlying rapid behaviour

abstract: Animals live in highly dynamic worlds, utilising sensorimotor circuits to rapidly process information and drive behaviours. For example, dragonflies are aerial predators which react to movements of prey within tens of milliseconds. These pursuits are likely controlled by identified neurons in the dragonfly, which have well-characterized physiological responses to moving targets. Predominantly, neural activity in these circuits are interpreted in the context of a rate code, where information is conveyed by changes in the number of spikes over a given time. However, such a description of neuronal activity is difficult to achieve in real-world, real-time scenarios. Here, we contrast a neuroscientists post-hoc view of spiking activity with the information available to the animal in real-time. We describe how performance of a rate code is readily overestimated and outline a rate codes significant limitations in driving rapid behaviours.


title: Molecular hydrogen is an overlooked energy source for marine bacteria

abstract: Molecular hydrogen (H2) and carbon monoxide (CO) are supersaturated in seawater relative to the atmosphere and hence are readily accessible energy sources for marine microbial communities. Yet while marine CO oxidation is well-described, it is unknown whether seawater communities consume H2. Here we integrated genome-resolved metagenomics, biogeochemistry, thermodynamic modelling, and culture-based analysis to profile H2 and CO oxidation by marine bacteria. Based on analysis of 14 surface water samples, collected from three locations spanning tropical to subantarctic fronts, three uptake hydrogenase classes are prevalent in seawater and encoded by major marine families such as Rhodobacteraceae, Flavobacteriaceae, and Sphingomonadaceae. However, they are less abundant and widespread than carbon monoxide dehydrogenases. Consistently, microbial communities in surface waters slowly consumed H2 and rapidly consumed CO at environmentally relevant concentrations, with H2 oxidation most active in subantarctic waters. The cell-specific power from these processes exceed bacterial maintenance requirements and, for H2, can likely sustain growth of bacteria with low energy requirements. Concordantly, we show that the polar ultramicrobacterium Sphingopyxis alaskensis grows mixotrophically on H2 by expressing a group 2a [NiFe]-hydrogenase, providing the first demonstration of atmospheric H2 oxidation by a marine bacterium. Based on TARA Oceans metagenomes, genes for trace gas oxidation are globally distributed and are fourfold more abundant in deep compared to surface waters, highlighting that trace gases are important energy sources especially in energy-limited waters. Altogether, these findings show H2 is a significant energy source for marine communities and suggest that trace gases influence the ecology and biogeochemistry of oceans globally.


title: Feedback in the β-catenin destruction complex imparts bistability and cellular memory

abstract:
Wnt ligands are considered classical morphogens, for which the strength of the cellular response is proportional to the concentration of the ligand. Herein, we show an emergent property of bistability arising from feedback among the Wnt destruction complex proteins that target the key transcriptional co-activator {beta}-catenin for degradation. Using biochemical reconstitution, we identified positive feedback between the scaffold protein Axin and the kinase GSK3. Theoretical modeling of this feedback between Axin and GSK3 predicted that the activity of the destruction complex exhibits bistable behavior. We experimentally confirmed these predictions by demonstrating that cellular cytoplasmic {beta}-catenin concentrations exhibit an "all-or-none" response with sustained memory (hysteresis) of the signaling input. This bistable behavior was transformed into a graded response and memory was lost through inhibition of GSK3. These findings provide a mechanism for establishing decisive, switch-like cellular response and memory upon Wnt pathway stimulation.

One Sentence SummaryPositive feedback within the {beta}-catenin destruction complex gives rise to bistability and memory in response to Wnt stimulation, imparting signal transduction accuracy and insulation.


title: Modular and programmable RNA sensing using ADAR editing in living cells

abstract: With the increasing availability of single-cell transcriptomes, RNA signatures offer a promising basis for targeting living cells. Molecular RNA sensors would enable the study of and therapeutic interventions for specific cell types/stats in diverse contexts, particularly in human patients and non-model organisms. Here we describe a modular and programmable design for live RNA sensing using adenosine deaminases acting on RNA (RADAR). We validated and then expanded our basic design, characterized its performance, and thoroughly analyzed its compatibility with the human/mouse transcriptomes. We also identified strategies to further boost output levels and improve the dynamic range. We show that RADAR is programmable and modular, and uniquely enables compact AND logic. In addition to being quantitative, RADAR can distinguish disease-relevant point mutations. Finally, we demonstrate that RADAR is a self-contained system with the potential to function in diverse organisms.

category: bioengineering


title: maxATAC: genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks

abstract: Transcription factors read the genome, fundamentally connecting DNA sequence to gene expression across diverse cell types. Determining how, where, and when TFs bind chromatin will advance our understanding of gene regulatory networks and cellular behavior. The 2017 ENCODE-DREAM in vivo Transcription-Factor Binding Site (TFBS) Prediction Challenge highlighted the value of chromatin accessibility data to TFBS prediction, establishing state-of-the-art methods. Yet, while Assay-for-Transposase-Accessible-Chromatin (ATAC)-seq datasets grow exponentially, suboptimal motif scanning is commonly used for TFBS prediction from ATAC-seq. Here, we present "maxATAC", a suite of user-friendly, deep neural network models for genome-wide TFBS prediction from ATAC-seq in any cell type. With models available for 127 human TFs, maxATAC is the largest collection of state-of-the-art TFBS models to date. maxATAC performance extends to primary cells and single-cell ATAC-seq, enabling state-of-the-art TFBS prediction in vivo. We demonstrate maxATACs capabilities by identifying TFBS associated with allele-dependent chromatin accessibility at atopic dermatitis genetic risk loci.


title: Protein-Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations

abstract: RNA polymerase II (Pol II) forms a complex with elongation factors to proceed the elongation stage of the transcription process. In this work, we studied elongation factor SPT5 and explored protein nucleic acid interactions for the isolated systems of KOW1 and KOW4 domains of SPT5 with DNA and RNA, respectively. We performed molecular dynamics (MD) simulations using three commonly used force fields that are CHARMM c36m, AMBER ff14sb and ff19sb. These simulations showed that most of the protein-nucleic acid interactions in the native state were retained with an increased electrostatic binding free energy for all force fields used. RNA was found highly dynamic with all force fields while DNA had relatively more stable conformations with the AMBER force fields compared to CHARMM. Furthermore, we performed MD simulations of the complete elongation complex using CHARMM c36m force field to compare the dynamics and interactions in the isolated systems. Similar strong KOW1 and DNA interactions were observed in the complete elongation complex simulations and DNA was further stabilized by a network of interactions involving SPT5-KOW1, SPT4 and rpb2 of Pol II. Overall, our study showed that the accuracy of force fields and the presence of the entire interaction network are important for elucidating the dynamics of protein-nucleic acid systems.


title: An allosteric agonist activates BK channels by perturbing coupling between Ca2+ binding and pore opening

abstract: BK type Ca2+-activated K+ channels activate in response to both the membrane voltage and intracellular Ca2+ with distinct mechanisms. Ca2+ binds to the cytosolic domain (CTD) to open the pore across the membrane, but the mechanism that couples Ca2+ binding to pore opening is not clear. Here we show that a compound, BC5, identified using in silico screening, interacts with BK channels at the interface between the CTD and the transmembrane voltage sensing domain (VSD) and enhances channel activity by specifically affecting the Ca2+ dependent mechanism. BC5 activates the channel in the absence of Ca2+ binding but Ca2+ binding inhibits BC5 effects. Thus, BC5 perturbs the pathway that couples Ca2+ binding to pore opening to allosterically affect both, which is supported by atomistic simulations and mutagensis. The results suggest that the CTD- VSD interaction makes a major contribution to the mechanism of Ca2+ dependent activation and is an important site for allosteric agonists to modulate BK channel activation.


title: Mass-Sensitive Particle Tracking to Characterize Membrane-Associated Macromolecule Dynamics

abstract:
Short-lived or transient interactions of macromolecules at and with lipid membranes, an interface where a multitude of essential biological reactions take place, are inherently difficult to assess with standard biophysical methods. The introduction of mass-sensitive particle tracking (MSPT) constitutes an important step towards a thorough quantitative characterization of such processes. Technically, this was made possible through the advent of interferometric scattering microscopy (iSCAT)-based mass photometry (MP). When the background removal strategy is optimized to reveal the two-dimensional motion of membrane-associated particles, this technique allows the real-time analysis of both diffusion and molecular mass of unlabeled macromolecules on biological membranes. Here, a detailed protocol to perform and analyze mass-sensitive particle tracking of membrane-associated systems is described. Measurements performed on a commercial mass photometer achieve time resolution in the millisecond regime and, depending on the MP system, a mass detection limit down to 50 kDa. To showcase the potential of MSPT for the in-depth analysis of membrane-catalyzed macromolecule dynamics in general, results obtained for exemplary protein systems such as the native membrane interactor annexin V are presented.

SUMMARYThis protocol describes an iSCAT-based image processing and single-particle tracking approach that enables the simultaneous investigation of the molecular mass and the diffusive behavior of macromolecules interacting with lipid membranes. Step-by-step instructions for sample preparation, mass-to-contrast conversion, movie acquisition, and post-processing are provided along-side directions to prevent potential pitfalls.


title: No priming, just fighting - endophytic yeast attenuates the defense response and the stress induced by Dutch elm disease in Ulmus minor

abstract: One century after the first report of Dutch Elm Disease (DED), there is still no practical solution for this problem threatening European and American elms (Ulmus spp.). The long breeding cycles needed to select resistant genotypes and the lack of efficient treatments keep disease incidence at high levels. In the present work, the expression of defense-related genes to the causal agent of DED, Ophiostoma novo-ulmi, were analyzed in in vitro clonal plantlets from two DED-resistant and two DED-susceptible U. minor trees. In addition, the effect of the inoculation of an endophytic pink-pigmented yeast (Cystobasidium sp.) on the plants defense system was tested both individually and in combination with O. novo-ulmi. The multifactorial nature of the resistance to DED was confirmed, as no common molecular response was found in the two resistant genotypes. However, the in vitro experimental system allowed to discriminate the susceptible from the resistant genotypes, showing higher levels of oxidative stress and phenolic compounds in the susceptible genotypes after pathogen inoculation. Inoculation of the endophyte before O. novo-ulmi attenuated the plant molecular response induced by the pathogen and moderated oxidative stress levels. Niche competition, endophyte-pathogen antagonism, and molecular crosstalk between the host and the endophyte are discussed as possible mechanisms of stress reduction. In sum, our results confirm the multifactorial nature of DED resistance mechanisms and highlight the possibility of using certain endophytic yeasts as biological tools to improve tree resilience against biotic stress.


title: Circadian volume changes in hippocampal glia studied by label-free interferometric imaging

abstract: Complex brain functions, including learning and memory, arise in part from the modulatory role of astrocytes on neuronal circuits. Functionally, the dentate gyrus (DG) exhibits differences in the acquisition of long-term potentiation (LTP) between day and night. We hypothesize that the dynamic nature of astrocyte morphology plays an important role in the functional circuitry of hippocampal learning and memory, specifically in the DG. Standard microscopy techniques, such as differential interference contrast (DIC), present insufficient contrast for detecting changes in astrocyte structure and function and are unable to inform on the intrinsic structure of the sample in a quantitative manner. Recently, gradient light interference microscopy (GLIM) has been developed to upgrade a DIC microscope with quantitative capabilities such as single-cell dry mass and volume characterization. Here, we present a methodology for combining GLIM and electrophysiology to quantify the astrocyte morphological behavior over the day-night cycle. Colocalized measurements of GLIM and fluorescence allowed us to quantify the dry masses and volumes of hundreds of astrocytes. Our results indicate that, on average, there is a 25% cell volume reduction during the nocturnal cycle. Remarkably, this cell volume change takes place at constant dry mass, which suggests that the volume regulation occurs primarily through aqueous medium exchange with the environment.

category: neuroscience


title: Modelling non-local neural information processing in the brain

abstract:
The representation of the surrounding world emerges through integration of sensory information and actions. We present a novel neural model which implements non-local, parallel information processing on a neocolumnar architecture with lateral interconnections. Information is integrated into a holographic wave interference pattern. We compare the simulated in silico pattern with observed in vivo invasive and non-invasive electrophysiological data in human and non-human primates. Our model replicates the modulation of neural high-frequency activity during visual perception showing that phase-locked low and high-frequency oscillations self-organize efficiently and carry high information content. The simulation further models how criticality (high content) of information processing emerges given a sufficiently high number of correlated neurons. Non-local information processing, forming one holographic wave pattern, suggests a platform for emergence of conscious perception.

One sentence summarySimulated non-local information processing on a neocolumnar architecture models well multiple electrophysiological observations of brain activity, including high-frequency activity during visual perception in primates.


title: Learning the Vector Coding of Egocentric Boundary Cells from Visual Data

abstract: The use of spatial maps to navigate through the world requires a complex ongoing transformation of ego-centric views of the environment into position within the allocentric map. Recent research has discovered neurons in retrosplenial cortex and other structures that could mediate the transformation from egocentric views to allocentric views. These egocentric boundary cells (EBCs) respond to the egocentric direction and distance of barriers relative to an animals point of view. This egocentric coding based on the visual features of barriers would seem to require complex dynamics of cortical interactions. However, computational models presented here show that egocentric boundary cells can be generated with a remarkably simple synaptic learning rule that forms a sparse representation of visual input as an animal explores the environment. Simulation of this simple sparse synaptic modification generates a population of egocentric boundary cells with distributions of direction and distance coding that strikingly resemble those observed within the retrosplenial cortex. This provides a framework for understanding the properties of neuronal populations in the retrosplenial cortex that may be essential for interfacing egocentric sensory information with allocentric spatial maps of the world formed by neurons in downstream areas including the grid cells in entorhinal cortex and place cells in the hippocampus.


title: Categorization and discrimination of human and non-human primate affective vocalizations: investigation of the frontal cortex activity through fNIRS.

abstract: Many species, including humans and non-human primates, react differently to threatening or pleasant situations. Because of its adaptiveness, recognizing affective signals is likely to be reflected in a capability of modern humans to recognize other closely related species call content. However, at both behavioural and neural levels, only few studies have used a comparative approach to understand affective decoding processes in humans, particularly with respect to affective vocalizations. Previous research in neuroscience about the recognition of human affective vocalizations has shown the critical involvement of temporal and frontal regions. In particular, frontal regions have been reported as crucial in the explicit decoding of vocal emotions especially in different task complexity such as discrimination or categorization. The aim of this study using functional Near Infrared Spectroscopy (fNIRS) was to specifically investigate the neural activity of the inferior frontal cortex pars triangularis (IFGtri) and the prefrontal cortex (PFC) underlying categorization (A versus B) and discrimination (A versus non-A) mechanisms of positive and negative affects in human, great apes (chimpanzee and bonobo), and monkey (rhesus macaque) vocalizations. We also analysed participants behavioural responses and correlated them with the recorded frontal activations. While performing the tasks, fNIRS data revealed a clear distinction between the two frontal regions, with a general positive activation of IFGtri compared to a decrease of PFC activity. We also found a modulation of IFGtri and PFC activations depending on both the species considered and on task complexity; with generally more activity in the IFGtri during discrimination compared to categorization, and a more intense decrease of the PFC in categorization compared to discrimination. Behaviourally, participants recognized almost all affective cues in all species vocalizations at above chance levels in the discrimination task (except for threatening bonobo calls). For categorization, they mostly correctly identified at levels significantly above chance affective contents in human and great ape vocalizations but not in macaque calls. Overall, these findings support the hypothesis of a pre-human origin of affective recognition processing inherited from our common ancestor with other great apes and processed in the frontal cortex. Our results also highlight behavioural differences related to task complexity, i.e. between categorization and discrimination processes, and the differential involvement of the PFC and the IFGtri, which seems necessary to explicitly decode affects in all primate vocalizations.


title: GABABR agonist baclofen promotes central nervous system remyelination

abstract: Promoting remyelination - the endogenous response by which lost myelin sheaths are regenerated - is considered as a potential neuroprotective strategy to prevent/limit the development of permanent neurological disability in patients with multiple sclerosis (MS). To this end, a number of clinical trials are investigating the potential of existing drugs to enhance oligodendrocyte progenitor cell (OPC) differentiation, the process that fails in chronic MS lesions. As we previously reported that oligodendroglia lineage cells express GABAB receptors (GABABRs) both in vitro and in vivo, and that GABABR-mediated signaling enhances OPC differentiation and myelination in vitro, here we focused on the remyelinating potential of the best-known GABABR agonist baclofen (Bac), already approved to treat spasticity in MS. We demonstrated that Bac increases myelin protein production following lysolecithin (LPC)-induced demyelination in cerebellar ex vivo slices. In addition, Bac administration enhanced OPC differentiation and remyelination in LPC-induced spinal cord lesions in adult mice. Thus, our results suggest that Bac should be considered as a potential therapeutic agent, not only to treat spasticity, but also to improve remyelination in patients with MS.


title: Synthetic glycans that control gut microbiome structure mitigate colitis in mice

abstract: Relative abundances of bacterial species in the gut microbiome have been linked to many diseases. Species of gut bacteria are ecologically differentiated by their abilities to metabolize different glycans, making glycan delivery a powerful way to alter the microbiome to promote health. We describe the properties and therapeutic potential of chemically diverse synthetic glycans (SGs). Fermentation of SGs by gut microbiome cultures resulted in compound-specific shifts in taxonomic and metabolite profiles not observed with reference glycans, including prebiotics. Model enteric pathogens grow poorly on most SGs, potentially increasing their safety for at-risk populations. SGs increased survival, reduced weight loss, and improved clinical scores in mouse models of colitis. Synthetic glycans are thus a promising modality to improve health through selective changes to the gut microbiome.

category: microbiology


title: Return of the Tbx5; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart

abstract:
The single curative measure for heart failure patients is total heart transplantation, which is limited due to a shortage of donors, the need for immunosuppression and economic costs. Therefore, there is an urgent unmet need for identifying cell populations capable of cardiac regeneration that we will be able to trace and monitor. Injury to the adult mammalian cardiac muscle, often leads to a heart attack through the irreversible loss of a large number of cardiomyocytes, due to an idle regenerative capability. Recent reports in zebrafish indicate that Tbx5a is a vital transcription factor for cardiomyocyte regeneration. Preclinical data underscore the cardioprotective role of Tbx5 upon heart failure. Data from our earlier murine developmental studies have pinpointed a prominent unipotent Tbx5-expressing embryonic cardiac precursor cell population able to form cardiomyocytes, in vivo, in vitro and ex vivo.

Using a developmental approach to an adult heart injury model and by employing a lineage-tracing mouse model as well as the use of single-cell RNA-seq technology, we identify a Tbx5-expressing ventricular cardiomyocyte-like precursor population, in the injured adult mammalian heart. The transcriptional profile of that precursor cell population is closer to that of neonatal than embryonic cardiomyocyte precursors. Tbx5, a cardinal cardiac development transcription factor, lies in the centre of a ventricular adult precursor cell population, which seems to be affected by neurohormonal spatiotemporal cues.

The identification of a Tbx5-specific cardiomyocyte precursor-like cell population, which is capable of dedifferentiating and potentially deploying a cardiomyocyte regenerative program, provides a clear target cell population for translationally-relevant heart interventional studies.


title: Naive Bayes Assessment of Mediterranean Basin Ecosystem Wildfires Associated With Vegetation Vigor in August 2021

abstract: The Mediterranean basin, located in the Southern Mediterranean Sea in the North of Africa, is one of the ecosystems that are vulnerable to wildfire hazards. A massive wildfire occurred in this ecosystem in August 2021. Here, this study aims to detect the burnt areas and assess the ecosystem covariates related to the wildfire occurrences. Wildfire assessments were conducted using remote sensing (RS) analysis. Measured ecosystem covariates include vegetation cover, moisture, and the Normalized Difference Vegetation Index (NDVI). The RS analysis confirms at least 17090 ha of vegetation cover were damaged. The burnt vegetation cover was associated with the vegetation moisture and NDVI. The result shows 61.93% of burnt areas were observed within areas that had low vegetation moisture. While 51.75% of burnt areas occurred within areas that had low NDVI values. Naive Bayes classifier confirms that vegetation moisture and NDVI covariates can be used to estimate the presences of wildfires with values of Kappa, accuracy, precision, recall, and F1 score are 0.7, 0.85, 0.89, 0.8, and 0.84. The area under (AUC) the receiver operating characteristic (ROC) curve values for vegetation moisture and NDVI covariates were 0.945 and 0.399. This value indicates that low vegetation moisture contributes more to the wildfire presences than low NDVI.


title: Sensory plasticity in a socially plastic bee

abstract: The social Hymenoptera have contributed much to our understanding of the evolution of sensory systems. Attention has focussed chiefly on how sociality and sensory systems have evolved together. In the Hymenoptera, the antennal sensilla are important for optimising the perception of olfactory social information. Social species have denser antennal sensilla than solitary species, which is thought to enhance social cohesion through nest-mate recognition. In the current study, we test whether sensilla numbers vary between regional populations of the socially plastic sweat bee Halictus rubicundus. We found region level differences in both olfactory and hygro/thermoreceptive sensilla numbers. We also found evidence that olfactory sensilla density is developmentally plastic: when we transplanted bees from Scotland to the south-east of England, their offspring (which developed in the south) had more olfactory hairs than the transplanted individuals themselves (which developed in Scotland). The transplanted bees displayed a mix of social (a queen plus workers) and solitary nesting, but neither individual nor nest phenotype was related to sensilla density. We suggest that this general, rather than caste-specific sensory plasticity provides a flexible means to optimise sensory perception according to the most pressing demands of the environment, and may support social plasticity in H. rubicundus.

category: evolutionary biology


title: A guide to using GPS-based tracking to study animal societies

abstract: GPS-based tracking is a widely used automated data collection method for studying wild animals. Much like traditional observational methods, using GPS devices to study social animals requires making a number of decisions about sampling that can affect the robustness of a studys conclusions. For example, sampling fewer individuals per group across many distinct social groups may not be informative enough for inferring behavioural patterns at a finer social organizational scale, while sampling more individuals per group across fewer groups limits the ability to draw conclusions about populations. Here, we integrate previous insights from animal social network analysis with simulated and empirical data to provide quantitative recommendations when designing GPS-based tracking studies of animal societies. We outline the trade-offs faced by researchers, and how these trade-offs should vary across social organizational scales and social systems in relation to questions of interest, such as those defined within versus among groups, and spanning from cohesive, stable groups through to more open societies. We discuss three fundamental axes of sampling effort requiring consideration when deploying GPS devices to study animal societies: 1) Sampling coverage--the number and allocation of GPS devices among individuals in one or more social groups; 2) Sampling duration-- the total amount of time over which devices collect data; 3) Sampling frequency--the temporal resolution at which GPS devices record data. Exploring each axis, we quantify the relationship between sampling effort and sampling error, giving recommendations on GPS sampling design to address research questions across social organizational scales and social systems--from group movement to social network structure and collective decision-making. In doing so, we also highlight practical limitations on deploying GPS tracking. Our study provides practical advice for empiricists to navigate their decision-making processes when designing GPS-based field studies of animal social behaviours, and highlights the importance of identifying the optimal deployment decisions for drawing informative and robust conclusions.


title: 3D Printable High Performance Conducting Polymer Hydrogel for All-Hydrogel Bioelectronics

abstract: Owing to the unique combination of electrical conductivity and tissue-like mechanical properties, conducting polymer hydrogels have emerged as a promising candidate for bioelectronic interfacing with biological systems. However, despite the recent advances, the development of hydrogels with both excellent electrical and mechanical properties in physiological environments remains a lingering challenge. Here, we report a bi-continuous conducting polymer hydrogel (BC-CPH) that simultaneously achieves high electrical conductivity (over 11 S cm-1), stretchability (over 400%) and fracture toughness (over 3,300 J m-2) in physiological environments, and is readily applicable to advanced fabrication methods including 3D printing. Enabled by the BC-CPH, we further demonstrate multi-material 3D printing of monolithic all-hydrogel bioelectronic interfaces for long-term electrophysiological recording and stimulation of various organs. This study may offer promising materials and a platform for future bioelectronic interfacing.


title: Development of an Ultra Low-Cost SSVEP-based BCI Device for Real-Time On-Device Decoding

abstract: This study details the development of a novel, approx. {pound}20 electroencephalogram (EEG)-based brain-computer interface (BCI) intended to offer a financially and operationally accessible device that can be deployed on a mass scale to facilitate education and public engagement in the domain of EEG sensing and neurotechnologies. Real-time decoding of steady-state visual evoked potentials (SSVEPs) is achieved using variations of the widely-used canonical correlation analysis (CCA) algorithm: multi-set CCA and generalised CCA. All BCI functionality is executed on board an inexpensive ESP32 microcontroller. SSVEP decoding accuracy of 95.56 {+/-} 3.74% with an ITR of 102 bits/min was achieved with modest calibration.


title: Characterization of the minimal residual disease state reveals distinct evolutionary trajectories of human glioblastoma

abstract: Recurrence of solid tumors renders patients vulnerable to a distinctly advanced, highly treatment-refractory disease state that has an increased mutational burden and novel oncogenic drivers not detected at initial diagnosis. Improving outcomes for recurrent cancers requires a better understanding of cancer cell populations that expand from the post-therapy, minimal residual disease (MRD) state. We profiled barcoded tumor stem cell populations through therapy at tumor initiation/engraftment, MRD and recurrence in our therapy-adapted, patient-derived xenograft models of glioblastoma (GBM). Tumors showed distinct patterns of recurrence in which clonal populations exhibited either an a priori, pre-existing fitness advantage, or a priori equipotency fitness acquired through therapy. Characterization of the MRD state by single-cell and bulk RNA sequencing revealed a tumor-intrinsic immunomodulatory signature with strong prognostic significance at the transcriptomic level and in proteomic analysis of cerebrospinal fluid (CSF) collected from GBM patients at all stages of disease. Our results provide insight into the innate and therapy-driven dynamics of human GBM, and the prognostic value of interrogating the MRD state in solid cancers.


title: Transcriptome Analysis of the Nematode Caenorhabditis elegans and Litoditis marina in a Chemically Defined Food Environment

abstract: Diets regulate animal development, reproduction, and lifespan. However, the underlying molecular mechanisms remain elusive. A chemically defined CeMM diet attenuates development and promotes longevity of C. elegans, but whether it impact on other nematodes is unknown. Here, we studied the effect of the CeMM diet on the development and longevity of the marine nematode Litoditis marina, which belongs to the same family as C. elegans. We further investigated genome-wide transcriptional responses to CeMM and OP50 diet for both nematodes, respectively. We observed that the CeMM diet attenuated L. marina development but did not extend its lifespan. We found that many of the FOXO DAF-16 target genes, lysosome and xenobiotic metabolism related genes were significantly increased on the CeMM, which might contribute to the lifespan extension of C. elegans. Notably, we found that the expression of lysosome and xenobiotic metabolism pathway genes was significantly down regulated in L. marina on CeMM, which might explain why the CeMM diet could not promote the lifespan of L. marina compared to bacterial feeding. Additionally, down-regulation of several RNA transcription and protein generation and related processes genes might not only be involved in extending longevity but also contribute to attenuating development of C. elegans on CeMM, while down-regulation of unsaturated fatty acids synthesis genes might contribute to slow down the growth of L. marina on CeMM. Further genetic analysis of candidate gene(s) of longevity and development in C. elegans and L. marina will provide the molecular mechanisms underlying how diets regulate animal physiology and health in the context of global climate change with variable nutritional environments.

category: zoology


title: Nonlinear super-resolution signal processing for subcellular analysis of calcium dynamics

abstract:
Optical (fluorescence) imaging of ionic dynamics has revolutionized neuroscience as it allows the study of neural activity across spatially identified populations. Quantification of fluorescence signals is commonly performed using ratiometric measures, like the {Delta}F/F. Although these measures are robust and easy to implement, they do not take advantage of the temporal information available in time-varying signals. Moreover, since a baseline (reference) period needs to be selected, their application is often limited to the quantification of stimulus-evoked activity. Here, we present a new approach, called ARES, based on the quantification of residuals after linear autoregression. We demonstrate the utility of ARES to quantify the functional dynamics of stimulus representation in cortical networks and show that it improves the spatial and temporal resolution with respect to {Delta}F/F. We further show that ARES can be used to study subcellular calcium dynamics and exemplify its utility to describe the spatiotemporal dynamics of calcium signal localization in compartmental network recordings. ARES offers a novel method for quantitative analysis of optical imaging data

Author summaryTwo-photon calcium imaging is a powerful and non-invasive method to measure and visualize the activity of neural populations in single cell and subcellular resolution. However, the slow dynamics of both the calcium signal itself and its indicators make it difficult to relate the timing and origin of the neural activity to the calcium signal. The most commonly used analysis method, {Delta}F/F, uses a reference baseline to quantify signal ratiometrically. This results in several limitations, especially in accounting for the time varying fluctuations in fluorescence values. Here we present a new method for the analysis of calcium signals, called ARES, in which a sliding window is used to predict the future values of the signal and deviations from this prediction are recorded as the signal. This has the advantage that shifts in baseline do not affect the processing, and that the method has an improved spatial and temporal resolution with respect to {Delta}F/F.