Biology subjects

Zhao, F.

Publications and source records attributed to Zhao, F..

At least 127 records · Page 7Linked to original sources

bioRxiv2021

Identifying long non-coding RNAs and characterizing their functional roles in swine mammary gland from colostrogenesis to lactogenesis

Long non-coding RNAs (lncRNAs) play important regulatory roles in milk biological processes. While, little is known about the identification and function of swine lncRNAs in response to mammary gland development. Here, we identified 286 differentially expressed (DE) lncRNAs in mammary gland at different stages from 14 days prior to (-) parturition to day 1 after (+) parturition using the published RNA-seq data. The expression pattern of these DE lncRNAs was examined, and most of lncRNAs expressions were strongly changed from Day -2 to Day +1. Functional annotation revealed that the DE lncRNAs were mainly involved in the mammary gland developing, lactation developing, milk composition metabolism and colostrum function. By performing the weighted gene co-expression network analysis (WGCNA), we identified 7 out of 12 lncRNA-mRNA modules, including 35 lncRNAs and 319 mRNAs, which were highly associated with the mammary gland at Day -14, Day -2 and Day +1. Integrated analysis of the DE lncRNAs expression pattern examination, targets prediction, function annotation and WGCNA suggested that 18 lncRNAs (such as, XLOC_020627, ENSSSCG00000051193, XLOC_025150, ENSSSCG00000042618, XLOC_963181, ENSSSCG00000051701, XLOC_018030, and XLOC_025146) and their 20 target genes (such as, ACTN4, ADCY1, CSN3, SMO, CSN2, PRKAG2, FIBCD1, and GALNT7), were considered as the promising candidates for swine parturition and colostrum occurrence processes. Our research provided the insights into lncRNA profiles and their regulating mechanisms from colostrogenesis to lactogenesis in swine.

genetics↗

bioRxiv2020

Body site-specific and disease-specific virulome in the human microbiome

Human body habitats are home to a diverse array of microbes, and within these microbial ecosystems, there are exchanges of genetic material, including virulence factors (VFs). Little is known about the diversity and abundance of VFs in different body sites and different types of diseases. We developed a virulome analysis pipeline using the species-specific sequence identity inferred from intraspecies ANI values to precisely assign reads to virulence factors. We characterized the human virulome from four body habitats, including the gut, oral cavity, skin, and vagina. Specifically, the diversity and abundance of VFs in the oral cavity were significantly higher than those in other body sites, including stool. We highlight the importance of sex-specific analysis when studying the human virulome. We analyzed data from more than 4,000 samples across healthy and diseased subjects and 13 types of diseases from different metagenomic sequencing studies to characterize the disease-specific virulome. Atherosclerotic cardiovascular disease (ACVD) has a more diverse virulome than other diseases tested. Notably, many VFs, including genes for secretion systems and toxins, are more abundant in diseased subjects than in healthy controls. We present, to our knowledge, the most comprehensive healthy and diseased virulome dataset yet created.

genomics↗

bioRxiv2020

First Glimpse of Gut Microbiota of Quarantine Insects in China

Quarantine insects are economically important pests that frequently invade new habitats. A rapid and accurate monitoring method to trace the geographical source of invaders is therefore needed for prevention, detection, and eradication. Current methods based on insect genetics are often too slow. We developed a novel tracing method based on insect gut microbiota. The source location of microbiota of insects can be used to rapidly determine the insects geographic origin. We analyzed 179 gut microbiota samples belonging to 591 individuals of 22 quarantine insect species collected from 36 regions in China and abroad. The gut microbiotas of these insects mainly included Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Proteobacteria, and Tenericutes. The diversity of the insect gut microbiota was closely related to geographic and environmental factors. Different insect species could be distinguished at the phylum level of microbiota. Populations of individual insect species from different regions could be distinguished at the genus level of microbiota. A method for determining the geographical origin of invasive insect species was tentatively established, but its practical applicability requires further study.

microbiology↗

bioRxiv2020

Environmental conditions and diffusion-limited microbial transfer drive specific microbial communities detected at different sections in oil-production reservoir with water-flooding

This study investigated the distribution of microbial communities in the oilfield production facilities of a water-flooding petroleum reservoir and the roles of environmental variation, microorganisms in injected water, and diffusion-limited microbial transfer in structuring the microbial communities. Similar bacterial communities were observed in surface water-injection facilities dominated by aerobic or facultative anaerobic Betaproteobacteria, Alphaproteobacteria, and Flavobacteria. Distinct bacterial communities were observed in downhole of the water-injection wells dominated by Clostridia, Deltaproteobacteria, Anaerolineae, and Synergistia, and in the oil-production wells dominated by Gammaproteobacteria, Betaproteobacteria, and Epsilonproteobacteria. Methanosaeta, Methanobacterium, and Methanolinea were dominant archaeal taxa in the water-injection facilities, while the oil-production wells were predominated by Methanosaeta, Methanomethylovorans, and Methanocalculus. Energy, nucleotide, translation, and glycan biosynthesis metabolisms were more active in the downhole of the water-injection wells, while bacterial chemotaxis, biofilm formation, two-component system, and xenobiotic biodegradation was associated with the oil-production wells. The number of shared OTUs and its positive correlation with formation permeability revealed differential diffusion-limited microbial transfer in oil-production facilities. The overall results indicate that environmental variation and microorganisms in injected water are the determinants that structure microbial communities in water-injection facilities, and the determinants in oil-bearing strata are environmental variation and diffusion-limited microbial transfer. IMPORTANCEWater-flooding continually inoculates petroleum reservoirs with exogenous microorganisms, nutrients, and oxygen. However, how this process influences the subsurface microbial community of the whole production process remains unclear. In this study, we investigated the spatial distribution of microbial communities in the oilfield production facilities of a water-flooding petroleum reservoir, and comprehensively illustrate the roles of environmental variation, microorganisms in injected water, and diffusion-limited microbial transfer in structuring the microbial communities. The results advance fundamental understanding on petroleum reservoir ecosystems that subjected to anthropogenic perturbations during oil production processes.

microbiology↗

bioRxiv2020

High-resolution electrochemistry of the extracellular electron transfer of Escherichia coli

Escherichia coli is one of the most important model bacteria in microorganism research and is broadly encountered in nature. In the present study, a wild-type E. coli strain K-12 was used for electrochemical investigations. Differential pulse voltammetry showed five pairs of redox peaks both for K-12 cells and the supernatant with potentials (anodic/cathodic) at -0.450/-0.378, -0.125/-0.105, -0.075/-0.055, +0.192/+0.264, and +0.300/+0.414 V (vs. Ag/AgCl), respectively. Chronoamperometry indicates that K-12 cells can produce immediate current by addition of glucose. The current production from K-12 can be 8-fold enhanced by 10.0 M exogenetic vitamin K3, but addition of 10.0 M riboflavin did not enhance the current production. Medium replacement experiments show that 50 % of the K-12 biofilm current was produced via direct extracellular electron transfer pathways. The study provides new insight in the voltammetry of strain K-12 and confirms that E. coli is an electrochemically active bacterium. E. coli has the potential to serve as a model bacterium for studying microbial extracellular electron transfer mechanisms.

microbiology↗

bioRxiv2020

Gene replacement of α-globin with β-globin restores hemoglobin balance in β-thalassemia-derived hematopoietic stem and progenitor cells

{beta}-thalassemia pathology is not only due to loss of {beta}-globin (HBB), but also erythrotoxic accumulation and aggregation of the {beta}-globin binding partner, -globin (HBA1/2). Here we describe a Cas9/AAV6-mediated genome editing strategy that can replace the entire HBA1 gene with a full-length HBB transgene in {beta}-thalassemia-derived hematopoietic stem and progenitor cells (HSPCs), which is sufficient to normalize {beta}-globin:-globin mRNA and protein ratios and restore functional adult hemoglobin tetramers in patient-derived red blood cells. Edited HSPCs were capable of long-term and bi-lineage hematopoietic reconstitution in mice, establishing proof-of-concept for replacement of HBA1 with HBB as a novel therapeutic strategy for curing {beta}-thalassemia.

molecular biology↗

bioRxiv2020

MiRNA-223 Inhibits MouseGallstone Formation by Targeting Key Transporters in Hepatobiliary Cholesterol Secretion Pathway

BackgroudMiRNA-223 has previously been reported to play an essential role in hepatic cholesterol homeostasis by suppressing cholesterol synthesis, attenuating cholesterol uptake by hepatocyte from and promoting cholesterol efflux into the blood. However, its role in regulation of biliary cholesterol secretion and gallstone formation remains unknown. MethodsMice with conventional knockout (KO), hepatocyte-specific knockout ({Delta}Hepa) / knockdown (KD) or gain expression of miRNA-223 were included in the study and were subjected to lithogenic diet (LD) for various weeks. The gallbladders were harvested and subjected to cholesterol crystal imaging and gallstone mass measurement. Liver tissues were collected for western blotting, RT-qPCR, and immunohistochemistry staining. Levels of cholesterol, bile salt, phospholipids, and triglyceride were determined in serum, liver tissues, and bile by enzyme color reactive assays. 3 UTR reporter gene assays were used to verify the direct target genes for miRNA-223. ResultsLD-induced gallstone formation was remarkably accelerated in miRNA-223 KO, {Delta}Hepa, and KD mice with concurrent enhancement in total cholesterol levels in liver tissue and bile. Key biliary cholesterol transporters ABCG5 and ABCG8 were identified as direct targets of miRNA-223. Reversely, AAV-mediated hepatocyte-specific miRNA-223 overexpression prevented gallstone progression with reduced targets protein expression. ConclusionThe present study demonstrates a novel role of miRNA-223 in the regulation of hepatic bile cholesterol secretion pathway and gallstone formation by targeting ABCG5 and ABCG8 expression. Therefore, elevating miRNA-223 would be a potentially novel approach to overcome the sternness of cholesterol gallstone disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=173 SRC="FIGDIR/small/344580v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1c418bforg.highwire.dtl.DTLVardef@134e20dorg.highwire.dtl.DTLVardef@e4e0d2org.highwire.dtl.DTLVardef@641b40_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2020

Auxin guides germ cell specification in Arabidopsis anthers

Germ cells (GCs) transmit genetic information from one generation to the next. Unlike animal GCs, plant GCs are induced post-embryonically, forming locally from somatic cells. This induction is coordinated with organogenesis and might be guided by positional cues. In angiosperms, male GCs initiate from the internal layers at the four corners of the anther primordia and are gradually enclosed by parietal cell (PC) layers, leading to a concentric GC-PC pattern.1,2 However, the underlying mechanism of GC initiation and GC-PC pattern formation is unclear. Auxin affects pattern formation3 and anther development.4-11 However, whether GC formation involves auxin remains unknown. We report that the auxin distribution in pre-meiotic anthers parallels GC initiation, forming a centripetal gradient between the outer primordial cells and the inner GCs. The auxin biosynthesis genes TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 (TAA1) and TRYPTOPHAN AMINOTRANSFERASE RELATED 2 (TAR2)5,12 are responsible for this patterning and essential for GC specification. SPOROCYTELESS/NOZZLE (SPL/NZZ, a determinant for GC specification)13-15 mediates the effect of auxin on GC specification, modulates auxin homeostasis, and maintains centripetal auxin patterning. Our results reveal that auxin is a key factor guiding GC specification in Arabidopsis anthers.

plant biology↗

bioRxiv2020

A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control

The link between gene regulation and morphogenesis of multicellular organisms is a fundamental problem in biology. We address this question in the floral meristem of Arabidopsis, which generates new tissues and organs through complex changes in growth patterns. Starting from high-resolution time-lapse images, we generated a comprehensive 4-D atlas of early flower development including cell lineage, cellular growth rates and the expression patterns of 28 regulatory genes. This information was introduced in MorphoNet, a web-based open-access platform. The application of mechanistic computational models indicated that the molecular network based on the literature only explained a minority of the expression patterns. This was substantially improved by adding single regulatory hypotheses for individual genes. We next used the integrated information to correlate growth with the combinatorial expression of multiple genes. This led us to propose a set of hypotheses for the action of individual genes in morphogenesis, not visible by simply correlating gene expression and growth. This identified the central transcription factor LEAFY as a potential regulator of heterogeneous growth, which was supported by quantifying growth patterns in a leafy mutant. By providing an integrated, multiscale view of flower development, this atlas should represent a fundamental step towards mechanistic multiscale-scale models of flower development.

developmental biology↗

bioRxiv2020

An Organoid for woven Bone

Bone formation (osteogenesis) is a complex process in which cellular differentiation and the generation of a mineralized organic matrix are synchronized to produce a hybrid hierarchical architecture. To study the mechanisms of osteogenesis in health and disease, there is a great need for functional model systems that capture in parallel both cellular and matrix formation processes. Stem cell-based organoids are promising as functional, self-organizing 3D in vitro models for studying the physiology and pathology of various tissues. However, for human bone, no such functional model system is yet available. This study reports the in vitro differentiation of human bone marrow stromal cells into a functional 3D self-organizing co-culture of osteoblasts and osteocytes, creating an organoid for early stage bone (woven bone) formation. It demonstrates the formation of an organoid where osteocytes are embedded within the collagen matrix that is produced by the osteoblasts and mineralized under biological control. Alike in vivo osteocytes the embedded osteocytes show network formation and communication via expression of sclerostin. The current system forms the most complete 3D living in vitro model system to investigate osteogenesis, both in physiological and pathological situations, as well as under influence of external triggers (mechanical stimulation, drug administration).

bioengineering↗

bioRxiv2020

Structural basis of a public antibody response to SARS-CoV-2

Molecular-level understanding of human neutralizing antibody responses to SARS-CoV-2 could accelerate vaccine design and facilitate drug discovery. We analyzed 294 SARS-CoV-2 antibodies and found that IGHV3-53 is the most frequently used IGHV gene for targeting the receptor binding domain (RBD) of the spike (S) protein. We determined crystal structures of two IGHV3-53 neutralizing antibodies +/- Fab CR3022 ranging from 2.33 to 3.11 [A] resolution. The germline-encoded residues of IGHV3-53 dominate binding to the ACE2 binding site epitope with no overlap with the CR3022 epitope. Moreover, IGHV3-53 is used in combination with a very short CDR H3 and different light chains. Overall, IGHV3-53 represents a versatile public VH in neutralizing SARS-CoV-2 antibodies, where their specific germline features and minimal affinity maturation provide important insights for vaccine design and assessing outcomes.

microbiology↗

bioRxiv2020

Rapid isolation of potent SARS-CoV-2 neutralizing antibodies and protection in a small animal model

The development of countermeasures to prevent and treat COVID-19 is a global health priority. In under 7 weeks, we enrolled a cohort of SARS-CoV-2-recovered participants, developed neutralization assays to interrogate serum and monoclonal antibody responses, adapted our high throughput antibody isolation, production and characterization pipeline to rapidly screen over 1000 antigen-specific antibodies, and established an animal model to test protection. We report multiple highly potent neutralizing antibodies (nAbs) and show that passive transfer of a nAb provides protection against high-dose SARS-CoV-2 challenge in Syrian hamsters. The study suggests a role for nAbs in prophylaxis, and potentially therapy, of COVID-19. The nAbs define protective epitopes to guide vaccine design.

immunology↗

bioRxiv2020

Systemic Bone Loss Following Myocardial Infarction in Mice is Mitigated by Treatment with a β3 Adrenergic Receptor Antagonist

Myocardial infarction (MI) and osteoporotic fracture (Fx) are leading causes of morbidity and mortality worldwide, and there is epidemiological evidence linking their incidence, suggesting possible crosstalk. MI can exacerbate underlying atherosclerosis through sympathetic nervous system activation and {beta}3 adrenoreceptor-mediated release of hematopoietic stem cells (HSCs), leading to monocytosis. We hypothesized that this same pathway may initiate systemic bone loss following MI, since osteoclasts differentiate from monocytes. In this study, MI was performed in 12-week-old male mice (n=24), and mice were randomized to treatment with a {beta}3-adrenergic receptor antagonist (SR 59230A) or no treatment for 10 days post-operatively; additional mice (n=21, treated and untreated) served as un-operated controls. Bone mineral density (BMD), bone mineral content (BMC), and body composition were quantified at baseline and 10 days post-MI using DXA; at 10 days post-MI circulating monocyte and neutrophil levels were quantified, and the L5 vertebral body and femur were analyzed with micro-computed tomography. We found that MI led to increases in circulating monocyte and neutrophil levels, but contrary to our initial hypothesis, {beta}3-antagonist treatment further increased circulating monocytes compared to untreated mice. BMD and BMC of MI mice decreased at the femur and lumbar spine (-6.9% femur BMD, -3.5% lumbar BMD); {beta}3-antagonist treatment diminished this bone loss response (-5.3% femur BMD, -1.2% lumbar BMD). Similarly, trabecular bone volume was decreased in MI mice compared to control mice, and this bone loss was partially attenuated by {beta}3-antagonist treatment. These results suggest that MI leads to bone loss at both the axial and appendicular skeleton, and that the sympathetic nervous system may be a modulator of this response. This study is the first to mechanistically show bone loss following an ischemic injury; these findings suggest that bone loss and increased fracture risk may be important clinical co-morbidities following MI or other ischemic injuries.

physiology↗

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↗

bioRxiv2020

Directed assembly and concentrating of micro/nanoparticles, cells, and vesicles via low-power near-infrared laser generated plasmonic microbubbles

Directed assembly and concentrating of micro- and nanoparticles via laser generated plasmonic microbubbles in a liquid environment is an emerging technology. For effective heating, visible light has been primarily employed in existing demonstrations. In this paper, we demonstrate a new plasmonic platform based on nanoporous gold disk (NPGD) array. Thanks to the highly tunable localized surface plasmon resonance of the NPGD array, microbubble of controlled size can be generated by near-infrared (NIR) light. Using NIR light provides several key advantages over visible light in less interference with standard microscopy and fluorescence imaging, preventing fluorescence photobleaching, less susceptible to absorption and scattering in turbid biological media, and much reduced photochemistry, phototoxicity and whatsoever. The large surface-to-volume ratio of NPGD further facilitates the heat transfer from these gold nanoheaters to the surroundings, achieving unprecedented low-power operation. While the microbubble is formed, the surrounding liquid circulates and direct microparticles randomly dispersed in the liquid to the bottom NPGD surface, yielding unique assemblies of microstructures. Such capability can also be employed in concentrating suspended colloidal nanoparticles at desirable sites and with preferred configuration, both enhancing the sensor performance. In addition to various micro- and nanoparticles, the plasmonic microbubbles are also shown to collect biological cells and nanovesicles. By using a spatial light modulator (SLM) to project the laser in arbitrary patterns, parallel assembly can be achieved to fabricate an array of clusters. These assemblies have been characterized using optical microscopy, scanning electron microscope, hyperspectral localized surface plasmon resonance imaging and hyperspectral Raman imaging.

bioengineering↗

bioRxiv2020

m6A Regulates Liver Metabolic Disorders and Hepatogenous Diabetes

N6-methyladenosine (m6A) RNA methylation is one of the most abundant modifications on mRNAs and plays an important role in various biological processes. The formation of m6A is catalysed by a methyltransferase complex containing a key factor methyltransferase-like 3 (Mettl3). However, the functions of Mettl3 and m6A modification in liver lipid and glucose metabolism remain unclear. Here, we show that both Mettl3 expression and m6A level increased in the liver of mice with High Fat Diet (HFD)-induced metabolic disorders, and overexpression of Mettl3 aggravated HFD-induced liver metabolic disorders and insulin resistance. Hepatocyte-specific knockout of Mettl3 significantly alleviated HFD-induced metabolic disorders by slowing weight gain, reducing lipid accumulation and improving insulin sensitivity. Mechanistically, Mettl3 depletion-mediated m6A loss causes extended RNA half-lives of metabolism-related genes, consequently protects mice against HFD-induced metabolic syndrome. Our findings reveal a critical role of Mettl3-mediated m6A in HFD-induced metabolic disorders and hepatogenous diabetes.

genetics↗

bioRxiv2019

Deep learning enables structured illumination microscopy with low light levels and enhanced speed

Using deep learning to augment structured illumination microscopy (SIM), we obtained a fivefold reduction in the number of raw images required for super-resolution SIM, and generated images under extreme low light conditions (100X fewer photons). We validated the performance of deep neural networks on different cellular structures and achieved multi-color, live-cell super-resolution imaging with greatly reduced photobleaching.

biophysics↗

bioRxiv2019

aCPSF1 controlled archaeal transcription termination: a prototypical eukaryotic model

Transcription termination defines RNA 3'-ends and guarantees programmed transcriptomes, thus is an essential biological process for life. However, transcription termination mechanisms remain almost unknown in Archaea. Here reported the first general transcription termination factor of Archaea, the conserved ribonuclease aCPSF1, and elucidated its 3'-end cleavage dependent termination mechanism. Depletion of Mmp-aCPSF1 in a methanoarchaeon Methanococcus maripaludis caused a genome-wide transcription termination defect and overall transcriptome chaos, and cold-sensitive growth. Transcript-3'end-sequencing (Term-seq) revealed transcriptions mostly terminated downstream of a uridine-rich terminator motif, where Mmp-aCPSF1 performed cleavage. The endoribonuclease activity was determined essential to terminate transcription in vivo as well. Through super-resolution photoactivated localization microscopy imaging, co-immunoprecipitation, and chromatin immunoprecipitation, we demonstrated that Mmp-aCPSF1 localizes within nucleoid and associates with RNAP and chromosomes. aCPSF1 appears to co-evolve with archaeal RNAPs, and two distant orthologs each from Lokiarchaeota and Thaumarchaeota could replace Mmp-aCPSF1 to termination transcription. Thus, aCPSF1 dependent termination mechanism could be universally employed in Archaea, including Lokiarchaeota, one supposed archaeal ancestor of Eukaryotes. Therefore, the reported aCPSF1 cleavage-dependent termination mode not only hints an archetype of Eukaryotic 3'-end processing/cleavage triggered RNAP II termination, but also would shed lights on understanding the complex eukaryotic termination based on the simplified archaeal model.

microbiology↗