Biology subjects

Chen, X.

Publications and source records attributed to Chen, X..

At least 1,315 records · Page 73Linked to original sources

bioRxiv2020

Dorsal raphe dopamine neurons signal motivational salience dependent on internal and external states

The ability to recognize motivationally salient events and respond to them adaptively is critical for survival. Here we tested whether dopamine (DA) neurons in the dorsal raphe nucleus (DRN) contribute to this process. Population recordings of DRNDA neurons during associative learning tasks showed that their activity dynamically tracks salience, developing excitation to both reward- and punishment-paired cues. The DRNDA response to reward-predicting cues was diminished after satiety, suggesting modulation by internal states. DRNDA activity was also greater for unexpected outcomes than for expected outcomes. Two-photon imaging of DRNDA neurons demonstrated that the majority of individual neurons developed activation to reward-predicting cues but not to punishment-predicting cues, which was surprising and qualitatively distinct from the population results. Head-fixation during fear learning abolished the neural response to aversive cues, indicating modulation by behavioral context. Overall, these results suggest that DRNDA neurons encode motivational salience, dependent on internal and external factors.

neuroscience↗

bioRxiv2020

A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis

Multiple sclerosis (MS) is a disease characterized by a targeted immune attack on myelin in the central nervous system (CNS). We have previously shown that oligodendrocytes (OLs), myelin producing cells in the CNS, and their precursors (OPCs), ac-quire disease-specific transcriptional states in MS 1,2. To under-stand how these alternative transcriptional programs are acti-vated in disease, we performed single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) on the OL lineage in the experimental autoimmune encephalomyeli-tis (EAE) mouse model of MS. We identified regulatory regions with increased accessibility in oligodendroglia (OLG) in EAE, some of which in the proximity of immune genes. A similar re-modeling of chromatin accessibility was observed upon treat-ment of postnatal OPCs with interferon-gamma (IFN{gamma}), but not with dexamethasone. These changes in accessibility were not exclusive to distal enhancers, but also occurred at promoter re-gions, suggesting a role for promoters in mediating cell-state transitions. Notably, we found that a subset of immune genes al-ready exhibited chromatin accessibility in OPCs ex vivo and in vivo, suggesting a primed chromatin state in OLG compatible with rapid transitions to an immune-competent state. Several primed genes presented bivalency of H3K4me3 and H3K27me3 at promoters in OPCs, with loss of H3K27me3 upon IFN{gamma} treatment. Inhibition of JMJD3/Kdm6b, mediating removal of H3K27me3, led to the inability to activate these genes upon IFN{gamma} treatment. Importantly, OLGs from the adult human brain showed chromatin accessibility at immune gene loci, par-ticularly at MHC-I pathway genes. A subset of single-nucleotide polymorphisms (SNPs) associated with MS susceptibility over-lapped with these primed regulatory regions in OLG from both mouse and human CNS. Our data suggest that susceptibility for MS may involve activation of immune gene programs in OLG. These programs are under tight control at the chromatin level in OLG and may therefore constitute novel targets for immunological-based therapies for MS.

neuroscience↗

bioRxiv2020

Protein Structure Refinement Guided by Atomic Packing Frustration Analysis

1Recent advances in machine learning, bioinformatics and the understanding of the folding problem have enabled efficient predictions of protein structures with moderate accuracy, even for targets when there is little information from templates. All-atom molecular dynamics simulations provide a route to refine such predicted structures, but unguided atomistic simulations, even when lengthy in time, often fail to eliminate incorrect structural features that would allow the structure to become more energetically favorable owing to the necessity of making large scale motions and overcoming energy barriers for side chain repacking. In this study, we show that localizing packing frustration at atomic resolution by examining the statistics of the energetic changes that occur when the local environment of a site is changed allows one to identify the most likely locations of incorrect contacts. The global statistics of atomic resolution frustration in structures that have been predicted using various algorithms provide strong indicators of structural quality when tested over a database of 20 targets from previous CASP experiments. Residues that are more correctly located turn out to be more minimally frustrated than more poorly positioned sites. These observations provide a diagnosis of both global and local quality of predicted structures, and thus can be used as guidance in all-atom refinement simulations of the 20 targets. Refinement simulations guided by atomic packing frustration turn out to be quite efficient and significantly improve the quality of the structures.

biophysics↗

bioRxiv2020

HiFi-SIM: reconstructing high-fidelity structured illumination microscope images

Structured illumination microscopy (SIM) has been a widely-used super-resolution (SR) fluorescence microscopy technique, but artifacts often appear in reconstructed SR images which reduce its fidelity and might cause misinterpretation of biological structures. We present HiFi-SIM, a high-fidelity SIM reconstruction algorithm, by engineering the effective point spread function (PSF) into an ideal form. HiFi-SIM can effectively reduce commonly-seen artifacts without loss of fine structures and improve the axial sectioning. Since results of HiFi-SIM are not sensitive to used PSF and reconstruction parameters, it lowers the requirements for dedicated PSF calibration and complicated parameter adjustment, thus promoting SIM as a daily imaging tool.

biophysics↗

bioRxiv2020

Acidosis, Zinc and HMGB1 in Sepsis: A Common Connection Involving Sialoglycan Recognition

Blood pH is tightly regulated between 7.35-7.45, with values below 7.3 during sepsis being associated with lactic acidosis, low serum zinc, and release of proinflammatory HMGB1 from activated and/or necrotic cells. Using an ex vivo whole blood system to model lactic acidosis, we show that while HMGB1 does not engage leukocyte receptors at physiological pH, lowering pH with lactic acid facilitates binding. At normal pH, micromolar zinc supports plasma sialoglycoprotein binding by HMGB1, which is markedly reduced when pH is adjusted with lactic acid to sepsis levels. Glycan array studies confirmed zinc and pH-dependent HMGB1 binding to sialoglycans typical of plasma glycoproteins. Thus, proinflammatory effects of HMGB1 are suppressed via plasma sialoglycoproteins until drops in pH and zinc release HMGB1 to trigger downstream immune activation. Significance StatementHMGB1 sequestered by plasma sialoglycoproteins at physiological pH is released when pH and zinc concentrations fall in sepsis.

immunology↗

bioRxiv2020

Autographa californica Multiple Nucleopolyhedrovirus orf13 is Required for Efficient Nuclear Egress of Nucleocapsids

Autographa californica multiple nucleopolyhedrovirus (AcMNPV) orf13 (ac13) is a conserved gene in all sequenced alphabaculoviruses. However, its function in the viral life cycle remains unknown. In this study we found that ac13 was a late gene and that the encoded protein, bearing a putative nuclear localization signal motif in the DUF3627 domain, colocalized with the nuclear membrane. Deletion of ac13 did not affect viral DNA replication, gene transcription, nucleocapsid assembly or occlusion body (OB) formation, but reduced virion budding from infected cells by approximately 400-fold compared with the wild-type virus. Deletion of ac13 substantially impaired the egress of nucleocapsids from the nucleus to the cytoplasm, while the number of occlusion-derived viruses embedded within OBs was unaffected. Taken together, our results indicated that ac13 was required for efficient nuclear egress of nucleocapsids during virion budding, but was dispensable for OB formation. IMPORTANCEEgress of baculovirus nucleocapsids from the nucleus is an essential process for morphogenesis of mature budded viruses, which is required to spread infection within susceptible cells and tissues. Although many viral and host proteins are required for nucleocapsid egress, the specific mechanisms underlying this process in baculoviruses remain somewhat enigmatic. In the present study, we found that the ac13 gene, in addition to ac11, ac51, ac66, ac75, ac78, gp41, ac93, p48, exon0 and ac142, was required for efficient nuclear egress of nucleocapsids. Our results contribute to a better understanding of nucleocapsid egress in baculoviruses.

microbiology↗

bioRxiv2020

DNNBrain: a unifying toolbox for mapping deep neural networks and brains

Deep neural networks (DNNs) have attained human-level performance on dozens of challenging tasks through an end-to-end deep learning strategy. Deep learning gives rise to data representations with multiple levels of abstraction; however, it does not explicitly provide any insights into the internal operations of DNNs. Its success appeals to neuroscientists not only to apply DNNs to model biological neural systems, but also to adopt concepts and methods from cognitive neuroscience to understand the internal representations of DNNs. Although general deep learning frameworks such as PyTorch and TensorFlow could be used to allow such cross-disciplinary studies, the use of these frameworks typically requires high-level programming expertise and comprehensive mathematical knowledge. A toolbox specifically designed for cognitive neuroscientists to map DNNs and brains is urgently needed. Here, we present DNNBrain, a Python-based toolbox designed for exploring internal representations in both DNNs and the brain. By integrating DNN software packages and well-established brain imaging tools, DNNBrain provides application programming and command line interfaces for a variety of research scenarios, such as extracting DNN activation, probing DNN representations, mapping DNN representations onto the brain, and visualizing DNN representations. We expect that our toolbox will accelerate scientific research in applying DNNs to model biological neural systems and utilizing paradigms of cognitive neuroscience to unveil the black box of DNNs.

neuroscience↗

bioRxiv2020

Molecular Functions of Conserved Developmentally-Regulated GTP-Binding Protein Drg1 in Translation

Conserved developmentally-regulated GTP-binding (Drg) proteins and their binding partner Dfrp proteins are known to be important for embryonic development, cellular growth control, differentiation and proliferation. Here, we report that the yeast Drg1/Dfrp1 ortholog, Rbg1/Tma46, facilitates translational initiation, elongation and termination via suppressing prolonged ribosome pausing. Consistent with the genome-wide observations, Rbg1 reverses the growth defect resulting from translation stalling and stabilizes mRNAs against no-go decay. Furthermore, we provide a cryoEM structure of the 80S ribosome bound with Rbg1/Tma46 that reveals the molecular interactions responsible for Rbg1/Tma46 function. The Rbg1 subunit binds to the GTPase association center of the ribosome and the A-tRNA, and the N-terminal zinc finger domain of Tma46 subunit binds to the 40S, establishing an interaction critical for the complex ribosomal association. Our results answer the fundamental question on how a paused ribosome resumes translation and show that Drg1/Dfrp1 proteins play a critical role in ensuring orderly translation.

biophysics↗

bioRxiv2020

The Evolution of Sex Chromosome Dosage Compensation in Animals

The evolution of sex chromosomes in the XY or ZW systems shall lead to gene expression dosage problems, as in at least one of the sexes, the sex-linked gene dose has been reduced by half. It has been proposed, most notably by Susumu Ohno for mammals, that the transcriptional output of the whole sex chromosome should be doubled for a complete dosage compensation. However, due to the variability of the existing methods to determine the transcriptional differences between Sex chromosomes and Autosomes (S:A ratios) in different studies, whether clade-specific results are comparable and whether there is a more general model to explain dosage compensation states remain unanswered. In this study, we collected more than 500 public RNA-seq datasets from multiple tissues and species in major clades (including mammals, birds, fishes, insects, and worms) and proposed a unified computational framework for unbiased and comparable measurement of the S:A ratios of multiple species. We also tested the evolution of dosage compensation more directly by assessing changes in the expression levels of the current sex-linked genes relative to those of the ancestral sex-linked genes. We found that in mammals and birds, the S:A ratio is approximately 0.5, while in insects, fishes and flatworms, the S:A ratio is approximately 1. Further analysis showed that the fraction of dosage-sensitive housekeeping genes on the sex chromosome is significantly correlated with the S:A ratio. In addition, the degree of degradation of the Y chromosome may be responsible for the change in the S:A ratio in mammals without a dosage-compensation mechanism. Our observations offer unequivocal support for the sex chromosome insensitivity hypothesis in animals and suggest that the dosage sensitivity states of sex chromosomes is a major factor underlying different evolutionary strategies of dosage compensation.

evolutionary biology↗

bioRxiv2020

Berberine reverses multidrug resistance in Candida albicans by hijacking the drug efflux pump Mdr1p

Clinical use of antimicrobials faces great challenges from the emergence of multidrug resistant (MDR) pathogens. The overexpression of drug efflux pumps is one of the major contributors to MDR. It is considered as a promising approach to overcome MDR by reversing the function of drug efflux pumps. In the life-threatening fungal pathogen Candida albicans, the major facilitator superfamily (MFS) transporter Mdr1p can excrete many structurally unrelated antifungals, leading to multidrug resistance. Here we report a counterintuitive case of reversing multidrug resistance in C. albicans by using a natural product berberine to hijack the overexpressed Mdr1p for its own importation. Moreover, we illustrate that the imported berberine accumulates in mitochondria, and compromises the mitochondrial function by impairing mitochondrial membrane potential and mitochondrial Complex I. It results in the selective elimination of Mdr1p overexpressed C. albicans cells. Furthermore, we show that berberine treatment can prolong the mean survival time (MST) of mice with a blood-borne dissemination of Mdr1p overexpressed multidrug resistant candidiasis. This study provided a potential direction of novel anti-MDR drug discovery by screening for multidrug efflux pump converters.

microbiology↗

bioRxiv2020

Simple cloning of large natural product biosynthetic gene cluster by CRISPR/Cas12a-mediated fast direct capturing strategy

Directly cloning of biosynthetic gene clusters (BGCs) from microbial genomes has been revolutionizing the natural product-based drug discovery. However, it is still very challenging to efficiently clone, for example, large (> 80kb) and GC-rich (> 70%), streptomycete originating BGCs. In this study, we developed a simple, fast yet efficient and low-cost in vitro platform for direct cloning large BGCs from streptomycete genomic DNA, named as CAT-FISHING (CRISPR/Cas12a- and Agarose plug-based sysTem for Fast bIoSyntHetIc geNe cluster cloninG), by combining the advantages of CRISPR/Cas12a cleavage and bacterial artificial chromosome (BAC) library construction. CAT-FISHING was demonstrated by directly cloning large DNA fragments ranging from 47 to 139 kb with GC content of > 70% from the S. albus J1074 genome in a relatively efficient manner. Moreover, surugamides, encoded by a captured 87-kb BGC with GC content of 76%, was heterologously expressed in a Streptomyces chassis. These results indicate that CAT-FISHING is a powerful platform for BGCs batch cloning, which would be greatly beneficial to the natural products-based drug discovery. We believe that this system will lead a renaissance of interest in microorganisms as a source for drug development.

synthetic biology↗

bioRxiv2020

Characterization of a gene-trap knockout mouse model of Scn2a encoding voltage-gated sodium channel Nav1.2

Recent large-scale genomic studies have revealed SCN2A as one of the most frequently mutated gene in patients with neurodevelopmental disorders including autism spectrum disorder and intellectual disability. SCN2A encodes for voltage-gated sodium channel isoform 1.2 (Nav1.2), which is mainly expressed in the central nervous system and responsible for the propagation of neuronal action potentials. Homozygous knockout (null) of Scn2a is perinatal lethal, whereas heterozygous knockout of Scn2a results in mild behavior abnormalities. To achieve a more substantial, but not complete, reduction of Scn2a expression, we characterized a Scn2a deficient mouse model using a targeted gene trap knockout (gtKO) strategy to recapitulate loss-of-function SCN2A disorders. This model produces viable homozygous mice (Scn2agtKO/gtKO) that can survive to adulthood, with markedly low but detectable Nav1.2 expression. Although Scn2agtKO/gtKO adult mice possess normal olfactory, taste, hearing, and mechanical sensitivity, they have decreased thermal and cold tolerance. Innate behaviors are profoundly impaired including impaired nesting, marble burying, and mating. These mice also have increased food and water intake with subsequent increases in fecal excretion of more but smaller fecal boli. This novel Scn2a gene trap knockout mouse thus provides a unique model to study pathophysiology associated with Scn2a deficiency.

neuroscience↗

bioRxiv2020

RND3/RhoE deficiency in preeclamptic women impairs placental mitochondrial function via regulation of the PPARgamma-UCP2 pathway

Preeclampsia (PE) is a life-threatening disease of pregnant women associated with severe hypertension, proteinuria, or multi-organ injuries. Mitochondrial-mediated placental oxidative stress plays a key role in the pathogenesis of PE. However, the underlying mechanism remains to be revealed. Here, we identify Rnd3, a small Rho GTPase, regulating placental mitochondrial reactive oxygen species (ROS). We showed that Rnd3 is down-regulated in primary trophoblasts isolated from PE patients. Loss of Rnd3 in trophoblasts resulted in excessive ROS generation, cell apoptosis, mitochondrial injury, and proton leakage from the respiratory chain. Moreover, Rnd3 overexpression partially rescues the mitochondrial defects and oxidative stress in human PE primary trophoblasts. Rnd3 physically interacts with the peroxisome proliferators-activated receptor {gamma} (PPAR{gamma}) and promotes the PPAR{gamma}-mitochondrial uncoupling protein 2 (UCP2) cascade. Forced expression of PPAR{gamma} rescues deficiency of Rnd3-mediated mitochondrial dysfunction. We conclude that Rnd3 acts as a novel protective factor in placental mitochondria through PPAR{gamma}-UCP2 signaling and highlight that downregulation of Rnd3 is a potential factor involved in PE pathogenesis.

pathology↗

bioRxiv2020

Predicting Antibody Developability from Sequence using Machine Learning

Antibodies are prominent therapeutic agents but costly to develop. Existing approaches to predict developability depend on structure, which requires expensive laboratory or computational work to obtain. To address this issue, we present a machine learning pipeline to predict developability from sequence alone using physicochemical and learned embedding features. Our approach achieves high sensitivity and specificity on a dataset of 2400 antibodies. These results suggest that sequence is predictive of developability, enabling more efficient development of antibodies.

bioinformatics↗

bioRxiv2020

A simple canonical circuitry for non-stationary normalization by inhibition to explain and predict change detection in monkey area MT

Sudden changes in visual scenes often indicate important events for behavior. For their quick and reliable detection, the brain must be capable to process these changes as independent as possible from its current activation state. In motion-selective area MT, neurons respond to instantaneous speed changes with pronounced transients, often far exceeding the expected response as derived from their speed tuning profile. We here show that this complex, non-linear behavior emerges from the combined temporal dynamics of excitation and divisive inhibition, and provide a comprehensive formal analysis. A central prediction derived from this investigation is that attention increases the steepness of the transient response irrespective of the activation state prior to a stimulus change, and irrespective of the sign of the change. Extracellular recordings of attention-dependent representation of both speed increments and decrements confirmed this prediction and suggest that improved change detection derives from basic computations in a canonical cortical circuitry.

neuroscience↗

bioRxiv2020

stLFRsv: a germline SV analysis pipeline using co-barcoded reads

Co-barcoded reads originated from long DNA fragment (mean length larger than 50Kbp) with barcodes, maintain both single base level accuracy and long range genomic information. We propose a pipeline stLFRsv to detect structure variation using co-barcoded reads. stLFRsv identifies abnormally large gaps between co-barcoded reads to detect potential breakpoints and reconstruct complex structure variations. The barcodes enabled co-barcoded reads phasing increases the signal to noise ratio and barcode sharing profiles are used to filter out false positives. We integrate the short reads SV caller smoove for smaller variations with stLFRsv. The integrated pipeline was evaluated on the well characterized genome HG002/NA24385 and obtained precision and recall rate of 74.2% and 22.3% for deletion on the whole genome. stLFR found some large variations not included in the benchmark set and verified by means of long reads or assembly. Our work indicates that co-barcoded reads technology has the potential to improve genome completeness.

bioinformatics↗

bioRxiv2020

Reward-based invigoration of sequential reaching

Seeking reward is a powerful tool for shaping human behaviour. While it has been demonstrated that reward invigorates performance of simple movements, its effect on more complex sequential actions is less clear. In addition, it is unknown why reward-based improvements for discrete actions are transient, i.e. performance gains are lost once reward is removed, but appear long lasting for sequential actions. We show across three experiments that reward invigorates sequential reaching performance. Driven by a reward-based increase in speed, movements also exhibited greater coarticulation, smoothness and a closer alignment to a minimum jerk trajectory. Critically, these performance gains were maintained across multiple days even after the removal of reward. We propose that coarticulation, the blending together of sub-movements into a single continuous action, provides a mechanism by which reward can invigorate sequential performance whilst also increasing efficiency. This change in efficiency appears essential for the retention of reward-based improvements in motor behaviour.

neuroscience↗

bioRxiv2020

Antigenic evolution on global scale reveals potential natural selection of SARS-CoV-2 by pre-existing cross-reactive T cell immunity

The mutation pattern of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is constantly changing with the places of transmission, but the reason remains to be revealed. Here, we presented the study that comprehensively analyzed the potential selective pressure of immune system restriction, which can drive mutations in circulating SARS-CoV-2 isolates. The results showed that the most common mutation sites of SARS-CoV-2 proteins were located on the non-structural protein ORF1ab and the structural protein Spike. Further analysis revealed mutations in cross-reactive epitopes between SARS-CoV-2 and seasonal coronavirus may help SARS-CoV-2 to escape cellular immunity under the long-term and large-scale community transmission. Meanwhile, the mutations on Spike protein may enhance the ability of SARS-CoV-2 to enter the host cells and escape the recognition of B-cell immunity. This study will increase the understanding of the evolutionary direction and warn about the potential immune escape ability of SARS-CoV-2, which may provide important guidance for the potential vaccine design.

bioinformatics↗