Biology subjects

Zhang, S.

Publications and source records attributed to Zhang, S..

At least 631 records · Page 35Linked to original sources

bioRxiv2023

Integrative Transcriptomic Analysis of Anterior and Posterior IOP-Controlling Tissues in Glaucoma Reveals Enrichment of MHC-II Pathway and T-Cell Infiltration Signatures

BackgroundGlaucoma is a multifactorial neurodegenerative disease indicating by abnormalities in the whole eye, apart from optic neuropathy, and is often associated with abnormal intraocular pressure (IOP). However, the underlying pathological mechanisms of glaucoma and the management of IOP remain largely unaddressed. Emerging evidence suggests the involvement of immune changes in glaucoma. Therefore, characterizations of immune alternations by molecular profiling of IOP-controlling tissues from both anterior and posterior eye segments including trabecular meshwork (TM) and choroid may provide insights to the disease mechanism. MethodsBulk TM microarray data (GSE138125 and GSE27276) from primary open-angle glaucoma (POAG) and choroid single-cell transcriptome data (GSE203499) from glaucoma were downloaded from Gene Expression Omnibus (GEO) database. The two qualified TM datasets were integrated. Analyses of differential expression genes (DEGs), functional and pathway annotations, immune infiltration, and disease-related modules were performed using the POAG bulk data. Similarly, DEGs and pathway annotations, single-cell trajectory and switch gene analysis, and cell-cell communications were conducted using the choroid single-cell RNA-sequencing data. Finally, integrated analyses from the two studies were conducted to determine the glaucomatous changes between anterior and posterior IOP-controlling eye tissues. ResultsA total of 102 DEGs between POAG and healthy tissues were identified from the TM data. Gene set enrichment analysis revealed five glaucoma-enriched pathways: ATP generation and metabolism, cornification and keratinization, metabolism of reactive oxygen species (ROS), humoral immune response, and platelet aggregation. Significant immune infiltrations were observed in POAG tissue, including total T cells (excluding CD8+ T cells), NK cells, monocytic lineage, endothelial cells, and fibroblasts. Furthermore, the POAG enriched pathways are primarily from T-cell infiltrations. On the other hand, fourteen distinct cell clusters were identified from the choroid single-cell data. The most evident findings were fibrosis, represented by extracellular matrix (ECM), the actin-binding pathways enrichment in pericyte-fibroblast transition, reduction in light sensitivity of melanocytes, and complex immune changes among all cell types in the pathological conditions compared to control. Taken together, an integrated analyses between the TM microarray and choroid single-cell data result in 111 significantly dysregulated genes in the disease state. These key genes participated in immune and inflammatory reactions (DUSP1, ADM, CD74, CEBPD, HLA-DPA1, ZNF331), served as potential biomarkers for neurodegenerative and autoimmune diseases (such as NR4A2), or regulated membrane integrity, vasculature calcification, ECM interactions, and cell morphology (PTP4A1, MGP, and RASD1). Overall, our integrated data analyses might provide insight to the understanding of the disease mechanism. ConclusionBy integrating bulk microarray data from TM and single-cell transcriptome data from the choroid, we systematically evaluated the glaucomatous transcriptomic changes between the anterior and posterior IOP-controlling tissue from ocular. Results indicated there was a significantly enrichment of genes belonging to the MHC-II pathway and T-cell infiltration in the disease state, opening new avenues for biomarkers discovery and therapeutic interventions to glaucoma.

bioinformatics↗

bioRxiv2023

GeneCompass: Deciphering Universal Gene Regulatory Mechanisms with Knowledge-Informed Cross-Species Foundation Model

Deciphering the universal gene regulatory mechanisms in diverse organisms holds great potential to advance our knowledge of fundamental life process and facilitate research on clinical applications. However, the traditional research paradigm primarily focuses on individual model organisms, resulting in limited collection and integration of complex features on various cell types across species. Recent breakthroughs in single-cell sequencing and advancements in deep learning techniques present an unprecedented opportunity to tackle this challenge. In this study, we developed GeneCompass, the first knowledge-informed, cross-species foundation model pre-trained on an extensive dataset of over 120 million single-cell transcriptomes from human and mouse. During pre-training, GeneCompass effectively integrates four types of biological prior knowledge to enhance the understanding of gene regulatory mechanisms in a self-supervised manner. Fine-tuning towards multiple downstream tasks, GeneCompass outperforms competing state-of-the-art models in multiple tasks on single species and unlocks new realms of cross-species biological investigation. Overall, GeneCompass marks a milestone in advancing knowledge of universal gene regulatory mechanisms and accelerating the discovery of key cell fate regulators and candidate targets for drug development.

bioinformatics↗

bioRxiv2023

CellPolaris: Decoding Cell Fate through Generalization Transfer Learning of Gene Regulatory Networks

Cell fate changes are determined by gene regulatory network (GRN), a sophisticated system regulating gene expression in precise spatial and temporal patterns. However, existing methods for reconstructing GRNs suffer from inherent limitations, leading to compromised accuracy and application generalizability. In this study, we introduce CellPolaris, a computational system that leverages transfer learning algorithms to generate high-quality, cell-type-specific GRNs. Diverging from conventional GRN inference models, which heavily rely on integrating epigenomic data with transcriptomic information or adopt causal strategies through gene co-expression networks, CellPolaris employs high-confidence GRN sources for model training, relying exclusively on transcriptomic data to generate previously unknown cell-type-specific GRNs. Applications of CellPolaris demonstrate remarkable efficacy in predicting master regulatory factors and simulating in-silico perturbations of transcription factors during cell fate transition, attaining state-of-the-art performance in accurately predicting candidate key factors and outcomes in cell reprogramming and spermatogenesis with validated datasets. It is worth noting that, with a transfer learning framework, CellPolaris can perform GRN based predictions in all cell types even across species. Together, CellPolaris represents a significant advancement in deciphering the mechanisms of cell fate regulation, thereby enhancing the precision and efficiency of cell fate manipulation at high resolution.

bioinformatics↗

bioRxiv2023

Alteration of mechanical stresses in the murine brain by age and hemorrhagic stroke

Residual mechanical stresses in tissues arise during rapid differential growth or remodeling such as in morphogenesis and cancer. These residual stresses, also known as solid stresses, are distinct from fluid pressures and dissipate in most healthy adult organs as the rate of growth decreases. However, studies have shown that residual stresses remain substantially high even in mature, healthy brains. The genesis and consequences of these mechanical stresses in a healthy brain, and in aging and disease remain to be explored. Here, we utilized and validated our previously developed method to map residual mechanical stresses in the brains of mice in three different age groups: 5-7 days, 8-12 weeks, and 22 months old. We found that residual solid stress increases rapidly from 5-7 days to 8-12 weeks in mice, and remains high even in mature 22-month-old mice brains. Three-dimensional mapping of the residual stresses revealed an increasing trend from anterior to posterior in coronal sections of the brain. Since the brain is rich in negatively charged hyaluronic acid, we evaluated the contribution of charged extracellular matrix (ECM) constituents in maintaining solid stress levels. We found that lower ionic strength leads to elevated solid stresses, a finding consistent with the unshielding effect of low ionic strength and the subsequent expansion of charged ECM components. Lastly, we demonstrated that hemorrhagic stroke, accompanied by loss of cellular density, resulted in decreased levels of residual stress in the murine brain. Our findings contribute to a better understanding of the spatiotemporal alteration of residual solid stresses in healthy and diseased brains, a crucial step toward uncovering the biological and immunological consequences of this understudied mechanical phenotype in the brain. Significance StatementWhile emerging evidence highlights the importance of solid stresses in embryogenesis and tumor growth, the genesis and consequences of residual solid stresses in the adult normal brain remain poorly understood. Understanding the spatiotemporal distribution and alteration of the residual solid stresses as the brain ages and is impacted by neuropathologies, such as a stroke, will elucidate the biological and immunological consequences of maintaining these stresses. This study suggests solid stress could serve as a potential biomarker in aging and diseases associated to the brain.

biophysics↗

bioRxiv2023

Germline-targeting chimpanzee SIV Envelopes induce V2-apex broadly neutralizing-like B cell precursors in a rhesus macaque infection model

Eliciting broadly neutralizing antibodies-(bnAbs) remains a major goal of HIV-1 vaccine research. Previously, we showed that a soluble chimpanzee SIV Envelope-(Env) trimer, MT145K, bound several human V2-apex bnAb-precursors and stimulated an appropriate response in V2-apex bnAb precursor-expressing knock-in mice. Here, we tested the immunogenicity of three MT145 variants (MT145, MT145K, MT145K.dV5) expressed as chimeric simian-chimpanzee-immunodeficiency-viruses-(SCIVs) in rhesus macaques-(RMs). All three viruses established productive infections with high setpoint vRNA titers. RMs infected with the germline-targeting SCIV_MT145K and SCIV_MT145K.dV5 exhibited larger and more clonally expanded B cell lineages featuring long anionic heavy chain complementary-determining-regions-(HCDR3s) compared with wildtype SCIV_MT145. Moreover, antigen-specific B cell analysis revealed enrichment for long-CDHR3-bearing antibodies in SCIV_MT145K.dV5 infected animals with paratope features resembling prototypic V2-apex bnAbs and their precursors. Although none of the animals developed bnAbs, these results show that germline-targeting SCIVs can activate and preferentially expand B cells expressing V2-apex bnAb-like precursors, the first step in bnAb elicitation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=180 HEIGHT=200 SRC="FIGDIR/small/558743v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@17673c8org.highwire.dtl.DTLVardef@1ab61a8org.highwire.dtl.DTLVardef@98781forg.highwire.dtl.DTLVardef@1f63e9b_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

MMD-DTA: A multi-modal deep learning framework for drug-target binding affinity and binding region prediction

AbstractThe prediction of drug-target affinity (DTA) plays an important role in the development of drugs and the discovery of potential drug targets. In recent years, computer-assisted DTA prediction has become an important method in this field. In this work, we propose a multi-modal deep learning framework for drug-target binding affinity and binding region prediction, namely MMD-DTA. The model can predict DTA while unsupervised learning of drug-target binding regions. The experimental results show that MMD-DTA performs better than the existing models on the main evaluation metrics. In addition, external validation results show that MMD-DTA improves the generalization ability of the model by integrating sequence information and structural information of drugs and targets, and the model trained on the benchmark dataset can be well generalized to independent virtual screening tasks. Visualization of drug-target binding region prediction shows the powerful interpretability of MMD-DTA, which has important implications for exploring the functional regions of drug molecules acting on proteins.

bioinformatics↗

bioRxiv2023

GENOMES UNCOUPLED1: an RNA-binding protein required for early PSII biogenesis

Genomes Uncoupled1 (GUN1), a nuclear-encoded chloroplast pentatricopeptide repeat (PPR) protein, serves as a master integrator of diverse retrograde signals, mediating chloroplast-to-nucleus retrograde signaling. Although PPR proteins primarily function in organelle RNA metabolism, a target RNA of GUN1 remained unknown. This study reveals that GUN1 recognizes psbD transcripts derived from a blue light-responsive promoter (BLRP), transcripts referred to as psbD BLRP. Overexpression of GUN1 significantly reduces the levels of psbD BLRP, whereas the loss of GUN1 leads to the accumulation of the putative target RNA. The in vitro RNA and in vivo genetic studies further demonstrate the critical role of the C-terminal small MutS-related (SMR) domain in stimulating psbD BLRP processing and PsbD (D2, a PSII core protein) synthesis. The GUN1-dependent psbD BLRP processing promotes PSII biogenesis during the early seedling development and de-etiolation phase. This finding underscores the role of GUN1 as an RNA-binding protein, highlighting the essential function of the SMR domain in processing the target RNA. SignificanceBiogenic retrograde signaling is essential in regulating chloroplast biogenesis, and it entails a nuclear-encoded chloroplast protein, Genomes Uncoupled1 (GUN1). Since its initial discovery in 1993, the gun1 mutant has been widely used to reveal the precise function of GUN1 in plastids as well as its downstream signaling components. Although GUN1 contains pentatricopeptide repeat motifs, it has been considered a non-canonical PPR protein because no one could demonstrate GUN1-RNA interaction in planta. However, through our computational analysis of PPR codes and subsequent biochemical studies, we were able to unravel its putative target RNA, namely psbD BLRP. Therefore, our finding may lead to a reevaluation of GUN1 research in the context of RNA metabolism and a revision of our current understanding of GUN1.

plant biology↗

bioRxiv2023

Inverse and Proportional trans Modulation of Gene Expression in Human Aneuploidies

Genomic imbalance in aneuploidy is often detrimental to organisms. To gain insight into the molecular basis of aneuploidies in humans, we analyzed transcriptome data from several autosomal and sex chromosome aneuploidies. The results showed that in human aneuploid cells, genes located on unvaried chromosomes are inversely or proportionally trans-modulated, while a subset of genes on the varied chromosomes are compensated. Less genome-wide modulation is found for sex chromosome aneuploidy compared with autosomal aneuploidy due to X inactivation and the retention of dosage sensitive regulators on both sex chromosomes to limit the effective dosage change. We also found that lncRNA and mRNA can have different responses to aneuploidy. Furthermore, we analyzed the relationship between dosage-sensitive transcription factors and their targets, which illustrated the modulations and indicates genomic imbalance is related to stoichiometric changes of components of gene regulatory complexes.

genetics↗

bioRxiv2023

A phage nucleus-associated RNA-binding protein is required for jumbo phage infection

Large-genome bacteriophages (jumbo phages) of the Chimalliviridae family assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and CRISPR/Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. Here we identify a conserved phage nuclear shell-associated protein that we term Chimallin C (ChmC), which adopts a nucleic acid-binding fold, binds RNA with high affinity in vitro, and binds phage mRNAs in infected cells. ChmC also forms phase-separated condensates with RNA in vitro. Targeted knockdown of ChmC using mRNA-targeting dCas13d halts infections at an early stage. Taken together, our data suggest that the conserved ChmC protein acts as a chaperone for phage mRNAs, potentially stabilizing these mRNAs and driving their translocation through the nuclear shell to promote translation and infection progression.

microbiology↗

bioRxiv2023

Mapping Cell-to-cell Interactions from Spatially Resolved Transcriptomics Data

Cell-cell communication (CCC) is essential to how life forms and functions. However, accurate, high-throughput mapping of how expression of all genes in one cell affects expression of all genes in another cell is made possible only recently, through the introduction of spatially resolved transcriptomics technologies (SRTs), especially those that achieve single cell resolution. However, significant challenges remain to analyze such highly complex data properly. Here, we introduce a Bayesian multi-instance learning framework, spacia, to detect CCCs from data generated by SRTs, by uniquely exploiting their spatial modality. We highlight spacias power to overcome fundamental limitations of popular analytical tools for inference of CCCs, including losing single-cell resolution, limited to ligand-receptor relationships and prior interaction databases, high false positive rates, and most importantly the lack of consideration of the multiple-sender-to-one-receiver paradigm. We evaluated the fitness of spacia for all three commercialized single cell resolution ST technologies: MERSCOPE/Vizgen, CosMx/Nanostring, and Xenium/10X. Spacia unveiled how endothelial cells, fibroblasts and B cells in the tumor microenvironment contribute to Epithelial-Mesenchymal Transition and lineage plasticity in prostate cancer cells. We deployed spacia in a set of pan-cancer datasets and showed that B cells also participate in PDL1/PD1 signaling in tumors. We demonstrated that a CD8+ T cell/PDL1 effectiveness signature derived from spacia analyses is associated with patient survival and response to immune checkpoint inhibitor treatments in 3,354 patients. We revealed differential spatial interaction patterns between {gamma}{delta} T cells and liver hepatocytes in healthy and cancerous contexts. Overall, spacia represents a notable step in advancing quantitative theories of cellular communications.

bioinformatics↗

bioRxiv2023

Morphological, molecular, and functional characterization of mouse glutamatergic myenteric neurons

The enteric nervous system (ENS) functions largely independently of the central nervous system (CNS). Correspondingly, glutamate, the dominant neurotransmitter in the CNS and sensory afferents, is not a primary neurotransmitter in the ENS. Only a fraction (approximately 2%) of myenteric neurons in the mouse distal colon and rectum (colorectum) are positive for vesicular glutamate transporter type 2 (VGLUT2), the structure and function of which remain undetermined. Here, we systematically characterized VGLUT2-positive enteric neurons (VGLUT2-ENs) through sparse labeling with adeno-associated virus, single-cell mRNA sequencing (scRNA-seq), and GCaMP6f calcium imaging. Our results reveal that the majority of VGLUT2-ENs (29 out of 31, 93.5%) exhibited Dogiel type I morphology with a single aborally projecting axon; most axons (26 out of 29, 89.7%) are between 4 and 10 mm long, each traversing 19 to 34 myenteric ganglia. These anatomical features exclude the VGLUT2-ENs from being intrinsic primary afferent or motor neurons. The scRNA-seq conducted on 52 VGLUT2-ENs suggests different expression profiles from conventional descending interneurons. Ex vivo GCaMP6f recordings from flattened colorectum indicate that almost all VGLUT2-EN (181 out of 215, 84.2%) are indirectly activated by colorectal stretch via nicotinic cholinergic neural transmission. In conclusion, VGLUT2-ENs are a functionally unique group of enteric neurons with single aborally projecting long axons that traverse multiple myenteric ganglia and are activated indirectly by colorectal mechanical stretch. This knowledge will provide a solid foundation for subsequent studies on the potential interactions of VGLUT2-EN with extrinsic colorectal afferents via glutamatergic neurotransmission. New & NoteworthyWe reveal that VGLUT2-positive enteric neurons (EN), although constituting a small fraction of total EN, are homogeneously expressed in the myenteric ganglia, with a slight concentration at the intermediate region between the colon and rectum. This concentration coincides with the entry zone of extrinsic afferents into the colorectum. Given that VGLUT2-ENs are indirectly activated by colorectal mechanical stretch, they are likely to participate in visceral nociception through glutamatergic neural transmission with extrinsic afferents.

neuroscience↗

bioRxiv2023

The Neural Correlates of Ambiguity and Risk in Human Decision-Making under an Active Inference Framework

Active inference integrates perception, decision-making, and learning into a united theoretical frame-work, providing an efficient way to trade off exploration and exploitation by minimizing (expected) free energy. In this study, we asked how the brain represents values and uncertainties (novelty and variability), and resolves these uncertainties under the active inference framework in the exploration-exploitation trade-off. 25 participants performed a contextual two-armed bandit task, with electroen-cephalogram (EEG) recordings. By comparing the model evidence for active inference and rein-forcement learning models of choice behavior, we show that active inference better explains human decision-making under novelty and variability, which entails exploration or information seeking. The EEG sensor-level results show that the activity in the frontal, central, and parietal regions is associated with novelty, while activity in the frontal and central brain regions is associated with variability. The EEG source-level results indicate that the expected free energy is encoded in the frontal pole and middle frontal gyrus and uncertainties are encoded in different brain regions but with overlap. Our study dissociates the expected free energy and uncertainties in active inference theory and their neural correlates, speaking to the construct validity of active inference in characterizing cognitive processes of human decisions. It provides behavioral and neural evidence of active inference in decision processes and insights into the neural mechanism of human decisions under uncertainties.

neuroscience↗

bioRxiv2023

OBIA: An Open Biomedical Imaging Archive

With the development of artificial intelligence (AI) technologies, biomedical imaging data play an important role in scientific research and clinical application, but the available resources are limited. Here we present Open Biomedical Imaging Archive (OBIA), a repository for archiving biomedical imaging and related clinical data. OBIA adopts five data objects (Collection, Individual, Study, Series, and Image) for data organization, accepts the submission of biomedical images of multiple modalities, organs, and diseases. In order to protect personal privacy, OBIA has formulated a unified de-identification and quality control process. In addition, OBIA provides friendly and intuitive web interface for data submission, browsing and retrieval, as well as image retrieval. As of September 2023, OBIA has housed data for a total of 937 individuals, 4136 studies, 24,701 series, and 1,938,309 images covering 9 modalities and 30 anatomical sites. Collectively, OBIA provides a reliable platform for biomedical imaging data management and offers free open access to all publicly available data to support research activities throughout the world. OBIA can be accessed at https://ngdc.cncb.ac.cn/obia.

bioinformatics↗

bioRxiv2023

Inhibition of human immunodeficiency virus (HIV-1) infectivity by expression of poorly or broadly neutralizing antibodies against Env in virus-producing cells

The human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) precursor (gp160) trimerizes, is modified by high-mannose glycans in the endoplasmic reticulum, and is transported via Golgi and non-Golgi secretory pathways to the infected cell surface. In the Golgi, gp160 is partially modified by complex carbohydrates and proteolytically cleaved to produce the mature functional Env trimer, which is preferentially incorporated into virions. Broadly neutralizing antibodies (bNAbs) generally recognize the cleaved Env trimer, whereas poorly neutralizing antibodies (pNAbs) bind the conformationally flexible gp160. We found that expression of bNAbs, pNAbs or soluble/membrane forms of the receptor, CD4, in cells producing HIV-1 all decreased viral infectivity. Four patterns of co-expressed ligand:Env were observed: 1) Ligands (CD4, soluble CD4-Ig and some pNAbs) that specifically recognize the CD4-bound Env conformation resulted in uncleaved Envs lacking complex glycans that were not incorporated into virions; 2) Other pNAbs produced Envs with some complex carbohydrates and severe defects in cleavage, which were relieved by brefeldin A treatment; 3) bNAbs that recognize gp160 as well as mature Envs resulted in Envs with some complex carbohydrates and moderate decreases in virion Env cleavage; and 4) bNAbs that preferentially recognize mature Envs produced cleaved Envs with complex glycans in cells and on virions. The low infectivity observed upon co-expression of pNAbs or CD4 could be explained by disruption of Env trafficking, reducing the level of Env and/or increasing the fraction of uncleaved Env on virions. In addition to bNAb effects on virion Env cleavage, the secreted bNAbs neutralized the co-expressed viruses. IMPORTANCEThe envelope glycoprotein (Env) trimers on the human immunodeficiency virus (HIV-1) mediate virus entry into host cells. Env is synthesized in infected cells, modified by complex sugars and cleaved to form a mature, functional Env, which is incorporated into virus particles. Env elicits antibodies in infected individuals, some of which can neutralize the virus. We found that antibodies co-expressed in the virus-producing cell can disrupt Env transit to the proper compartment for cleavage and sugar modification and, in some cases, block incorporation into viruses. These studies provide insights into the processes by which Env becomes functional in the virus-producing cell and may assist attempts to interfere with these events to inhibit HIV-1 infection.

microbiology↗

bioRxiv2023

Overexpression of ZmSTOP1-A Enhances Aluminum Tolerance in Arabidopsis by Stimulating Organic Acid Secretion and Reactive Oxygen Species Scavenging

Aluminum (Al) toxicity and low pH are major factors limiting plant growth in acidic soils. Sensitive to Proton Rhizotoxicity 1 (STOP1) transcription factor respond to these stresses by regulating the expression of multiple Al- or low pH-responsive genes. ZmSTOP1-A, a STOP1-like protein from maize (Zea mays), was localized to the nucleus and had transactivation activity. ZmSTOP1-A was expressed moderately in both roots and shoots of maize seedlings, but was not induced by Al stress or low pH. Overexpression of ZmSTOP1-A in Arabidopsis Atstop1 mutant partially restored Al tolerance and completely low pH tolerance with respect to root growth. Regarding Al tolerance, ZmSTOP1-A/Atstop1 plants showed clear upregulation of organic acid transporter genes, and leading to increased organic acid secretion and reduced Al accumulation in roots. Besides, the antioxidant enzyme activity in roots and shoots of ZmSTOP1-A/Atstop1 plants was significantly enhanced, ultimately alleviating Al toxicity via scavenging reactive oxygen species. Similarly, ZmSTOP1-A could directly activate ZmMATE1 expression in maize, positively correlated with the number of Al-responsive GGNVS cis-element in the ZmMATE1 promoter. Our results revealed that ZmSTOP1-A antagonizes Al toxicity by enhancing organic acid secretion and reactive oxygen species scavenging in Arabidopsis, demonstrating that it is an important transcription factor conferring Al tolerance. Our findings help to comprehensively elucidate the role of STOP1-like transcript factor in enabling plants to detoxifying Al.

molecular biology↗

bioRxiv2023

STASCAN deciphers fine-resolution cell-distribution maps in spatial transcriptomics by deep learning

BackgroundThe spatial transcriptomics (ST) technologies have been widely applied to decode the spatial distribution of cells by resolving gene expression profiles in tissues. However, a fine-resolved spatial cell map is still limited by algorithmic tools and sequencing techniques. ResultsHere we develop a novel deep learning approach, STASCAN, which could define the spatial cellular distribution of both captured and uncharted areas by cell feature learning that combines gene expression profiles and histology images. STASCAN additionally adopts optional transfer learning and pseudo-labeling methods to improve the accuracy of the cell-type prediction from images. We have successfully applied STASCAN to enhance cell resolution, and revealed finer organizational structures across diverse datasets from various species and tissues generated from 10x Visium technology. STASCAN improves cell resolution of Schmidtea mediterranea datasets by six times and reconstructs more detailed 3D cell-type models. Furthermore, STASCAN could accurately pinpoint the boundaries of distinct cell layers in human intestinal tissue, specifically identify a micrometer-scale smooth muscle bundle structure in consistent with anatomic insights in human lung tissue, and redraw the spatial structural variation with enhanced cell patterns in human myocardial infarction tissue. Additionally, through STASCAN on embryonic mouse brain datasets generated by DBiT-derived MISAR-seq technology, the increased cellular resolution and distinct anatomical tissue domains with cell-type niches are revealed. Collectively, STASCAN is compatible with different ST technologies and has notable advantages in generating cell maps solely from histology images, thereby enhancing the spatial cellular resolution. ConclusionsIn short, STASCAN displays significant advantages in deciphering higher-resolution cellular distribution, resolving enhanced organizational structures and demonstrating its potential applications in exploring cell-cell interactions within the tissue microenvironment.

bioinformatics↗

bioRxiv2023

Mechanistic implications of the ternary complex structural models for the photoenzyme protochlorophyllide oxidoreductase.

The photoenzyme protochlorophyliide oxidoreductase (POR) is an important enzyme for understanding biological H-transfer mechanisms. It uses light to catalyse the reduction of protochlorophyllide (Pchlide) to chlorophyllide, a key step in chlorophyll biosynthesis. Although a wealth of spectroscopic data have provided crucial mechanistic insight about the light-driven reaction chemistry, a structural rationale for POR photocatalysis has proved more challenging and remains hotly debated. Recent structural models of the ternary enzyme-substrate complex, derived from crystal and electron microscopy data, show differences in the orientation of the Pchlide substrate and the architecture of the POR active site that have significant implications for the catalytic mechanism of Pchlide reduction. Here, we have used a combination of computational and experimental approaches to investigate the compatibility of each of these structural models with the hypothesised reaction mechanisms and propose an alternative structural model for the cyanobacterial POR-Pchlide-NADPH ternary complex based on these findings. Through detailed site-directed mutagenesis studies we show that a strictly conserved Tyr residue, which has previously been proposed to act as the proton donor in POR photocatalysis, is not likely to be involved in this step of the reaction but is crucial for Pchlide binding. Instead, an active site Cys residue is important for both hydride and proton transfer reactions in POR and is proposed to act as the proton donor, either directly or through a water-mediated network. Moreover, a conserved Gln residue is found to be important for Pchlide binding and ensuring efficient photochemistry by tuning its electronic properties, likely by interacting with the central Mg atom of the substrate. This optimal binding pose for the POR ternary enzyme-substrate complex illustrates how light energy can be harnessed to facilitate enzyme catalysis by this unique enzyme.

biochemistry↗

bioRxiv2023

Rof is a key regulator of Rho and transcription termination in bacteria

Transcription is crucial for the expression of genetic information and its efficient and accurate termination is required for all living organisms. Rho-dependent termination could rapidly terminate unwanted premature RNAs and play important roles in bacterial adaptation to changing environments. Although Rho has been discovered for about five decades, the regulation mechanisms of Rho-dependent termination are still not fully elucidated. Here we report the cryogenic electron microscopy structure of Rho-Rof antitermination complex. The structure shows that Rof binds to the open-ring Rho hexamer and inhibits the initiation of Rho-dependent termination. Rofs N-terminal -helix is key in facilitating Rof-Rho interactions. Rof binds to Rhos primary binding site (PBS) and excludes Rho from binding with PBS ligand RNA at the initiation step. Further in vivo assays in Salmonella Typhimurium show that Rof is required for virulence gene expression and host cell invasion, unveiling a novel physiological function of Rof and transcription termination in bacterial pathogenesis.

microbiology↗