Biology subjects

Sun, Z.

Publications and source records attributed to Sun, Z..

At least 253 records · Page 14Linked to original sources

bioRxiv2021

Molecular mechanism behind the involvement of apple flavonoid glycosyltransferase gene MdGT1 in the color of apple leaves

Nowadays, the plant family 1 UDP-glycosyltransferases (UGTs) are more and more investigated owing to their contribution to the plant secondary metabolism and diverse biological roles. Apple (Malus domestica) is one of the most widely cultivated fruit trees with great economical importance. However, poor knowledge is known about the apple UGTs. In this study, we identified 229 members of family 1 through a genome-wide analysis of the apple UGTs, which were clustered into 18 groups, from A to R. We also performed detailed analysis to 34 apple UGTs with quantitavive RT-PCR, and discovered a number of stress-regulated UGTs. Among them, we characterized the role of MD09G1064900, also named as MdUGT83L3, which is significantly induced by salt and cold. In vivo analysis showed that it has high activity towards cyanidin, and moderate activity towards quercetin and keampferol. The transgenic callus and regenerated apple plants overexpressing MdUGT83L3 showed enhanced tolerance to salt and cold treatments. Overexpression of MdUGT83L3 also increased anthocyanin accumulation in the callus tissues and enhanced ROS clearing upon exposed to salt and cold stresses. Futhermore, via yeast-two-hybrid assay, EMSA and CHIP analysis, we also found that MdUGT83L3 could be directly regualted by MdMYB88. Our study indicated that MdUGT83L3, under the regulation of MdMYB88, plays important roles in salt and cold stress adaptation via modulating flavonoid metabolism in apple.

molecular biology↗

bioRxiv2021

LRH-1 NUTRIGENOMICS: The Provision of Lauric Acid Results in the Endogenous Production of the Liver Receptor Homolog-1 Ligand, Dilauroylphosphatidylcholine, and LRH-1 Transactivation

BackgroundThe unusual phosphatidylcholine species, dilauroylphosphatidylcholine (DLPC), has been reported to bind and activate the orphan nuclear receptor, liver receptor homolog-1 (LRH-1). To date, DLPC has not been reported endogenously in metabolomic databases. ObjectiveHerein, we test the hypothesis that the provision of the acyl constituent of DLPC, lauric acid (C12:0), a saturated fatty acid rich in tropical oils such as coconut oil, will 1) result in endogenous DLPC production and 2) enhance LRH-1 transcriptional activity. MethodsWe measured DLPC following provision of C12:0 to HepG2 cells, C57/BL6J mice, and to healthy human participants in an acute, randomized, controlled cross-over trial. LRH-1fl/fl and LRH-1fl/fl Albumin-Cre mice were used in ex vivo and in vivo approaches. to assess the impact of C12:0 on LRH-1 target gene expression. 1-13C-lauric acid and methyl-d9-choline were used to assess DLPC production dynamics. ResultsDLPC was not observed in any C12:0-free approach. Provision of C12:0 in the culture media or to C57/BL6J mice resulted in the rapid production of DLPC, including DLPCs presence in multiple LRH-1 expressing tissues. Coconut oil-fed human participants exhibited DLPC in postprandial serum samples. Ex vivo and in vivo C12:0 provision resulted in increased mRNA expression of LRH-1 target genes, an effect that was not observed in hepatic knockout mice. Methyl-d9-choline administration revealed a complex reliance on CDP-choline-derived DLPC. ConclusionC12:0 provision results in endogenous production of the LRH-1 ligand, DLPC, and LRH-1 transcriptional activation phenotypes. Our findings highlight pleiotropic effects of lauric acid, a common hypercholesterolemic dietary saturated fatty acid, secondary to LRH-1 agonism.

physiology↗

bioRxiv2021

Dendritic cell CX3CR1 and macrophages F4/80 play a central role in between gut micro biome and inflammation in Arsenic induced mice

Microbiota plays a crucial role to protect the intestine contrary to the harmful foreign microorganisms and organize the immune system via numerous mechanisms, which include either direct or indirect environmental factors. The underlying mechanism arsenic (As) influenced immune system and regulates inflammation by altering gut microbiome in ileum remains unclear. However, chronic exposure to arsenic (at doses of 0.15 mg or 1.5 mg or 15 mg As2O3/ L in drinking water) significantly increased mRNA and protein levels of F4/80 and CX3CR1, concurrently, the increased levels of mRNA and protein IFN{gamma}, TNF, IL-18 and decreased levels of IL-10 were found in both 3 and 6 months exposure periods. High-throughput sequencing analysis revealed that gut microbiota at phylum; family and taxonomical levels were showed the abundance of gut microbiota. Evidentially, the ultra-structure of intestinal villi, microbes engulfed and immune cell migration were showed by the transmission electron microscopy. Chronic exposure to As influenced the inflammation by changing immune system and altered gut microbiota. In this study we conclude that chronic exposure to As breakdown the normal gut microbial community and increase the pathogenicity, the resultant risk pathogen direct contact with intestinal immune system and regulate the inflammation.

molecular biology↗

bioRxiv2020

Universal Spectrum Identifier for mass spectra

Mass spectra provide the ultimate evidence for supporting the findings of mass spectrometry (MS) proteomics studies in publications, and it is therefore crucial to be able to trace the conclusions back to the spectra. The Universal Spectrum Identifier (USI) provides a standardized mechanism for encoding a virtual path to any mass spectrum contained in datasets deposited to public proteomics repositories. USIs enable greater transparency for providing spectral evidence in support of key findings in publications, with more than 1 billion USI identifications from over 3 billion spectra already available through ProteomeXchange repositories.

bioinformatics↗

bioRxiv2020

Species-resolved sequencing of low-biomass microbiomes by 2bRAD-M

Microbiome samples with low microbial biomass or severe DNA degradation remain challenging for amplicon-based (e.g., 16S/18S-rRNA) or whole-metagenome sequencing (WMS) approaches. Here, we introduce 2bRAD-M, a highly reduced and cost-effective metagenome-sequencing strategy which only sequences ~1% of metagenome and can simultaneously produce species-level bacterial, archaeal, and fungal profiles for low-biomass and highly degraded samples. For mock communities, 2bRAD-M can accurately generate species-level taxonomic profiles for otherwise hard-to-sequence samples with (i) low biomass of merely 1 pg of total DNA, (ii) high host DNA contamination (99%), and (iii) severely fragmented DNA (50-bp) from degraded samples. Tests of 2bRAD-M on stool, skin and environment-surface samples deliver successful reconstruction of comprehensive, high-resolution microbial profiles with agreement across 16S-rRNA, WMS and existing literature. In addition, it enables microbial profiling in formalin-fixed paraffin-embedded (FFPE) cervical tissue samples which were recalcitrant to conventional approaches due to the low amount and heavy degradation of microbial DNA, and discriminated healthy tissue, pre-invasive cancer and invasive cancer via species-level microbial profiles with 91.1% accuracy. Therefore, 2bRAD-M greatly expands the reach of microbiome sequencing.

microbiology↗

bioRxiv2020

A wide-ranging Pseudomonas aeruginosa PeptideAtlas build: a useful proteomic resource for a versatile pathogen.

Pseudomonas aeruginosa is an important opportunistic pathogen with high prevalence in nosocomial infections. This microorganism is a good model for understanding biological processes such as the quorum-sensing response, the metabolic integration of virulence, the mechanisms of global regulation of bacterial physiology, and the evolution of antibiotic resistance. Till now, P. aeruginosa proteomic data, although available in several on-line repositories, were dispersed and difficult to access. In the present work, proteomes of the PAO1 strain grown under very different conditions and from diverse cellular compartments have been analyzed and joined to build the Pseudomonas PeptideAtlas. This resource is a comprehensive mass spectrometry-derived peptide and inferred protein database with 71.3% coverage of the total predicted proteome of P. aeruginosa PAO1. This is the highest published coverage among the eight bacterial PeptideAtlas datasets currently available. The proteins in the Pseudomonas PeptideAtlas cover 84% of metabolic proteins, 71% of proteins involved in genetic information processing, 72% of proteins responsible for environmental information processing, more than 80% of proteins related to quorum sensing and biofilm formation, and 81% of proteins responsible for antimicrobial resistance. It exemplifies a necessary tool for targeted proteomics studies, system-wide observations, and cross-species observational studies. Here we describe how this resource was built and some of the physiologically important proteins of this pathogen. SignificancePseudomonas aeruginosa is among the most versatile bacterial pathogens. Studies of its proteome are very important as they can reveal virulence factors and mechanisms of antibiotic resistance. The construction of a proteomic resource such as the PeptideAtlas enables targeted proteomics studies, system-wide observations, and cross-species observational studies.

microbiology↗

bioRxiv2020

Challenges in Benchmarking Metagenomic Profilers

Accurate microbial identification and abundance estimation are crucial for metagenomics analysis. Various methods for classifying metagenomic data and estimating taxonomic profiles, broadly referred to as metagenomic profilers, have been developed. Yet, benchmarking metagenomic profilers remains challenging because some tools are designed to report relative sequence abundance while others report relative taxonomic abundance. Here, we show how misleading conclusions can be drawn by neglecting this distinction between relative abundance types when benchmarking metagenomic profilers. Moreover, we show compelling evidence that interchanging sequence abundance and taxonomic abundance will influence both per-sample summary statistics and cross-sample comparisons. We suggest that the microbiome research community should pay attention to potentially misleading biological conclusions arising from this issue when benchmarking metagenomic profilers, by carefully considering the type of abundance data that was analyzed and interpreted, and clearly stating the strategy used for metagenomic profiling.

bioinformatics↗

bioRxiv2020

A scale-free, fully connected global transition network underlies known microbiome diversity

Microbiomes are inherently linked by their structural similarity, yet the global features of such similarity are not clear. Here we propose as solution a search-based microbiome transition network. By traversing a composition-similarity based network of 177,022 microbiomes, we show that although the compositions are distinct by habitat, each microbiome is on-average only seven neighbors from any other microbiome on Earth, indicating the inherent homology of microbiome at the global scale. This network is scale-free, suggesting a high degree of stability and robustness in microbiome transition. By tracking the minimum spanning tree in this network, a global roadmap of microbiome dispersal was derived that tracks the potential paths of formulating and propagating microbiome diversity. Such search-based global microbiome networks, reconstructed within hours on just one computing node, provide a readily expanded reference for tracing the origin and evolution of existing or new microbiomes.

microbiology↗

bioRxiv2020

Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria

Promoter-proximal pausing regulates expression of many eukaryotic genes and serves as checkpoints for assembly of elongation/splicing machinery. Little is known how broadly the pausing is employed in transcriptional regulation in bacteria. We applied NET-seq combined with RNase I footprinting for genome-wide analysis of {sigma}70-dependent transcription pauses in Escherichia coli. Many E. coli genes appear to contain clusters of strong backtracked pauses at 10-20-bp distance from the transcription start site caused by retention of {sigma}70 subunit in RNA polymerase. The pauses in 10-15-bp register of the promoter are dictated by binding of {sigma}70 to canonical -10 element, 6-7 nt spacer and "YR+1Y" motif centered at transcription start site all characteristic for strong E. coli promoters. The promoters for the pauses in 16-20-bp register contain an additional -10-like sequence positioned on the same face of the DNA duplex as the original -10 element suggesting that {sigma}70 hopping was responsible for these pauses. Our in vitro analysis reveals that RNA polymerase backtracking and DNA scrunching are involved in these pauses that are relieved by Gre transcript cleavage factors. The genes coding for transcription factors are enriched in these pauses suggesting that {sigma}70 and Gre proteins regulate transcription in response to changing environmental cues.

microbiology↗

bioRxiv2020

CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing

Sample multiplexing facilitates single cell sequencing by reducing costs, revealing subtle difference between similar samples, and identifying artifacts such as cell doublets. However, universal and cost-effective strategies are rather limited. Here, we reported a Concanavalin A-based Sample Barcoding strategy (CASB), which could be followed by both single-cell mRNA and ATAC (assay for transposase accessible chromatin) sequencing techniques. The method involves minimal sample processing, thereby preserving intact transcriptomic or epigenomic patterns. We demonstrated its high labeling efficiency, high accuracy in assigning cells/nuclei to samples regardless of cell type and genetic background, as well as high sensitivity in detecting doublets by two applications: 1) CASB followed by scRNA-seq to track the transcriptomic dynamics of a cancer cell line perturbed by multiple drugs, which revealed compound-specific heterogeneous response; 2) CASB together with both snATAC-seq and scRNA-seq to illustrate the IFN-{gamma}-mediated dynamic changes on epigenome and transcriptome profile, which identified the transcription factor underlying heterogeneous IFN-{gamma} response.

genomics↗

bioRxiv2020

Longitudinal multi-omics along gingivitis development reveal a suboptimal-health gum state with periodontitis-like microbiome

Most adults experience episodes of gingivitis, which can progress to the irreversible, chronic state of periodontitis. However the mechanistic roles of plaque in gingivitis onset and progression to periodontitis remain elusive. Here, we integrated the longitudinal multi-omics data from plaque metagenome, metabolome and salivary cytokines in 40 adults who transit from naturally-occurring gingivitis (NG), to healthy gingivae (baseline) and then to experimental gingivitis (EG). During EG, rapid and consistent alterations in plaque microbiota, metabolites and salivary cytokines emerged as early as 24-72 hours after pause of oral hygiene, defining an asymptomatic sub-optimal health (SoH) stage. SoH also features a steep and synergetic decrease of plaque-derived betaine and Rothia spp., suggesting an anti-gum-inflammation mechanism by health-promoting microbial residents. Global, cross-cohort meta-analysis revealed a high Microbiome-based Periodontitis Index at SoH state, due to its convergent taxonomical and functional profiles towards those of periodontitis. In contrast, caries SoH features a microbial signature very distinct from caries. Thus SoH is a universal state of polymicrobial inflammations with disease-specific features, which is key to maintaining a disease-preventive plaque.

microbiology↗

bioRxiv2020

Genetic manipulation of insulin/insulin-like growth factor signaling pathway activity has sex-biased effects on Drosophila body size

In Drosophila, female body size is approximately 30% larger than male body size due to an increased rate of larval growth. While the mechanisms that control this sex difference in body size remain incompletely understood, recent studies suggest that the insulin/insulin-like growth factor signaling pathway (IIS) plays a role in the sex-specific regulation of growth during development. In larvae, IIS activity differs between the sexes, and there is evidence of sex-specific regulation of IIS ligands. Yet, we lack knowledge of how changes to IIS activity impact growth in each sex, as the majority of studies on IIS and body size use single- or mixed-sex groups of larvae and/or adult flies. The goal of our current study was to clarify the requirement for IIS activity in each sex during the larval growth period. To achieve this goal we used established genetic approaches to enhance, or inhibit, IIS activity, and quantified body size in male and female larvae. Overall, genotypes that inhibited IIS activity caused a female-biased decrease in body size, whereas genotypes that augmented IIS activity caused a male-specific increase in body size. This data extends our current understanding of larval growth by showing that most changes to IIS pathway activity have sex-biased effects on body size, and highlights the importance of analyzing data by sex in larval growth studies.

physiology↗

bioRxiv2020

The S1/S2 boundary of SARS-CoV-2 spike protein modulates cell entry pathways and transmission

The global spread of SARS-CoV-2 is posing major public health challenges. One unique feature of SARS-CoV-2 spike protein is the insertion of multi-basic residues at the S1/S2 subunit cleavage site, the function of which remains uncertain. We found that the virus with intact spike (Sfull) preferentially enters cells via fusion at the plasma membrane, whereas a clone (Sdel) with deletion disrupting the multi-basic S1/S2 site instead utilizes a less efficient endosomal entry pathway. This idea was supported by the identification of a suite of endosomal entry factors specific to Sdel virus by a genome-wide CRISPR-Cas9 screen. A panel of host factors regulating the surface expression of ACE2 was identified for both viruses. Using a hamster model, animal-to-animal transmission with the Sdel virus was almost completely abrogated, unlike with Sfull. These findings highlight the critical role of the S1/S2 boundary of the SARS-CoV-2 spike protein in modulating virus entry and transmission.

microbiology↗

bioRxiv2020

The N34S mutation of SPINK1 may impact the kinetics of trypsinogen activation to cause early trypsin release in the pancreas

The N34S variant of the trypsin inhibitor SPINK1 is the clinically most significant risk factor for chronic pancreatitis, but the underlying molecular mechanism could not be identified. Molecular dynamics simulations and docking of the generated conformational ensemble of SPINK1 to trypsin show that the mutation reduces the fraction of conformations that can directly participate in productive association, thereby reducing the association rate. The small change is difficult to detect by measuring the kinetics of SPINK1 binding to trypsin. However, kinetic modeling reveals that even a small change in the inhibition rate affects the trypsinogen to trypsin conversion rate at the early stage of the reaction when the trypsin concentration is very low, and the impact is substantially amplified by the autocatalytic mechanism of the conversion. Thus, the slightly reduced inhibition rate shortens the delay in the activation of trypsin release, which is therefore occurs within the pancreas.

biophysics↗

bioRxiv2020

Microbiota in milk from healthy and mastitis cows varies greatly in diversity, species richness and composition, as revealed by PacBio sequencing

Mastitis is the most economically important disease of dairy cows. This study used PacBio single-molecule real-time sequencing technology to sequence the full-length of the l6S rRNA from the microbiota in 27 milk samples (18 from mastitis and 9 from healthy cows; the cows were at different stages of lactation). We observed that healthy or late stage milk microbiota had significantly higher microbial diversity and richness. The community composition of the microbiota from different groups also varied greatly. In milk from healthy cows the microbiota was predominantly comprised of Lactococcus lactis, Acinetobacter johnsonii and Bacteroides dorei, while from mastitis cows it was predominantly comprised of Bacillus cereus, Clostridium cadaveris and Streptococcus suis. The prevalence of La. lactis and B. cereus in milk from healthy and mastitis cows was confirmed by digital droplets PCR. Differences in milk microbiota composition could suggest an important role for these microbes in protecting the host from mastitis. Based on the milk microbiota profiles, the Udder Health Index was constructed to predict the risk of bovine mastitis. Application of this predictive model could aid early identification and prevention of mastitis in dairy cows, though the model requires further optimisation using a larger dataset.

microbiology↗

bioRxiv2020

Constitutive Androstane Receptor and Hepatitis B Virus X Protein Cooperatively Induce β-catenin-Activated Liver Tumors

Background and AimsThe xenobiotic nuclear receptor Constitutive Androstane Receptor (CAR) is essential for xenobiotic tumor promotion in mouse models. In these models, {beta}-catenin is genetically activated in approximately 80% of tumors. Chronic Hepatitis B Virus (HBV) infection is a major risk factor for hepatocellular carcinoma (HCC), and {beta}-catenin activation is also frequently activated in HBV-associated HCCs. The goal of this research was to determine whether activation of CAR in a mouse model of chronic HBV infection would result in tumor formation and whether these tumors would display increased {beta}-catenin activation. Approach and ResultsWe treated transgenic mice expressing the HBV X protein (HBx) in hepatocytes with a single dose of the potent CAR agonist TCPOBOP. After 10 months, these mice developed large liver tumors that are characterized by {beta}-catenin nuclear localization and upregulation of {beta}-catenin targets. The {beta}-catenin regulator FoxM1 and the oxidative stress master regulator Nrf2, both of which are CAR gene targets, were also overactivated in tumors. The CAR/HBx tumors share a conserved gene signature with HBV-related human hepatocellular carcinoma. ConclusionsActivation of CAR in the presence of HBx results in tumors with strong {beta}-catenin activation. The mouse model we have described reflects the gene expression patterns seen in human HBV-associated HCC and presents an attractive basis for future studies.

cancer biology↗

bioRxiv2020

A simple Ca2+-imaging approach to neural network analysis in cultured neurons

BackgroundCa2+-imaging is a powerful tool to measure neuronal dynamics and network activity. To monitor network-level changes in cultured neurons, neuronal activity is often evoked by electrical or optogenetic stimulation and assessed using multi-electrode arrays or sophisticated imaging. Although such approaches allow detailed network analyses, multi-electrode arrays lack single-cell precision, whereas optical physiology generally requires advanced instrumentation. New MethodHere we developed a simple, stimulation-free protocol with associated Matlab algorithms that enables scalable analyses of network activity in cultured human and mouse neurons. The approach allows analysis of overall networks and single-neuron dynamics, and is amenable to scale-up for screening purposes. ResultsWe validated the protocol by assessing human neurons with a heterozygous conditional deletion of Munc18-1, and mouse neurons with a homozygous conditional deletion of neurexins. The approach described here enabled identification of differential changes in these mutant neurons at the network level and of the amplitude and frequency of calcium peaks at the single-neuron level. These results demonstrate the utility of the approach. Comparison with existing methodCompared with current imaging platforms, our method is simple, scalable, and easy to implement. It enables quantification of more detailed parameters than multi-electrode arrays, but does not have the resolution and depth of more sophisticated yet labour-intensive analysis methods, such as electrophysiology. ConclusionThis method is scalable for a rapid assessment of neuronal function in culture, and can be applied to both human and mouse neurons. Thus, the method can serve as a basis for phenotypical analysis of mutations and for drug discovery efforts.

neuroscience↗

bioRxiv2020

Probiotic consumption relieved human stress and anxiety symptoms via modulating the gut microbiota and neuroactive potential

Stress has been shown to disturb the balance of human intestinal microbiota and subsequently cause mental health problems, such as anxiety and depression. The gut microbial communities are able to synthesize and/or consume various neuroactive metabolites, and preliminary human studies have also demonstrated the ability of probiotics to modulate the levels of neurotransmitter. However, the study and interpretation of the biological significance of microbial neuroactive compounds have been hindered by the lack of dedicated reference databases and corresponding human intestinal microbiota reference genomes. Our previous study showed that ingesting the probiotic strain, Lactobacillus (L.) plantarum P-8, for 12 weeks could alleviate stress and anxiety of stressed adults. The current study was a follow-up work aiming to further elucidate mechanisms behind the observed beneficial effects by performing deep analysis of the fecal metagenomes of the probiotic (n = 43) and placebo (n = 36) groups. Comparing with the probiotic group, the gut microbiomes of the placebo group showed significantly higher Bray-Curtis dissimilarity between weeks 0 and 12 (p < 0.05). Comparing with week 0, the Shannon diversity index of the placebo group decreased significantly at week 12 (t-test; p < 0.05), but such decrease was non-significant for the probiotic group. Additionally, the fecal metagenomes of the probiotic group showed significant increases in the species-level genome bins (SGBs) of Bifidobacterium adolescent, Bifidobacterium longum, and Fecalibacterium prausnitzii increased, while decreases in the SGBs of Roseburia faeci and Fusicatenibacter saccharivorans. Furthermore, the 12-week probiotic supplementation enhanced the diversity of neurotransmitter-synthesizing and/or -consuming SGBs, and the levels of some predicted microbial neuroactive metabolites (short chain fatty acids, gamma-aminobutyric acid, arachidonic acid, and sphingomyelin et.al). In conclusion, this study revealed the potential mechanism of probiotics in alleviating stress and anxiety via the gut-brain axis. The modulation of the intestinal microbiota by probiotics is an attractive strategy for managing stress and anxiety.

neuroscience↗