title: Saturated reconstruction of living brain tissue

abstract: Complex wiring between neurons underlies the information-processing network enabling all brain functions, including cognition and memory. For understanding how the network is structured, processes information, and changes over time, comprehensive visualization of the architecture of living brain tissue with its cellular and molecular components would open up major opportunities. However, electron microscopy (EM) provides nanometre-scale resolution required for full in-silico reconstruction, yet is limited to fixed specimens and static representations. Light microscopy allows live observation, with super-resolution approaches facilitating nanoscale visualization, but comprehensive 3D-reconstruction of living brain tissue has been hindered by tissue photo-burden, photobleaching, insufficient 3D-resolution, and inadequate signal-to-noise ratio (SNR). Here we demonstrate saturated reconstruction of living brain tissue. We developed an integrated imaging and analysis technology, adapting stimulated emission depletion (STED) microscopy in extracellularly labelled tissue for high SNR and near-isotropic resolution. Centrally, a two-stage deep-learning approach leveraged previously obtained information on sample structure to drastically reduce photo-burden and enable automated volumetric reconstruction down to single synapse level. Live reconstruction provides unbiased analysis of tissue architecture across time in relation to functional activity and targeted activation, and contextual understanding of molecular labelling. This adoptable technology will facilitate novel insights into the dynamic functional architecture of living brain tissue.


title: Geometry of spiking activity in early visual cortex: a Topological Data Analytic approach

abstract: In the brain, spiking patterns live in a high-dimensional space of neurons and time. Thus, determining the intrinsic structure of this state space for neural activity presents a theoretical and experimental challenge. To address this challenge, we introduce a new framework for applying topological data analysis (TDA) to spike train data to determine the geometry of neural activity space. Key to our approach is a parametrized family of distances based on the timing of spikes to determine the dissimilarity between neuronal responses. We applied TDA to visually driven single-unit and multiple single-unit spiking activity in macaque V1 and V2. TDA across timescales reveals a common geometry in V1 and V2 that is most consistent with a low-dimensional space endowed with Euclidean or hyperbolic geometry with modest curvature. Remarkably, the inferred geometry depends on timescale, and is most distinct for the timescales that are important for encoding contrast, orientation, and spatial correlations.

category: neuroscience


title: Glocal dendritic spikes: variation in branch activity during dendritic spiking indicates multiple functional units in the pyramidal neuron apical tuft

abstract:
There is a lively debate on how many functional units exist within the dendritic tree of pyramidal neurons (PNs). The classical view that the PNs dendritic tree comprises several computational units 1-4 was challenged by recent in-vivo studies that identified mainly widespread dendritic spikes 5-10, suggesting a low degree of dendritic compartmentalization. We reasoned that global spikes do not rule out dendritic compartmentalization if these spikes contain a high variation in branch activity. Therefore, we turned to image Ca2+ activity in many apical dendrites from individual layer (L) 5 PNs of the primary motor cortex (M1). For proper dendritic morphology and Ca2+ activity analysis, we used mice with sparse double labeling of PNs with a structural marker (tdTomato) and a GCaMP6s probe. We first collected data for complete registration of the apical tuft dendritic structure. We then used 3D two-photon microscopy to image Ca2+ activity within these tufts during treadmill running. Using these, we imaged up to 30 apical branches from individual L5 PNs, including branches separated by as many as 11 bifurcations and more than 1000 {micro}m of intracellular distance. We found that local spikes were rare, but global spikes often displayed heterogeneous Ca2+ elevation across branches, giving rise to an activity pattern across the tuft. This spiking pattern was dynamic and according to unsupervised hierarchical cluster analysis, fitted to 2-6 distinct patterns, even over short imaging periods. Taken together, we find a considerable variation in branch activity within and between global dendritic spikes, supporting multiple dendritic functional units.

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC="FIGDIR/small/484426v1_ufig1.gif" ALT="Figure 1">
View larger version (21K):
org.highwire.dtl.DTLVardef@103ceeaorg.highwire.dtl.DTLVardef@1058a19org.highwire.dtl.DTLVardef@ad7c24org.highwire.dtl.DTLVardef@1b13d94_HPS_FORMAT_FIGEXP  M_FIG C_FIG We detected three main spike types. Local spikes were evident in a minority of the branches and had low amplitude. Contrastingly, global spikes often displayed homogeneous levels of branch activity and were the strongest and most prolonged spikes. An intermediate pattern was the "glocal spike," where a global spike exhibited heterogeneous branch activity. Spikes with heterogeneous Ca2+ elevation across branches constituted at least a quarter of all spikes. In the social sciences, the term "glocalization" refers to global phenomena that are adjusted locally, such as food items sold worldwide but attuned to local tastes 11. Influenced by that, we refer to global spikes with heterogeneous branch activity as "glocal spikes."


title: Axisymmetric diffusion kurtosis imaging with Rician bias correction: A simulation study

abstract:
PurposeTo compare the estimation accuracy of axisymmetric diffusion kurtosis imaging (DKI) and standard DKI in combination with Rician bias correction (RBC) under the influence of noise.

MethodsAxisymmetric DKI is more robust against noise-induced variation in the measured signal than standard DKI because of its reduced parameter space. However, its susceptibility to Rician noise bias at low signal-to-noise ratios (SNRs) is unknown. Here, we investigate two main questions: first, does Rician bias correction improve estimation accuracy of axisymmetric DKI?; second, is the estimation accuracy of axisymmetric DKI increased compared to standard DKI? Estimation accuracy was investigated on the five axisymmetric DKI tensor metrics (AxTM): the parallel and perpendicular diffusivity and kurtosis and the mean kurtosis, using a simulation study based on synthetic and in-vivo data.

ResultsWe found that RBC was most effective for increasing accuracy of the parallel AxTM in highly to moderately aligned white matter. For the perpendicular AxTM, axisymmetric DKI without RBC performed slightly better than with RBC. However, the combination of axisymmetric DKI with RBC was the overall best performing algorithm across all five AxTM and the axisymmetric DKI framework itself substantially improved accuracy in tissues with low fiber alignment.

ConclusionThe combination of axisymmetric DKI with RBC facilitates accurate DKI parameter estimation at unprecedented low SNRs ({approx} 15), possibly making it a valuable tool for neuroscience and clinical research studies where scan time is a limited resource. The tools used in this paper are publicly available in the open-source ACID toolbox for SPM.


title: T cell migration requires ion and water influx to regulate actin polymerization

abstract:
Migration of T cells is essential for their ability to mount immune responses. Chemokine-induced T cell migration requires WNK1, a kinase that regulates ion influx into the cell. However, it is not known why ion entry is necessary for T cell movement. We show that signaling from the chemokine receptor CCR7 leads to activation of WNK1 and its downstream pathway at the leading edge of migrating CD4+ T cells, leading to ion influx and consequent water entry by osmosis through AQP3. This WNK1-induced water entry is required to swell the membrane at the leading edge, generating space into which actin filaments can polymerize, thereby facilitating forward movement of the cell.

One Sentence SummaryChemokine-induced migration of T cells requires water entry at the leading edge to facilitate actin polymerization.

category: immunology


title: VEGFR3 modulates brain microvessel branching in a mouse model of 22q11.2 deletion syndrome

abstract: The loss of a single copy of TBX1 accounts for most of the clinical signs and symptoms of 22q11.2 deletion syndrome (22q11.2DS), a common genetic disorder that is characterized by multiple congenital anomalies and brain-related clinical problems, some of which likely have vascular origins. Tbx1 mutant mice have brain vascular anomalies, thus making them a useful model to gain insights into the brain disorders associated with the human disease. Here, we found that Tbx1 has a dynamic expression pattern in brain endothelial cells (ECs), including tip cells, during early vascularization, but it is not expressed in EC progenitors. Its main morphogenetic function in the brain is to regulate negatively filopodia biogenesis and vessel branching. Because of similar phenotypes reported for Vegfr3 loss of function, we pursued a mouse genetic approach to test TBX1-VEGFR3 interaction through gain and loss of function experiments. Vegfr3 is expressed in brain ECs with extensive overlap with Tbx1 expression. We demonstrate that inactivating Vegfr3 in the Tbx1 expression domain in a Tbx1 mutant background enhances vessel branching and filopodia formation to a greater extent than that observed in the individual mutants. Furthermore, using a mouse transgenic line, we show that increasing Vegfr3 expression in the Tbx1 expression domain fully rescued the vessel branching and filopodia phenotypes caused by Tbx1 loss of function. Similar results were obtained using an in vitro model of endothelial tubulogenesis. Overall, these results provide genetic evidence that Vegfr3 is a regulator of early vessel branching and filopodia formation in the brain, and is a likely critical effector of the brain vascular phenotype caused by Tbx1 loss of function.

category: developmental biology


title: Sex and size matter: foraging ecology of offshore harbour porpoises in waters around Greenland

abstract: Individuals of different sex or age can vary in their resource use due to differences in behaviour, life history, energetic need, or size. Harbour porpoises are small cetaceans that rely on a constant prey supply to survive. Here, we use bone collagen carbon ({delta}13C) and nitrogen ({delta}15N) isotope compositions to elucidate sex and size differences in the foraging ecology of harbour porpoises from West Greenland. In this region, populations have a unique offshore, deep-water ecology. Female harbour porpoises are larger than males and we find that females have a higher trophic level than males, and {delta}15N positively correlates with size for females only. This indicates that size may matter in the ability of females to handle larger prey and/or dive deeper to catch higher trophic level prey. These results suggest that females, which also feed their calves, may be under different ecological constraints than males. We also analysed the harbour porpoise data with comparable stable isotope data from Greenland populations of belugas and narwhals. Consistent with their small body size, and a diet consisting primarily of capelin, we find that harbour porpoises have a lower trophic level than belugas and narwhals. Furthermore, harbour porpoises have the largest ecological niche of the three species, which is in accordance with tagging studies indicating they have a wide range in shelf and deep offshore waters of the sub-arctic and North Atlantic.

category: ecology


title: Engineering ecologically complementary rhizosphere probiotics using consortia of specialized bacterial mutants

abstract: While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between inoculated consortia members create conflicts for their survival and functioning. To circumvent this, we used transposon mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth-promotion by assembling consortia of closely related but functionally specialized mutants. While most insertion mutations were harmful, some improved strains plant growth-promotion traits without increasing antagonism between them. Crucially, plant growth-promotion could be improved by applying these specialist mutants as consortia, leading to clear positive relationships between consortia richness, plant root colonization and protection from bacterial wilt disease. Together, our results suggest that increasing intra-species diversity could be an effective way to increase probiotic consortia multifunctionality, leading to more stable plant growth-promotion throughout growth cycle via insurance effects.


title: Beyond inappropriate fire regimes: a synthesis of fire-driven declines of threatened mammals in Australia

abstract: Fire can promote biodiversity but changing patterns of fire threaten species worldwide. While scientific literature often describes  inappropriate fire regimes as a significant threat to biodiversity, less attention has been paid to the characteristics that make a fire regime inappropriate. We go beyond this generic description and synthesize how inappropriate fire regimes contribute to declines of animal populations, using threatened mammals as a case study. We developed a demographic framework for classifying mechanisms by which fire regimes cause population decline, and applied the framework in a systematic review to identify fire characteristics and interacting threats associated with population declines in Australian threatened land mammals (n=99). Inappropriate fire regimes threaten 88% of Australian threatened land mammals. Our review indicates that intense, large, and frequent fires are the primary cause of fire-related population declines, particularly through their influence on survival rates. However, several species are threatened by a lack of fire and there is considerable uncertainty in the evidence base for fire-related declines. Climate change and predation are documented or predicted to interact with fire to exacerbate mammalian declines. This demographic framework will help target conservation actions globally and would be enhanced by empirical studies of animal survival, dispersal, and reproduction.


title: Xanthomonas indica sp. nov., a non-pathogenic bacterium isolated from healthy rice (Oryza sativa) seeds from India

abstract: Two yellow pigmented bacterial strains were isolated from healthy rice seeds. The strains designated as PPL560T and PPL568 were identified as members of genus Xanthomonas based on analysis of biochemical and 16S rRNA gene sequence retrieved from whole genome sequence. Isolates formed a distinct monophyletic lineage with X. sontii and X. sacchari as the closest relatives in the phylogenetic tree based on core gene content shared by reported species in genus Xanthomonas. Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridisation values calculated against other species of Xanthomonas were below their respective cut-offs. In planta studies revealed that PPL560T and PPL568 are non-pathogenic to rice plants upon leaf clip inoculation. Absence of type III secretion system related genes and effectors further supported their non-pathogenic status. Herein, we propose Xanthomonas indica sp. nov. as novel species of genus Xanthomonas with PPL560T=MTCC13185 as its type strain and PPL568 as another constituent member.

category: evolutionary biology


title: Transcriptional control of the lacZ promoter is under directional and diversifying selection

abstract: Bacterial cells often respond to changes in the environment by modifying protein expression. This can be achieved through changes in transcriptional or translational activity, or both. Recent research has shed some light on how natural selection shapes overall protein expression. Still, little is known about how selection acts on transcription or translation individually. To address part of this question, we implement an experimental system which allows us to measure how genetic changes affect transcription only, excluding the effects on translation. We use this system to quantify changes in three regulatory phenotypes of the lacZ promoter: transcriptional activity, plasticity, and cell-to-cell variability. We compare these phenotypes from segregating variants that have been subject to natural selection, and random variants that have never been subjected to natural selection. We show that natural selection filters out mutations causing large changes in transcriptional levels from the lacZ promoter. Further, we detect directional selection acting on transcriptional plasticity in combinations of glucose, galactose and lactose environments. Focusing on cell-to-cell variability in transcription, we describe both directional and diversifying selection acting on this phenotype depending on the environment used. We also observe a link between the phylogeny of the environmental E. coli strains and high and low transcriptional noise levels in glucose which are mediated by just one or two SNPs. Our results thus provide new insight into how one of the most well-characterized bacterial promoters is shaped in nature by selection.


title: Case-only rare variant analysis of severe alcohol dependence (AD) using a multivariate hierarchical gene clustering approach.

abstract:
BackgroundVariation in genes involved in ethanol metabolism has been shown to influence risk for alcohol dependence (AD) including protective loss of function alleles in ethanol metabolizing genes. We therefore hypothesized that people with severe AD would exhibit different patterns of rare functional variation in genes with strong prior evidence for influencing ethanol metabolism and response when compared to genes not meeting these criteria.

ObjectiveApply a novel analysis method to leverage a case only design and Whole Exome Sequencing (WES) of severe AD cases from Ireland in order to quantify the difference in functional variation between ethanol-metabolizing genes and their matched controls.

MethodsFirst, three sets of genes known to influence ethanol metabolism or response were generated. Set 1 comprised genes involved in alcohol metabolism in human including alcohol dehydrogenase (ADH), aldehyde dehydrogenase (ALDH), the Cytochrome P450 Family 2 Subfamily E Member 1 (CYP2E1), and catalase (CAT) genes (n=11). Set 2 comprised set 1, in addition to genes showing altered expression in mouse brain after alcohol exposure (n=117). Set 3 comprised sets 1 and 2, in addition to genes shown to alter ethanol behavioral response in invertebrate models (n=358). These sets of genes of interest (GOI) were then matched to sets of control genes using multivariate hierarchical clustering of gene-level summary features obtained from the gnomAD database. Using WES data from 195 individuals with severe alcohol dependence, GOI were then compared to their matched control gene sets using multivariate logistic regression to detect aggregate differences in abundance of synonymous, missense, and loss of function (LOF) variants, respectively.

ResultsA significant difference was not found in the number of functional variants in the primary set of 10 ethanol-metabolizing genes, compared to a matched set of control genes. In both the mouse expression and invertebrate sets, we observed an increased number of synonymous variants in GOI over matched control genes.

ConclusionThe proposed method demonstrates a computationally viable and statistically appropriate approach for genetic analysis of case-only data.

category: genetics


title: QTLs analysis for cold tolerance in rice (Oryza sp.) at the seedling stage using F2 population developed from cross between the genotypes NERICA L-19 and Diamante

abstract: Rice (Oryza sp.) is the most important food crop of the developing world and the staple food of more than half of the world population. It is produced in about 110 countries, including Africa under traditional production systems where field conditions are often variable and yield is low. This is due to the preponderance of abiotic stresses such as cold in these systems. The aim of this study was to identify QTLs associated with cold tolerance at the seedling stage. It was obtained: a phylogenetic tree showing individuals tolerant and sensitive to cold in the Sahel conditions at the seedling stage; 5 majors QTLs associated with cold tolerance located on chromosome 4; QTLs associated with cold tolerance at the seedling stage using F2 population developed from cross between NERICA L-19 X Diamante. All these results are interesting, because to pass local varieties sensitive to cold tolerant varieties through the identification of QTLs associated with cold tolerance that might be introduced. This will enable African producers; especially small producers which have low resource to buy a plant material adapted to the cold period to optimize their rice yields.


title: DNA methylation signatures of Alzheimer's disease neuropathology in the cortex are primarily driven by variation in non-neuronal cell-types

abstract: Alzheimers disease (AD) is a chronic neurodegenerative disease characterized by the progressive accumulation of amyloid-beta and neurofibrillary tangles of tau in the neocortex. Utilizing extensive neuropathology data from the Brains for Dementia Research (BDR) cohort we performed the most systematic epigenome-wide association study (EWAS) of multiple measures of AD neuropathology yet undertaken, profiling DNA methylation in two cortical regions from 631 donors. We meta-analyzed our results with those from previous studies of DNA methylation in AD cortex (total n = 2,013 donors), identifying 334 cortical differentially methylated positions (DMPs) associated with AD pathology including methylomic variation at novel loci not previously implicated in dementia. We subsequently characterized DNA methylation in purified nuclei populations - enriched for neurons, oligodendrocytes and microglia - exploring the extent to which cortex AD-associated DMPs reflect differences manifest in specific cell populations. We find that the majority of DMPs identified in  bulk cortex tissue actually reflect DNA methylation differences occurring in non-neuronal cells, with dramatically increased effect sizes observed in microglia-enriched nuclei populations. Our study highlights the power of utilizing multiple measures of neuropathology to identify epigenetic signatures of AD and the importance of characterizing disease-associated variation in purified neural cell-types.


title: Integrated protein and transcriptome high-throughput spatial profiling

abstract: Spatial transcriptomics and proteomics have independently transformed our understanding of complex biological processes; however, integration of these modalities is currently limited. To overcome this challenge, we developed Spatial PrOtein and Transcriptome Sequencing (SPOTS) for high-throughput integration of transcriptome and protein profiling within the spatial context. Applying SPOTS to spleen and breast cancer samples revealed that spatially-resolved multi-omic integration provides a comprehensive perspective on key biological processes in health and disease.

category: genomics


title: Integration of visual and antennal mechanosensory feedback during head stabilization in hawkmoths

abstract:
During flight maneuvers, insects exhibit compensatory head movements which are essential for stabilizing the visual field on their retina, reducing motion blur, and supporting visual self-motion estimation. In Diptera, such head movements are mediated via visual feedback from their compound eyes that detect retinal slip, as well as rapid mechanosensory feedback from their halteres - the modified hindwings that sense the angular rates of body rotations. Because non-Dipteran insects lack halteres, it is not known if mechanosensory feedback about body rotations plays any role in their head stabilization response. Diverse non-Dipteran insects are known to rely on visual and antennal mechanosensory feedback for flight control. In hawkmoths, for instance, reduction of antennal mechanosensory feedback severely compromises their ability to control flight. Similarly, when the head movements of freely-flying moths are restricted, their flight ability is also severely impaired. The role of compensatory head movements as well as multimodal feedback in insect flight raises an interesting question: in insects that lack halteres, what sensory cues are required for head stabilization? Here, we show that in the nocturnal hawkmoth Daphnis nerii, compensatory head movements are mediated by combined visual and antennal mechanosensory feedback. We subjected tethered moths to open-loop body roll rotations under different lighting conditions, and measured their ability to maintain head angle in the presence or absence of antennal mechanosensory feedback. Our study suggests that head stabilization in moths is mediated primarily by visual feedback during roll movements at lower frequencies, whereas antennal mechanosensory feedback is required when roll occurs at higher frequency. These findings are consistent with the hypothesis that control of head angle results from a multimodal feedback loop that integrates both visual and antennal mechanosensory feedback, albeit at different latencies. At adequate light levels, visual feedback is sufficient for head stabilization. However, under dark conditions, antennal mechanosensory feedback is essential for the control of head movements.

HighlightsO_LIVisual feedback contributes to head stabilization primarily during slower body rotation in hawkmoths.
C_LIO_LIAntennal mechanosensors contribute to head stabilization primarily during faster body roll.
C_LIO_LIAntennal mechanosensory feedback in head stabilization is mediated via Johnstons organ.
C_LIO_LIRestricting head movements affects flight control.
C_LI

category: animal behavior and cognition


title: Optimization of the precursor supply for an enhanced FK-506 production in Streptomyces tsukubaensis

abstract: Tacrolimus (FK-506) is a macrolide widely used as immunosuppressant to prevent transplant rejection. Synthetic production of FK-506 is not efficient and costly, whereas the biosynthesis of FK-506 is complex and the level produced by the wild type strain, Streptomyces tsukubaensis, is very low. We therefore engineered FK-506 biosynthesis and the supply of the precursor L-lysine to generate strains with improved FK-506 yield. To increase FK-506 production, first the intracellular supply of the essential precursor lysine was improved in the native host S. tsukubaensis by engineering the lysine biosynthetic pathway. Therefore, a feedback deregulated aspartate kinase AskSt* of S. tsukubaensis was generated by site directed mutagenesis. Whereas overexpression of AskSt* resulted only in a 17% increase in FK-506 yield, heterologous overexpression of a feedback deregulated AskCg* from Corynebacterium glutamicum was proven to be more efficient. Combined overexpression of AskCg* and DapASt, showed a strong enhancement of the intracellular lysine pool following increase in the yield by approximately 73% compared to the wild type. Lysine is coverted into the FK-506 building block pipecolate by the lysine cyclodeaminase FkbL. Construction of a {Delta}fkbL mutant led to a complete abolishment of the FK-506 production, confirming the indispensability of this enzyme for FK-506 production. Chemical complementation of the {Delta}fkbL mutant by feeding pipecolic acid and genetic complementation with fkbL as well as with other lysine cyclodeaminase genes (pipAf, pipASt, originating from Actinoplanes friuliensis and Streptomyces pristinaespiralis, respectively) completely restored FK-506 production. Subsequently, FK-506 production was enchanced by heterologous overexpression of PipAf and PipASp in S. tsukubaensis. This resulted in a yield increase by 65% compared to the WT in the presence of PipAf from A. friuliensis. For further rational yield improvement, the crystal structure of PipAf from A. friuliensis was determined at 1.3 [A] resolution with the cofactor NADH bound and at 1.4 [A] with its substrate lysine. Based on the structure the Ile91 residue was replaced by Val91 in PipAf, which resulted in an overall increase of FK-506 production by approx. 100% compared to the WT.

category: bioengineering


title: 3D Bioprinted perfusable and vascularized breast tumor model for dynamic screening of chemotherapeutics and CAR-T cells

abstract:
Despite substantial advancements in development of cancer treatments, lack of standardized and physiologically-relevant in vitro testing platforms limit the rapid and early screening of anti-cancer agents. A major barrier in this endeavor, is the complex interplay between the tumor microenvironment and host immune response and lack of predictive biomarkers for clinical benefit. To tackle this challenge, we have developed a dynamic-flow based three-dimensionally (3D) bioprinted vascularized breast tumor model, responding to chemo and immunotherapeutic treatments. Heterotypic tumor spheroids, comprising metastatic breast cancer cells (MDA-MB-231), human umbilical vein endothelial cells (HUVECs) and human dermal fibroblasts (HDFs), precisely bioprinted at pre-defined distances from a perfused vasculature, exhibited tumor angiogenesis and cancer invasion. Proximally bioprinted tumors ([~]100 m) exhibited enhanced capillary sprouting, anastomosis to perfused vasculature and increased cancer cell migration as compared to distally bioprinted spheroids ([~]500 m). Proximally bioprinted tumors treated with varying dosages of doxorubicin for 72 h enabled functional analysis of drug response, wherein, tumors portrayed a dose-dependent drug response behavior with [~]70% decrease in tumor volume for 1 M dose. Additionally, a cell based immune therapy approach was explored by perfusing HER2-targeting chimeric antigen receptor (CAR) modified CD8+ T cells for 24 or 72 h through the central vasculature. Extensive CAR-T cell recruitment to the endothelium and substantial T cell activation and infiltration in the tumor site, resulted in [~]70% reduction in tumor growth for high CAR treatment densities, after 72 h of treatment. The presented 3D model paves the way for a robust, precisely fabricated and physiologically-relevant 3D tumor microenvironment platform for future translation of anti-cancer therapies to personalized medicine for cancer patients.

One Sentence SummaryA physiologically-relevant 3D bioprinted perfusable vascularized tumor model capable of dynamic screening of chemo and immunotherapeutics.


title: Case-control analysis of single-cell RNA-seq studies

abstract: Single-cell RNA-seq (scRNA-seq) assays are being increasingly utilized to investigate specific hypotheses in both basic biology and clinically-applied studies. The design of most such studies can be often reduced to a comparison between two or more groups of samples, such as disease cases and healthy controls, or treatment and placebo. Comparative analysis between groups of scRNA-seq samples brings additional statistical considerations, and currently there is a lack of tools to address this common scenario. Based on our experience with comparative designs, here we present a computational suite (Cacoa - case-control analysis) to carry out statistical tests, exploration, and visualization of scRNA-seq sample cohorts. Using multiple example datasets, we demonstrate how application of these techniques can provide additional insights, and avoid issues stemming from inter-individual variability, limited sample size, and high dimensionality of the data.

category: bioinformatics


title: Drug Mechanism Enrichment Analysis: A tool to link molecular signatures with sensitivity to drug mechanisms of action

abstract:
MotivationTargeted therapeutics have the potential for efficacy against tumors with minimal effects on normal tissues. However, predicting effective drugs from molecular signatures remains a challenge. Here, we present Drug Mechanism Enrichment Analysis (DMEA), a method that uses a transcriptomic signature to predict drug mechanism(s) of action to which a tumor cell may be sensitive or resistant. The method derives its power by aggregating data from many drugs with a shared mechanism of action.

ResultsWe first tested the sensitivity of DMEA using synthetic data. We next validated that DMEA recapitulated known sensitivities to HMGCR, EGFR, and RAF inhibitors while also identifying drug mechanisms for resistant cancers. Finally, we predicted tissue-dependent drug sensitivity for tumors with high and low expression of the cystine/glutamate antiporter xCT. Collectively, DMEA is a novel bioinformatic tool that uses molecular signatures to predict targeted therapeutics sharing a common mechanism of action.

Availability and implementationDMEA is freely available to download as an R package at: https://github.com/BelindaBGarana/DMEA.


title: EsMeCaTa: Estimating metabolic capabilities from taxonomic affiliations

abstract:
SummaryPredicting the functional potential of microorganisms in environmental samples from cultivation-independent techniques is a major challenge. A persistent difficulty lies in associating taxonomic profiles obtained from metabarcoding experiment with accurate functional profiles, particularly for poorly-resolved taxonomic groups. In this paper, we present EsMeCaTa a python package predicting shared proteins from taxonomic affiliations. EsMeCaTa relies on the UniProt database to retrieve the public proteomes associated with a taxon and then uses MMseqs2 in order to compute the set of proteins shared in the taxon. Finally, Es-MeCaTa extracts the functional annotations of these proteins to provide an accurate estimate of the functional potential associated to taxonomic affiliations.

AvailabilityEsMeCaTa is available at: https://github.com/AuReMe/esmecata under the GPL-3 license.


title: Feature selection and aggregation for antibiotic resistance GWAS in Mycobacterium tuberculosis: a comparative study.

abstract:
Drug resistance (DR) remains a global healthcare concern. In contrast to other human bacterial pathogens, acquiring mutations in the genome is the main mechanism of drug resistance for Mycobacterium tuberculosis (MTB). For some antibiotics resistance of a particular isolate can be predicted with high confidence knowing whether specific mutations occurred, but for some antibiotics our knowledge of resistance mechanism is moderate. Statistical machine learning (ML) methods are used in attempts to infer new genes implicated in drug resistance. These methods use large collections of isolates with known whole-genome sequences and resistance status for different drugs. However, high correlations between the presence or absence of resistance to drugs that are used together in one treatment regimen complicate inference of causal mutations by traditional ML. Recently, several new methods were suggested to deal with the problem of correlations of response variables in training data. In this study, we applied the following methods to tackle the confounding effect of resistance co-occurrence in a dataset of approximately 13 000 complete genomes of MTB with characterized resistance status for 13 drugs: logistic regression with different regularization penalty functions, a polynomial-time algorithm for best-subset selection problem (ABESS), and "Hungry, Hungry SNPos" (HHS) method. We compared these methods by the ability to select known causal mutations for the resistance to each particular drug and not to select mutations in genes that are known to be associated with resistance to other drugs. ABESS significantly outperformed the others selecting more relevant sets of mutations. We also showed that aggregation of rare mutations into features indicating changes of PFAM domains increased the quality of prediction and these features were majorly selected by ABESS.

Data SummaryThe dataset unifies characterized whole-genome sequences of M. tuberculosis from multiple studies [1-10]. Short Illumina reads are available in public repositories (SRA or ENA). Sample ids, phenotypes and links to the source papers are summarized and listed in Table S1.


title: -Labeled PARP-1 PET Imaging of PSMA Targeted Alpha Particle Radiotherapy Response

abstract:
MotivationThe growing interest and clinical translation of alpha particle () therapies brings with it new challenges to assess target cell engagement and to monitor therapeutic effect. Noninvasive imaging has great potential to guide -treatment and to harness the potential of these agents in the complex environment of disseminated disease. Poly(ADP) ribose polymerase 1 (PARP-1) is among the most abundantly expressed DNA repair enzymes with key roles in multiple repair pathways - such as those induced by irradiation.

Materials and MethodsHere, we used a third-generation PARP1-specific radiotracer, [18F]-PARPZ, to delineate castrate resistant prostate cancer xenografts. Following treatment with the clinically applied [225Ac]-PSMA-617, positron emission tomography was performed and analyzed, along with and correlative autoradiography and histology acquired.

Results[18F]-PARPZ was able to distinguish treated from control (saline) xenografts by uptake. Kinetic analysis of tracer accumulation also suggests that the localization of the agent to sites of increased PARP-1 expression is a consequence of DNA damage response.

ConclusionsTogether, these data support expanded investigation of [18F]-PARPZ to facilitate clinical translation in the -therapy space.

category: cancer biology


title: Comparison of co-immunoprecipitation techniques for effective identification of SNTA1 interacting proteins in breast cancer cells

abstract: Diverse signal transduction pathways involve thousands of proteins acting in concert that contribute to breast cancer pathology. SNTA1 has emerged as a common link that functions to wire various complex signaling circuits within the cell. In our study we used endogenous SNTA1 protein as bait in pull-down assays to identify SNTA1 interactome from breast cancer cell extract. We compared the utility of two co-immunoprecipitation techniques conventional co-IP and cross-linking co-IP coupled to mass spectrometry (IP-MS) that intriguingly generated valuable inventory of SNTA1 associated proteins in breast cancer cells that may or may not interact physically but contribute to shared functions in breast cancer pathology. We observed that Pierce cross-link IP kit enhanced sensivity of the analysis as it decreased the number of background proteins with a remarkable increase in identified list of proteins. We have also observed that different approaches are able to consistently detect the same signaling outcome as observed by Gene Ontology. Identification of interacting partners of SNTA1 in breast cancer cell lines may depict the possible signaling mechanism of this protein in molecular pathogenesis of breast cancer and its possible use as a therapeutic target.


title: SciCV, the Swiss National Science Foundation's new CV format

abstract:
BackgroundThe Swiss National Science Foundation (SNSF) tested a new CV format called SciCV to encourage fair, DORA-compliant assessment of grant applicants. It was developed in close collaboration with the academic evaluation community and international experts, introduced through detailed change management and finally tested in its utility by an independent research team of the Center for Science and Technology Studies Leiden (CWTS).

MethodsWe present the development of the SciCV pilot and its evaluation by the CWTS research group. The analysis comprised both quantitative and qualitative methods, with (i) surveys and semi-structured interviews with applicants and reviewers, (ii) text analysis of the narrative elements of SciCV, and (iii) participant observation in ten evaluation panel meetings.

ResultsNarrative elements and the inclusion of the academic age were rated as most useful new CV elements, while the inclusion of two metrics, the h-index and the relative citation ratio, were received more critically. The omission of a full publication list had similar numbers of supporters and opponents among applicants and reviewers. Less experienced and junior applicants and reviewers rated the new format generally more positively than more senior applicants and reviewers. The text analysis of narrative elements yielded no significant gender specific differences. The participant observation revealed that the new elements in SciCV broadened the information base used in the evaluation of applicants but did not fundamentally alter traditional, publication-centred evaluation practices.

ConclusionSciCV was a relevant and successful initiative for the SNSF, which showed that the implementation of a new, well-structured CV format is not only feasible but also something that many stakeholders welcome.The extensive experience and results obtained during the change process formed the basis for the development of SciCV 2.0 at the SNSF. It also offers a basis and guidance for other funding organisations planning similar initiatives.

category: scientific communication and education


title: Robust group- but limited individual-level (longitudinal) reliability and insights into cross-phases response prediction of conditioned fear

abstract: Here we follow the call to target measurement reliability as a key prerequisite for individual-level predictions in translational neuroscience by investigating i) longitudinal reliability at the individual and ii) group level, iii) cross-sectional reliability and iv) response predictability across experimental phases. 120 individuals performed a fear conditioning paradigm twice six month apart. Analyses of skin conductance responses, fear ratings and BOLD-fMRI with different data transformations and included numbers of trials were conducted. While longitudinal reliability was generally poor to moderate at the individual level, it was good for acquisition but not extinction at the group-level. Cross-sectional reliability was satisfactory. Higher responding in preceding phases predicted higher responding in subsequent experimental phases at a weak to moderate level depending on data specifications. In sum, the results suggest the feasibility of individual-level predictions for (very) short time intervals (e.g., cross-phases) while predictions for longer time intervals may be problematic.


title: Resolving the mesoscopic missing link: Biophysical modeling of EEG from cortical columns in primates

abstract:
Event-related potentials (ERP) are among the most widely measured indices for studying human cognition. While their timing and magnitude provide valuable insights, their usefulness is limited by our understanding of their neural generators at the circuit level. Inverse source localization offers insights into such generators, but their solutions are not unique. To address this problem, scientists have assumed the source space generating such signals comprises a set of discrete equivalent current dipoles, representing the activity of small cortical regions. Based on this notion, theoretical studies have employed forward modeling of scalp potentials to understand how changes in circuit-level dynamics translate into macroscopic ERPs. However, experimental validation is lacking because it requires in vivo measurements of intracranial brain sources. Laminar local field potentials (LFP) offer a mechanism for estimating intracranial current sources. Yet, a theoretical link between LFPs and intracranial brain sources is missing. Here, we present a forward modeling approach for estimating mesoscopic intracranial brain sources from LFPs and predict their contribution to macroscopic ERPs. We evaluate the accuracy of this LFP-based representation of brain sources utilizing synthetic laminar neurophysiological measurements and then demonstrate the power of the approach in vivo to clarify the source of a representative cognitive ERP component. To that end, LFP was measured across the cortical layers of visual area V4 in macaque monkeys performing an attention demanding task. We show that area V4 generates dipoles through layer-specific transsynaptic currents that biophysically recapitulate the ERP component through the detailed forward modeling. The constraints imposed on EEG production by this method also revealed an important dissociation between computational and biophysical contributors. As such, this approach represents an important bridge from the mesoscopic activity of cortical columns to the patterns of EEG we measure at the scalp.

HighlightsO_LICognitive EEG production was accurately modeled from empirically measured cortical activity in awake macaques.
C_LIO_LIV4 laminar activity plausibly generates the attention-related signal indexed by the EEG.
C_LIO_LIModels demonstrate the importance of biophysical geometry in cognitive EEG production.
C_LI


title: Tuning of motor outputs produced by spinal stimulation during voluntary control of torque directions in monkeys

abstract: Spinal stimulation is a promising method to restore motor function after impairment of descending pathways. While paresis, a weakness of voluntary movements driven by surviving descending pathways, can benefit from spinal stimulation, the effects of descending commands on motor outputs produced by spinal stimulation are unclear. Here, we show that descending commands amplify stimulus-evoked joint torque and the function of intraspinal elements. During the wrist torque tracking task, optimized currents of spinal stimulation over the cervical enlargement facilitated and/or suppressed activities of forelimb muscles. Magnitudes of these effects were dependent on directions of voluntarily-produced torque and positively correlated with levels of voluntary muscle activity. Furthermore, the directions of evoked wrist torque corresponded to the directions of voluntarily-produced torque. These results suggest that spinal stimulation is beneficial in cases of partial lesion of descending pathways by compensating for reduced descending commands through activation of excitatory and inhibitory synaptic connections to motoneurons.


title: High-level visual areas act like domain-general filters with strong selectivity and functional specialization

abstract: Investigation of the visual system has mainly relied on a-priori hypotheses to restrict experimental stimuli or models used to analyze experimental data. Hypotheses are an essential part of scientific inquiry, but an exclusively hypothesis-driven approach might lead to confirmation bias towards existing theories and away from novel discoveries not predicted by them. This paper uses a hypothesis-neutral computational approach to study four high-level visual regions of interest (ROIs) selective to faces, places, letters, or body parts. We leverage the unprecedented scale and quality of the Natural Scenes Dataset to constrain neural network models of these ROIs with functional Magnetic Resonance Imaging (fMRI) measurements. We show that using only the stimulus images and the associated activity in an ROI, we are able to train from scratch a neural network that can predict the activity in each voxel of that ROI with an accuracy that beats state-of-the-art models. Moreover, once trained, the ROI-specific networks can reveal what kinds of functional properties emerge spontaneously in their training. Strikingly, despite no category-level supervision, the units in the trained networks act strongly as detectors for semantic concepts like  faces or  words, thereby providing sub-stantial pieces of evidence for categorical selectivity in these visual areas. Importantly, this selectivity is maintained when training the networks with selective deprivations in the training diet, by excluding images that contain their preferred category. The resulting selectivity in the trained networks strongly suggests that the visual areas do not function as exclusive category detectors but are also sensitive to visual patterns that are typical to their preferred categories, even in the absence of these categories. Finally, we show that our response-optimized networks have distinct functional properties. Together, our findings suggest that response-optimized models combined with model interpretability techniques can serve as a powerful and unifying computational framework for probing the nature of representations and computations in the brain.


title: Subjectivity of time perception alters choice preference for future rewards through fronto-striatal value signal dynamics

abstract: Our preference for a reward depends on the time of delay for its delivery. Here we show that changes in the external environment can manipulate the perceived duration of time, which alters the formation of the choice preference through value signals in the cortical and subcortical brain regions. Humans anticipated a real liquid reward delayed by tens of seconds, during which colors of visually presented panels gradually changed. The color-change delay was perceived as shorter than a control color-constant delay. Interestingly, participants with greater perceptual bias of the delay showed stronger preference for rewards with the color-change delay. The ventrolateral prefrontal cortex (vlPFC) and ventral striatum (VS) showed dynamic neural signatures of value components that were modulated by subjectively perceived duration. Crucially, these effects were specifically observed while a future reward was anticipated, and moreover, the vlPFC activity was weaker in participants with greater bias in the duration perception. These results demonstrate that subjective time experience leads to biased choice preference of delayed rewards, which is regulated by dynamic value signals of future rewards and accurate perception of the external world in the vlPFC-VS systems.


title: IRON REGULATORY PROTEIN (IRP)-MEDIATED IRON HOMEOSTASIS IS CRITICAL FOR NEUTROPHIL DEVELOPMENT AND DIFFERENTIATION IN THE BONE MARROW

abstract: Iron is mostly devoted to the hemoglobinization of erythrocytes for oxygen transport. Yet, emerging evidence points to a broader role for the metal in hematopoiesis, including the formation of the immune system. Iron availability in mammalian cells is controlled by iron-regulatory proteins (IRP)-1 and -2. We report that global disruption of both IRP1 and IRP2 in adult mice impairs neutrophil development and differentiation in the bone marrow, yielding immature neutrophils with abnormally high glycolytic and autophagic activity, resulting in neutropenia. IRPs promote neutrophil differentiation in a cell intrinsic manner by securing cellular iron supply together with transcriptional control of neutropoiesis to facilitate differentiation to fully mature neutrophils. Unlike neutrophils, monocyte count was not affected by IRP and iron deficiency, suggesting a lineage-specific effect of iron on myeloid output. This study unveils the previously unrecognized importance of IRPs and iron metabolism in the formation of a major branch of the innate immune system.


title: Minicollagens play the governing role in polar capsule formation in parasitic cnidarians, the Myxozoa

abstract: Minicollagens are major structural components in the biogenesis of nematocysts in Cnidaria. Sequence mining and recent proteomic analysis of polar capsules, homologues of cnidarian nematocysts, have confirmed the presence of minicollagens in this evolutionarily ancient cnidarian endoparasitic group. Nonetheless, the role of nematocyst-associated proteins in polar capsule morphogenesis has never been studied in myxozoans. Here, we report the gene expression of three myxozoan minicollagens, ncol-1, ncol-3, and the recently identified ncol-5, during the intrapiscine development of Myxidium lieberkuehni, the myxozoan parasite of Northern pike Esox lucius. Moreover, we determined the abundance and localisation of Ncol-1 and Ncol-5 proteins in the developing myxozoan stages by western blotting and by immunofluorescence and immunogold electron microscopy. We found that expression of minicollagens was spatiotemporally restricted to developing polar capsules in sporogonic stages. Intriguingly, Ncol-1 and Ncol-5 were localised as major components of the polar capsule wall and polar tubule. These results support the common origin of nematocysts and myxozoan polar capsules. Furthermore, our findings have practical implications for a more accurate identification of developmental stages of myxozoan parasites.


title: Gut microbiota composition in colorectal cancer patients is genetically regulated

abstract:
The risk of colorectal cancer (CRC) depends on environmental and genetic factors. Among environmental factors, an imbalance in the gut microbiota can increase CRC risk. Also, microbiota is influenced by host genetics. However, it is not known if germline variants influence CRC development by modulating microbiota composition. We investigated germline variants associated with the abundance of bacterial populations in the normal (non-involved) colorectal mucosa of 93 CRC patients and evaluated their possible role in disease. Using a multivariable linear regression, we assessed the association between germline variants identified by genome wide genotyping and bacteria abundances determined by 16S rRNA gene sequencing.

We identified 37 germline variants associated with the abundance of the genera Bacteroides, Ruminococcus, Akkermansia, Faecalibacterium and Gemmiger and with alpha diversity. These variants are correlated with the expression of 58 genes involved in inflammatory responses, cell adhesion, apoptosis and barrier integrity. Genes and bacteria appear to be involved in the same processes. In fact, expression of the pro-inflammatory genes GAL, GSDMD and LY6H was correlated with the abundance of Bacteroides, which has pro-inflammatory properties; abundance of the anti-inflammatory genus Faecalibacterium correlated with expression of KAZN, with barrier-enhancing functions.

Both the microbiota composition and local inflammation are regulated, at least partially, by the same germline variants. These variants may regulate the microenvironment in which bacteria grow and predispose to the development of cancer. Identification of these variants is the first step to identifying higher-risk individuals and proposing tailored preventive treatments that increase beneficial bacterial populations.

Authors summaryGenetic variants describe the variation in the DNA sequence in our genomes and are unique for each person. These variants modify the risk of developing colorectal cancer (CRC) by regulating genes that participate in CRC-associated mechanisms. CRC risk is also affected by microbiota (the microorganisms residing in ourselves). A balanced microbiota helps perform our normal body functions, but can induce cancer, if this balance is lost. Microbiota is affected by factors such as pollution and diet, but is also regulated by genetic variants. However, can genetic variants predispose to cancer risk by regulating microbiota? To answer this question, we sequenced the genetic variants of 93 CRC patients and examined the composition of their intestinal microbiota. We identified variants that regulate the presence of benefic or pathogenic bacteria. The same variants also affect the expression of genes that participate in inflammation, immunity and integrity of intestinal tissue. We found that genetic variants regulate gene expression and microbiota at the same time, predisposing to a higher or lower CRC risk. People with variants predisposing to a higher risk may be benefitted by tailored preventive treatments that increase beneficial bacteria.


title: Cytokine and chemokine profile in patients hospitalized with COVID-19: A comparative study

abstract:
Abnormal cytokine and chemokine concentrations during SARS-CoV-2 infection may represent disease severity. We aimed to assess plasma cytokine and chemokine concentrations in patients with SARS-CoV-2 in Addis Ababa, Ethiopia. In this study, 260 adults: 126 hospitalized patients with confirmed COVID-19 sorted into severity groups: severe (n=68) and mild or moderate (n=58), and 134 healthy controls were enrolled. We quantified 39 plasma cytokines and chemokines using multiplex ELISA. Spearman rank correlation and Mann-Whitney U test were used to identify mechanistically coupled cytokines/chemokines and compare disease severity. Compared to healthy controls, patients with COVID-19 had significantly higher levels of interleukins 1, 2, 6, 7, 8, 10 and 15, C-reactive protein (CRP), serum amyloid A (SAA), intercellular adhesion molecule 1 (ICAM-1), vascular cell adhesion protein 1 (VCAM-1), IFN-{gamma}-inducible protein-10 (IP-10), macrophage inflammatory protein-1 alpha (MIP-1), eotaxin-3, interferon-gamma (IFN-{Upsilon}), tumor necrosis factor- (TNF-), basic fibroblast growth factor (bFGF), placental growth factor (PlGF), and fms-like tyrosine kinase 1 (Flt-1). Patients with severe COVID-19 had higher IL-10 and lower macrophage-derived chemokine (MDC) compared to the mild or moderate group (P<0.05). In the receiver operating characteristic curve, SAA, IL-6 and CRP showed strong sensitivity and specificity predicting the severity and prognosis of COVID-19. Greater age and higher CRP had a significant association with disease severity (P<0.05). Our findings reveal that CRP, SAA, VCAM-1, IP-10, MDC and IL-10 levels are promising biomarkers for COVID-19 disease severity, suggesting that plasma cytokines/chemokines could be used as warning indicators of COVID-19 severity, aid in COVID-19 prognosis and treatment.

IMPORTANCESARS-CoV-2 triggers inflammatory reaction resulting in respiratory discomfort and in critical case may result in death. Cytokines and chemokines are inflammatory biomarkers that regulate and determine the nature of immune responses. Measuring cytokine and chemokine levels is useful in stratification, management and treatment of COVID-19 patients as well as guide resource allocations and therapeutic options. Here, we examined ctytokine and chemokine profiles in COVID-19 patients. Understanding how distinct cytokines and chemokines change over time as COVID-19 disease progresses might aid clinicians in detecting severe illness earlier and thereby improve patient prognosis.

category: biochemistry


title: Potent and specific human monoclonal antibodies against SARS-CoV-2 Omicron variant by rapid mRNA immunization of humanized mice

abstract: The Omicron variant (B.1.1.529) of SARS-CoV-2 rapidly becomes dominant globally. Its extensive mutations confer severe efficacy reduction to most of existing antibodies or vaccines. Here, we developed RAMIHM, a highly efficient strategy to generate fully human monoclonal antibodies (mAbs), directly applied it with Omicron-mRNA immunization, and isolated three potent and specific clones against Omicron. Rapid mRNA immunization elicited strong anti-Omicron antibody response in humanized mice, along with broader anti-coronavirus activity. Customized single cell BCR sequencing mapped the clonal repertoires. Top-ranked clones collectively from peripheral blood, plasma B and memory B cell populations showed high rate of Omicron-specificity (93.3%) from RAMIHM-scBCRseq. Clone-screening identified three highly potent neutralizing antibodies that have low nanomolar affinity for Omicron RBD, and low ng/mL level IC50 in neutralization, more potent than majority of currently approved or authorized clinical RBD-targeting mAbs. These lead mAbs are fully human and ready for downstream IND-enabling and/or translational studies.


title: Dynamical Systems Models for Plasma Dilution

abstract: Recent experiments provide evidence that diluting the blood plasma restores the plasma environment to a more youthful level at least partially restoring the health of organs and tissues throughout the body. We propose that a dynamical-systems model representing the plasma constituents could support the optimization process and help determine the appropriate dilution level, frequency and any simultaneous plasma infusions to achieve the most favorable outcome. We use a combination of a gradient descent, a simulated annealing and a genetic algorithm to find a population of models that fit illustrative data. We analyze this population and present distributions of the model parameters and include a collection of plots of the dilution process for illustrative models. We then consider modifications of the dilution in order to illustrate what predictions might be possible had we more data to disambiguate the model.

category: biophysics


title: Automated neuron tracking inside moving and deforming animals using deep learning and targeted augmentation

abstract: Advances in functional brain imaging now allow sustained rapid 3D visualization of large numbers of neurons inside behaving animals. To decode circuit activity, imaged neurons must be individually segmented and tracked. This is particularly challenging when the brain itself moves and deforms inside a flexible body. The field has lacked general methods for solving this problem effectively. To address this need, we developed a method based on a convolutional neural network (CNN) Awith specific enhancements which we apply to freely moving Caenorhabditis elegans. For a traditional CNN to track neurons across images of a brain with different postures, the CNN must be trained with ground truth (GT) annotations of similar postures. When these postures are diverse, an adequate number of GT annotations can be prohibitively large to generate manually. We introduce  targeted augmentation, a method to automatically synthesize reliable annotations from a few manual annotations. Our method effectively learns the internal deformations of the brain. The learned deformations are used to synthesize annotations for new postures by deforming the manual annotations of similar postures in GT images. The technique is germane to 3D images, which are generally more difficult to analyze than 2D images. The synthetic annotations, which are added to diversify training datasets, drastically reduce manual annotation and proofreading. Our method is effective both when neurons are represented as individual points or as 3D volumes. We provide a GUI that incorporates targeted augmentation in an end-to-end pipeline, from manual GT annotation of a few images to final proofreading of all images. We apply the method to simultaneously measure activity in the second-layer interneurons in C. elegans: RIA, RIB, and RIM, including the RIA neurite. We find that these neurons show rich behaviors, including switching entrainment on and off dynamically when the animal is exposed to periodic odor pulses.


title: Targeted Anatomical and Functional Identification of Antinociceptive and Pronociceptive Serotonergic Neurons that project to the Superficial Dorsal Horn

abstract: Spinally-projecting serotonergic neurons play a key role in controlling pain sensitivity and can either increase or decrease nociception depending on physiological context. It is currently unknown how serotonergic neurons mediate these opposing effects. Utilizing virus-based strategies, we identified two anatomically separated populations of serotonergic hindbrain neurons located in the lateral paragigantocellularis (LPGi) and the medial hindbrain, which respectively innervate the superficial and deep spinal dorsal horn and have contrasting effects on pain perception. Our tracing experiments revealed an unexpected high selectivity of serotonergic neurons of the LPGi for transduction with spinally injected AAV2retro vectors while medial hindbrain serotonergic neurons were largely resistant to AAV2retro transduction. Taking advantage of this selectivity, we employed intersectional chemogenetic approaches to demonstrate that activation of the LPGi serotonergic projections decreases thermal sensitivity, whereas activation of medial serotonergic neurons increases sensitivity to mechanical von Frey stimulation. Together these results suggest that there are functionally distinct classes of serotonergic hindbrain neurons that differ in their anatomical location in the hindbrain, their postsynaptic targets in the spinal cord, and impact on nociceptive sensitivity. At least the LPGi neurons give rise to rather global and bilateral projections throughout the rostrocaudal extent of the spinal cord suggesting that they contribute to widespread systemic pain control.


title: Prime-boost vaccinations with two serologically distinct chimpanzee adenovirus vectors expressing SARS-CoV-2 spike or nucleocapsid tested in a hamster COVID-19 model

abstract: Two serologically distinct replication-defective chimpanzee-origin adenovirus (Ad) vectors (AdC) called AdC6 and AdC7 expressing the spike (S) or nucleocapsid (N) proteins of an early SARS-CoV-2 isolate were tested individually or as a mixture in a hamster COVID-19 challenge model. The N protein, which was expressed as a fusion protein within herpes simplex virus glycoprotein D (gD) stimulated antibodies and CD8+ T cells. The S protein expressing AdC (AdC-S) vectors induced antibodies including those with neutralizing activity that in part cross-reacted with viral variants. Hamsters vaccinated with the AdC-S vectors were protected against serious disease and showed accelerated recovery upon SARS-CoV-2 challenge. Protection was enhanced if AdC-S vectors were given together with the AdC vaccines that expressed the gDN fusion protein (AdC-gDN). In contrast hamsters that just received the AdC-gDN vaccines showed only marginal lessening of symptoms compared to control animals. These results indicate that immune response to the N protein that is less variable that the S protein may potentiate and prolong protection achieved by the currently used genetic COVID-19 vaccines.


title: SARS-CoV-2 Omicron potently neutralized by a novel antibody with unique Spike binding properties

abstract: The SARS-CoV-2 Omicron variant exhibits very high levels of transmission, pronounced resistance to authorized therapeutic human monoclonal antibodies and reduced sensitivity to vaccine-induced immunity. Here we describe P2G3, a human monoclonal antibody (mAb) isolated from a previously infected and vaccinated donor, which displays picomolar-range neutralizing activity against Omicron BA.1, BA.1.1, BA.2 and all other current variants, and is thus markedly more potent than all authorized or clinically advanced anti-SARS-CoV-2 mAbs. Structural characterization of P2G3 Fab in complex with the Omicron Spike demonstrates unique binding properties to both down and up spike trimer conformations at an epitope that partially overlaps with the receptor-binding domain (RBD), yet is distinct from those bound by all other characterized mAbs. This distinct epitope and angle of attack allows P2G3 to overcome all the Omicron mutations abolishing or impairing neutralization by other anti-SARS-COV-2 mAbs, and P2G3 accordingly confers complete prophylactic protection in the SARS-CoV-2 Omicron monkey challenge model. Finally, although we could isolate in vitro SARS-CoV2 mutants escaping neutralization by P2G3 or by P5C3, a previously described broadly active Class 1 mAb, we found these viruses to be lowly infectious and their key mutations extremely rare in the wild, and we could demonstrate that P2G3/P5C3 efficiently cross-neutralized one anothers escapees. We conclude that this combination of mAbs has great prospects in both the prophylactic and therapeutic settings to protect from Omicron and other VOCs.


title: Resilience of S309 and AZD7442 monoclonal antibody treatments against infection by SARS-CoV-2 Omicron lineage strains

abstract: Omicron variant strains encode large numbers of changes in the spike protein compared to historical SARS-CoV-2 isolates. Although in vitro studies have suggested that several monoclonal antibody therapies lose neutralizing activity against Omicron variants1-4, the effects in vivo remain largely unknown. Here, we report on the protective efficacy against three SARS-CoV-2 Omicron lineage strains (BA.1, BA.1.1, and BA.2) of two monoclonal antibody therapeutics (S309 [Vir Biotechnology] monotherapy and AZD7442 [AstraZeneca] combination), which correspond to ones used to treat or prevent SARS-CoV-2 infections in humans. Despite losses in neutralization potency in cell culture, S309 or AZD7442 treatments reduced BA.1, BA.1.1, and BA.2 lung infection in susceptible mice that express human ACE2 (K18-hACE2). Correlation analyses between in vitro neutralizing activity and reductions in viral burden in K18-hACE2 or human Fc{gamma} R transgenic mice suggest that S309 and AZD7442 have different mechanisms of protection against Omicron variants, with S309 utilizing Fc effector function interactions and AZD7442 acting principally by direct neutralization. Our data in mice demonstrate the resilience of S309 and AZD7442 mAbs against emerging SARS-CoV-2 variant strains and provide insight into the relationship between loss of antibody neutralization potency and retained protection in vivo.

category: microbiology


title: Rethinking the role of intraspecific variability in species coexistence

abstract: Intraspecific variability (IV) has been proposed as a new track to explain species coexistence. Previous studies generally assumed, although often non-explicitely, that IV results from intrinsic differences between conspecific individuals. Under this hypothesis, IV either (i) blurred species differences, thus promoting transient or unstable coexistence, (ii) disproportionately advantaged the strongest competitor, thus hindering coexistence, or (iii) promoted coexistence. Based on a body of evidence, we here emphasize that IV does not necessarily imply inherent differences among conspecific individuals, nor species niches overlap. Conspecific individuals can also differ in their measured attributes due to differences in the micro-environment they thrive in. If this source of variation is predominant, which we suggest it is in many cases given the variation of the environment in numerous dimensions at fine scales and the observed spatial structure of IV, it implies that conspecific individuals respond more similarly to environmental variation than heterospecific individuals, thereby concentrating competition within species -- a necessary condition for species coexistence. Importantly, as the number of environmental dimensions that are typically observed and characterized in the field is generally much lower than the actual number of environmental dimensions that influence individual attributes, a great part of observed IV can often be misinterpreted as random variation across individuals while being environmentally-driven, with radically different consequences for community dynamics. We call for new studies exploring observed IV as an outcome of species-specific responses to high-dimensional environmental variations that can lead to inversions of species hierarchy in space and time promoting stable coexistence.


title: Adaptive Magnetic Resonance

abstract: Nuclear magnetic resonance is one of the cornerstones of modern medicine and biomedical research. Over the past several decades, the speed and precision of in-vivo magnetic resonance imaging (MRI) and spectroscopy (MRS) have increased by leaps and bounds, by utilizing sophisticated excitation and acquisition techniques, from parallel imaging and compressed sensing to magnetic resonance fingerprinting. However, these approaches have all been static in nature, fixing measurement parameters in advance, in anticipation of a wide range of expected tissue parameter values, and are therefore sub-optimal for any given subject. We depart from the conventional framework of magnetic resonance and propose a new approach - termed adaptive magnetic resonance - which binds acquisition and excitation, by using the measured signal to update and fine-tune the measurement parameters in real time. This targets the specific tissue characteristics of the subject while they are being scanned. Adaptive magnetic resonance provides a completely new and previously-untapped avenue for improving the sensitivity and specificity of in-vivo magnetic resonance across all tissue contrast mechanisms. Equivalently, it can accelerate data acquisition compared to non-adaptive schemes, by obtaining the same precision using fewer, optimally tuned excitations. We demonstrate that an adaptive pulse sequence for measuring the transverse relaxation time (T2) of metabolites in-vivo improves upon the precision of static approaches by a factor of {approx} 1.7 - or, alternatively, accelerates acquisition 2.5-fold.


title: Patch2Self denoising of Diffusion MRI with Self-Supervision and Matrix Sketching

abstract: Diffusion-weighted magnetic resonance imaging (DWI) is the only noninvasive method for quantifying microstructure and reconstructing white-matter pathways in the living human brain. Fluctuations from multiple sources create significant additive noise in DWI data which must be suppressed before subsequent microstructure analysis. We introduce a self-supervised learning method for denoising DWI data, Patch2Self (P2S), which uses the entire volume to learn a full-rank locally linear denoiser for that volume. By taking advantage of the oversampled q-space of DWI data, P2S can separate structure from noise without requiring an explicit model for either. The setup of P2S however can be resource intensive, both in terms of running time and memory usage, as it uses all voxels (n) from all-but-one held-in volumes (d - 1) to learn a linear mapping {Phi} : [R]nx(d-1) [↦] [R]n for denoising the held-out volume. We exploit the redundancy imposed by P2S to alleviate its performance issues and inspect regions that influence the noise disproportionately. Specifically we introduce P2S-sketch, which makes a two-fold contribution: (1) P2S-sketch uses matrix sketching to perform self-supervised denoising. By solving a sub-problem on a smaller sub-space, so called, coreset, we show how P2S can yield a significant speedup in training time while using less memory. (2) We show how the so-called statistical leverage scores can be used to interpret the denoising of dMRI data, a process that was traditionally treated as a black-box. Our experiments conducted on simulated and real data clearly demonstrate that P2S via matrix sketching (P2S-sketch) does not lead to any loss in denoising quality, while yielding significant speedup and improved memory usage by training on a smaller fraction of the data. With thorough comparisons on real and simulated data, we show that Patch2Self outperforms the current state-of-the-art methods for DWI denoising both in terms of visual conspicuity and downstream modeling tasks. We demonstrate the effectiveness of our approach via multiple quantitative metrics such as fiber bundle coherence, R2 via cross-validation on model fitting, mean absolute error of DTI residuals across a cohort of sixty subjects.


title: The cGAS-STING pathway affects vertebral bone but does not promote intervertebral disc cell senescence or degeneration

abstract: The DNA-sensing cGAS-STING pathway promotes the senescence-associated secretory phenotype (SASP) and mediates type-I interferon inflammatory responses to foreign viral and bacterial DNA as well as self-DNA. Studies of the intervertebral disc in humans and mice demonstrate associations between aging, increased cell senescence, and disc degeneration. Herein we assessed the role of STING in SASP promotion in STING gain- (N153S) and loss-of-function mouse models. N153S mice evidenced elevated circulating levels of proinflammatory markers including IL-1{beta}, IL-6, and TNF- and exhibited a mild trabecular and cortical bone phenotype in caudal vertebrae. Interestingly, despite systemic inflammation, the structural integrity of the disc and knee articular joint remained intact, and cells did not show a loss of their phenotype or elevated SASP. Transcriptomic analysis of N153S tissues demonstrated an upregulated immune response by disc cells, which did not closely resemble inflammatory changes in human tissues. Interestingly, STING-/- mice also showed a mild vertebral bone phenotype, but the absence of STING did not improve the age-associated disc phenotype or reduce the abundance of SASP markers. Overall, the analyses of N153S and STING-/- mice that the cGAS-STING pathway is not a major contributor to SASP induction and consequent disc aging and degeneration but may play a minor role in the maintenance of trabecular bone in the vertebrae. This work contributes to a growing body of work demonstrating that systemic inflammation is not a key driver of disc degeneration.

category: cell biology


title: Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model.

abstract: Mitochondria are extremely pleomorphic organelles. Automatically annotating each one accurately and precisely in any 2D or volume electron microscopy (EM) image is an unsolved computational challenge. Current deep learning-based approaches train models on images that provide limited cellular contexts, precluding generality. To address this, we amassed a highly heterogeneous [~]1.5 x 106 image 2D unlabeled cellular EM dataset, and segmented [~]135,000 mitochondrial instances therein. MitoNet, a model trained on these resources, performs well on challenging benchmarks and on previously unseen volume EM datasets containing tens of thousands of mitochondria. We release a new Python package and napari plugin, empanada, to rapidly run inference, visualize, and proofread instance segmentations.


title: Two different phospholipases C, Isc1 and Pgc1, cooperate to regulate mitochondrial function

abstract: Absence of inositolphosphosphingolipid phospholipase C, Isc1, a yeast homologue of mammalian neutral sphingomyelinase type 2, leads to severe mitochondrial dysfunction. We show that the defect can be largely rescued by deletion of another type-C phospholipase, the phosphatidylglycerol (PG)-specific Pgc1. The reduced phosphatidylethanolamine (PE) levels, as well as reduced cytochrome c oxidase activity, observed in isc1{Delta} cells were restored to wild-type levels in the pgc1{Delta}isc1{Delta} mutant. We found that Pgc1 substrate, PG, inhibits in vitro activity of Isc1 and phosphatidylserine decarboxylase Psd1, an enzyme crucial for PE biosynthesis. We also identified a mechanism by which the balance between the current demand for PG and its consumption is controlled. We document that the product of PG hydrolysis, diacylglycerol, competes with the substrate of PG-phosphate synthase, Pgs1, and thereby inhibits the biosynthesis of excess PG. This feedback loop does not work in the absence of Pgc1, which catalyzes PG degradation. Finally, Pgc1 activity is partially inhibited by products of Isc1-mediated hydrolysis. The described functional interconnection of the two phospholipases contributes significantly to lipid homeostasis throughout the cellular architecture.


title: Local actuation of organoids by magnetic nanoparticles

abstract: Tissues take shape during development through a series of morphogenetic movements guided by local cell-scale forces. While current in vitro approaches subjecting tissues to homogenous stresses, it is currently no possible to recapitulate highly local spatially varying forces. Here we develop a method for local actuation of organoids using embedded magnetic nanoparticles. Sequential aggregation of magnetically labelled human pluripotent stem cells followed by actuation by a magnetic field produces localized magnetic clusters within the organoid. These clusters impose local mechanical forces on the surrounding tissue in response to applied global magnetic fields. We show that precise, spatially defined actuation provides short-term mechanical tissue perturbations as well as long-term cytoskeleton remodeling. We demonstrate that local magnetically-driven actuation guides asymmetric growth and proliferation, leading to enhanced patterning in human neural organoids. We show that this approach is applicable to other model systems by observing polarized patterning in paraxial mesoderm organoids upon local magnetic actuation. This versatile approach allows for local, controllable mechanical actuation in multicellular constructs, and is widely applicable to interrogate the role of local mechanotransduction in developmental and disease model systems.


title: Modelling global mRNA dynamics during Drosophila embryogenesis reveals a relationship between mRNA degradation and P-bodies

abstract: Regulation of mRNA degradation is critical for a diverse array of cellular processes and developmental cell fate decisions. Although many methods for determining mRNA half-lives rely on transcriptional inhibition or metabolic labelling, these manipulations can influence half-lives or introduce errors in the measurements. Here we use a non-invasive method for estimating mRNA half-lives globally in the early Drosophila embryo using a total RNA-seq time series and Gaussian process regression to model the dynamics of premature and mature mRNAs. We show how regulation of mRNA stability is used to establish a range of mature mRNA dynamics during embryogenesis, despite shared transcription profiles. Our data suggest that mRNA half-life is not dependent on translation efficiency, but instead we provide evidence that short half-life mRNAs are more strongly associated with P-bodies. Moreover, we detect an enrichment of mRNA 3 ends in P-bodies in the early embryo, consistent with 5 to 3 degradation occurring in P-bodies for at least a subset of mRNAs. We discuss our findings in relation to recently published data suggesting that the primary function of P-bodies in other biological contexts is mRNA storage.


title: A naturally arising broad and potent CD4-binding site antibody with low somatic mutation

abstract:
The induction of broadly neutralizing antibodies (bNAbs) is a potential strategy for a vaccine against HIV-1. However, most bNAbs exhibit features such as unusually high somatic hypermutation, including insertions and deletions, which make their induction challenging. VRC01-class bNAbs exhibit extraordinary breadth and potency, but also rank among the most highly somatically-mutated bNAbs. Here we describe a VRC01-class antibody isolated from a viremic controller, BG24, that has less than half the mutations of most other relatives of its class, while achieving comparable breadth and potency. A 3.8 [A] X-ray crystal structure of a BG24-BG505 Env trimer complex revealed conserved contacts at the gp120 interface characteristic of the VRC01-class Abs, despite lacking common CDR3 sequence motifs. The existence of moderately-mutated CD4-binding site (CD4bs) bNAbs such as BG24 provides a simpler blueprint for CD4bs antibody induction by a vaccine, raising the prospect that such an induction might be feasible with a germline-targeting approach.

TeaserAn anti-HIV-1 antibody with comparable neutralization breadth and potency to similarly-classed antibodies, with half as many mutations.


title: Reproductive tradeoffs govern sexually dimorphic tubular lysosome induction in C. elegans

abstract: Animals of different sexes often exhibit unique behaviors that benefit their specific reproductive interests. In the nematode Caenorhabditis elegans, self-fertilizing hermaphrodites can reproduce without a mate and thus prioritize feeding to satisfy the high energetic costs of reproduction. However, males, which rely on finding potential mates for reproduction, sacrifice feeding and instead prioritize exploratory behavior. Here, we demonstrate that these differences in behavior are linked to sexual dimorphism at the cellular level; young males raised on a rich food source show constitutive induction of gut tubular lysosomes, a non-canonical lysosome morphology that typically forms in the gut of young hermaphrodites only when food is limited. We find that male-specific induction of gut tubular lysosomes on abundant food is due to self-imposed dietary restriction through daf-7/TGF{beta} signaling, which promotes mate-searching at the cost of feeding. While gut tubular lysosomes are largely absent from well-fed hermaphrodites at the start of adulthood, their induction accelerates in hermaphrodites in early aging, dependent on the presence of sperm and, partly, on embryo production. These findings identify tubular lysosome induction as a sexually dimorphic cellular event that may integrate animal physiology with sex-specific behavioral differences important for reproductive success.


title: Gene mutations and molecular evolution of the chikungunya virus E1 and E2 from 2014 to 2019

abstract:
Chikungunya virus (CHIKV), a mosquito-borne Alphavirus, is the etiological agent of chikungunya fever. To investigate the prevalence and genetic characteristics of CHIKV in China, we performed a molecular epidemiological study during the 2014-2019 period. Phylogenetic analysis of CHIKV in the 2014-2019 shows that it is currently clustered geographically, which means that CHIKVs local adaptability is gradually strengthening. Focusing on CHIKV adaptive mutation E1-A226V is not obvious in our study. The CHIKV E1 amino acid non-synonymous mutation results revealed the common mutation site M343I. Most mutation sites belong to the American epidemic strains, and the mutation rate is 2.8%. In 31 sequences, 19 non-synonymous mutations were found in CHIKV E1 (total mutation rate 20/499 = 4%), and 37 non-synonymous mutations in CHIKV E2 (total mutation rate 30/425 = 7%). It is worth noting that the mutation of CHIKV E2 has changed more than that of CHIKV E1 between 2014 and 2019. CHIKV E2 screened out common mutation sites, and the results showed that there are five common mutation sites, namely S119G, L182M, G206D, S300N, and A345T. Eighty-three percent of the CHIKV E2 receptor binding domain mutations in the American strains, namely T3I and N6H, may cause immune escape.

We constructed a new luciferase immunosorbent assay using CHIKV E2 antigen and mutant E2 antigen to test the serum of the CHIKV infected patients, and the detected samples and dilution ratios were different. The T3I, N6H, S119G, L182M, G206D, S300N, and A345T mutations in CHIKV E2 could explain these differences between patients.

IMPORTANCECHIKV originated in Africa more than 500 years ago, with a common lineage dividing into two distinct branches called West Africa (West African, WA) and East/Central/South Africa (East/Central/South African, ECSA). Moreover, the E1-A226V mutation enhanced the replication and transmission capacity of CHIKV in Aedes albopictus. However, it should be noted that E1-A226V does not explain the CHIKV epidemic that has occurred in the Americas in recent years. We analyzed CHIKV samples in the 2014-2019, and the results showed that the mutation of CHIKV E1 protein occurred was not mainly concentrated in E1-A226V, but concentrated in M343I. This also means that CHIKV constantly mutates in the natural environment and is formed under natural conditions. Analysis of the common mutation sites of CHIKV E2 showed that there were seven common mutation sites S119G/L182M/ G206D /S300N/A345T, and the new mutation of CHIKV E2 may affect serological antibody detection.


title: Per-Pathogen Virulence of HIV-1 subtypes A, C and D

abstract:
HIV-1 subtypes differ, among other things, in their clinical manifestations and the speed in which they spread. In particular, the frequency of subtype C is increasing relative to subtype A and D. We aim to investigate whether HIV-1 subtype A, C and D differ in their per-pathogen virulence and to what extend this can explain the difference in spread between these subtypes.

We use data from the Hormonal Contraception and HIV-1 Genital Shedding and Disease Progression among Women with Primary HIV Infection (GS) Study. For each study participant, we determine the set-point viral load value, CD4+ T cell level after primary infection and CD4+ T cell decline. Based on both the CD4+ T cell count after primary infection and CD4+ T cell decline, we estimate the time until AIDS for each individual. We then obtain our newly introduced measure of virulence as the inverse of the estimated time until AIDS. This new measure of virulence has an improved correlation with the set-point viral load compared to the decline of CD4+ T cells alone. After fitting a model to the measured virulence and set-point viral load values, we tested if this relation varies per subtype. We found that subtype C has a significantly higher per-pathogen virulence than subtype A. Based on an evolutionary model, we then hypothesize that differences in the primary length of infection period cause the observed variation in the speed of spread of the subtypes.

Author summaryHIV-1 subtype C is currently spreading relatively fast in various parts of the world. Data from a study that followed many women infected with different HIV-1 subtypes (A, C and D) before they started treatment shows that neither their viral load nor the disease duration are increased for subtype C compared to subtype A and D. Thus, it seems that subtype C does not have a transmission advantage, neither per contact nor due to longer infection, making the observed relative rise in subtype C a puzzle. We used the same data to test if subtype C has optimized its potential to spread by decreasing the disease duration per unit of viral load (per-pathogen virulence) compared to subtype A and D. However, we find that subtype C has a significantly higher per-pathogen virulence than subtype A and D. This result makes the rise of subtype C even more counter-intuitive.

In a last step, we develop an evolutionary model, in which we synthesize all our empirical results. With this model we can show that the most likely explanation for the global spread of subtype C is a difference in the duration of primary infection between the subtypes.


title: Maintaining hypoxia environment of subchondral bone alleviates osteoarthritis progression

abstract:
Abnormal subchondral bone remodeling featured by over-activated osteoclastogenesis leads to articular cartilage degeneration and osteoarthritis (OA) progression, but the mechanism is still unclear. In this study, we used lymphocyte cytosolic protein 1 (Lcp1) knock-out mice to suppress subchondral osteoclast formation in mice OA model with anterior cruciate ligament transection (ACLT) and Lcp1-/- mice showed decreased bone remodeling and sensory innervation in subchondral bone accompanied by retarded cartilage degeneration. For mechanisms, in wildtype mice with ACLT the activated osteoclasts in subchondral bone induced type-H vessels and elevated oxygen concentration which ubiquitylated hypoxia-inducible factor 1 (HIF-1), vital for maintaining chondrocyte homeostasis in articular chondrocytes and led to cartilage degeneration. Deletion of Lcp1 impeded osteoclast-mediated angiogenesis, which maintained the low levels of oxygen partial pressure (pO2) in subchondral bone as well as the whole joint and delayed the OA progression. Stabilization of HIF-1 delayed cartilage degeneration and knockdown of Hif1a abolished the protective effects of Lcp1 knockout. Notably, we identified a novel subgroup of hypertrophic chondrocytes highly associated with OA by single cell sequencing analysis of human articular chondrocytes. Lastly, we showed that Oroxylin A, an Lcp1-encoded protein L-plastin (LPL) inhibitor, could alleviate OA progression. In conclusion, maintaining hypoxic environment in subchondral bone is an attractive strategy for OA treatment.

TeaserInhibiting subchondral osteoclastogenesis alleviates OA progression via maintaining joint hypoxia environment.


title: Hiplot: a comprehensive and easy-to-use web service boosting publication-ready biomedical data visualization

abstract: Modern web techniques provide an unprecedented opportunity for leveraging complex biomedical data generating in clinical, omics, and mechanism experiments. Currently, the functions for carrying out publication-ready biomedical data visualization represent primary technical hurdles in the state-of-art omics-based web services, whereas the demand for visualization-based interactive data mining is ever-growing. Here, we propose an easy-to-use web service, Hiplot (https://hiplot.com.cn), equipping with comprehensive and interactive biomedical data visualization functions (230+) including basic statistics, multi-omics, regression, clustering, dimensional reduction, meta-analysis, survival analysis, risk modeling, etc. We used the demo and real datasets to demonstrate the usage workflow and the core functions of Hiplot. It permits users to conveniently and interactively complete a few specialized visualization tasks that previously could only be done by senior bioinformatics or biostatistics researchers. A modern web client with efficient user interfaces and interaction methods has been implemented based on the custom components library and the extensible plugin system. The versatile output can also be produced in different environments via using the cross-platform portable command-line interface (CLI) program, Hctl. A switchable view between the editable data table and the file uploader/path selection could facilitate data importing, previewing, and exporting, while the plumber-based response strategy significantly reduced the time costs for generating basic scientific graphics. Diversified layouts, themes/styles, and color palettes in this website allow users to create high-quality and publication-ready graphics. Researchers devoted to both life and data science may benefit from the emerging web service.


title: Loop extrusion driven volume phase transition of entangled chromosomes

abstract: Mitotic chromosomes without nucleosomes have been reconstituted in recent experiments. When topo II is depleted from the reconstituted chromosomes, these chromosomes are entangled and form  sparklers, where DNA is condensed in the core with linker histone H1.8 and condensin is localized at the periphery. To understand the mechanism of the assembly of sparklers, we here take into account the loop extrusion by condensin in an extension of the theory of entangled polymer gels. The loop extrusion stiffens an entangled DNA network because DNA segments in the elastically effective chains are translocated to loops, which are elastically ineffective. Our theory predicts that the loop extrusion by condensin drives the volume phase transition that collapses a swollen entangled DNA gel as the stiffening of the network destabilizes the swollen phase. This is an important element to understand the mechanism of the assembly of the reconstituted chromosomes.


title: A model for determining the length distribution of actin filaments in cells

abstract: Tensional homeostasis is a cellular process whereby nonmuscle cells such as fibroblasts keep a constant level of intracellular tension and signaling activities. Cells are allowed thanks to tensional homeostasis to adapt to mechanical stress, but the detailed mechanism remains unclear. Here we address from a theoretical point of view what is required for maintaining cellular tensional homeostasis. A constrained optimization problem is formulated to analytically determine the probability function of the length of individual actin filaments (AFs) responsible for sustaining cellular tension. An objective function composed of two entropic quantities measuring the extent of formation and dispersion of AFs within cells is optimized under two constraint functions dictating a constant amount of actin molecules and tension that are arguably the two most salient features of tensional homeostasis. We then derive a specific probability function of AFs that is qualitatively consistent with previous experimental observations, in which short AF populations preferably appear. Regarding the underlying mechanism, our analyses suggest that the constraint for keeping the constant tension level makes long AF populations smaller in number because long AFs have a higher chance to be involved in bearing larger forces. The specific length distribution of AFs is thus required for achieving the constrained objectives, by which individual cells are endowed with the ability to stably maintain a homeostatic tension throughout the cell, thereby potentially allowing cells to locally detect deviation in the tension, keep resulting biological functions, and hence enable subsequent adaptation to mechanical stress. Although minimal essential factors are included given the actual complexity of cells, our approach would provide a theoretical basis for understanding complicated homeostatic and adaptive behavior of the cell.