Biology subjects

Zhang, S.

Publications and source records attributed to Zhang, S..

At least 919 records · Page 51Linked to original sources

bioRxiv2021

Unconventional tonicity-regulated nuclear trafficking of NFAT5 mediated by KPNB1, XPOT and RUVBL2

NFAT5 is the only known mammalian tonicity-responsive transcription factor functionally implicated in diverse physiological and pathological processes. NFAT5 activity is tightly regulated by extracellular tonicity but the underlying mechanisms remain elusive. We demonstrated that NFAT5 enters the nucleus via the nuclear pore complex. We also found that NFAT5 utilizes a non-canonical nuclear localization signal (NFAT5-NLS) for nuclear imports. siRNA screening revealed that karyopherin {beta}1 (KPNB1) drives nuclear import of NFAT5 via directly interacting with NFAT5-NLS. Proteomics analysis and siRNA screening further revealed that nuclear export of NFAT5 under hypotonicity is mediated by Exportin-T, and that it requires RuvB-Like AAA type ATPase 2 (RUVBL2) as an indispensable chaperone. Our findings have identified KPNB1 and RUVBL2 as key molecules responsible for the unconventional tonicity-regulated nucleocytoplasmic shuttling of NFAT5. These findings offer an opportunity for developing novel NFAT5 targeting strategies that are potentially useful for the treatment of diseases associated with NFAT5 dysregulation.

cell biology↗

bioRxiv2021

A single-cell transcriptomic atlas characterizes liver non-parenchymal cells in healthy and diseased mice

The heterogeneity of liver non-parenchymal cells (NPCs) is essential for liver structure and function. However, the current understanding of liver NPCs, especially in different liver diseases, remains incompletely elucidated. Here, a single-cell transcriptome atlas of 171,814 NPCs from healthy and 5 typical liver disease mouse models, including alcoholic liver disease, nonalcoholic steatohepatitis (NASH), drug-induced liver injury, cholestatic, and ischemia-reperfusion liver injury is constructed. The inter- and intra-group heterogeneity of 12 types (and numerous subtypes) of NPCs involving endothelial cells, hepatic stellate cells (HSCs), neutrophils, T cells, and mononuclear phagocytes (MPs) are summarized. A protective subtype of neutrophils characterized by Chil3high is validated and found significantly increasing only in drug-induced and cholestatic liver injury models. Transcriptional regulatory network analysis reveals disease-specific transcriptional reprogramming. Metabolic activity analysis indicates that fibrosis is accompanied by increases in glycolysis and retinol metabolism in activated HSCs and MPs. Moreover, we found that cell-cell interactions between cholangiocytes and immune cells contribute more to cholestatic liver fibrosis compared with NASH, while HSCs are more important for NASH fibrosis. Our atlas, together with an interactive website provides a systematic view of highly heterogeneous NPCs and a valuable resource to better understand pathological mechanisms underlying liver diseases.

genomics↗

bioRxiv2021

Based on the identification of tumor antigens and immune subtypes in renal clear cell carcinoma for mRNA vaccine development

BackgroundCancer vaccine based on mRNA is considered as a promising strategy and has become a new hot spot in cancer immunotherapy. However, its application to KIRC is not clear. A growing body of research has shown that immunotyping can reflect the comprehensive immune status and immune microenvironment of tumor, which is closely related to treatment response and vaccination potential. The aim of this study was to identify the potential antigens of KIRC for the development of anti-KIRC mRNA vaccines, and to further differentiate the immune subtypes of KIRC to construct an immune landscape for the selection of appropriate patients for vaccination. MethodsGene expression profiles and corresponding clinical information of 265 KIRC patients and RNA-seq data of 539 KIRC patients were retrieved from were collected from GEO and TCGA. cBioPortal was used to visualize and compare genetic alterations, while GEPIA2 was used to calculate the prognostic index of selected antigens. The relationship between the infiltration of antigen presenting cells and the expression of the identified antigen was visualized with TIMER, and consensus clustering analysis was used to determine the immune subtypes. Finally, the immune landscape of KIRC is visualized through the dimensionality reduction analysis based on graph learning. ResultsTwo tumor antigens associated with prognostic and antigen-presenting infiltrating cells were identified in KIRC, including LRP2, and DOCK8. KIRC patients were classified into six immune subtypes based on different molecular, cellular, and clinical characteristics. Patients with IS5 and IS6 tumors had an immune "hot" and immunosuppressive phenotype, which was associated with better survival compared to other subtypes, whereas patients with IS1-4 tumors had an immune "cold" phenotype, which was associated with a higher tumor mutation burden. In addition, the expression of immune checkpoints and immunogenic cell death modulators differed significantly in different immunosubtypes of tumors. Finally, the immune landscape of KIRC shows a high degree of heterogeneity across patients. ConclusionsLRP2 and FEM2 are potential KIRC antigens for mRNA vaccine development, and patients with immune subtypes IS1-4 are suitable for vaccination.

bioinformatics↗

bioRxiv2021

The Genome Sequence Archive Family: Towards Explosive Data Growth and Diverse Data Types

The Genome Sequence Archive (GSA) is a data repository for archiving raw sequence data, which provides data storing and sharing services for worldwide scientific communities. Considering explosive data growth with diverse data types, here we present the GSA family by expanding into a set of resources for raw data archive with different purposes, namely, GSA (https://ngdc.cncb.ac.cn/gsa/), GSA for Human (GSA-Human, https://ngdc.cncb.ac.cn/gsa-human/), and Open Archive for Miscellaneous Data (OMIX, https://ngdc.cncb.ac.cn/omix/). Compared with the 2017 version, GSA has been significantly updated in data model, online functionalities, and web interfaces. GSA-Human, as a new partner of GSA, is a data repository specialized in human genetics-related data with controlled access and security. OMIX, as a critical complement to the two resources mentioned above, is an open archive for miscellaneous data. Together, all these resources form a family of resources dedicated to archiving explosive data with diverse types, accept data submissions from all over the world and provide free open access to all publicly available data in support of worldwide research activities.

bioinformatics↗

bioRxiv2021

Room-temperature Storage of Lyophilized Engineered Bacteria using Tardigrade Intrinsically Disordered Proteins

Tardigrades, which live in transiently wet environments such as moss, are well-known for their extreme resistance to desiccation. Tardigrade intrinsically disordered proteins (TDPs) have been reported to also protect bacteria and yeast under desiccation [4, 5, 32]. In this study, we utilized lyophilization to achieve room-temperature storage of engineered bacteria. By using TDPs, engineered bacteria are protected under lyophilization and their original functions are preserved [12, 17, 18]. This study shows that TDPs can be expressed in the Escherichia coli (E. coli) BL21 and DH5, and bacteria treated with Cytosolic-abundant heat soluble protein (CAHS) 106094 displayed the highest survival rate after lyophilization [16, 41, 44]. Moreover, this study shows that the co-expression of TDPs can improve the preservation of bacteria and maintain high survival rates after prolonged room temperature storage. Additionally, the TDPs can be expressed using different vectors, which means that they can be used in different types of engineered bacteria. This study offers a new storage method that not only improves the storage of biological material for industrial and daily usage, but also for future iGEM (International Genetically Engineered Machine Competition) teams to store and use their engineered bacteria in different applications.

synthetic biology↗

bioRxiv2021

The Cost of Untracked Diversity in Brain-Imaging Prediction

Brain-imaging research enjoys increasing adoption of supervised machine learning for singlesubject disease classification. Yet, the success of these algorithms likely depends on population diversity, including demographic differences and other factors that may be outside of primary scientific interest. Here, we capitalize on propensity scores as a composite confound index to quantify diversity due to major sources of population stratification. We delineate the impact of population heterogeneity on the predictive accuracy and pattern stability in two separate clinical cohorts: the Autism Brain Imaging Data Exchange (ABIDE, n=297) and the Healthy Brain Network (HBN, n=551). Across various analysis scenarios, our results uncover the extent to which cross-validated prediction performances are interlocked with diversity. The instability of extracted brain patterns attributable to diversity is located preferentially to the default mode network. Our collective findings highlight the limitations of prevailing deconfounding practices in mitigating the full consequences of population diversity.

neuroscience↗

bioRxiv2021

Timing of meristem initiation and maintenance determines the morphology of fern gametophytes

The alternation of generations in land plants occurs between the sporophyte phase and the gametophyte phase. The sporophytes of seed plants develop self-maintained, multicellular meristems, and these meristems determine plant architecture. The gametophytes of seed plants lack meristems and are heterotrophic. In contrast, the gametophytes of seed-free vascular plants, including ferns, are autotrophic and free-living, developing meristems to sustain their independent growth and proliferation. Compared to meristems in the sporophytes of seed plants, the cellular mechanisms underlying meristem development in fern gametophytes remain largely unknown. Here, using confocal time-lapse live imaging and computational segmentation and quantification, we determined different patterns of cell divisions associated with the initiation and proliferation of two distinct types of meristems in fern gametophytes. Our results reveal how the simple timing of a switch between two meristems has considerable consequences for the divergent gametophyte morphologies of two closely related ferns from Pteridaceae (Pteris and Ceratopteris). Our result provides evolutionary insight into the function and regulation of gametophyte meristems in seed-free vascular plants. HighlightLive-imaging of cell growth and division in apical initials and lateral meristems reveals that the timing of a switch between the two meristem identities drives morphology variation in fern gametophytes.

plant biology↗

bioRxiv2021

A secondary metabolite drives intraspecies antagonism in a gut symbiont that is inhibited by peptidoglycan acetylation

The mammalian microbiome encodes numerous secondary metabolite biosynthetic gene clusters, yet their role in microbe-microbe interactions is unclear. Here, we characterized two polyketide synthase gene clusters (fun and pks) in the gut symbiont Limosilactobacillus reuteri. The pks, but not the fun cluster, encodes antimicrobial activity. Forty-one out of 51 L. reuteri strains tested are sensitive to Pks products, which was independent of strains host origin. The sensitivity to Pks was also established in intraspecies competition experiments in gnotobiotic mice. Comparative genome analyses between Pks-resistant and sensitive strains identified an acyltransferase gene (act) that is unique to Pks-resistant strains. Subsequent cell wall analysis of the wild-type and the act mutant strains showed that Act acetylates cell wall components. The pks mutants lost their competitive advantage and act mutants lost their Pks resistance in vivo. Thus, our findings provide insight into how closely related gut symbionts can compete and co- exist in the gastrointestinal tract.

microbiology↗

bioRxiv2021

Single Cell Raman-Deuterium Isotope Probing for Drug Resistance of Elizabethkingia spp.

Nosocomial infection associated with Elizabethkingia spp. is an emerging clinical concern characterized by multi-drug resistance and severe clinical consequences particularly in immunocompromised individuals and infants. Efficient control of this infection demands quick and reliable methods to determine the right drugs for the treatment. In this study, E. meningoseptica ATCC 13253 and four clinical isolates of Elizabethkingia spp. obtained from China, were subjected to single cell Raman spectroscopy analysis coupling with deuterium probing (single cell Raman-DIP). The results demonstrated that single cell Raman-DIP could generate an antimicrobial susceptibility testing result for Elizabethkingia spp. colonies within 4 hours based on their metabolisms variations at single cell level, and the drug resistant spectra of Elizabethkingia spp. determined by single cell Raman-DIP were consistent with the classical MIC method. Meanwhile single cell Raman spectroscopy (single cell RS) was applied to analyze Raman spectra of Elizabethkingia spp., which were revealed that their ratios of nucleic acid/protein were lower than other gram-negative pathogens and isolates from different origins could be distinguished by their Raman fingerprint. The in vitro results confirmed that minocycline and levofloxacin are first-line antimicrobials for Elizabethkingia spp. infection.

microbiology↗

bioRxiv2021

Differential Bcd activation of two hunchback promoters emerges from unified kinetics of enhancer-promoter interaction

Many eukaryotic genes contain alternative promoters with distinct expression patterns. How these promoters are differentially regulated remains elusive. Here, we apply single-molecule imaging to quantify the transcriptional regulation of two alternative promoters (P1 and P2) of the Bicoid (Bcd) target gene hunchback in syncytial blastoderm Drosophila embryos. Contrary to the previous notion that Bcd only activates P2, we find that Bcd activates both promoters via the same two enhancers. P1 activation is less frequent and requires binding of more Bcd molecules than P2 activation. Using a theoretical model to relate promoter activity to enhancer states, we show that the two promoters follow common transcription kinetics driven by sequential Bcd binding at the two enhancers. Bcd binding at either enhancer primarily activates P2, while P1 activation relies more on Bcd binding at both enhancers. These results provide a quantitative framework for understanding the kinetic mechanisms of complex eukaryotic gene regulation.

biophysics↗

bioRxiv2021

Elastic Network Modeling of Cellular Networks Unveils Sensor and Effector Genes that Control Information Flow

The high-level organization of the cell is embedded in long-range interactions that connect distinct cellular processes. Existing approaches for detecting long-range interactions consist of propagating information from source nodes through cellular networks, but the selection of source nodes is inherently biased by prior knowledge. Here, we sought to derive an unbiased view of long-range interactions by adapting a perturbation-response scanning strategy initially developed for identifying allosteric interactions within proteins. We deployed this strategy onto an elastic network model of the yeast genetic network. The genetic network revealed a superior propensity for long-range interactions relative to simulated networks with similar topology. Long-range interactions were detected systematically throughout the network and found to be enriched in specific biological processes. Furthermore, perturbation-response scanning identified the major sources and receivers of information in the network, named effector and sensor genes, respectively. Effectors formed dense clusters centrally integrated into the network, whereas sensors formed loosely connected antenna-shaped clusters. Long-range interactions between effector and sensor clusters represent the major paths of information in the network. Our results demonstrate that elastic network modeling of cellular networks constitutes a promising strategy to probe the high-level organization of the cell.

systems biology↗

bioRxiv2021

Unbiased screen of human transcriptome reveals an unexpected role of 3'UTRs in translation initiation

Although most eukaryotic mRNAs require a 5'-cap for translation initiation, some can also be translated through a poorly studied cap-independent pathway. Here we developed a circRNA-based system and unbiasedly identified more than 10,000 sequences in the human transcriptome that contain Cap-independent Translation Initiators (CiTIs). Surprisingly, most of the identified CiTIs are located in 3'UTRs, which mainly promote translation initiation in mRNAs bearing highly structured 5'UTR. Mechanistically, CiTI recruits several translation initiation factors including eIF3 and DHX29, which in turn unwind 5'UTR structures and facilitate ribosome scanning. Functionally, we showed that the translation of HIF1A mRNA, an endogenous DHX29 target, is antagonistically regulated by its 5'UTR structure and a new 3'-CiTI in response to hypoxia. Therefore, deletion of 3'-CiTI suppresses cell growth in hypoxia and tumor progression in vivo. Collectively, our study uncovers a new regulatory mode for translation where the 3'UTR actively participate in the translation initiation.

molecular biology↗

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

Divergent early antibody responses define COVID-19 disease trajectories

A damaging inflammatory response is strongly implicated in the pathogenesis of severe COVID-19 but mechanisms contributing to this response are unclear. In two prospective cohorts, early non-neutralizing, afucosylated, anti-SARS-CoV-2 IgG predicted progression from mild, to more severe COVID-19. In contrast to the antibody structures that predicted disease progression, antibodies that were elicited by mRNA SARS-CoV-2 vaccines were low in Fc afucosylation and enriched in sialylation, both modifications that reduce the inflammatory potential of IgG. To study the biology afucosylated IgG immune complexes, we developed an in vivo model which revealed that human IgG-Fc{gamma}R interactions can regulate inflammation in the lung. Afucosylated IgG immune complexes induced inflammatory cytokine production and robust infiltration of the lung by immune cells. By contrast, vaccine elicited IgG did not promote an inflammatory lung response. Here, we show that IgG-Fc{gamma}R interactions can regulate inflammation in the lung and define distinct lung activities associated with the IgG that predict severe COVID-19 and protection against SARS-CoV-2. One Sentence SummaryDivergent early antibody responses predict COVID-19 disease trajectory and mRNA vaccine response and are functionally distinct in vivo.

immunology↗

bioRxiv2021

MLC Seq: De novo sequencing of full-length tRNA isoforms by mass ladder complementation

tRNAs can exist in distinct isoforms because of different chemical modifications, which confounds attempts to accurately sequence individual tRNA species using next generation sequencing approaches or to quantify different RNA modifications at specific sites on a tRNA strand. Herein, we develop a mass spectrometric (MS) ladder complementation sequencing (MLC-Seq), allowing for direct and simultaneous sequencing of full-length tRNA molecules, including those with low abundance. MLC-seq is achieved by improved instrumentation, and advanced algorithms that identify each tRNA species and related isoforms in an RNA mixture, and assemble full MS ladders from partial ladders with missing ladder components. Using MLC-Seq, we successfully obtained the sequence of tRNA-Phe from yeast and tRNA-Glu from mouse hepatocytes, and simultaneously revealed new tRNA isoforms derived from nucleotide modifications. Importantly, MLC-Seq pinpointed the location and stoichiometry changes of RNA modifications in tRNA-Glu upon the treatment of dealkylated enzyme AlkB, which confirmed its known enzymatic activity and suggested previously unidentified effects in RNA editing.

biochemistry↗

bioRxiv2021

Understanding Microbeads Stacking in Deformable Nano-Sieve for Efficient Plasma Separation and Blood Cell Retrieval

Efficient separation of blood cells and plasma is key for numerous molecular diagnosis and therapeutics applications. Despite various microfluidics-based separation strategies have been developed, a simple, reliable, and multiplexing separation device that can process a large volume of blood is still missing. Here we show a microbead packed deformable microfluidic system that can efficiently separate highly purified plasma from whole blood as well as retrieve blocked blood cells from the device. Combining microscope imaging, optical tomography scanning, and computational fluidic modeling, a highly accurate model is constructed to understand the link between the mechanical properties of the microfluidics, flow rate, and microbeads packing/leaking, which supports and rationalizes the experimental observations. This deformable nano-sieve device establishes a key technology for centrifuge-free diagnosis and treatment of bloodborne diseases and may be important for the design of next-generation deformable microfluidics for separation applications.

bioengineering↗

bioRxiv2021

Interferon-armed RBD dimer enhances the immunogenicity of RBD for sterilizing immunity against SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global crisis, urgently necessitating the development of safe, efficacious, convenient-to-store, and low-cost vaccine options. A major challenge is that the receptor-binding domain (RBD)-only vaccine fails to trigger long-lasting protective immunity if used solely for vaccination. To enhance antigen processing and cross-presentation in draining lymph nodes (DLNs), we developed an interferon (IFN)-armed RBD dimerized by immunoglobulin fragment (I-R-F). I-R-F efficiently directs immunity against RBD to DLN. A low dose of I-R-F induces not only high titer long-lasting neutralizing antibodies but also comprehensive T cell responses than RBD, and even provides comprehensive protection in one dose without adjuvant. This study shows that the I-R-F vaccine provides rapid and complete protection throughout upper and lower respiratory tracts against high dose SARS-CoV-2 challenge in rhesus macaques. Due to its potency and safety, this engineered vaccine may become one of the next-generation vaccine candidates in the global race to defeat COVID-19.

immunology↗

bioRxiv2021

Biofilm self-patterning: mechanical force landscaping drives a collective reorientation cascade

In growing active matter systems, a large collection of engineered or living autonomous units metabolize free energy and create order at different length scales as they proliferate and migrate collectively. One such example is bacterial biofilms, which are surface-attached aggregates of bacterial cells embedded in an extracellular matrix. However, how bacterial growth coordinates with cell-surface interactions to create distinctive, long-range order in biofilms remains elusive. Here we report a collective cell reorientation cascade in growing Vibrio cholerae biofilms, leading to a differentially ordered, spatiotemporally coupled core-rim structure reminiscent of a blooming aster. Cell verticalization in the core generates differential growth that drives radial alignment of the cells in the rim, while the radially aligned rim in turn generates compressive stresses that expand the verticalized core. Such self-patterning disappears in adhesion-less mutants but can be restored through opto-manipulation of growth. Agent-based simulations and two-phase active nematic modeling reveal the strong interdependence of the driving forces for the differential ordering. Our findings provide insight into the collective cell patterning in bacterial communities and engineering of phenotypes and functions of living active matter.

biophysics↗