Biology subjects

Zhang, D.

Publications and source records attributed to Zhang, D..

At least 415 records · Page 23Linked to original sources

bioRxiv2020

BDdb: a comprehensive platform for exploration and utilization of birth defect multi-omics data

Birth defect, not only poses a major challenge for infant health but also attracts the attention of countless people in the world. Chromosome abnormality directly results in diverse birth defects which are generally deleterious and even lethal. Therefore, gaining molecular regulatory insights into these diseases is important and necessary for effective prenatal screening. Recently, with the advance of next-generation sequencing (NGS) techniques, a myriad of treatises and data associated with these diseases are now constantly produced from different laboratories across the world. To meet the increasing requirements for birth-related data resources, we developed a birth defect multi-omics database (BDdb), freely accessible at http://t21omics.cngb.org and consisting of multi-omics data, circulating free DNA (cfDNA) data, as well as diseases biomarkers. Omics data sets from 138 GSE samples, 5271 GSM samples and 328 entries, and more than 2000 biomarkers of 22 birth-defect diseases in 5 different species were integrated into BDdb, which provides a user-friendly interface for searching, browsing and downloading selected data. Additionally, we re-analyzed and normalized the raw data so that users can also customize the analysis using the data generated from different sources or different High-Throughput Sequencing (HTS) methods. To our knowledge, BDdb is the first comprehensive database associated with birth-defect-related diseases. which would benefit the diagnosis and prevention of birth defects.

bioinformatics↗

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

Proto-sex locus in large yellow croaker provides insights into early evolution of the sex chromosome

Autosomal origins of heterogametic sex chromosomes have been inferred frequently from suppressed recombination and gene degeneration manifested in incompletely differentiated sex chromosomes. However, the initial transition of an autosome region to a proto-sex locus has been not explored in depth. By assembling and analyzing a chromosome-level draft genome, we found a recent (evolved 0.26 million years ago), highly homologous, and dmrt1 containing sex-determination locus with slightly reduced recombination in large yellow croaker (Larimichthys crocea), a teleost species with genetic sex determination (GSD) and with undifferentiated sex chromosomes. We observed genomic homology and polymorphic segregation of the proto-sex locus between sexes. Expression of dmrt1 showed a stepwise increase in the development of testis, but not in the ovary. We infer that the inception of the proto-sex locus involves a few divergences in nucleotide sequences and slight suppression of recombination in an autosome region. In androgen-induced sex reversal of genetic females, in addition to dmrt1, genes in the conserved dmrt1 cluster, and the rest of the sex determination network were activated. We provided evidence that broad functional links were shared by genetic sex determination and environmental sex reversal.

evolutionary biology↗

bioRxiv2020

A chromosome-level genome assembly of the yellowfin seabream (Acanthopagrus latus) (Hottuyn, 1782) provides insights into its osmoregulation and sex reversal

The yellowfin seabream Acanthopagrus latus is the economically most important Sparidae fish species in the northern South China Sea. As euryhaline fish, they are perfect model for investigating osmoregulatory mechanisms in teleosts. Moreover, the reproductive biology of hermaphrodites has long been intriguing; however, very little is known about the molecular pathways underlying their sex change. To elucidate genetic mechanisms of osmoregulation and sex reversal in this fish, a high-quality reference genome of the yellowfin seabream was generated by a combination of Illumina and PacBio technologies. The draft genome of yellowfin seabream was 806 Mb, with 732 Mb scaffolds anchored on 24 chromosomes. The contig N50 and scaffold N50 were 2.6 Mb and 30.17 Mb, respectively. The assembly is of high integrity and includes 92.23% universal single-copy orthologues based on benchmarking universal single-copy orthologs (BUSCO) analysis. Moreover, among the 19,631 protein-coding genes, we found that the ARRDC3 and GSTA gene families related to osmoregulation underwent an extensive expansion in two euryhaline Sparidae fish genomes compared to other teleost genomes. Moreover, integrating sex-specific transcriptome analyses, several genes related to the transforming growth factor beta (TGF-{beta}) signalling pathway involved in sex differentiation and development. This genomic resource will not only be valuable for studying the osmoregulatory mechanisms in estuarine fish and sex determination in hermaphrodite vertebrate species, but also provide useful genomic tools for facilitating breeding of the yellowfin seabream.

genomics↗

bioRxiv2020

A high-quality genome assembly and annotation of the humpback grouper Cromileptes altivelas

Cromileptes altivelas that belongs to Serranidae in the order Perciformes, is widely distributed throughout the tropical waters of the Indo-West Pacific regions. Due to their excellent food quality and abundant nutrients, it has become a popular marine food fish with high market values. Here, we reported a chromosome-level genome assembly and annotation of the humpback grouper genome using more than 103X PacBio long-reads and high-throughput chromosome conformation capture (Hi-C) technologies. The N50 contig length of the assembly is as large as 4.14 Mbp, the final assembly is 1.07 Gb with N50 of scaffold 44.78 Mb, and 99.24% of the scaffold sequences were anchored into 24 chromosomes. The high-quality genome assembly also showed high gene completeness with 27,067 protein coding genes and 3,710 ncRNAs. This high accurate genome assembly and annotation will not only provide an essential genome resource for C. altivelas breeding and restocking, but will also serve as a key resource for studying fish genomics and genetics.

genomics↗

bioRxiv2020

FEM-Based Mechanics Modeling of Bio-Inspired Compliant Mechanisms for Medical Applications

Compliant mechanisms are widely used in the design of medical robotics and devices because of their monolithic structure and high flexibility. Many compliant mechanisms derive their design ideas from nature, since the structure of biological organisms sometimes offers a better solution than the conventional mechanisms. However, the bio-inspired structures usually have very complex geometries which cannot be easily modeled and analyzed using traditional methods. In this paper, we present a novel finite element method (FEM) based modeling framework in Matlab to analyze the mechanics of different bio-inspired compliant mechanisms. Since the basic linear FEM formulation can only be employed to model small displacements of compliant mechanisms, a non-linear FEM formulation that integrates the modeling of large displacements, tendon-driven mechanisms and contact problems was implemented in the proposed framework to overcome the limitations. Simulations and experiments were also conducted to evaluate the performance of the modeling framework. Results have demonstrated the accuracy and plausibility of the proposed non-linear FEM formulation. Furthermore, the proposed framework can also be used to achieve structural optimization of bio-inspired compliant mechanisms.

bioengineering↗

bioRxiv2020

Enzymatic RNA Biotinylation for Affinity Purification and Identification of RNA-protein Interactions

Throughout their cellular lifetime, RNA transcripts are bound to proteins, playing crucial roles in RNA metabolism, trafficking, and function. Despite the importance of these interactions, identifying the proteins that interact with an RNA of interest in mammalian cells represents a major challenge in RNA biology. Leveraging the ability to site-specifically and covalently label an RNA of interest using E. Coli tRNA guanine transglycosylase and an unnatural nucleobase substrate, we establish the identification of RNA-protein interactions and the selective enrichment of cellular RNA in mammalian systems. We demonstrate the utility of this approach through the identification of known binding partners of 7SK snRNA via mass spectrometry. Through a minimal 4-nucleotide mutation of the long noncoding RNA HOTAIR, enzymatic biotinylation enables identification putative HOTAIR binding partners in MCF7 breast cancer cells that suggest new potential pathways for oncogenic function. Furthermore, using RNA sequencing and qPCR, we establish that an engineered enzyme variant achieves high levels of labeling selectivity against the human transcriptome allowing for 145-fold enrichment of cellular RNA directly from mammalian cell lysates. The flexibility and breadth of this approach suggests that this system could be routinely applied to the functional characterization of RNA, greatly expanding the toolbox available for studying mammalian RNA biology.

biochemistry↗

bioRxiv2020

Evolutionary history of inversions in the direction of architecture-driven mutational pressures in crustacean mitochondrial genomes

Inversions of the origin of replication (ORI) of mitochondrial genomes produce asymmetrical mutational pressures that can cause artefactual clustering in phylogenetic analyses. It is therefore an absolute prerequisite for all molecular evolution studies that use mitochondrial data to account for ORI events in the evolutionary history of their dataset. The number of ORI events in crustaceans remains unknown; several studies reported ORI events in some crustacean lineages on the basis of fully inversed (e.g. negative vs. positive) GC skew patterns, but studies of isolated lineages could have easily overlooked ORI events that produced merely a reduction in the skew magnitude. In this study, we used a comprehensive taxonomic approach to systematically study the evolutionary history of ORI events in crustaceans using all available mitogenomes and combining signals from lineage-specific skew magnitude and direction (+ or -), cumulative skew diagrams, and gene rearrangements. We inferred 24 putative ORI events (14 of which have not been proposed before): 17 with relative confidence, and 7 speculative. Most of these were located at lower taxonomic levels, but there are indications of ORIs that occurred at or above the order-level: Copepoda, Isopoda, and putatively in Branchiopoda and Poecilostomatida+Cyclopoida. Several putative ORI events did not result in fully inversed skews. In many lineages skew plots were not informative for the prediction of replication origin and direction of mutational pressures, but inversions of the mitogenome fragment comprising the ancestral CR (rrnS-CR-trnI) were rather good predictors of skew inversions. We also found that skew plots can be a useful tool to indirectly infer the relative strengths of mutational/purifying pressures in some crustacean lineages: when purifying pressures outweigh mutational, GC skew plots are strongly affected by the strand distribution of genes, and when mutational > purifying, GC skew plots can be even completely (apparently) unaffected by the strand distribution of genes. This observation has very important repercussions for phylogenetic and evolutionary studies, as it implies that not only the relatively rare ORI events, but also much more common gene strand switches and same-strand rearrangements can produce mutational bursts, which in turn affect phylogenetic and evolutionary analyses. We argue that such compositional biases may produce misleading signals not only in phylogenetic but also in other types of evolutionary analyses (dN/dS ratios, codon usage bias, base composition, branch length comparison, etc.), and discuss several such examples. Therefore, all studies aiming to study the evolution of mtDNA sequences should pay close attention to architectural rearrangements.

evolutionary biology↗

bioRxiv2020

Role of 1'-Ribose Cyano Substitution for Remdesivir to Effectively Inhibit both Nucleotide Addition and Proofreading in SARS-CoV-2 Viral RNA Replication

COVID-19 has recently caused a global health crisis and an effective interventional therapy is urgently needed. SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) is a promising but challenging drug target due to its intrinsic proofreading exoribonuclease (ExoN). Remdesivir targeting SARS-CoV-2 RdRp exerts high drug efficacy in vitro and in vivo. However, its underlying inhibitory mechanisms remain elusive. Here, we performed all-atom molecular dynamics simulations with an accumulated simulation time of 24 microseconds to elucidate the molecular mechanisms underlying the inhibitory effects of Remdesivir. We found that Remdesivirs 1-cyano group of possesses the dual role of inhibiting nucleotide addition and proofreading. The presence of its polar 1-cyano group at an upstream site in RdRp causes instability and hampers RdRp translocation. This leads to a delayed chain termination of RNA extension, which may also subsequently reduce the likelihood for Remdesivir to be cleaved by ExoN acting on the 3-terminal nucleotide. In addition, our simulations suggest that Remdesivirs 1-cyano group can also disrupt the cleavage active site of ExoN via steric interactions, leading to a further reduced cleavage efficiency. Our work provides plausible molecular mechanisms on how Remdesivir inhibits viral RNA replication and may guide rational design for new treatments of COVID-19 targeting viral replication.

biophysics↗

bioRxiv2020

Single-cell transcriptomic analysis identifies neocortical developmental differences between human and mouse

BackgroundThe specification and differentiation of neocortical projection neurons is a complex process under precise molecular regulation; however, little is known about the similarities and differences in cerebral cortex development between human and mouse at single-cell resolution. ResultsHere, using single-cell RNA-seq (scRNA-seq) data we explore the divergence and conservation of human and mouse cerebral cortex development using 18,446 and 7,610 neocortical cells. Systematic cross-species comparison reveals that the overall transcriptome profile in human cerebral cortex is similar to that in mouse such as cell types and their markers genes. By single-cell trajectories analysis we find human and mouse excitatory neurons have different developmental trajectories of neocortical projection neurons, ligand-receptor interactions and gene expression patterns. Further analysis reveals a refinement of neuron differentiation that occurred in human but not in mouse, suggesting that excitatory neurons in human undergo refined transcriptional states in later development stage. By contrast, for glial cells and inhibitory neurons we detected conserved developmental trajectories in human and mouse. ConclusionsTaken together, our study integrates scRNA-seq data of cerebral cortex development in human and mouse, and uncovers distinct developing models in neocortical projection neurons. The earlier activation of cognition -related genes in human may explain the differences in behavior, learning or memory abilities between the two species.

bioinformatics↗

bioRxiv2020

Human-lineage-specific genomic elements: relevance to neurodegenerative disease and APOE transcript usage

Knowledge of genomic features specific to the human lineage may provide insights into brain-related diseases. We leverage high-depth whole genome sequencing data to generate a combined annotation identifying regions simultaneously depleted for genetic variation (constrained regions) and poorly conserved across primates. We propose that these constrained, non-conserved regions (CNCRs) have been subject to human-specific purifying selection and are enriched for brain-specific elements. We find that CNCRs are depleted from protein-coding genes but enriched within lncRNAs. We demonstrate that per-SNP heritability of a range of brain-relevant phenotypes are enriched within CNCRs. We find that genes implicated in neurological diseases have high CNCR density, including APOE, highlighting an unannotated intron-3 retention event. Using human brain RNA-sequencing data, we show the intron-3-retaining transcript/s to be more abundant in Alzheimers disease with more severe tau and amyloid pathological burden. Thus, we demonstrate the importance of human-lineage-specific sequences in brain development and neurological disease. We release our annotation through vizER (https://snca.atica.um.es/browser/app/vizER).

neuroscience↗

bioRxiv2020

Room-temperature-storable PCR Mixes for SARS-CoV-2 Detection

A novel coronavirus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2) emerged in late 2019, causing an outbreak of pneumonia [coronavirus disease 2019 (COVID-19)] in Wuhan, China, which then rapidly spread globally. Although the use of ready-made reaction mixes can enable more rapid PCR-based diagnosis of COVID-19, the need to transport and store these mixes at low temperatures presents challenges to already overburdened logistics networks. Here, we present an optimized freeze-drying procedure that allows SARS-CoV-2 PCR mixes to be transported and stored at ambient temperatures, without loss of activity. Additive-supplemented PCR mixes were freeze-dried. The residual moisture of the freeze-dried PCR mixes was measured by Karl-Fischer titration. We found that freeze-dried PCR mixes with [~]1.2% residual moisture are optimal for storage, transport, and reconstitution. The sensitivity, specificity, and repeatability of the freeze-dried reagents were similar to those of freshly prepared, wet reagents. The freeze-dried mixes retained activity at room temperature (18[~]25{degrees}C) for 28 days, and for 14 and 10 days when stored at 37{degrees}C and 56{degrees}C, respectively. The uptake of this approach will ease logistical challenges faced by transport networks and make more cold storage space available at diagnosis and hospital laboratories. This method can also be applied to the generation of freeze-dried PCR mixes for the detection of other pathogens.

microbiology↗

bioRxiv2020

ZmCLA4 regulates leaf angle through multiple plant hormone-mediated signal pathways in maize

Leaf angle in cereals is an important agronomic trait contributing to plant architecture and grain yield by determining the plant compactness. Although ZmCLA4 was identified to shape plant architecture by affecting leaf angle, the detailed regulatory mechanism of ZmCLA4 in maize remains unclear. ZmCLA4 was identified as a transcriptional repressor using the Gal4-LexA/UAS system and transactivation analysis in yeast. The DNA affinity purification (DAP)-seq assay showed that ZmCLA4 not only acts as a repressor containing the EAR motif (CACCGGAC), but was also found to have two new motifs, CCGARGS and CDTCNTC. On analyzing the ZmCLA4-bound targeted genes, we found that ZmCLA4, as a cross node of multiple plant hormone-mediated pathways, directly bound to ARF22 and IAA26 to regulate auxin transport and mediated brassinosteroid signaling by directly binding to BZR3 and 14-3-3. ZmCLA4 bound two WRKY genes involved with abscisic acid, two genes (CYP75B1, CYP93D1) involved with jasmonic acid, B3 involved in the response to ethylene, and thereby negatively regulated leaf angle formation. We built a new regulatory network for the ZmCLA4 gene controlling leaf angle in maize, which contributed to the understanding of ZmCLA4s regulatory mechanism and will improve grain yields by facilitating optimization of plant architecture.

molecular biology↗

bioRxiv2020

Multiplexed photo-activation of mRNA with single-cell resolution

We demonstrate sequential optical activation of two types of mRNAs in the same mammalian cell through the sequential photocleavage of small molecule caging groups ( photo-cages) tethered to the 5' untranslated region (5'-UTR) of an mRNA. Synthetic photo-cages were conjugated onto target mRNA using RNA-TAG, an enzymatic site-specific RNA modification technique. Translation of mRNA was severely reduced upon conjugation of the photo-cages onto the 5'-UTR. However, subsequent photo-release of the cages from the mRNA transcript triggered activation of translation with single-cell spatiotemporal resolution. To achieve sequential photo-activation of two mRNAs in the same cell, we synthesized a pair of photo-cages which can be selectively cleaved from mRNA upon photo-irradiation with different wavelengths of light. Sequential photo-activation of two mRNAs enabled precise optical control of translation of two unique transcripts. We believe that this modular approach to precisely and rapidly control gene expression will serve as a powerful tool in future biological studies that require controlling translation of multiple transcripts with high spatiotemporal resolution.

biochemistry↗

bioRxiv2020

A single cell atlas reveals distinct immune landscapes in transplant and primary tumors that determine response or resistance to immunotherapy

Despite impressive responses in some patients, immunotherapy fails to cure most cancer patients. Preclinical studies indicate that radiotherapy synergizes with immunotherapy, promoting radiation-induced antitumor immunity. Nearly all preclinical immunotherapy studies utilize transplant tumor models, but cure rates of transplant tumor models treated with immunotherapy often overestimate patient responses. Here, we show that transplant tumors are cured by PD-1 blockade and radiotherapy, but identical treatment fails in autochthonous tumors. We generated a single-cell atlas of tumor-infiltrating immune cells from transplant and primary tumors treated with radiation and immunotherapy, which reveals striking differences in their immune landscapes. Although radiotherapy remodels myeloid cell phenotypes in primary and transplant tumors, only transplant tumors are enriched for CD8+ T cells that mediate tumor clearance while mice with primary sarcomas demonstrate tumor-specific tolerance. These results identify distinct microenvironments in tumors that coevolve with the immune system, which promote tolerance that must be overcome for immune-mediated cancer cures.

cancer biology↗

bioRxiv2020

Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis Mechanisms of SARS-Related Coronaviruses

A novel coronavirus (SARS-CoV-2) is the causative agent of an emergent severe respiratory disease (COVID-19) in humans that is threatening to result in a global health crisis. By using genomic, sequence, structural and evolutionary analysis, we show that Alpha- and Beta-CoVs possess several novel families of immunoglobulin (Ig) domain proteins, including ORF8 and ORF7a from SARS-related coronaviruses and two protein groups from certain Alpha-CoVs. Among them, ORF8 is distinguished in being rapidly evolving, possessing a unique insert and a hypervariable position among SARS-CoV-2 genomes in its predicted ligand-binding groove. We also uncover many Ig proteins from several metazoan viruses which are distinct in sequence and structure but share an architecture comparable to that of CoV Ig domain proteins. Hence, we propose that deployment of Ig domain proteins is a widely-used strategy by viruses, and SARS-CoV-2 ORF8 is a potential pathogenicity factor which evolves rapidly to counter the immune response and facilitate the transmission between hosts.

microbiology↗

bioRxiv2020

SMRT sequencing generates the chromosome-scale reference genome of tropical fruit mango, Mangifera indica

Mango (Mangifera indica), a member of the family Anacardiaceae, is one of the worlds most popular tropical fruits. Here we sequenced the variety, "Hong Xiang Ya", and generated a 371.6-Mb mango genome assembly with 34,529 predicted protein-coding genes. Aided with the published genetic map, for the first time, we assembled the M. indica genome to the chromosomes, and finally about 98.77% of the genome assembly was anchored to 20 pseudo-chromosomes. The availability of the chromosome-length genome assembly of M. indica will provide novel insights into genome evolution, understand the genetic basis of specialized phytochemical composites relevant to fruit quality, and enhance allele mining in genomics-assisted breeding for mango genetic improvement.

genomics↗

bioRxiv2020

Common postzygotic mutational signature in multiple healthy adult tissues related to embryonic hypoxia

Postzygotic mutations are acquired in all of the normal tissues throughout an individuals lifetime and hold clues for identifying mutagenesis causing factors. The process and underlying mechanism of postzygotic mutations in normal tissues is still poorly understood. In this study, we investigated postzygotic mutation spectra in healthy individuals by optimized ultra-deep exome sequencing of time series samples from the same volunteer and samples from different individuals. In cells of blood, sperm, and muscle, we resolved three common types of mutational signature. Two of them are known to represent clock-like mutational processes, and their proportions in mutation profiles associated with polymorphisms of epigenetic regulation genes, suggesting the contribution of personal genetic backgrounds to underlying biological process. Notably, the third signature, characterized by C>T transitions at GpCpN sites, tends to be a feature of diverse normal tissues. Mutations of this type were likely to occur early in embryo development even before the tissue differentiation, as indicated by their relatively high allele frequencies, sharing variants between multiple tissues, and lacking of age-related accumulation. Almost all tumors shown in public datasets did not have this signature detected except for 19.6% of clear cell renal cell carcinoma samples, which featured by activation of the hypoxia-induced signaling pathway. Moreover, in vitro activation of HIF signaling pathway successfully introduced the corresponding mutation profile of this signature in a culture-expanded human embryonic stem cell line. Therefore, embryonic hypoxia may explain this novel signature across multiple normal tissues. Our study suggest hypoxic conditions in the early stage of embryo development may be a crucial factor for the C>T transitions at GpCpN sites and individual genetic background also related to shaping human postzygotic mutation profiles.

genetics↗