Biology subjects

Zhang, H.

Publications and source records attributed to Zhang, H..

At least 955 records · Page 53Linked to original sources

bioRxiv2022

Manganese-dependent microRNA trimming by 3'->5' exonucleases generates 14-nucleotide or shorter tiny RNAs

MicroRNAs (miRNAs) are about 22-nucleotide (nt) non-coding RNAs forming the effector complexes with Argonaute (AGO) proteins to repress gene expression. Although tiny RNAs (tyRNAs) shorter than 19 nt have been found to bind to plant and vertebrate AGOs, their biogenesis remains a long-standing question. Here, our in vivo and in vitro studies show several 3[->]5 exonucleases, such as interferon-stimulated gene 20 kDa (ISG20), three prime repair exonuclease 1 (TREX1), and ERI1 (enhanced RNAi, also known as 3hExo), capable of trimming AGO-associated full-length miRNAs to 14 nt or shorter tyRNAs. Their guide trimming occurs in a manganese-dependent manner but independently of the guide sequence and the loaded four human AGO paralogs. We also show that ISG20-mediated guide trimming makes Argonaute3 (AGO3) a slicer. Given the high Mn2+ concentrations in stressed cells, virus-infected cells, and neurodegeneration, our study sheds light on the roles of the Mn2+-dependent exonucleases in remodeling gene silencing.

molecular biology↗

bioRxiv2022

Feasibility Analyses and Experimental Confirmation of Dove Prism Based Dual-fiberscope Rotary Joint

Two-photon fluorescence microscopy has enjoyed its wide adoption in neuroscience. Head-mounted miniaturized fiberscopes offered an exciting opportunity for enabling neural imaging in freely-behaving animals with high 3D resolution. Here we propose a dual-fiberscope rotary joint based on a Dove prism, for enabling simultaneous two-photon imaging of two brain regions with two fiberscopes in freely-walking/rotating mice. Analytic proof has confirmed the key properties of a Dove prism. Feasibility analyses and proof-of-concept experimental results have demonstrated the feasibility of such a rotary joint for allowing two fiberscopes to rotate simultaneously while maintaining an excellent single-mode fiber-to-fiber coupling for the excitation femtosecond laser. Fiberscopes with a dual-probe rotary joint offer an exciting opportunity to explore neural network dynamics of multiple interconnected brain regions in freely-walking rotating animals.

neuroscience↗

bioRxiv2022

The giant diploid faba genome unlocks variation in a global protein crop

Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emission and loss of biodiversity. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value. Faba bean (Vicia faba L.) has a high yield potential and is well-suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has grown to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, though with significant copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association (GWA) analysis to dissect the genetic basis of hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate improvement of sustainable protein production across Mediterranean, subtropical, and northern temperate agro-ecological zones.

plant biology↗

bioRxiv2022

Down-regulated GAS6 impairs synovial macrophage efferocytosis and promotes obesity-associated osteoarthritis

Obesity has always been considered a significant risk factor in OA progression, but the underlying mechanism of obesity-related inflammation in OA synovitis remains unclear. The present study found that synovial macrophages infiltrated and polarized in the obesity microenvironment and identified the essential role of M1 macrophages in impaired macrophage efferocytosis using pathology analysis of obesity-associated OA. The present study revealed that obese OA patients and ApoE-/- mice showed a more pronounced synovitis and enhanced macrophage infiltration in synovial tissue, accompanied by dominant M1 macrophage polarization. Obese OA mice had a more severe cartilage destruction and increased levels of synovial apoptotic cells than OA mice in the control group. Enhanced M1-polarized macrophages in obese synovium decreased growth arrest-specific 6 (GAS6) secretion, resulting in impaired macrophage efferocytosis in synovial apoptotic cells. Intracellular contents released by accumulated apoptotic cells further triggered an immune response and lead to a release of inflammatory factors, such as TNF-, IL-1{beta}, and IL-6, which induce chondrocyte homeostasis dysfunction in obese OA patients. Intra-articular injection of GAS6 restored the phagocytic capacity of macrophages, reduced the accumulation of local apoptotic cells, and decreased the levels of TUNEL- and caspase-3-positive cells, preserving cartilage thickness and preventing the progression of obesity-associated OA. Therefore, blocking M1 macrophage polarization or intra-articular injection of GAS6 is a potential therapeutic strategy for obesity-associated OA.

immunology↗

bioRxiv2022

origamiFISH allows universal, label-free, single molecule visualization of DNA origami nanodevices across biological samples

Structural DNA nanotechnology enables user-prescribed design of DNA nanostructures (DNs) for biological applications, but how DN design determines their bio-distribution and cellular interactions remain poorly understood. One challenge is that current methods for tracking DN fates in situ, including fluorescent-dye labeling, suffer from low sensitivity and dye-induced artifacts. Here we present origamiFISH, a label-free and universal method for single-molecule fluorescence detection of DNA origami nanostructures in cells and tissues. origamiFISH targets pan-DN scaffold sequences with hybridization chain reaction (HCR) probes to achieve thousand-fold signal amplification. We identify cell-type and shape-specific spatiotemporal uptake patterns within 1 minute of uptake and at picomolar DN concentrations, 10,000x lower than field standards. We additionally optimized compatibility with immunofluorescence and tissue clearing to visualize DN distribution within tissue cryo/vibratome-sections, slice cultures, and whole-mount organoids. Together, origamiFISH enables faithful mapping of DN interactions across subcellular and tissue barriers for guiding the development of DN-based therapeutics.

synthetic biology↗

bioRxiv2022

Synthetic maize centromeres transmit chromosomes across generations

Centromeres are long, often repetitive regions of genomes that bind kinetochore proteins and ensure normal chromosome segregation. Engineering centromeres that function in vivo has proven to be difficult. Here we describe a LexA-CENH3 tethering approach that activates functional centromeres at maize synthetic repeat arrays containing LexO binding sites. The synthetic centromeres are sufficient to cause chromosome breakage and release of chromosome fragments that are passed through meiosis and into progeny. Several independent chromosomes were identified, each with newly created centromeres localized over the repeat arrays where they were directed. The new centromeres were self-sustaining and stably transmitted chromosomes to progeny in the absence of the LexA-CENH3 activator. Our results demonstrate the feasibility of using synthetic centromeres for karyotype engineering applications.

genetics↗

bioRxiv2022

Multi-omics data integration via novel interpretable k-hop graph attention network for signaling network inference

With the advent of sequencing technology, large-scale multi-omics data have been generated to understand the diversity and heterogeneity of genetic targets and associated complex signaling pathways at multiple levels in diseases, which are critical targets to guide the development of personalized precision medicine. However, it remains a challenging task to computationally mine a few essential targets and pathways from a large number of variables characterized by the multi-level multi-omics data. In this study, we proposed a novel interpretable k-hop graph attention network model, k-hop GAT, to integrate the multi-omics data to infer the essential targets and related signaling networks. We evaluated the proposed model using the multi-omics data, i.e., genetic mutation, copy number variation, methylation, gene expression data, of 332 cancer lines; and the experimentally identified essential targets. The validation and comparison results indicated that the proposed model outperformed the GAT and graph convolutional network (GCN) models.

systems biology↗

bioRxiv2022

Droplet microfluidics forward for tracing target cells at single-cell transcriptome resolution

The rapid promotion of single-cell omics in various fields has begun to help solve many problems encountered in research including precision medicine, prenatal diagnosis, and embryo development. Meanwhile, single-cell techniques are also constantly updated with increasing demand. For some specific target cells, the workflow from droplet screening to single-cell sequencing is a preferred option, which also should reduce the impact of operation steps such as demulsification and cell recovery. We developed an all-in-droplet method integrating cell encapsulation, target sorting, droplet picoinjection, and single-cell transcriptome profiling on chips to achieve a labor-saving monitor of TCR-T cells. As a proof of concept, in this research, TCR-T cells were encapsulated, sorted, and performed single-cell transcriptome sequencing (scRNA-seq) by injecting reagents into droplet. It avoided the tedious operation of droplet breakage and re-encapsulation between droplet sorting and scRNA-seq. Moreover, convenient device operation will accelerate the progress of chip marketization. The strategy achieved an excellent recovery performance of single cell transcriptome with a median gene number over 4000 and a cross-contamination rate of 8.2 {+/-} 2%. Furthermore, this strategy allows us to develop a device with high integrability to monitor infused TCR-T cells, which will promote the development of adoptive T cell immunotherapy and their clinical application.

cell biology↗

bioRxiv2022

CTCF and R-loops are boundaries of cohesin-mediated DNA looping

Cohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional (3D) genome organization. Cohesin extrudes DNA loops that are anchored by CTCF in a polar orientation. Here, we present direct evidence that CTCF binding polarity controls cohesin-mediated DNA looping. Using single-molecule imaging of CTCF-cohesin collisions, we demonstrate that a critical N-terminal motif of CTCF blocks cohesin translocation and DNA looping. The cryo-electron microscopy structure of the intact cohesin-CTCF complex reveals that this CTCF motif ahead of zinc-fingers can only reach its binding site on the STAG1 cohesin subunit when the N-terminus of CTCF faces cohesin. Remarkably, a C-terminally oriented CTCF accelerates DNA compaction by cohesin. DNA-bound Cas9 and Cas12a ribonucleoproteins are also polar cohesin barriers, indicating that stalling is intrinsic to cohesin itself, and other proteins can substitute for CTCF in fruit flies and other eukaryotes. Finally, we show that RNA-DNA hybrids (R-loops) block cohesin-mediated DNA compaction in vitro and are enriched with cohesin subunits in vivo, likely forming TAD boundaries. Our results provide direct evidence that CTCF orientation and R-loops shape the 3D genome by directly regulating cohesin.

molecular biology↗

bioRxiv2022

Discovery of a novel monoclonal PD-L1 antibody H1A that promotes T-cell mediated tumor killing activity in renal cell carcinoma

In the last decade, the therapeutic landscape of renal cell carcinoma has rapidly evolved with the addition of PD-1/PD-L1 immune checkpoint inhibitors in the armamentarium of oncologists. Despite clinical evidence of improved oncological outcomes, only a minority of patients experience long-lasting antitumor immune response and complete response. The intrinsic and acquired resistance to PD-1/PD-L1 immune checkpoint blockade is an important challenge for patients and clinicians as no reliable tool has been developed to predict individualized response to immunotherapy. In this study, we demonstrate the translational relevance of an ex-vivo functional assay that measure the tumor cell killing ability of patient-derived CD8 T cells isolated from peripheral blood. Cytotoxic activity of CD8 T cells was improved at 3-month post-radical nephrectomy compared to baseline and it was associated with higher circulating levels of tumor-reactive effector CD8 T cells (CD11ahighCX3CR1+GZMB+). Pretreatment of peripheral immune cells with FDA-approved PD-1/PD-L1 inhibitors enhanced tumor cell killing activity of CD8 T cells but differential response was observed at the individual patient level. Finally, we found a newly developed monoclonal antibody (H1A), which induces PD-L1 degradation, demonstrated superior efficacy in promoting T-cell mediated tumor killing activity compared to FDA-approved PD-1/PD-L1 inhibitors. PBMC immunophenotyping by mass cytometry revealed enrichment of effector CD8 T cells in H1A-treated PBMC. To conclude, our study lays the ground for future investigation of the therapeutic value of H1A as a next-generation immune checkpoint inhibitor. Furthermore, further work is needed to evaluate the potential of measuring T-cell cytotoxicity activity as a tool to predict individual response to immune checkpoint inhibitors in patients with advanced renal cell carcinoma.

immunology↗

bioRxiv2022

A Meta-learning based Graph-Hierarchical Clustering Method for Single Cell RNA-Seq Data

Single cell sequencing techniques enable researchers view complex bio-tissues from a more precise perspective to identify cell types. However, more and more recent works have been done to find more detailed subtypes within already known cell types. Here, we present MeHi-SCC, a method which utilized meta-learning protocol and brought in multi scRNA-seq datasets information in order to assist graph-based hierarchical sub-clustering process. In result, MeHi-SCC outperformed current-prevailing scRNA clustering methods and successfully identified cell subtypes in two large scale cell atlas. Our codes and datasets are available online at https://github.com/biomed-AI/MeHi-SCC

bioinformatics↗

bioRxiv2022

The tea plant (Camellia sinensis) FLOWERING LOCUS C-like gene CsFLC1 is correlated with bud dormancy and triggers early flowering in Arabidopsis

Flowering and bud dormancy are crucial stages in the life cycle of perennial angiosperms in temperate climates. MADS-box family genes are involved in many plant growth and development processes. Here, we identified 3 MADS-box genes in tea plant belonging to the FLOWERING LOCUS C (CsFLC) family. We monitored CsFLC1 transcription throughout the year and found that CsFLC1 was expressed at a higher level during the winter bud dormancy and flowering phases. To clarify the function of CsFLC1, we developed transgenic Arabidopsis thaliana plants heterologously expressing 35S::CsFLC1. These lines bolted and bloomed earlier than the WT (Col-0), and the seed germination rate was inversely proportional to the increased CsFLC1 expression level. RNA-seq of 35S::CsFLC1 transgenic Arabidopsis showed that many genes responding to ageing, flower development and leaf senescence were affected, and phytohormone-related pathways were especially enriched. According to the results of hormone content detection and RNA transcript level analysis, CsFLC1 controls flowering time possibly by regulating SOC1, AGL42, SEP3 and AP3 and hormone signalling, accumulation and metabolism. Our results suggest that CsFLC1 might play dual roles in flowering and winter bud dormancy and provide new insight into the molecular mechanisms of FLC in tea plants as well as other plant species. HighlightThree FLOWERING LOCUS C-like genes were identified in tea plants, among them CsFLC1 played dual roles in flowering and winter bud dormancy.

plant biology↗

bioRxiv2022

A small-molecule lycorine derivative reveals Na+/K+-ATPase α3 as an anti-obesity target

Obesity remains a severe global public health challenge, with contemporary therapeutic approaches primarily focusing on appetite suppression. Here, we discovered HLY72, a lycorine-derived small molecule that potently counteracts obesity in mice at doses without affecting food intake, by promoting sympathetic activation-mediated lipolysis and thermogenesis in adipose tissues. Mass spectrometry identified Na+/K+-ATPase (NKA) 3, the brain-specific isoform, as HLY72s target. Only blood-brain barrier-permeable NKA inhibitors reproduce HLY72s anti-obesity effects, and resistance to HLY72 treatment occurs specifically in NKA 3 (not 1) knockin mice harboring a HLY72-binding mutation. Similar to the chemical inhibition by HLY72, genetic inhibition of NKA 3 also effectively protects mice from diet-induced obesity. These findings point NKA 3 as a potent anti-obesity drug target and highlight HLY72s potential in treating and preventing obesity independent of appetite control.

physiology↗

bioRxiv2022

A phased, chromosome-scale genome of 'Honeycrisp' apple (Malus domestica)

Honeycrisp is one of the most valuable apple cultivars grown in the United States and a popular breeding parent due to its superior fruit quality traits, high levels of cold hardiness, and disease resistance. However, it suffers from a number of physiological disorders and is susceptible to production and postharvest issues. Although several apple genomes have been sequenced in the last decade, there is still a substantial knowledge gap in understanding the genetic mechanisms underlying cultivar-specific traits. Here we present a fully phased, chromosome-level genome of Honeycrisp apples, using PacBio HiFi, Omni-C, and Illumina sequencing platforms. Our genome assembly is by far the most contiguous among all the apple genomes. The sizes of the two assembled haplomes are 674 Mb and 660 Mb, with contig N50s of 32.8 Mb and 31.6 Mb, respectively. In total, 47,563 and 48,655 protein coding genes were annotated from each haplome, capturing 96.8-97.4% complete BUSCOs in the eudicot database, the most complete among all Malus annotations. A gene family analysis using seven Malus genomes shows that a vast majority of Honeycrisp genes are assigned into orthogroups shared with other genomes, but it also reveals 121 Honeycrisp-specific orthogroups. We provide a valuable resource for understanding the genetic basis of horticulturally important traits in apples and other related tree fruit species, including at-harvest and postharvest fruit quality, abiotic stress tolerance, and disease resistance, all of which can enhance breeding efforts in Rosaceae.

genomics↗

bioRxiv2022

Myxococcus xanthus, a nonpathogenic bacterium, eliminates Cryptococcus neoformans, a fungal pathogen of human, independent of cell-cell contact

Each year an estimated 1.2 billion people suffer from fungal diseases and 1.5 - 2 million die from fungal infections - surpassing the loss from malaria and tuberculosis1-3. Due to the similarities between fungal and human cells, the lack of fungal-specific targets has become the major hurdle for antifungal discovery. Many fungi, including the deadly human pathogen Cryptococcus neoformans, are found in soil, where they compete with other microorganisms, including bacteria. However, most bacteria that inhibit fungal growth are pathogens and their antifungal effects strictly rely on cell-cell contact. Here we show that Myxococcus xanthus, a nonpathogenic, soil-dwelling bacterium, efficiently eliminates C. neoformans and strongly inhibits the production of fungal virulence factors. Remarkably, these antifungal activities do not require cell-cell contact. Using fluorescence microscopy, we found that M. xanthus increases the permeability of C. neoformans cells. Our results on the cross-kingdom interaction between M. xanthus and C. neoformans will reveal fundamental mechanisms for bacterial-fungal interactions and suggest novel strategies for antifungal therapies.

microbiology↗

bioRxiv2022

Dinoflagellate Proton-Pump Rhodopsin Gene in Long Island Sound: Diversity and Spatiotemporal Distribution

Microbial proton-pump rhodopsin (PPR), an alternative light-harvesting mechanism to chlorophyll-based photosystems, may contribute significantly to solar energy entry into the marine ecosystem. PPR transforms solar energy to cellular energy used for various metabolic processes in the cells or flagellar movement. Although rhodopsins or their encoding genes have been documented in a wide phylogenetic range of cultured dinoflagellates, information is limited about how widespread and how spatiotemporally dynamical dinoflagellate PPR (DiPPR) are in the marine ecosystem. In this study, using the quantitative PCR method, we investigated the abundance and diversity of DiPPR genes in Long Island Sound (LIS), a temperate estuary, both spatially and temporally in 2010. DiPPR genes were found year-round and throughout LIS, with higher abundances in the eutrophic Western Sound and during April and July. The gene diversity data suggest that there are at least five distinct rhodopsin-harboring groups of dinoflagellates throughout the year. The abundance of DiPPR genes, measured as copy number per mL seawater, appeared not to be influenced by water temperature and nitrogen nutrient concentration; however, weak negative correlations with orthophosphate concentration and salinity and a positive correlation with the abundance of typical-DiPPR-harboring dinoflagellates were observed. The association of DiPPR with phosphorus nutrition warrants further studies.

molecular biology↗

bioRxiv2022

Detection of Frog virus 3 via the system integrating RPA-CRISPR/Cas12a-SPM with deep learning

Frog virus 3 (FV3, genera Ranavirus, family Iridoviridae), a double-stranded DNA virus, results in irreparable damage to biodiversity and significant economic losses to aquaculture. Although the existing FV3 detection methods are of high sensitivity and specificity, the complex procedure and requirement of expensive instruments limit their practical implantation. Herein, we develop a fast, easy-to-implement, highly sensitive, and point-of-care (POC) detection system for FV3. Combining recombinase polymerase amplification (RPA) and CRISPR/Cas12a, we achieve a limit of detection (LoD) of 100 aM (60.2 copies/L) by optimizing RPA primers and CRISPR RNAs (crRNAs). For POC detection, we build a smartphone microscopy (SPM) and achieve an LoD of 10 aM within 40 minutes. Four positive animal-derived samples with a quantitation cycle (Cq) value of quantitative PCR (qPCR) in the range of 13 to 32 are detectable by the proposed system. In addition, we deploy deep learning models for binary classification (positive or negative samples) and multiclass classification (different concentrations of FV3 and negative samples), achieving 100% and 98.75% accuracy, respectively. Without temperature regulation and expensive equipment, RPA-CRISPR/Cas12a combined with a smartphone readout and artificial intelligence (AI) assisted classification shows great potential for FV3 detection. This integrated system holds great promise for POC detection of aquatic DNA pathogens. HighlightsO_LIAn integrated DNA detection system is developed by combining RPA, CRISPR/Cas12a, smartphone microscopy, and deep learning. C_LIO_LIThe LoD of frog virus 3 is 10 aM within 40 min. C_LIO_LIThe detection system shows good performance on animal-derived samples. C_LI

molecular biology↗

bioRxiv2022

DNA capture and loop extrusion dynamics by cohesin-NIPBL

3D chromatin organization plays a critical role in regulating gene expression, DNA replication, recombination, and repair. While initially discovered for its role in sister chromatid cohesion, emerging evidence suggests that the cohesin complex (SMC1, SMC3, RAD21, and SA1/SA2), facilitated by NIPBL, mediates topologically associating domains (TADs) and chromatin loops through DNA loop extrusion. However, information on how conformational changes of cohesin-NIPBL drive its loading onto DNA, initiation, and growth of DNA loops is still lacking. Using high-speed AFM (HS-AFM) imaging, we show that cohesin-NIPBL captures DNA through arm extension, followed by transfer of DNA to its globular domain and DNA loop initiation independent of ATPase hydrolysis. Additional shorter protrusions (feet) from cohesin-NIPBL transiently bind to DNA, facilitating its loading onto DNA. Furthermore, HS-AFM imaging reveals distinct forward and reverse DNA loop extrusion steps by cohesin-NIPBL. These results provide critical missing links in our understanding of DNA binding and loop extrusion by cohesin-NIPBL.

biophysics↗