Biology subjects

Wang, M.

Publications and source records attributed to Wang, M..

At least 883 records · Page 49Linked to original sources

bioRxiv2019

Exploring the influence of surface proteins on probiotic activity of Lactobacillus pentosus HC-2 in Litopenaeus vannamei midgut via Label-free quantitative proteomic analysis

Our previously work showed that Lactobacillus pentosus HC-2 as probiotic could improve the growth performance, immune response, gut bacteria diversity and disease resistance of Litopenaeus vannamei. However, the probiotic mechanism of was not fully characterized. In the present study, histology and proteomic analysis was performed to explore the influence of HC-2 surface protein on its probiotic effects to L. vannamei after feeding the intact surface proteins or the probiotic treated with lithium chloride (LiCl) to remove non-covalently bound surface proteins or no probiotic for four weeks. Histological observation found that feeding with normal HC-2 obviously improved the intestinal histology and enhanced the protective effect against pathogens damages, but fed with LiCl-treated HC-2 didnt improve the intestinal environment. A total over 2,764 Peptides and 1,118 uniproteins were identified from L. vannamei midgut, 211 proteins were significant differentially expressed normal HC-2 group compared with control, 510 proteins were significant differentially expressed in LiCl-tread HC-2 group compared with control, and 458 proteins were significant differentially expressed in LiCl-tread HC-2 group compared with normal HC-2 group. GO/KEGG enrichment analysis of the significantly different proteins demonstrated that fed with normal HC-2 mainly induced immune response, metabolic, cell adhesion and cell-cell signaling related proteins up-regulation, which were contributed to bacteria adhesion and colonization in midgut to improve shrimp immune system and growth, but these proteins were suppressed after feeding with deprived surface proteins bacteria. Taken together, these results indicating that the surface proteins were indispensable for HC-2 to execute probiotic effects in midgut of shrimp.

microbiology↗

bioRxiv2019

\"Low-cost\" initial burst of root development in whole Fagus crenata seedlings: The key to survival?

Terrestrial plants are rooted in one place, and therefore their metabolism must be flexible to adapt to continuously changing environments. This flexibility is probably influenced by the divergent metabolic traits of plant organs. However, direct measurements on organ-specific metabolic rates are particularly scarce and little is known about their roles in determining whole-individual meatabolism. To reveal this on seedlings of Fagus crenata, which is one of the most widespread dominant genus in temperate deciduous broad leaf forests in the circum-polar Northern Hemisphere, we measured respiration, fresh mass and surface area for total leaves, stems and roots of 55 individuals in two years from germination and analyzed their relationships with individual metabolism. Proportion of roots to whole plant in mass increased from approximately 17% to 74%, and that in surface area increased from about 11% to 82% in the two years. Nonetheless, the increment of the proportion of root respiration to whole-plant respiration was from 9.2% to only 40%, revealing that the increment in mass and surface area of roots was much larger than the increment in energetic cost. As a result, only the roots showed a substantial decline in both respiration/surface area and respiration/mass among the three organs; roots had about 90% decline in their respiration/surface area, and 84% decline in their respiration/mass, while those in leaves and stems were relatively constant. The low-cost and rapid root development is specific to the two years after germination and would be effective for avoiding water and nutrient deficit, and possibly helps seedling survival. This drastic shift in structure and function with efficient energy use in developmental change from seeds to seedlings may underpin the establishment of F. crenata forests. We discuss significance of lowering energetic cost for various individual organisms to effectively acquire resources from a wide perspective of view.

plant biology↗

bioRxiv2019

Primary Studies on the Effect of Microbially Coalbed Methane Enhancement in Suit in the Qinshui Basin

Methods used to yield bio-methane with coal to increase coalbed methane reserves had researched, thus providing a means for improving gas drainage efficiency. One such method utilized to convert coal into gas involves coal biodegradation technology. In order to confirm the practical application of this technology, the experiments were conducted in wells, Z-159, Z-163, Z-167, and Z-7H, in the Qinshui Basin in China, and the duration of the experiments was 32 months. Cl- ion tracer, number changes of Methanogen sp., and coal bed biome evolution indicated that the culture medium diffused in the Z-159 and Z-7H wells. These wells resumed gas production separately. Gasification of coal lasted 635 and 799 days, and yielded 74817 m3 and 251754 m3 coalbed methane in Z-159 and Z-7H wells, respectively. Results demonstrate that coalbed methane enhancement with biogasification of coal is a potential technical to achieve the productivity improvement of coalbed methane wells.

bioengineering↗

bioRxiv2019

Fundamental contribution and host range determination of ANP32 protein family in influenza A virus polymerase activity

The polymerase of the influenza virus is part of the key machinery necessary for viral replication. However, the avian influenza virus polymerase is restricted in mammalian cells. The cellular protein ANP32A has been recently found to interact with viral polymerase, and to both influence polymerase activity and interspecies restriction. Here we report that either ANP32A or ANP32B is indispensable for influenza A virus RNA replication. The contribution of ANP32B is equal to that of ANP32A, and together they play a fundamental role in the activity of mammalian influenza A virus polymerase, while neither human ANP32A nor ANP32B support the activity of avian viral polymerase. Interestingly, we found that avian ANP32B was naturally inactive, leaving ANP32A alone to support viral replication. Two amino acid mutations at sites 129-130 in chicken ANP32B lead to the loss of support of viral replication and weak interaction with the viral polymerase complex, and these amino acids are also crucial in the maintenance of viral polymerase activity in other ANP32 proteins. Our findings strongly support ANP32A&B as key factors for both virus replication and adaption. IMPORTANCEThe key host factors involved in the influenza A viral the polymerase activity and RNA replication remain largely unknown. Here we provide evidence that ANP32A and ANP32B from different species are powerful factors in the maintenance of viral polymerase activity. Human ANP32A and ANP32B contribute equally to support human influenza virus RNA replication. However, unlike avian ANP32A, the avian ANP32B is evolutionarily non-functional in supporting viral replication because of a 129-130 site mutation. The 129-130 site plays an important role in ANP32A/B and viral polymerase interaction, therefore determine viral replication, suggesting a novel interface as a potential target for the development of anti-influenza strategies.

microbiology↗

bioRxiv2019

A chromosome-level genome of black rockfish, Sebastes schlegelii, provides insights into the evolution of live birth

Black rockfish (Sebastes schlegelii) is a teleost species where eggs are fertilized internally and retained in the maternal reproductive system, where they undergo development until live birth (termed viviparity). In the present study, we report a chromosome-level black rockfish genome assembly. High-throughput transcriptome analysis (RNA-seq and ATAC-seq), coupled with in situ hybridization (ISH) and immunofluorescence, identify several candidate genes for maternal preparation, sperm storage and release, and hatching. We propose that zona pellucida (ZP) genes retain sperm at the oocyte envelope, while genes in two distinct astacin metalloproteinase subfamilies serve to release sperm from the ZP and free the embryo from chorion at pre-hatching stage. Finally, we present a model of black rockfish reproduction, and propose that the rockfish ovarian wall has a similar function to uterus of mammals. Taken together, these genomic data reveal unprecedented insights into the evolution of an unusual teleost life history strategy, and provide a sound foundation for studying viviparity in non-mammalian vertebrates and an invaluable resource for rockfish ecology and evolution research.

genomics↗

bioRxiv2019

Immune gene expression profiling reveals heterogeneity in luminal breast tumors

Disease heterogeneity of immune gene expression patterns of luminal breast cancer (BC) has not been well studied. We performed immune gene expression profiling of tumor and adjacent normal tissue in 92 Asian luminal BC patients and identified three distinct immune subtypes. Tumors in one subtype exhibited signs of T-cell activation, lower ESR1/ESR2 expression ratio and higher expression of immune checkpoint genes, nonsynonymous mutation burden, APOBEC-signature mutations, and increasing body mass index compared to other luminal tumors. Tumors in a second subtype were characterized by increased expression of interferon-stimulated genes and enrichment for TP53 somatic mutations. The presence of three immune subtypes within luminal BC was replicated in cases drawn from The Cancer Genome Atlas and a Korean breast cancer study. Our findings suggest that immune gene expression and associated genomic features could be useful to further stratify luminal BC beyond the current luminal A/B classification.

genomics↗

bioRxiv2019

Time- and size-resolved bacterial aerosol dynamics in highly polluted air: new clues for haze formation mechanism

Aerosol chemistry is often studied without considering microbial involvements. Here, we have applied a high-volume (1 m3/min) aerosol sampler and the Micro-Orifice Uniform Deposit Impactor (NanoMoudi) along with molecular and microscopic methods to investigate time-and size-resolved bacterial aerosol dynamics in air. Under high particulate matter (PM) polluted episodes, bacterial aerosols were detected to have a viability up to 50-70% in the 0.56-1 m size range, at which elevated levels of SO42-, NO3- and NH4+ were concurrently observed. Engineered or acclimated for both pharmaceuticals and wastewater treatment, bacteria such as Psychrobacter spp., Massilia spp., Acinetobacter lwoffii, Exiguobacterium aurantiacum, and Bacillus megaterium were shown to have experienced massive abundance shifts in polluted air on early mornings and late afternoons, on which were previously reported to witness rapid new particle formation events. For example, Acinetobacter spp. were shown to account for > 96% abundance at a corresponding PM2.5 level of 208 ng/m3. The bacterial aerosol changes corresponded to the observed PM2.5 mass peak shift from 3.2-5.6 m to the high viability size range of 0.56-1m. Additionally, it is interesting that elevated levels of soluble Na, Ca, Mg, K, Al, Fe and P elements that are required for bacterial growth were observed to co-occur with those significant bacterial aerosol structure shifts in the air. For particular time-resolved PM2.5 pollution episodes, Acinetobacter and Massilia were shown to alternate in dominating the time-resolved aerosol community structures. The results from a HYSPLIT trajectory model simulation suggested that the role by air mass transport in affecting the observed bacterial aerosol dynamics could be minor. As an evidence, we found that Acinetobacter, Psychrobacter, Exiguobacterium, and Bacillus genera were emitted into the air with a level of > 3000 CFU/m3 from a pharmaceutical plant. In addition, high level of VOCs up to 15,030 ppbv, mainly Acetone (61%) and Acetaldehyde (11%), were also detected in the air inside the plant. All the data including size-resolved viability and time-resolved bacterial aerosol dynamics together with their growth conditions detected in the air suggested that airborne bacteria in the size range of 0.56- 1m could have played important roles for haze formation in Beijing. The results about time- and size-resolved bacterial aerosol dynamics from this work provide a fresh understanding of aerosol chemistry especially in highly polluted air. It is hoped that these findings could lend a support in future cost-effective air pollution control practices.

microbiology↗

bioRxiv2019

Gene Panel Sequencing in a Chinese High-risk Breast Cancer Cohort

Currently, over 20 genes have been defined that can confer susceptibility for high-risk breast cancer. Although research has proved the utility of multiple-gene sequencing in the assessment of breast cancer risk, there is little data from China patients. Here, we use a multiple-gene sequencing panel to identify the variant spectrum in Chinese high-risk breast cancer subjects.\n\nA total of 829 Chinese high-risk breast cancer patients participated in the research. The coding regions of 115 hereditary cancer susceptibility genes were sequenced using a next generation sequencing platform. In total, 193 pathogenic variants were identified in 45 genes from 177 patients. The pathogenic variant carrier rate is 21.4%: with 10.5% patients carrying a BRCA1 or BRCA2 mutation only, 10.0% of patients carried non-BRCA gene mutations only, while 1.0% of patients carried both a BRCA1/2 and a non-BRCA gene mutation. Variants of uncertain significance (VUS) totaling 2632 were identified in 115 genes from 787 of 829 patients: 82.5% patients carried more than one VUS, and only 5.1% patients did not carry any VUS. Families carrying pathogenic variants were tracked and adenoma was founded in three of them. Our data provide a comprehensive analysis of potential susceptibility variations of high-risk for breast cancer in a Chinese population. This data will be useful for the comparison of the susceptibility variation spectrum between different populations and to discover potential pathogenic variants to improve the prevention and treatment of high-risk breast cancer.

cancer biology↗

bioRxiv2019

iTALK: an R Package to Characterize and Illustrate Intercellular Communication

Crosstalk between tumor cells and other cells within the tumor microenvironment (TME) plays a crucial role in tumor progression, metastases, and therapy resistance. We present iTALK, a computational approach to characterize and illustrate intercellular communication signals in the multicellular tumor ecosystem using single-cell RNA sequencing data. iTALK can in principle be used to dissect the complexity, diversity, and dynamics of cell-cell communication from a wide range of cellular processes.

cancer biology↗

bioRxiv2019

Functional dissection of Alzheimer’s disease brain gene expression signatures in humans and mouse models

Human brain transcriptomes can highlight biological pathways associated with Alzheimers disease (AD); however, challenges remain to link expression changes with causal triggers. We have examined 30 AD-associated, gene coexpression modules from human brains for overlap with 251 differentially-expressed gene sets from mouse brain RNA-sequencing experiments, including from models of AD and other neurodegenerative disorders. Human-mouse overlaps highlight responses to amyloid versus neurofibrillary tangle pathology and further reveal age- and sex-dependent expression signatures for AD progression. Human coexpression modules enriched for neuronal and/or microglial genes overlap broadly with signatures from mouse models of AD, Huntingtons disease, Amyotrophic Lateral Sclerosis, and also aging. Several human AD coexpression modules, including those implicated in the unfolded protein response and oxidative phosphorylation, were not activated in AD models, but instead were detected following other, unexpected mouse genetic manipulations. Our results comprise a powerful, cross-species resource and pinpoint experimental models for diverse features of AD pathophysiology from human brain transcriptomes.

systems biology↗

bioRxiv2019

Meta-analysis of the human brain transcriptome identifies heterogeneity across human AD coexpression modules robust to sample collection and methodological approach

Alzheimers disease (AD) is a complex and heterogenous brain disease that affects multiple inter-related biological processes. This complexity contributes, in part, to existing difficulties in the identification of successful disease-modifying therapeutic strategies. To address this, systems approaches are being used to characterize AD-related disruption in molecular state. To evaluate the consistency across these molecular models, a consensus atlas of the human brain transcriptome was developed through coexpression meta-analysis across the AMP-AD consortium. Consensus analysis was performed across five coexpression methods used to analyze RNA-seq data collected from 2114 samples across 7 brain regions and 3 research studies. From this analysis, five consensus clusters were identified that described the major sources of AD-related alterations in transcriptional state that were consistent across studies, methods, and samples. AD genetic associations, previously studied AD-related biological processes, and AD targets under active investigation were enriched in only three of these five clusters. The remaining two clusters demonstrated strong heterogeneity between males and females in AD-related expression that was consistently observed across studies. AD transcriptional modules identified by systems analysis of individual AMP-AD teams were all represented in one of these five consensus clusters except ROS/MAP-identified Module 109, which was specific for genes that showed the strongest association with changes in AD-related gene expression across consensus clusters. The other two AMP-AD transcriptional analyses reported modules that were enriched in one of the two sex-specific Consensus Clusters. The fifth cluster has not been previously identified and was enriched for genes related to proteostasis. This study provides an atlas to map across biological inquiries of AD with the goal of supporting an expansion in AD target discovery efforts.

systems biology↗

bioRxiv2018

Integrative analysis with expanded DNA methylation data reveals common key regulators and pathways in cancers

The integration of genomic and DNA methylation data has been demonstrated as a powerful strategy in understanding cancer mechanisms and identifying therapeutic targets. The TCGA consortium has mapped DNA methylation in thousands of cancer samples using Illumina Infinium Human Methylation 450K BeadChip (Illumina 450K array) that only covers about 1.5% of CpGs in the human genome. Therefore, increasing the coverage of the DNA methylome would significantly leverage the usage of the TCGA data. Here, we present a new model called EAGLING that can expand the Illumina 450K array data 18 times to cover about 30% of the CpGs in the human genome. We applied it to analyze 13 cancers in TCGA. By integrating the expanded methylation, gene expression and somatic mutation data, we identified the genes showing differential patterns in each of the 13 cancers. Many of the triple-evidenced genes identified in the majority of the cancers are biomarkers or potential biomarkers. Pan-cancer analysis also revealed the pathways in which the triple-evidenced genes are enriched, which include well known ones as well as new ones such as axonal guidance signaling pathway and pathways related to inflammatory processing or inflammation response. Triple-evidenced genes, particularly TNXB, RRM2, CELSR3, SLC16A3, FANCI, MMP9, MMP11, SIK1, TRIM59, showed superior predictive power in both tumor diagnosis and prognosis. These results have demonstrated that the integrative analysis using the expanded methylation data is powerful in identifying critical genes/pathways that may serve as new therapeutic targets.

bioinformatics↗

bioRxiv2018

Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

Complete ammonia oxidizing bacteria (CAOB) have been recognized as a new member of ammonia-oxidizing microorganisms (AOMs) due to its single-step nitrification capability. However, the abundance and diversity of CAOB in environmental ecosystems were still far from known owing to the lack of specific molecular marker. Herein, a universal primer set specifically targeting the both clades of CAOB amoA gene with high specificity and coverage was successfully designed. Intriguingly, real-time quantitative PCR tests revealed that CAOB were ubiquitous and unexpectedly abundant in agricultural soils, river sediments, intertidal zones, drinking water and wastewater treatment systems. Phylogenetic analysis indicated that clade A existed in all the five types of ecosystems, while clade B were only detected in soil and sediment samples. Four sub-clusters were further classified within clade A, in which N. nitrosa cluster dominated CAOB amoA in activated sludge samples while the new recognized soil cluster was the primary constitute in soils. Moreover, the niche specialization between different CAOB species and the environmental conditions were supposed to be the primary driven force to shape the diversity and community of CAOB. This study provided a strong evidence in support of the ubiquities and high abundances of CAOB in various environmental ecosystems and highlighted the significance of including CAOB as the new member of AOMs to re-evaluate the biogeochemical nitrogen cycle.

microbiology↗

bioRxiv2018

Cell-to-cell variation in defective virus expression and effects on host responses during influenza virus infection

Virus and host factors contribute to cell-to-cell variation in viral infections and determine the outcome of the overall infection. However, the extent of the variability at the single cell level and how it impacts virus-host interactions at a systems level are not well understood. To characterize the dynamics of viral transcription and host responses, we used single-cell RNA sequencing to quantify at multiple time points the host and viral transcriptomes of human A549 cells and primary bronchial epithelial cells infected with influenza A virus. We observed substantial variability of viral transcription between cells, including the accumulation of defective viral genomes (DVGs) that impact viral replication. We show a correlation between DVGs and viral-induced variation of the host transcriptional program and an association between differential induction of innate immune response genes and attenuated viral transcription in subpopulations of cells. These observations at the single cell level improve our understanding of the complex virus-host interplay during influenza infection.\n\nIMPORTANCEDefective influenza virus particles generated during viral replication carry incomplete viral genomes and can interfere with the replication of competent viruses. These defective genomes are thought to modulate disease severity and pathogenicity of the influenza infection. Different defective viral genomes also introduce another source of variation across a heterogeneous cell population. Evaluating the impact of defective virus genomes on host cell responses cannot be fully resolved at the population level, requiring single cell transcriptional profiling. Here we characterized virus and host transcriptomes in individual influenza-infected cells, including that of defective viruses that arise during influenza A virus infection. We established an association between defective virus transcription and host responses and validated interfering and immunostimulatory functions of identified dominant defective virus genome species in vitro. This study demonstrates the intricate effects of defective viral genomes on host transcriptional responses and highlights the importance of capturing host-virus interactions at the single-cell level.

microbiology↗

bioRxiv2018

A novel polyphasic identification system for genus Trichoderma

As the rapid-changing in Trichoderma taxonomy, an efficient identification of Trichoderma species is an urgent issue for Trichoderma-based research. In this study, based on the current taxonomy of Trichoderma, we constructed curated databases including 338 ITS sequences, 435 TEF1 sequences, 415 RPB2 sequences and 28 phenotypic characters. In addition, a polyphasic identification system (PIST) was developed. Within PIST, the resolution ability of molecular and phenotype characters could be combined for species identification in a step-by-step way. Compared with other identification systems, the involved Trichoderma species were extended from 88 to 252 species and 175 from 188 tested Trichoderma species could be identified within PIST. In most tested cases, three nucleotide markers and phenotypic characters showed improved identification performance. The TEF1 sequences have superior resolution than other characters.\n\nImportanceThe genus Trichoderma is important to human society with a wide application in industry, agriculture and environment bio-remediation. Thus, a quick and accurate identification of Trichoderma spp. is paramount since it is usually the first step to conduct a Trichoderma-based scientific research and is an obstruction especially for those researchers as nematologist, chemists, nutritionist and the like, lacking of taxonomic knowledge of fungi.

microbiology↗

bioRxiv2018

From copy number alterations to structural variants: the evolutionary cascade of papillary renal cell carcinomas

Intratumor heterogeneity (ITH) and tumor evolution have been well described for clear cell renal cell carcinomas (ccRCC), but they are less studied for other kidney cancer subtypes. Here we investigate ITH and clonal evolution of papillary renal cell carcinoma (pRCC) and rarer kidney cancer subtypes, integrating whole-genome sequencing and DNA methylation data. In 29 tumors, up to 10 samples from the center to the periphery of each tumor, and metastatic samples in 2 cases, enable phylogenetic analysis of spatial features of clonal expansion, which shows congruent patterns of genomic and epigenomic evolution. In contrast to previous studies of ccRCC, in pRCC driver gene mutations and most arm-level somatic copy number alterations (SCNAs) are clonal. These findings suggest that a single biopsy would be sufficient to identify the important genetic drivers and targeting large-scale SCNAs may improve pRCC treatment, which is currently poor. While type 1 pRCC displays near absence of structural variants (SVs), the more aggressive type 2 pRCC and the rarer subtypes have numerous SVs, which should be pursued for prognostic significance.

genomics↗

bioRxiv2018

Genomic analysis of dingoes identifies genomic regions under reversible selection during domestication and feralization

Dingoes (Canis dingo) are wild canids living in Australia. They have lived isolated from both the wild and the domestic ancestor and are a unique model for studying feralization, the process in which a domestic species escapes human control, adapts to the wild, and diverges from the domestic ancestor into a genetically distinct population. Here, we sequenced the genomes of 10 dingoes and 2 New Guinea Singing Dogs, to study the origins and feralization process of the dingo. Phylogenetic and demographic analyses show that dingoes originate from domestic dogs in southern East Asia, which migrated via Island Southeast Asia to reach Australia 4300-5000 years ago, and subsequently diverged into a genetically distinct population. Selection analysis identified 99 positively selected genes enriched in starch and fat metabolism pathways, indicating a diet change during feralization of dingoes. Interestingly, we found that 14 genes have shifted allele frequencies compared to dogs but not compared to wolves. This suggests that the selection affecting these genes during domestication of the wolf was reversed in the feralization process. One of these genes, ARHGEF7, may promote the formation of neural spine and synapses in hippocampal neurons. Functional assays showed that an A to G mutation in ARHGEF7, located in a transcription factor-binding site, decreases the endogenous expression. This suggests that ARHGEF7 may have been under selection for behavioral adaptations related to the transitions in environment both from wild to domestic and from domestic back to wild. Our results indicate that adaptation to domestication and feralization primarily affected different genomic regions, but that some genes, related to neurodevelopment, metabolism and reproduction, may have been reversibly affected in the two processes.

genomics↗

bioRxiv2018

Multiscale causal network models of Alzheimer’s disease identify VGF as a key regulator of disease

Though discovered over 100 years ago, the molecular foundation of sporadic Alzheimers disease (AD) remains elusive. To elucidate its complex nature, we constructed multiscale causal network models on a large human AD multi-omics dataset, integrating clinical features of AD, DNA variation, and gene and protein expression into probabilistic causal models that enabled detection and prioritization of high-confidence key drivers of AD, including the top predicted key driver VGF. Overexpression of neuropeptide precursor VGF in 5xFAD mice partially rescued beta-amyloid-mediated memory impairment and neuropathology. Molecular validation of network predictions downstream of VGF was achieved, with significant enrichment for homologous genes identified as differentially expressed in 5xFAD brains overexpressing VGF versus controls. Our findings support a causal and/or protective role for VGF in AD pathogenesis and progression.\n\nOne sentence summaryVGF protects against Alzheimers disease

genomics↗