Biology subjects

Zhang, B.

Publications and source records attributed to Zhang, B..

At least 487 records · Page 27Linked to original sources

bioRxiv2021

An early signaling transcription factor regulates differentiation in Giardia

Transcriptional regulation of differentiation is critical for parasitic pathogens to adapt to environmental changes and regulate transmission. In response to encystation stimuli, Giardia lamblia cells shift from G1+S phase of the cell cycle to G2+M. By 2-4 hours, cyst wall proteins are upregulated, indicating that key regulatory steps occur within the first four hours of encystation. However, all characterized transcription factors (TFs) in Giardia have only been investigated at later time points of encystation. How TFs initiate encystation and link it to the cell cycle remains enigmatic. Here, we systematically screened six putative early upregulated TFs for nuclear localization, established their dynamic expression profiles, and determined their functional role in regulating encystation. We found a critical repressor, GLP4 that increases rapidly after 30 min of encystation stimuli and downregulates encystation specific markers, including Cyst Wall Proteins (CWPs) and enzymes in the cyst N-acetyl galactosamine (GalNAc) pathway. Depletion of GLP4 increases cyst production. Importantly, we observe that G2+M cells exhibit higher levels of CWP1 resulting from the activation of MYB2, a TF previously linked to encystation in Giardia. GLP4 upregulation occurs in G1+S cells, suggesting a role in repressing MYB2 and encystation specific genes in the G1+S phase of the cell cycle. Furthermore, we demonstrate that depletion of GLP4 upregulates MYB2 and promotes encystation while overexpression of GLP4 downregulates MYB2 and represses encystation. Together, these results suggest that Giardia employs a dose-dependent transcriptional response that involves the cell cycle regulated repressor GLP4 to orchestrate MYB2 and entry into the encystation pathway. ImportanceTransition between life cycle stages is a common feature among parasitic pathogens and its regulation must be optimized to balance persistence of infection with transmission. The early transcription factors (TFs) regulating commitment to differentiate are totally unknown in Giardia. In this work, we identified GLP4, a previously uncharacterized GARP-like TF, as an early-acting transcriptional repressor that inhibits G1+S cells from entering the encystation pathway. GLP4 is therefore a key regulator controlling the balance between proliferative growth and terminal differentiation into infective cysts.

developmental biology↗

bioRxiv2021

aCPSF1 in synergy with terminator U-tract dictates archaeal transcription termination efficiency via the KH domains recognizing U-tract

Recently, aCPSF1 was reported to function as the long-sought global transcription termination factor of archaea, while the working mechanism remains elusive. This work, through analyzing transcript-3'end-sequencing data of Methanococcus maripaludis, found positive correlations of both the terminator uridine(U)-tract and aCPSF1 with hierarchical transcription termination efficiencies (TTEs) at the genome-wide level. In vitro assays determined that aCPSF1 specifically binds to the terminator U-tract with U-tract number-related binding abilities, and in vivo assays demonstrated the two are indispensable in dictating high TTEs, revealing that aCPSF1 and the terminator U-tract in synergy determine high TTEs. The N-terminal KH domains equip aCPSF1 of specific binding to terminator U-tract and the in vivo aCPSF1-terminator U-tract synergism; aCPSF1s nuclease activity was also required for TTEs. aCPSF1 also functioned as back-up termination for transcripts with weak intrinsic terminator signals. aCPSF1 orthologs from Lokiarchaeota and Thaumarchaeota exhibited similar U-tract synergy in dictating TTEs. Therefore, aCPSF1 and the intrinsic U-rich terminator could work in a noteworthy two-in-one termination mode in Archaea, which could be widely employed by archaeal phyla; using one factor recognizing U-rich terminator signal and cleaving transcript 3'-end, the archaeal aCPSF1-dependent transcription termination could display a simplified archetypal mode of the eukaryotic RNA polymerase II termination machinery.

microbiology↗

bioRxiv2021

CellMap: Characterizing the types and composition of iPSC-derived cells from RNA-seq data

Induced pluripotent stem cell (iPSC) derived cell types are increasingly employed as in vitro model systems for drug discovery. For these studies to be meaningful, it is important to understand the reproducibility of the iPSC-derived cultures and their similarity to equivalent endogenous cell types. Single-cell and single-nucleus RNA sequencing (RNA-seq) are useful to gain such understanding, but they are expensive and time consuming, while bulk RNA-seq data can be generated quicker and at lower cost. In silico cell type decomposition is an efficient, inexpensive, and convenient alternative that can leverage bulk RNA-seq to derive more fine-grained information about these cultures. We developed CellMap, a computational tool that derives cell type profiles from publicly available single-cell and single-nucleus datasets to infer cell types in bulk RNA-seq data from iPSC-derived cell lines.

bioinformatics↗

bioRxiv2021

VP-Detector: A 3D convolutional neural network for automated macromolecule localization and classification in cryo-electron tomograms

MotivationCryo-electron tomography (Cryo-ET) with sub-tomogram averaging (STA) is indispensable when studying macromolecule structures and functions in their native environments. However, current tomographic reconstructions suffer the low signal-to-noise (SNR) ratio and the missing wedge artifacts. Hence, automatic and accurate macromolecule localization and classification become the bottleneck problem for structural determination by STA. Here, we propose a 3D multi-scale dense convolutional neural network (MSDNet) for voxel-wise annotations of tomograms. Weighted focal loss is adopted as a loss function to solve the class imbalance. The proposed network combines 3D hybrid dilated convolutions (HDC) and dense connectivity to ensure an accurate performance with relatively few trainable parameters. 3D HDC expands the receptive field without losing resolution or learning extra parameters. Dense connectivity facilitates the re-use of feature maps to generate fewer intermediate feature maps and trainable parameters. Then, we design a 3D MSDNet based approach for fully automatic macromolecule localization and classification, called VP-Detector (Voxel-wise Particle Detector). VP-Detector is efficient because classification performs on the pre-calculated coordinates instead of a sliding window. ResultsWe evaluated the VP-Detector on simulated tomograms. Compared to the state-of-the-art methods, our method achieved a competitive performance on localization with the highest F1-score. We also demonstrated that the weighted focal loss improves the classification of hard classes. We trained the network on a part of training sets to prove the availability of training on relatively small datasets. Moreover, the experiment shows that VP-Detector has a fast particle detection speed, which costs less than 14 minutes on a test tomogram. Contactzsh@amss.ac.cn, xfcui@email.sdu.edu.cn, zhangfa@ict.ac.cn Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2021

A hybridoma-derived monoclonal antibody with high homology to the aberrant myeloma light chain

The identification of antibody variable regions in the heavy (VH) and light (VL) chains from hybridomas is necessary for the production of recombinant, sequence-defined monoclonal antibodies (mAbs) and antibody derivatives. This process has received renewed attention in light of recent reports of hybridomas having unintended specificities due to the production of non-antigen specific heavy and/or light chains for the intended antigen. Here we report a surprising finding and potential pitfall in variable domain sequencing of an anti-human CD63 hybridoma. We amplified multiple VL genes from the hybridoma cDNA, including the well-known aberrant Sp2/0 myeloma VK and a unique, full-length VL. After finding that the unique VL failed to yield a functional antibody, we discovered an additional full-length sequence with surprising similarity (~95% sequence identify) to the non-translated myeloma kappa chain but with a correction of its key frameshift mutation. Expression of the recombinant mAb confirmed that this highly homologous sequence is the antigen-specific light chain. Our results highlight the complexity of PCR-based cloning of antibody genes and strategies useful for identification of correct sequences.

molecular biology↗

bioRxiv2021

Homogeneous environmental selection overturns distance-decay relationship of soil prokaryotic community

Though being fundamental to global diversity distribution, little is known about the geographic pattern of soil microorganisms across different biomes on a large scale. Here, we investigated soil prokaryotic communities from Chinese northern grasslands on a scale up to 4,000 km in both alpine and temperate biomes. Surprisingly, prokaryotic similarities increased with geographic distance after tipping points of 1,760 - 1,920 km, overturning the well-accepted distance-decay relationship and generating a significant U-shape pattern. Such U-shape pattern was likely due to decreased disparities in environmental heterogeneity along with geographic distance when across biomes, as homogeneous environmental selection dominated prokaryotic assembly based on {beta}NTI analysis. Consistently, short-term environmental heterogeneity also followed the U-shape pattern spatially, mainly attributed to dissolved nutrients. In sum, these results demonstrate that homogeneous environmental selection via dissolved nutrients overwhelmed the "distance" effect when across biomes, subverting the previously well-accepted geographic pattern for microbes on a large scale.

ecology↗

bioRxiv2021

A common SEC23B missense mutation in congenital dyserythropoietic anemia type II leads to growth restriction and symptoms of chronic pancreatitis in mice

Human loss-of-function mutations in SEC23B result in congenital dyserythropoietic anemia type II (CDAII). Complete deficiency of SEC23B in mice leads to perinatal death caused by massive degeneration of professional secretory tissues. Functions of SEC23B in postnatal mice are unclear. In this study, we generated knockout (KO) mice with deletion of exons 5 and 6 of Sec23b and knockin (KI) mice with the E109K mutation, the most common CDAII missense mutation. Despite decreased SEC23B protein level, Sec23bki/ki mice showed no obvious abnormalities. Hemizygous (Sec23bki/ko) mice exhibit a partial lethal phenotype, with only half of expected mice survive past weaning. Sec23bki/ko pancreas had exocrine insufficiency and chronic pancreatitis histology, as well as increased ER stress and apoptosis. Moreover, Sec23bki/ko mice exhibited severe growth restriction accompanied by growth hormone (GH) insensitivity, reminiscent of the Laron syndrome. Growth restriction is not associated with hepatocyte-specific Sec23b deletion, suggesting non-liver origin of the phenotype. Inflammation associated with chronic pancreatic deficiency may explain GH insensitivity in Sec23bki/ko mice. Our results indicate that phenotype severities are linked to the residual functions of SEC23B, demonstrating the importance of SEC23B in pancreatic acinar function in adult mice. The Sec23bki/ko mice provide a novel model of chronic pancreatitis and growth retardation.

cell biology↗

bioRxiv2021

Ultrapotent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants

Accumulating mutations in the SARS-CoV-2 Spike (S) protein can increase the possibility of immune escape, challenging the present COVID-19 prophylaxis and clinical interventions. Here, 3 receptor binding domain (RBD) specific monoclonal antibodies (mAbs), 58G6, 510A5 and 13G9, with high neutralizing potency blocking authentic SARS-CoV-2 virus displayed remarkable efficacy against authentic B.1.351 virus. Each of these 3 mAbs in combination with one neutralizing Ab recognizing non-competing epitope exhibited synergistic effect against authentic SARS-CoV-2 virus. Surprisingly, structural analysis revealed that 58G6 and 13G9, encoded by the IGHV1-58 and the IGKV3-20 germline genes, both recognized the steric region S470-495 on the RBD, overlapping the E484K mutation presented in B.1.351. Also, 58G6 directly bound to another region S450-458 in the RBD. Significantly, 58G6 and 510A5 both demonstrated prophylactic efficacy against authentic SARS-CoV-2 and B.1.351 viruses in the transgenic mice expressing human ACE2 (hACE2), protecting weight loss and reducing virus loads. These 2 ultrapotent neutralizing Abs can be promising candidates to fulfill the urgent needs for the prolonged COVID-19 pandemic.

immunology↗

bioRxiv2021

stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics

MotivationSingle-cell RNA sequencing (scRNA-seq) techniques have revolutionized the investigation of tran-scriptomic landscape in individual cells. Recent advancements in spatial transcriptomic technologies further enable gene expression profiling and spatial organization mapping of cells simultaneously. Among the tech-nologies, imaging-based methods can offer higher spatial resolutions, while they are limited by either the small number of genes imaged or the low gene detection sensitivity. Although several methods have been proposed for enhancing spatially resolved transcriptomics, inadequate accuracy of gene expression prediction and in-sufficient ability of cell-population identification still impede the applications of these methods. ResultsWe propose stPlus, a reference-based method that leverages information in scRNA-seq data to enhance spatial transcriptomics. Based on an auto-encoder with a carefully tailored loss function, stPlus performs joint embedding and predicts spatial gene expression via a weighted k-NN. stPlus outperforms baseline meth-ods with higher gene-wise and cell-wise Spearman correlation coefficients. We also introduce a clustering-based approach to assess the enhancement performance systematically. Using the data enhanced by stPlus, cell populations can be better identified than using the measured data. The predicted expression of genes unique to scRNA-seq data can also well characterize spatial cell heterogeneity. Besides, stPlus is robust and scalable to datasets of diverse gene detection sensitivity levels, sample sizes, and number of spatially meas-ured genes. We anticipate stPlus will facilitate the analysis of spatial transcriptomics. AvailabilitystPlus with detailed documents is freely accessible at http://health.tsinghua.edu.cn/software/stPlus/ and the source code is openly available on https://github.com/xy-chen16/stPlus. Contactruijiang@tsinghua.edu.cn Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2021

YhcB coordinates peptidoglycan and LPS biogenesis with phospholipid synthesis during Escherichia coli cell growth.

The cell envelope is essential for viability in all kingdoms of life. It retains enzymes and substrates within a confined space while providing a protective barrier to the external environment. Destabilising the envelope of bacterial pathogens is a common strategy employed by antimicrobial treatment. However, even in one of the most well studied organisms, Escherichia coli, there remain gaps in our understanding of how the synthesis of the successive layers of the cell envelope are coordinated during growth and cell division. Here, we used a whole genome phenotypic screen to identify mutants with a defective cell envelope. We report that loss of yhcB, a conserved gene of unknown function, results in loss of envelope stability, increased cell permeability and dysregulated control of cell size. Using whole genome transposon mutagenesis strategies we report the complete genetic interaction network of yhcB, revealing all genes with a synthetic negative and a synthetic positive relationship. These genes include those previously reported to have a role in cell envelope biogenesis. Surprisingly, we identified genes previously annotated as essential that became non-essential in a {Delta}yhcB background. Subsequent analyses suggest that YhcB sits at the junction of several envelope biosynthetic pathways coordinating the spatiotemporal growth of the cell, highlighting YhcB as an as yet unexplored antimicrobial target.

microbiology↗

bioRxiv2021

Statistical learning of frequent distractor locations in visual search involves regional signal suppression in early visual cortex

Observers can learn the locations where salient distractors appear frequently to reduce potential interference - an effect attributed to better suppression of distractors at frequent locations. But how distractor suppression is implemented in the visual cortex and frontoparietal attention networks remains unclear. We used fMRI and a regional distractor-location learning paradigm (Sauter et al. 2018, 2020) with two types of distractors defined in either the same (orientation) or a different (colour) dimension to the target to investigate this issue. fMRI results showed that BOLD signals in early visual cortex were significantly reduced for distractors (as well as targets) occurring at the frequent versus rare locations, mirroring behavioural patterns. This reduction was more robust with same-dimension distractors. Crucially, behavioural interference was correlated with distractor-evoked visual activity only for same- (but not different-) dimension distractors. Moreover, with different- (but not same-) dimension distractors, a colour-processing area within the fusiform gyrus was activated more when a colour distractor was present versus absent and with a distractor occurring at a rare versus frequent location. These results support statistical learning of frequent distractor locations involving regional suppression in the early visual cortex and point to differential neural mechanisms of distractor handling with different-versus same-dimension distractors.

neuroscience↗

bioRxiv2021

Transcriptional Inactivation of TP53 and the BMP Pathway Mediates Therapy-induced Dedifferentiation and Metastasis in Prostate Cancer

Unsupervised clustering and deconvolution analysis identifies a novel subtype of M-CRPC endowed with hybrid epithelial/mesenchymal (E/M) and luminal progenitor-like traits (Mesenchymal and Stem-like PC, MSPC). Analysis of patient datasets and mechanistic studies indicate that MSPC arises as a consequence of therapy-induced lineage plasticity. AR blockade instigates two separate and complementary processes: 1) transcriptional silencing of TP53 and hence acquisition of hybrid E/M and stem-like traits; and 2) inhibition of the BMP signaling, which promotes resistance to the pro-apoptotic and anti-proliferative effects of AR inhibition. The drug-tolerant prostate cancer cells generated through reprogramming are rescued by neuregulin and generate metastases in mice. Combined inhibition of HER2/3 and AR or mTORC1 exhibit efficacy in preclinical models of mixed ARPC/MSPC or MSPC, respectively. These results identify a novel subtype of M-CRPC, trace its origin to therapy-induced lineage plasticity, and reveal its dependency on HER2/3 signaling.

cancer biology↗

bioRxiv2021

Single-cell atlas of progressive supranuclear palsy reveals a distinct hybrid glial cell population

Progressive supranuclear palsy (PSP) is a neurodegenerative disorder whose molecular complexity at a single cell level has not been evaluated. Here we analyzed 45,559 high quality nuclei from the subthalamic nucleus and associated basal ganglia regions from post-mortem human PSP brains with varying degrees of tau pathology compared to controls (n=3 per group). We identified novel astrocyte-oligodendrocyte hybrid cell populations that overexpress neurotropic factors in conjunction with suppression of the unfolded protein response pathway. Notably, trajectory analysis identified subpopulations of hybrid cells with distinct astrocytic, oligodendrocytic and hybrid molecular states that change from a neuroprotective hybrid cell to an astrocytic cell with impaired homeostatic function in PSP. Our single nucleus transcriptomic data provides insights into the cell-type-specific contributions to the disease for investigating the molecular and cellular basis of PSP.

neuroscience↗

bioRxiv2021

DDN2.0: R and Python packages for differential dependency network analysis of biological systems

Data-driven differential dependency network analysis identifies in a complex and often unknown overall molecular circuitry a network of differentially connected molecular entities (pairwise selective coupling or uncoupling depending on the specific phenotypes or experimental conditions) (Herrington, et al. 2018; Zhang, et al., 2009; Zhang and Wang, 2010; Zhang, et al., 2016). Such differential dependency networks are typically used to assist in the inference of potential key pathways. Based on our previously developed Differential Dependency Network (DDN) method, we report here the fully implemented R and Python software tool packages for public use. The DDN2.0 algorithm uses a fused Lasso model and block-wise coordinate descent to estimate both the common and differential edges of dependency networks. The identified DDN can help to provide plausible interpretation of data, gain new insight of disease biology, and generate novel hypotheses for further validation and investigations. To address the imbalanced sample group problem, we propose a sample-size normalized formulation to correct systematic bias. To address high computational complexity, we propose four strategies to accelerate DDN2.0 learning. The experimental results show that new DDN2.0+ learning speed with combined four accelerating strategies is hundreds of times faster than that of DDN2.0 algorithm on medium-sized data (Fu, 2019). To detect intra-omics and inter-omics network rewiring, we propose multiDDN using a multi-layer signaling model to integrate multi-omics data. The simulation study shows that the multiDDN method can achieve higher accuracy of detecting network rewiring (Fu, 2019).

bioinformatics↗

bioRxiv2021

Decreased biofilm formation in Proteus mirabilis after short-term exposure to a simulated microgravity environment

BackgroundMicrobes threaten human health in space exploration. Studies have shown that P. mirabilis has been found in human space habitats. In addition, the biological characteristics of P. mirabilis in space have been studied unconditionally. The simulated microgravity environment provides a platform for understanding the changes in the biological characteristics of P. mirabilis. ObjectiveThis study intends to explore the effect of simulated microgravity on P. mirabilis, the formation of P. mirabilis biofilm and its related mechanism. MethodsThe strange deformable rods were cultured continuously for 14 days under the microgravity simulated by (HARVs) in a high-aspect ratio vessels. The morphology, growth rate, metabolism and biofilm formation of the strain were measured, and the phenotypic changes of P. mirabilis were evaluated. Transcriptome sequencing was used to detect differentially expressed genes under simulated microgravity and compared with phenotype. ResultsThe growth rate, metabolic ability and biofilm forming ability of P. mirabilis were lower than those of normal gravity culture under the condition of simulated microgravity. Further analysis showed that the decrease of growth rate, metabolic ability and biofilm forming ability may be caused by the down-regulation of related genes (pstS,sodB and fumC). ConclusionIt provides a certain reference for the prevention and treatment of P. mirabilis infection in the future space station by exploring the effect of simulated microgravity exposure on P. mirabilis.

microbiology↗

bioRxiv2021

Sex disparities in influenza: a multiscale network analysis

Sex differences in the pathogenesis of infectious diseases due to differential immune responses between females and males have been well documented for multiple pathogens. However, the molecular mechanism underlying the observed sex differences in influenza virus infection remains poorly understood. In this study, we used a network-based approach to characterize the blood transcriptome collected over the course of infection with influenza A virus from female and male ferrets to dissect sex-biased gene expression. We identified significant differences in the temporal dynamics and regulation of immune responses between females and males. Our results elucidate sex-differentiated pathways involved in the unfolded protein response (UPR), lipid metabolism, and inflammatory responses, including a female-biased IRE1/XBP1 activation and male-biased crosstalk between metabolic reprogramming and IL-1 and AP-1 pathways. Overall, our study provides molecular insights into sex differences in transcriptional regulation of immune responses and contributes to a better understanding of sex bias in influenza pathogenesis.

systems biology↗

bioRxiv2021

Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans

Condensins are molecular motors that compact DNA via linear translocation. In C. elegans, the X-chromosome harbors a specialized condensin that participates in dosage compensation (DC). Condensin DC is recruited to and spreads from a small number of recruit elements on the X-chromosome (rex) and is required for the formation of topologically associating domains (TADs). We take advantage of autosomes that are largely devoid of condensin DC and TADs to address how rex sites and condensin DC give rise to the formation of TADs. When an autosome and X-chromosome are physically fused, despite the spreading of condensin DC into the autosome, no TAD was created. Insertion of a strong rex on the X-chromosome results in the TAD boundary formation regardless of sequence orientation. When the same rex is inserted on an autosome, despite condensin DC recruitment, there was no spreading or features of a TAD. On the other hand, when a "super rex" composed of six rex sites or three separate rex sites are inserted on an autosome, recruitment and spreading of condensin DC led to formation of TADs. Therefore, recruitment to and spreading from rex sites are necessary and sufficient for recapitulating loop-anchored TADs observed on the X-chromosome. Together our data suggest a model in which rex sites are both loading sites and bidirectional barriers for condensin DC, a one-sided loop-extruder with movable inactive anchor.

genomics↗

bioRxiv2021

Single-stranded nucleic acid sensing and coacervation by linker histone H1

The linker histone H1 is the most abundant group of eukaryotic chromatin-binding proteins. The mechanism underlying the diverse physiological functions of H1 remains unclear. Here we used single-molecule fluorescence and force microscopy to observe the behavior of H1 on DNA under different tensions. Unexpectedly, we found that H1 coalesces around nascent ssDNA. Molecular dynamics simulations revealed that multivalent and transient interactions between H1 and ssDNA mediate their phase separation. We further showed that longer and unpaired nucleic acids result in more viscous, gel-like H1 droplets. Finally, we imaged H1 puncta in cells under normal and stressed conditions and observed that RPA and H1 occupy separate nuclear regions. Overall, our results provide a new perspective to understanding the role of H1 in genome organization and maintenance.

biophysics↗