Biology subjects

Zhang, M.

Publications and source records attributed to Zhang, M..

At least 667 records · Page 37Linked to original sources

bioRxiv2020

A fluorescent L-2-hydroxyglutarate biosensor

L-2-Hydroxyglutarate (L-2-HG) plays important roles in diverse physiological processes, such as carbon starvation response, tumorigenesis, and hypoxic adaptation. Despite its importance and intensively studied metabolism, regulation of L-2-HG metabolism remains poorly understood and a regulator specifically responded to L-2-HG has never been identified. Based on the genomic neighborhood analysis of the gene encoding L-2-HG oxidase (LhgO), LhgR, which represses the transcription of lhgO, was identified in Pseudomonas putida W619 in this study. LhgR was demonstrated to recognize L-2-HG as its specific effector molecule, and this allosteric transcription factor was then used as a biorecognition element for construction of L-2-HG-sensing FRET sensor. The newly developed L-2-HG sensor can conveniently monitor the concentrations of L-2-HG in various biological samples. In addition to bacterial L-2-HG generation during carbon starvation, biological functions of the L-2-HG dehydrogenase and hypoxia induced L-2-HG accumulation were also revealed by using the L-2-HG sensor in human cells.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biochemistry↗

bioRxiv2020

Astrocytes express DMT1 and transferrin receptors, which transport iron thus activating Ca2+ signalling: possible role in neuroprotection against iron overload?

ABSTRACTIron is the fundamental element for numerous physiological functions. Reduced ferrous (Fe2+) and oxidized ferric (Fe3+) are the two ionized iron states in the living organisms. In the cell membrane, divalent metal ion transporter 1 (DMT1) is responsible for cellular uptake of Fe2+, whereas transferrin receptors (TFR) carry transferrin (TF)-bound Fe3+. In this study we performed, for the first time, detailed analysis of the action of Fe ions on cytoplasmic free calcium ion concentration ([Ca2+]i) in astrocytes. Using qPCR and immunocytochemistry we identified DMT1 and TFR in astrocytes in primary cultures, in acutely isolated astrocytes and in brain tissue preparations; in situ both DMT1 and TFR are concentrated in astroglial perivascular endfeet. Administration of Fe2+ or Fe3+ in low μM concentrations evoked Ca2+ signals in astrocytes in vitro and in vivo. Iron ions triggered increase in [Ca2+]i by acting through two distinct molecular cascades. Uptake of Fe2+ by DMT1 inhibited astroglial Na+-K+-ATPase (NKA), which led to an elevation in cytoplasmic Na+ concentration (as measured by SBFI probe), thus reversing Na+/Ca2+ exchanger (NCX) thereby generating Ca2+ influx. Uptake of Fe3+ by TF-TFR stimulated phospholipase C to produce inositol 1,4,5-trisphosphate (InsP3), thus trigering InsP3 receptor-mediated Ca2+ release from the endoplasmic reticulum. Iron-induced Ca2+ signals promote astroglial release of arachidonic acid and prostaglandin E2 cytokines by activating cytosolic phospholipase A2 (cPLA2) and NF-κB signalling cascade. In summary, these findings reveal new mechanisms of iron-induced astrocytic signalling operational in conditions of iron overload, in response to which astrocytes actively accumulate excessive iron and activate neuroprotective pathways.Competing Interest StatementThe authors have declared no competing interest.View Full Text

molecular biology↗

bioRxiv2020

Biomimetic system design for engineering biofidelic 3-D respiratory tissues in vitro

Objective The structural and functional complexity of the respiratory system present significant challenges to capturing conditions vital for maintaining phenotypic cellular functions in vitro. Here we report a unique tissue engineering system that enables respiratory constructs to be cultured under physiological loading at an air-liquid interface (ALI).Methods The system consists of a porous poly-e-caprolactone scaffold mounted in a well insert, which articulates via magnetic coupling with a linear actuator device to strain attached scaffolds through a sterile barrier. For proof of concept, NCI-H460 human carcinoma cells were seeded on scaffold inserts which were subjected to 5-15% cyclic tensile strain at 0.2Hz within a six well plate. The dynamic constructs were cultured at an ALI in a standard incubator for up to 10 days along with unstimulated (static) ALI and static submerged control groups.Results High (near-100%) cell seeding efficiency was achieved within the scaffold-strain device. Both dynamic and static ALI groups yielded higher cell densities compared to the submerged control for all time points. Distinctly different patterns in cellular growth and behaviour between dynamic air-liquid interface and conventional static submerged culture groups were revealed by nuclei staining, where the actuated group displayed more uniform cellular distribution throughout the construct compared to both static controls.Conclusion Air-liquid interface culture and physiological strain are important for engineering respiratory tissue models.Significance The system described allows scalable and replicable culture of 3-D tissue engineered respiratory models under biologically-relevant conditions.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioengineering↗

bioRxiv2020

Fungi ligE-type glutathione S-transferases horizontally transferred into plants and a protozoan

Horizontal gene transfers (HGT) were considered as common evolution approaches for organisms. However, most HGT especially those HGT among distant species, like microbes to plants, were over-estimated because they were just identified based on the criteria of Blast searches and gene tree-species tree reconciliation. Recently, a ligE-type glutathione S-transferase (GST), Fhb7-GST was considered as an HGT from Epichloe to Thinopyrum elongatum. To confirm and clarify the occurring patterns of this HGT, homologue searches were conducted. Although TeFhb7-GST was not found in other plants, ligE-GSTs were found in not only plants but also an ameba protozoan. Additionally, ligE-GSTs were likely to horizontally transfer from fungi to other organisms. LigE-GSTs evolve in various fungi, but they only exist in some liverworts and green algae. Interestingly, all these ligE-GST genes in these plants share more than 90% similarities with that from fungus Coniosporium apollinis. More than that, the protozoan homologue from Acanthamoeba castellanii have 94.9% similiarity with that from C. apollinis. Actually, only a few substitutions were found in two homologues except a 111-bp lost in A. castellanii ligE-GST. All these results suggested HGT is an important evolutionary method for all organisms. Notably, natural HGT remind us to reevaluate the transgenic crops.

evolutionary biology↗

bioRxiv2020

A Mild Keratin 1 Decrease Leads to Cell Death and Increased Oxidative Stress in B16-F10 Melanoma Cell Lines

Keratins play multiple significant biological roles in epithelium. K1 / keratin 10 (K10) heterodimer is a hallmarker for keratinocyte differentiation. While keratins are absent in normal melanocyte, keratins have been found in both melanoma cell lines and human melanoma. The biological significance of the keratins in melanoma cells has remained unclear. In our current study we applied K1 siRNA to investigate the biological significance of the K1 in B16-F10 melanoma cells. We found that as low as a 16% decrease in the K1 level led to significant increases in both apoptosis and necrosis of the cells. Moreover, the mild K1 decrease led to significant increases in both dichlorofluorescein (DCF) and ethidium signals - two indicators of oxidative stress - in the cells. Collectively, our findings have provided the first evidence indicating both a critical role of the K1 in maintaining the survival of melanoma cells and an important role of the K1 in modulating the oxidative stress state of the cells. These findings have exposed new functions of keratins in cancer cells, suggesting that K1 may become a novel therapeutic target for melanoma.

cancer biology↗

bioRxiv2020

Cryo-EM structure of an activated GPCR-G protein complex in lipid nanodiscs

G protein coupled receptors (GPCRs) are the largest superfamily of transmembrane proteins and the targets of over 30% of currently marketed pharmaceuticals1,2. Although several structures have been solved for GPCR-G protein complexes3-17, structural studies of the complex in a physiological lipid membrane environment are lacking. Additionally, most previous studies required additional antibodies/nanobodies and/or engineered G proteins for complex stabilization. In the absence of a native complex structure, the underlying mechanism of G protein activation leading to GDP/GTP exchange remains unclear. Here, we report cryo-EM structures of lipid bilayer-bound complexes of neurotensin, neurotensin receptor 1, and Gi1{beta}1{gamma}1 protein in two conformational states, resolved to 4.1 and 4.2 [A] resolution. The structures were determined without any stabilizing antibodies/nanobodies, and thus provide a native-like platform for understanding the structural basis of GPCR-G protein complex formation. Our structures reveal an extended network of protein-protein interactions at the GPCR-G protein interface compared to in detergent micelles, defining roles for the lipid membrane in modulating the structure and dynamics of complex formation, and providing a molecular explanation for the stronger interaction between GPCR and G protein in lipid bilayers. We propose a detailed allosteric mechanism for GDP release, providing new insights into the activation of G proteins for downstream signaling under near native conditions.

molecular biology↗

bioRxiv2020

Assessment of metagenomic sequencing and qPCR for detection of influenza D virus in bovine respiratory tract samples

High throughput sequencing is currently revolutionizing the genomics field and providing new approaches to the detection and characterization of microorganisms. The objective of this study was to assess the detection of influenza D virus (IDV) in bovine respiratory tract samples using two sequencing platforms (MiSeq and Nanopore (GridION)), and species-specific qPCR. An IDV-specific qPCR was performed on 232 samples (116 nasal swabs and 116 tracheal washes) that had been previously subject to virome sequencing using MiSeq. Nanopore sequencing was performed on 19 samples positive for IDV by either MiSeq or qPCR. Nanopore sequence data was analyzed by two bioinformatics methods: Whats In My Pot (WIMP, on the EPI2ME platform), and an in-house developed analysis pipeline. The agreement of IDV detection between qPCR and MiSeq was 82.3%, between qPCR and Nanopore was 57.9% (in-house) and 84.2% (WIMP), and between MiSeq and Nanopore was 89.5% (in-house) and 73.7% (WIMP). IDV was detected by MiSeq in 14 of 17 IDV qPCR-positive samples with Cq (cycle quantification) values below 31, despite multiplexing 50 samples for sequencing. When qPCR was regarded as the gold standard, the sensitivity and specificity of MiSeq sequence detection were 28.3% and 98.9%, respectively. We conclude that both MiSeq and Nanopore sequencing are capable of detecting IDV in clinical specimens with a range of Cq values. Sensitivity may be further improved by optimizing sequence data analysis, improving virus enrichment, or reducing the degree of multiplexing.

microbiology↗

bioRxiv2020

VirusDIP: Virus Data Integration Platform

MotivationThe Coronavirus Disease 2019 (COVID-19) pandemic poses a huge threat to human public health. Viral sequence data plays an important role in the scientific prevention and control of epidemics. A comprehensive virus database will be vital useful for virus data retrieval and deep analysis. To promote sharing of virus data, several virus databases and related analyzing tools have been created. ResultsTo facilitate virus research and promote the global sharing of virus data, we present here VirusDIP, a one-stop service platform for archive, integration, access, analysis of virus data. It accepts the submission of viral sequence data from all over the world and currently integrates data resources from the National GeneBank Database (CNGBdb), Global initiative on sharing all influenza data (GISAID), and National Center for Biotechnology Information (NCBI). Moreover, based on the comprehensive data resources, BLAST sequence alignment tool and multi-party security computing tools are deployed for multi-sequence alignment, phylogenetic tree building and global trusted sharing. VirusDIP is gradually establishing cooperation with more databases, and paving the way for the analysis of virus origin and evolution. All public data in VirusDIP are freely available for all researchers worldwide. Availabilityhttps://db.cngb.org/virus/ Contactweixiaofeng@cngb.org

bioinformatics↗

bioRxiv2020

Molecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomics

A mammalian brain is comprised of numerous cell types organized in an intricate manner to form functional neural circuits. Single-cell RNA sequencing provides a powerful approach to identify cell types based on their gene expression profiles and has revealed many distinct cell populations in the brain1-3. Single-cell epigenomic profiling4,5 further provides information on gene-regulatory signatures of different cell types. Understanding how different cell types contribute to brain function, however, requires knowledge of their spatial organization and connectivity, which is not preserved in sequencing-based methods that involve cell dissociation3,6. Here, we used an in situ single-cell transcriptome-imaging method, multiplexed error-robust fluorescence in situ hybridization (MERFISH)7, to generate a molecularly defined and spatially resolved cell atlas of the mouse primary motor cortex (MOp). We profiled [~]300,000 cells in the MOp, identified 95 neuronal and non-neuronal cell clusters, and revealed a complex spatial map in which not only excitatory neuronal clusters but also most inhibitory neuronal clusters adopted layered organizations. Notably, intratelencephalic (IT) cells, the largest branch of neurons in the MOp, formed a continuous spectrum of cells with gradual changes in both gene expression profiles and cortical depth positions in a highly correlated manner. Furthermore, we integrated MERFISH with retrograde tracing to probe the projection targets for different MOp neuronal cell types and found that projections of MOp neurons to other cortical regions formed a many-to-many network with each target region receiving input preferentially from a different composition of IT clusters. Overall, our results provide a high-resolution spatial and projection map of molecularly defined cell types in the MOp. We anticipate that the imaging platform described here can be broadly applied to create high-resolution cell atlases of a wide range of systems.

neuroscience↗

bioRxiv2020

Immune Response Drives Outcomes in Prostate Cancer: Implications for Immunotherapy

BackgroundThe heterogeneity of the immune microenvironment leads to the different response results of immune checkpoint blockade therapy. We aimed to propose a robust molecular classification of prostate cancer microenvironment to identify ideal patients for delivering effective immunotherapy. MethodsA total of 1,557 prostate cancer patients were enrolled in the current study, including 69 real-world samples from the AHMU-PC cohort. Non-negative matrix factorization algorithm was employed to virtually microdissect the patients to immune and non-immune subclasses. The patients in the immune class were dichotomized to immune activated and suppressed subtypes by the nearest template prediction of activated stroma signature. The curative effects of different immune subclasses in response to immunotherapy were also predicted. ResultsWe termed the newly identified molecular class of tumors as "immune class", which was characterized by a high enrichment of T cell, B cell, NK cell, macrophage associated signatures, etc., compared with the non-immune class (all, P < 0.05). Subsequently, the immune class was subclassified into immune activated and suppressed subtypes determined by the activation status of WNT/TGF-{beta}, TGF-{beta}1, and C-ECM signatures. As a result, around 14.9% to 24.3% of overall patients belonged to the immune activated subgroup, and they were proved with the favorable recurrence-free survival outcomes than others and showed potential curative effects in response to the anti-PD-1/PD-L1 immunotherapy. ConclusionOur study identifies a novel immune class in prostate cancer, which is further described by active or exhausted immune responses. These findings provide novel insights into tailoring immunotherapeutic strategies for different prostate cancer subgroups. Highlights{blacksquare} Immunotherapy could trigger a durable response in advanced prostate cancer, but it only benefits a minority of patients; {blacksquare}Immune response drives recurrence-free survival outcomes in prostate cancer; {blacksquare}The robust molecular classification system helps identify more ideal patients for delivering anti-PD-1/PD-L1 immunotherapy.

immunology↗

bioRxiv2020

Non-Invasive Single-Cell Morphometry in Living Bacterial Biofilms

Fluorescence microscopy enables spatial and temporal measurements of live cells and cellular communities. However, this potential has not yet been fully realized for investigations of individual cell behaviors and phenotypic changes in dense, three-dimensional (3D) bacterial biofilms. Accurate cell detection and cellular shape measurement in densely packed biofilms are challenging because of the limited resolution and low signal to background ratios (SBRs) in fluorescence microscopy images. In this work, we present Bacterial Cell Morphometry 3D (BCM3D), an image analysis workflow that combines deep learning with mathematical image analysis to accurately segment and classify single bacterial cells in 3D fluorescence images. In BCM3D, deep convolutional neural networks (CNNs) are trained using simulated biofilm images with experimentally realistic SBRs, cell densities, labeling methods, and cell shapes. We systematically evaluate the segmentation accuracy of BCM3D using both simulated and experimental images. Compared to state-of-the-art bacterial cell segmentation approaches, BCM3D consistently achieves higher segmentation accuracy and further enables automated morphometric cell classifications in multi-population biofilms.

microbiology↗

bioRxiv2020

In-Vivo Toxicity Studies and In-Vitro Inactivation of SARS-CoV-2 by Povidone-iodine In-situ Gel Forming Formulations

To curb the spread of SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, we characterize the virucidal activity of long-acting Povidone Iodine (PVP-I) compositions developed using an in-situ gel forming technology. The PVP-I gel forming nasal spray (IVIEW-1503) and PVP-I gel forming ophthalmic eye drop (IVIEW-1201) rapidly inactivated SARS-CoV-2, inhibiting the viral infection of VERO76 cells. No toxicity was observed for the PVP-I formulations. Significant inactivation was noted with preincubation of the virus with these PVP-I formulations at the lowest concentrations tested. It has been demonstrated that both PVP-I formulations can inactivate SARS-CoV-2 virus efficiently in both a dose-dependent and a time-dependent manner. These results suggest IVIEW-1503 and IVIEW-1201 could be potential agents to reduce or prevent the transmission of the virus through the nasal cavity and the eye, respectively. Further studies are needed to clinically evaluate these formulations in early-stage COVID-19 patients.

microbiology↗

bioRxiv2020

Non-canonical proline-tyrosine interactions with multiple host proteins regulate Ebola virus infection

The Ebola virus VP30 protein interacts with the viral nucleoprotein and with host protein RBBP6 via PPxPxY motifs. In these interactions the largely alpha-helical carboxy-terminal domain of the EBOV VP30 engages with the motif such that the prolines adopt non-canonical orientations, as compared to other proline-rich motifs. Affinity tag-purification mass spectrometry identified additional PPxPxY-containing host proteins, including hnRNP L, hnRNPUL1 and PEG10, as VP30 interactors. Of these, hnRNP L and PEG10, like RBBP6, inhibit viral RNA synthesis and EBOV replication, whereas hnRNPUL1 enhances. Further, double knockdown studies support additive effects of RBBP6 and hnRNP L. Binding studies demonstrate variable capacity of PPxPxY motifs to bind VP30 and the extended motif PxPPPPxY is demonstrated to confer optimal binding and to inhibit RNA synthesis, with the fifth proline and the tyrosine being most critical. Competition binding and hydrogen-deuterium exchange studies demonstrate that each protein binds a similar interface on VP30 and impacts VP30 phosphorylation. VP30 therefore represents a novel proline recognition domain that allows multiple host proteins to target a single viral protein-protein interface to modulate viral transcription.

microbiology↗

bioRxiv2020

Lipid Droplet Is an Ancient and Inheritable Organelle in Bacteria

Lipid droplet (LD) is a monolayer phospholipid membrane-bound organelle found in all eukaryotes and several prokaryotes which plays key roles in cellular lipid homeostasis and human health. The origin and evolution of the organelle remains unknown. Here, we report that through screening over 660 bacteria using biophysical and biochemical methods, plus LD isolation and proteomic tool, LDs were identified in most of these microbes, affiliated with five main bacterial phyla. Moreover, LDs were also identified in E. coli overexpressing lipid synthesis enzymes, indicating that bacteria without detectable LDs possessed the ability of LD biogenesis. The similarity of isolated LDs from representative strains and evolutionary analysis of LD major protein PspA demonstrate that LDs were conserved in bacteria. Furthermore, time-lapse imaging revealed that LDs were inheritable accompanying with bacterial growth and division. Finally, a common ancestor of LD-containing bacteria was predicted to originate 3.19 billion years ago by a phylogenetic analysis. Our findings suggest that LD is a widespread and inheritable organelle from an ancient common ancestor.

cell biology↗

bioRxiv2020

LiBis: An ultrasensitive alignment method for low-input bisulfite sequencing

The cell-free DNA (cfDNA) methylation profile in liquid biopsies has been utilized to diagnose early-stage disease and estimate therapy response. However, in typical clinical settings, only very small amounts of cfDNA can be purified. Whole-genome bisulfite sequencing (WGBS) is the gold standard to measure DNA methylation; however, WGBS using small amounts of fragmented DNA introduces a critical challenge for data analysis, namely a low mapping ratio. This, in turn, generates low sequencing depth and low coverage for CpG sites genome wide. The lack of informative CpGs has become a bottleneck for the clinical application of cfDNA-based WGBS assays. Hence, we developed LiBis (Low-input Bisulfite Sequencing), a novel method for low-input WGBS data alignment. By dynamically clipping initially unmapped reads and remapping clipped fragments, we judiciously rescued those reads and uniquely aligned them to the genome. By substantially increasing the mapping ratio by up to 88%, LiBis dramatically improved the number of informative CpGs and the precision in quantifying the methylation status of individual CpG sites. The high sensitivity and cost effectiveness afforded by LiBis for low-input samples will allow the discovery of genetic and epigenetic features suitable for downstream analysis and biomarker identification using liquid biopsy.Competing Interest StatementThe authors have declared no competing interest.List of AbbreviationsLiBislow-input bisulfite sequencing alignmentcfDNAcell-free DNAWGBSwhole-genome bisulfite sequencingCpGcytosine nucleotide followed by a guanine nucleotidectDNAcirculating tumor DNAHTMLHyperText Markup LanguageHPVHuman papillomavirusView Full Text

bioinformatics↗

bioRxiv2020

Complexity of resting brain dynamics shaped by multiscale structural constraints

The brain is a complex system exhibiting ever-evolving activity patterns without any external inputs or tasks. Such intrinsic dynamics (or lack thereof) are thought to play crucial roles in typical as well as atypical cognitive functioning. Linking the ever-changing intrinsic dynamics to the rather static anatomy is a challenging endeavor. Dynamical systems models are important tools for understanding how structure and function are linked in the brain. Here, we provide a novel modeling framework to examine such structure-function relations. Our deterministic approach complements previous modeling frameworks, which typically focus on noise-driven (or stochastic) dynamics near a single attractor. We examine the overall organizations of and coordination between all putative attractors. Using our approach, we first provide evidence that examining cross-attractor coordination between brain regions could better predict human functional connectivity than examining noise-driven near-attractor dynamics. Further, we observed that structural connections across scales modulate the energy costs of such cross-attractor coordination. Overall, our work provides a systematic framework for characterizing intrinsic brain dynamics as a web of cross-attractor transitions and associated energy costs. The framework may be used to predict transitions and energy costs associated with experimental or clinical interventions.

neuroscience↗

bioRxiv2020

Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer

Neuroendocrine prostate cancer is one of the most aggressive subtypes of prostate tumor. Although much progress has been made in understanding the development of neuroendocrine prostate cancer, the cellular architecture associated with neuroendocrine differentiation in human prostate cancer remain incompletely understood. Here, we use single-cell RNA sequencing to profile the transcriptomes of 21,292 cells from needle biopsies of 6 castration-resistant prostate cancers. Our analyses reveal that all neuroendocrine tumor cells display a luminal-like epithelial phenotype. In particular, lineage trajectory analysis suggests that focal neuroendocrine differentiation exclusively originate from luminal-like malignant cells rather than basal compartment. Further tissue microarray analysis validates the generality of the luminal phenotype of neuroendocrine cells. Moreover, we uncover neuroendocrine differentiation-associated gene signatures that may help us to further explore novel intrinsic molecular mechanisms deriving neuroendocrine prostate cancer. In summary, our single-cell study provides direct evidence into the cellular states underlying neuroendocrine transdifferentiation in human prostate cancer.

cancer biology↗

bioRxiv2020

Chromosome-level genome assembly of the African pike, Hepsetus odoe

The order Characiformes is one of the largest components of the freshwater teleost fauna inhabiting exclusively in South America and Africa with great ecological and economical significance. Yet, quite limited genomic resources are available to study this group and their transatlantic vicariance. In this study we present a chromosome-level genome assembly of the African pike (Hepsetus odoe), a representative member of the African Characiformes. To this end, we generated 119, 11, and 67 Gb reads using the single tube long fragment read (stLFR), Oxford Nanopore, and Hi-C sequencing technologies, respectively. We obtained an 862.1 Mb genome assembly with the contig and scaffold N50 of 347.4 kb and 25.8 Mb, respectively. Hi-C sequencing produced 29 chromosomes with 742.5 Mb, representing 86.1% of the genome. 24,314 protein-coding genes were predicted and 23,999 (98.7%) genes were functionally annotated. The chromosomal-scale genome assembly will be useful for functional and evolutionary studies of the African pike and promote the study of Characiformes speciation and evolution.

genomics↗