Biology subjects

Zhou, W.

Publications and source records attributed to Zhou, W..

At least 307 records · Page 17Linked to original sources

bioRxiv2020

Prophylactic and therapeutic HBV vaccination by an HBs-expressing cytomegalovirus vector lacking an interferon antagonist

Cytomegalovirus (CMV)-based vaccines show promising effects against chronic infections in non-human primates. Therefore, we examined the potential of HBV vaccines based on mouse CMV (MCMV) vectors expressing the small HBsAg. Immunological consequences of vaccine virus attenuation were addressed by either replacing the dispensable gene m157 ( MCMV-HBs) or the gene M27 ( {Delta}M27-HBs), the latter encodes a potent interferon antagonist targeting the transcription factor STAT2. M27 was chosen, since human cytomegalovirus (HCMV) encodes an analogous gene product, which also induced proteasomal STAT2 degradation by exploiting Cullin RING ubiquitin ligases. Vaccinated mice were challenged with HBV through hydrodynamic injection. MCMV-HBs and {Delta}M27-HBs vaccination achieved accelerated HBV clearance in serum and liver as well as robust HBV-specific CD8+ T cell responses. When we explored the therapeutic potential of MCMV-based vaccines, especially the combination of {Delta}M27-HBs prime and DNA boost vaccination resulted in increased intrahepatic HBs-specific CD8+ T cell responses and HBV clearance in persistently infected mice. Our results demonstrated that vaccines based on a replication competent MCMV attenuated through the deletion of an interferon antagonist targeting STAT2 elicit robust anti-HBV immune responses and mediate HBV clearance in mice in prophylactic and therapeutic immunization regimes.

immunology↗

bioRxiv2020

An enhanced characterization of the human skin microbiome: a new biodiversity of microbial interactions

The healthy human skin microbiome is shaped by skin site physiology, individual-specific factors, and is largely stable over time despite significant environmental perturbation. Studies identifying these characteristics used shotgun metagenomic sequencing for high resolution reconstruction of the bacteria, fungi, and viruses in the community. However, these conclusions were drawn from a relatively small proportion of the total sequence reads analyzable by mapping to known reference genomes. Reference-free approaches, based on de novo assembly of reads into genome fragments, are also limited in their ability to capture low abundance species, small genomes, and to discriminate between more similar genomes. To account for the large fraction of non-human unmapped reads on the skin--referred to as microbial dark matter--we used a hybrid de novo and reference-based approach to annotate a metagenomic dataset of 698 healthy human skin samples. This approach reduced the overall proportion of uncharacterized reads from 42% to 17%. With our refined characterization, we revisited assumptions about the skin microbiome, and demonstrated higher biodiversity and lower stability, particularly in dry and moist skin sites. To investigate hypotheses underlying stability, we examined growth dynamics and interspecies interactions in these communities. Surprisingly, even though most skin sites were relatively stable, many dominant skin microbes, including Cutibacterium acnes and staphylococci, were actively growing in the skin, with poor or no relationship between growth rate and relative abundance, suggesting that host selection or interspecies competition may be important factors maintaining community homeostasis. To investigate other mechanisms facilitating adaptation to a specific skin site, we identified Staphylococcus epidermidis genes that are likely involved in stress response and provide mechanisms essential for growth in oily sites. Finally, horizontal gene transfer--another mechanism of competition by which strains may swap antagonistic or virulent coding regions--was relatively limited in healthy skin, but suggested exchange of different metabolic and environmental tolerance pathways. Altogether, our findings underscore the value of a combined reference-based and de novo approach to provide significant new insights into microbial composition, physiology, and interspecies interactions to maintain community homeostasis in the healthy human skin microbiome.

microbiology↗

bioRxiv2020

Molecular Choreography of Acute Exercise

Exercise testing is routinely used in clinical practice to assess fitness - a strong predictor of survival - as well as causes of exercise limitations. While these studies often focus on cardiopulmonary response and selected molecular pathways, the dynamic system-wide molecular response to exercise has not been fully characterized. We performed a longitudinal multi-omic profiling of plasma and peripheral blood mononuclear cells including transcriptome, immunome, proteome, metabolome and lipidome in 36 well-characterized volunteers before and after a controlled bout of acute exercise (2, 15, 30 min and 1 hour in recovery). Integrative analysis revealed an orchestrated choreography of biological processes across key tissues. Most of these processes were dampened in insulin resistant participants. Finally, we discovered biological pathways involved in exercise capacity and developed prediction models revealing potential resting blood-based biomarkers of fitness.

systems biology↗

bioRxiv2020

Human papillomavirus 16 positive cervical cancer in Guatemala: The D2 and D3 sublineages differ in integration rate and age of diagnosis

Human papillomavirus (HPV) 16 displays substantial sequence variation; four HPV16 lineages (A, B, C, D) have been described, as well as multiple sub-lineages. To identify molecular events associated with HPV16 carcinogenesis we evaluated viral variation, the integration of HPV16, and somatic mutation in 96 cervical cancer samples from Guatemala. A total of 64% (60/94) of the samples had integrated HPV16 sequences, and integration was associated with an earlier age of diagnosis (P=0.0007) and pre-menopausal disease. HPV16 integration sites were broadly distributed in the genome but in one tumor, HPV16 integrated into the promoter of the interferon regulatory factor 4 (IRF4) gene, which plays an important role in the regulation of the interferon response to viral infection. The HPV16 D2 and D3 sub-lineages were found in 23% and 30% of the tumors, respectively and were significantly associated with adenocarcinoma. D2-positive tumors had a higher rate of integration (P=0.011), earlier age of diagnosis (P=0.012), and a lower rate of somatic mutation (P=0.03). Whereas D3-positive tumors are less likely to integrate, have later age-of-diagnosis, and a higher rate of somatic mutation. In conclusion, Guatemalan cervical tumors have a high frequency of the very high-risk HPV16 D2 and D3 sub-lineages and cervical cancer patients with these variants of HPV16 differ in histology, age of- diagnosis, integration, and somatic mutation frequency. In summary, related lineages of HPV16 have different features of oncogenicity.

cancer biology↗

bioRxiv2020

A general role of zinc binding domain revealed by structures of σ28-dependent transcribing complexes

In bacteria, {sigma}28 is the flagella-specific sigma factor that controls the expression of flagella-related genes involving bacterial motility and chemotaxis. However, its transcriptional mechanism remains largely unclear. Here we report cryo-EM structures of {sigma}28-dependent transcribing complexes on a complete flagella-specific DNA promoter. The structures reveal how {sigma}28-RNA polymerase (RNAP) recognizes promoter DNA through strong interaction with -10 element but weak contact with -35 element to initiate transcription. In addition, we observed a distinct architecture in which the {beta}' zinc binding domain (ZBD) of RNAP stretches out from its canonical position to interact with the upstream non-template strand. Further in vitro and in vivo assays demonstrate that this interaction facilitates the isomerization of RNAP-promoter closed to open complex due to compensating the weak interaction between {sigma}4/-35 element, and suggest that ZBD-relocation is a general mechanism employed by the {sigma}70-family factors to enhance transcription from promoters with weak {sigma}4/-35 element interactions.

molecular biology↗

bioRxiv2019

Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

Gut microbial communities can respond to antibiotic perturbations by rapidly altering their taxonomic and functional composition. However, little is known about the strain-level processes that drive this collective response. Here we characterize the gut microbiome of a single individual at high temporal and genetic resolution through a period of health, disease, antibiotic treatment, and recovery. We used deep, linked-read metagenomic sequencing to track the longitudinal trajectories of thousands of single nucleotide variants within 36 species, which allowed us to contrast these genetic dynamics with the ecological fluctuations at the species level. We found that antibiotics can drive rapid shifts in the genetic composition of individual species, often involving incomplete genome-wide sweeps of pre-existing variants. These genetic changes were frequently observed in species without obvious changes in species abundance, emphasizing the importance of monitoring diversity below the species level. We also found that many sweeping variants quickly reverted to their baseline levels once antibiotic treatment had concluded, demonstrating that the ecological resilience of the microbiota can sometimes extend all the way down to the genetic level. Our results provide new insights into the population genetic forces that shape individual microbiomes on therapeutically relevant timescales, with potential implications for personalized health and disease.

microbiology↗

bioRxiv2019

Moxifloxacin efficacy against Mycobacterium abscessus in vivo using zebrafish model

Moxifloxacin (MFX) showed good activity in vitro against Mycobacterium abscessus (M. abscessus) and was suggested as one of the antibiotic regimens for adults with M. abscessus disease. However, some other studies showed that MFX showed less or none activity against M. abscessus. In our study we aim to evaluate MFX activity against M. abscessus using zebrafish (ZF) model in vivo. MIC of each drugs were determined by broth microdilution method. M. abscessus labeled by CM-DiI, were micro-injected into ZF. Survival curves were determined by recording dead ZF every day. After 4 days of incubation ZF were lysed. Colony-forming unit (CFU) were enumerated and results are expressed as mean log10 CFU per ZF. Bacteria dissemination and fluorescence intensity in ZF were observed and analyzed. Inhibition rate was also calculated. In our study MFX showed good activity in vitro. But in vivo MFX showed limited restriction to M. abscessus. The association between increased survival and high dose of MFX is not significant. Same results were observed in bacterial fluorescence intensity and inhibition rates, with no significant difference when compared with no drug group (P > 0.05). However, significant difference was observed in azithromycin (AZM) group. MFX showed limited efficacy on Mycobacterium abscessus in vivo using ZF model. MFXs activity in vivo need to be confirmed.

microbiology↗

bioRxiv2019

Biodiversity-based innovations fortify agricultural growth in Asia-Pacific economies

The Green Revolution (GR) is widely credited with alleviating famine, mitigating poverty and driving aggregate economic growth over the past 6 decades. In Asia, GR technologies secured a tripling of rice output, with one-off germplasm improvements providing benefits beyond US$ 4.3 billion/year. Here, we unveil the magnitude and macro-economic relevance of parallel biodiversity-induced productivity growth in non-rice crops from 1918 to 2018. We empirically demonstrate how biological control (BC) defused invasive pest threats in multiple agricultural commodities, ensuring annually-accruing (on-farm) benefits of US$ 22.6 billion/year. Scientifically-guided BC permitted 73-100% yield-loss recovery in critical food, feed and fiber crops including cassava, banana, breadfruit and coconut. As such, BC promoted rural growth and prosperity even in marginal, poorly-endowed, non-rice environments. By placing agro-ecological innovations on equal footing with input-intensive measures, our work provides lessons for future efforts to mitigate invasive species, restore ecological resilience and sustainably raise output of global agri-food systems.

ecology↗

bioRxiv2019

Spatiotemporal Control of CRISPR/Cas9 Function in Cells and Zebrafish using Light-Activated Guide RNA

We developed a new method for conditional regulation of CRISPR/Cas9 activity in mammalian cells and zebrafish embryos via photochemically activated, caged guide RNAs. Caged gRNAs are generated by substituting four nucleobases evenly distributed throughout the 5-protospacer region with caged nucleobases during synthesis. Caging confers complete suppression of gRNA:target dsDNA hybridization and rapid restoration of CRISPR/Cas9 function upon optical activation. This tool offers simplicity and complete programmability in design, high spatiotemporal specificity in cells and zebrafish embryos, excellent off to on switching, and stability by preserving the ability to form Cas9:gRNA ribonucleoprotein complexes. caged gRNAs are novel tools for conditional control of gene editing thereby enabling the investigation of spatiotemporally complex physiological events by obtaining a better understanding of dynamic gene regulation.

developmental biology↗

bioRxiv2019

Effects of CXCL12/CXCR4/CXCR7 axis on human sperm motility and chemotaxis

Mammalian spermatozoa undergo a series of functional changes in the female genital tract before they can fertilize oocytes. Chemokines and their receptors are involved in these complex biological events. However, the detailed molecular mechanisms on the modulation of chemokines on spermatozoa still need to be elucidated. CXCL12, a chemokine, has been widely studied in leukocyte migration and. Here we found that CXCL12 was existent in human cumulus cells and follicular fluid and its receptors CXCR4 and CXCR7 were co-expressed on human spermatozoa. We investigated the effects of CXCL12 on various biological functions of human sperm and which receptor plays a dominant role in these processes. We found that CXCL12 could promote human sperm chemotaxis, motility, penetration in the mucus, acrosome reaction and Ca2+ influx through CXCR4 rather than CXCR7. In addition, the simplified physical model reasonably explained the change of sperm velocity under the influence of CXCL12 concentration gradient, which was identical to their physiological motion patterns.

cell biology↗

bioRxiv2019

Single-cell ATAC-seq Signal Extraction and Enhancement with SCATE

Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) is the state-of-the-art technology for analyzing genome-wide regulatory landscape in single cells. Single-cell ATAC-seq data are sparse and noisy. Analyzing such data is challenging. Existing computational methods cannot accurately reconstruct activities of individual cis-regulatory elements (CREs) in individual cells or rare cell subpopulations. We present a new statistical framework, SCATE, that adaptively integrates information from co-activated CREs, similar cells, and publicly available regulome data to substantially increase the accuracy for estimating activities of individual CREs. We show that using SCATE, one can better reconstruct the regulatory landscape of a heterogeneous sample.

genomics↗

bioRxiv2019

GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling

Transcriptional repression needs to be rapidly reversible during embryonic development. This extends to the Hedgehog pathway, which primarily serves to counter GLI repression by processing GLI proteins into transcriptional activators. In investigating the mechanisms underlying GLI repression, we find that a subset of these regions, termed HH-responsive enhancers, specifically loses acetylation in the absence of HH signaling. These regions are highly enriched around HH target genes and primarily drive HH-specific limb activity. They also retain H3K27ac enrichment in limb buds devoid of GLI activator and repressor, indicating that their activity is primarily regulated by GLI repression. The Polycomb repression complex is not active at most of these regions, suggesting it is not a major mechanism of GLI repression. We propose a model for tissue-specific enhancer activity in which an HDAC-associated GLI repression complex regulates target gene expression by altering the acetylation status at enhancers.

developmental biology↗

bioRxiv2019

Age-related Gene Expression Signatures (AGES) in rats demonstrate early, late, and linear transcriptional changes from multiple tissues

In order to understand changes in gene expression that occur as a result of age, which might create a permissive or causal environment for age-related diseases, we produced a multi-timepoint Age-related Gene Expression Signature (AGES) from liver, kidney, skeletal muscle and hippocampus of rats, comparing 6, 9, 12, 18, 21, 24 and 27-month old animals. We focused on genes that changed in one direction throughout the lifespan of the animal, either early in life (early logistic changes); at mid-age (mid-logistic); late in life (late-logistic); or linearly, throughout the lifespan. The pathways perturbed as a result of chronological age demonstrate organ-specific and more global effects of aging, and point to mechanisms that might be counter-regulated pharmacologically in order to treat age-associated diseases. A small number of genes were regulated by aging in the same manner in every tissue, suggesting they may be more universal markers of aging.

systems biology↗

bioRxiv2019

Minor QTLs mining through the combination of GWAS and machine learning feature selection

IntroductionMinor QTLs mining has a very important role in genomic selection, pathway analysis and trait development in agricultural and biological research. Since most individual loci contribute little to complex trait variations, it remains a challenge for traditional statistical methods to identify minor QTLs with subtle phenotypic effects. Here we applied a new framework which combined the GWAS analysis and machine learning feature selection to explore new ways for the study of minor QTLs mining.\n\nResultsWe studied the soybean branching trait with the 2,137 accessions from soybean (Glycine max) diversity panel, which was sequenced by 50k SNP chips with 42,080 valid SNPs. First as a baseline study, we conducted the GWAS GAPIT analysis, and we found that only one SNP marker significantly associated with soybean branching was identified. We then combined the GWAS analysis and feature importance analysis with Random Forest score analysis and permutation analysis. Our analysis results showed that there are 36,077 features (SNPs) identified by Random Forest score analysis, and 2,098 features (SNPs) identified by permutation analysis. In total, there are 1,770 features (SNPs) confirmed by both of the Random Forest score analysis and the permutation analysis. Based on our analysis, 328 branching development related genes were identified. A further analysis on GO (gene ontology) term enrichment were applied on these 328 genes. And the gene location and gene expression of these identified genes were provided.\n\nConclusionsWe find that the combined analysis with GWAS and machine learning feature selection shows significant identification power for minor QTLs mining. The presented research results on minor QTLs mining will help understand the biological activities that lie between genotype and phenotype in terms of causal networks of interacting genes. This study will potentially contribute to effective genomic selection in plant breeding and help broaden the way of molecular breeding in plants.

bioinformatics↗

bioRxiv2019

Prolonged podocyte depletion in larval zebrafish resembles mammalian focal and segmental glomerulosclerosis

Although FSGS has been in the scientific focus for many years, it is still a massive burden for patients with no causal therapeutic option. In FSGS, podocytes are injured, parietal epithelial cells (PECs) are activated and engage in the formation of cellular lesions leading to progressive glomerular scarring. Herein we show that podocyte-depleted zebrafish larvae develop acute proteinuria, severe foot process effacement and activate PECs which create cellular lesions and deposit extracellular matrix on the glomerular tuft. We therefore propose that this model shows features of human FSGS and show its applicability for a high-throughput drug screening assay.

pathology↗

bioRxiv2019

Minor QTLs mining through the combination of GWAS and machine learning feature selection

bioinformatics↗

bioRxiv2019

UK-Biobank Whole Exome Sequence Binary Phenome Analysis with Robust Region-based Rare Variant Test

In biobank data analysis, most binary phenotypes have unbalanced case-control ratios, which can cause inflation of type I error rates. Recently, a saddlepoint approximation (SPA) based single variant test has been developed to provide an accurate and scalable method to test for associations of such phenotypes. For gene- or region-based multiple variant tests, a few methods exist which adjust for unbalanced case-control ratios; however, these methods are either less accurate when case-control ratios are extremely unbalanced or not scalable for large data analyses. To address these problems, we propose SKAT/SKAT-O type region-based tests, where the single-variant score statistic is calibrated based on SPA and Efficient Resampling (ER). Through simulation studies, we show that the proposed method provides well-calibrated p-values. In contrast, the unadjusted approach has greatly inflated type I error rates (90 times of exome-wide =2.5x10-6) when the case-control ratio is 1:99. Additionally, the proposed method has similar computation time as the unadjusted approaches and is scalable for large sample data. Our UK Biobank whole exome sequence data analysis of 45,596 unrelated European samples and 791 PheCode phenotypes identified 10 rare variant associations with p-value < 10-7, including the associations between JAK2 and myeloproliferative disease, TNC and large cell lymphoma and F11 and congenital coagulation defects. All analysis summary results are publicly available through a web-based visual server.

genetics↗

bioRxiv2019

Different Expressions of IL-1 TNF-α P-selectin mRNA by Endothelial Cells after Vein Thrombosis

[Abstract]O_ST_ABSObjectiveC_ST_ABSExperiments were designed to compare the expressions of IL-1 TNF- P-selectin mRNA by porcine endothelial cells after vein thrombosis.\n\nMethodsIVC under the renal vein of 20 porcines were ligated to induce thrombosis modes. These thrombosed veins were divided into three groups:group A-one day after thrombosis, group B-four days after thrombosis and group C-seven days after thrombosis. The other pigs were given the shame operation as a contro group (group D). The mRNA levels of IL-1 TNF- and P-selectin expressed by porcine endothelial cells in three groups were analy sed by semi quantitative RT-PCR. Endothelial cells were harvested with collagenase II.\n\nResultsThe purity of endothelial cells harvested was 99.42 {+/-}0.07. The expression of IL-1 was detained only in group A while TNF-reached its peak in group B(P <0.05) and P-selectin increased gradually with the days passing by(P <0.05).\n\nConclusionEndothelial cells are not only the target cells of inflammatory mediators, but also can express a variety of active factors to promote venous thrombosis. Expression of TNF- mRNA is increased gradually in the early period of vein thrombosis while P-selectin in the acute period; IL-1 mRNA was transiently expressed only in the early stage of thrombosis.

microbiology↗