Biology subjects

Xiong, X.

Publications and source records attributed to Xiong, X..

6 recordsLinked to original sources

bioRxiv2018

Dietary lysozyme supplement alters serum biochemical makers and milk metabolite profile of sows via gut microbiota

Lysozyme is an important antimicrobial agent with promising future in replacing antibiotics in livestok production. The aim of current study was to determine variations in sows gut microbiota, serum immunity and breast milk metabolite profile mediated by lysozyme supplementation.Thirty-six pregnant sows were assigned to a control group without supplementation and two treatments with 0.5 g/kg and 1.0 g/kg lysozyme provided in formula feed for 21days. Microbiota analysis based on 16s RNA high-throughput sequencing and untargeted liquid chromatography tandem mass spectrometry were applied and combined in analysis. Serum biochemical indicators and immunoglobulins were also determined. Sows received 1.0kg/t lyszoyme treatment shown significant redution in microbial diversity. Spirochaetes, Euryarchaeota and Actinobacteria significantly increased while Firmicutes showed a remarkable reduction in 1.0kg/t treated group compared with control. Pyrimidine metabolism,Purine metabolism and Amino acid related enzymes were significantly upregulated in 1.0kg/t lysozyme treated group. The richness of gram-positive bacteria were significantly down-regulated by lysozyme treatments. Serum aspartate transaminase (AST) activity was significantly un-regulated. Serum IgM levels were significantly higher in the 1.0 kg/t group compared with control, while IgA levels was significantly lower in 1.0kg/t group. Over thirty metabolites from sows breast milk including L-Glutamine,creatine and L-Arginine were sigficantly altered by lysozyme treatment. There existed crucial correlations among gut microbiota, serum immunity and breast milk metabolites where lactobacillus and prevotella may play a key role in lysozyme mediated host-microbial interactions. Overall, lysozyme supplementation could effectively improve the composition, metabolic functions and phenotypes of sows gut microbiota and it also benefit sows with better immune status and breast milk composition.\n\nImportanceEnteric infections caused by pathogens have a significant negative effect on neonatal survival and animal health in swine production. The application of antibiotics in feeds at subtherapeutic levels could improve performance and overall health and is used extensively throughout the industry. However, abuse of antibiotics is contributing to the high level of drug resistance in microbial communities and rising concerns regarding human health. Here, we revealed that lysozyme supplementation could effectively improve the composition, metabolic functions and phenotypes of sows gut microbiota and it also benefit sows with better immune status and breast milk composition. These findings confirmed that lysozyme could be a suitable alternative to antibiotics in swine production.

microbiology↗

bioRxiv2018

Genetic Architecture of Collective Behaviors in Zebrafish

Collective behaviors of groups of animals, such as schooling and shoaling of fish, are central to species survival, but genes that regulate these activities are not known. Here we parsed collective behavior of groups of adult zebrafish using computer vision and unsupervised machine learning into a set of highly reproducible, unitary, several hundred millisecond states and transitions, which together can account for the entirety of relative positions and postures of groups of fish. Using CRISPR-Cas9 we then targeted for knockout 35 genes associated with autism and schizophrenia. We found mutations in three genes had distinctive effects on the amount of time spent in the specific states or transitions between states. Mutation in immp2l (inner mitochondrial membrane peptidase 2-like gene) enhances states of cohesion, so increases shoaling; mutation in in the Nav1.1 sodium channel, scn1lab+/- causes the fish to remain scattered without evident social interaction; and mutation in the adrenergic receptor, adra1aa-/-, keeps fish close together and retards transitions between states, leaving fish motionless for long periods. Motor and visual functions seemed relatively well-preserved. This work shows that the behaviors of fish engaged in collective activities are built from a set of stereotypical states. Single gene mutations can alter propensities to collective actions by changing the proportion of time spent in these states or the tendency to transition between states. This provides an approach to begin dissection of the molecular pathways used to generate and guide collective actions of groups of animals.

animal behavior and cognition↗

bioRxiv2018

Metabolic Reaction Network-based Recursive Metabolite Identification for Untargeted Metabolomics

Metabolite identification is a long-standing challenge in untargeted metabolomics and a major hurdle for functional metabolomics studies. Here, we developed a metabolic reaction network-based recursive algorithm and webserver called MetDNA for the large-scale and unambiguous identification of metabolites (available at http://metdna.zhulab.cn). We showcased the versatility of our workflow using different instrument platforms, data acquisition methods, and biological sample types and demonstrated that over 2,000 metabolites could be identified from one experiment.

bioinformatics↗

bioRxiv2018

Combining high-throughput micro-CT-RGB phenotyping and genome-wide association study to dissect the genetic architecture of tiller growth in rice

Traditional phenotyping of rice tillers is time consuming and labor intensive and lags behind the rapid development of rice functional genomics. Thus, dynamic phenotyping of rice tiller traits at a high spatial resolution and high-throughput for large-scale rice accessions is urgently needed. In this study, we developed a high-throughput micro-CT-RGB (HCR) imaging system to non-destructively extract 730 traits from 234 rice accessions at 9 time points. We used these traits to predict the grain yield in the early growth stage, and 30% of the grain yield variance was explained by 2 tiller traits in the early growth stage. A total of 402 significantly associated loci were identified by GWAS, and dynamic and static genetic components were found across the nine time points. A major locus associated with tiller angle was detected at nine time points, which contained a major gene TAC1. Significant variants associated with tiller angle were enriched in the 3'-UTR of TAC1. Three haplotypes for the gene were found and tiller angles of rice accessions containing haplotype H3 were much smaller. Further, we found two loci contained associations with both vigor-related HCR traits and yield. The superior alleles would be beneficial for breeding of high yield and dense planting.\n\nHighlightCombining high-throughput micro-CT-RGB phenotyping facility and genome-wide association study to dissect the genetic architecture of rice tiller development by using the indica subpopulation.

genetics↗

bioRxiv2017

Base-resolution mapping reveals distinct m1A methylome in nuclear- and mitochondrial-encoded transcripts

Gene expression can be post-transcriptionally regulated via dynamic and reversible RNA modifications. N1-methyladenosine (m1A) is a recently identified mRNA modification; however, little is known about its precise location, regulation and function. Here, we develop a base-resolution m1A profiling method, based on m1A-induced misincorporation during reverse transcription, and report distinct classes of m1A methylome in the human transcriptome. m1A in 5-UTR, particularly those at the first nucleotide of mRNA, associate with increased translation efficiency. A different subset of m1A exhibit a GUUCRA tRNA-like motif, are evenly distributed in the transcriptome and are dependent on the methyltransferase TRMT6/61A. Additionally, we show for the first time that m1A is prevalent in the mitochondrial-encoded transcripts. Manipulation of m1A level via TRMT61B, a mitochondria-localizing m1A methyltransferase, demonstrates that m1A in mitochondrial mRNA interferes with translation. Collectively, our approaches reveal distinct classes of m1A methylome and provide a resource for functional studies of m1A-mediated epitranscriptomic regulation.

biochemistry↗

bioRxiv2017

Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem Cells

The CCCTC-binding factor (CTCF) is widely regarded as a key player in chromosome organization in mammalian cells, yet direct assessment of the impact of loss of CTCF on genome architecture has been difficult due to its essential role in cell proliferation and early embryogenesis. Here, using auxin-inducible degron techniques to acutely deplete CTCF in mouse embryonic stem cells, we show that cell growth is severely slowed yet chromatin organization remains largely intact after loss of CTCF. Depletion of CTCF reduces interactions between chromatin loop anchors, diminishes occupancy of cohesin complex genome-wide, and slightly weakens topologically associating domain (TAD) structure, but the active and inactive chromatin compartments are maintained and the vast majority of TAD boundaries persist. Furthermore, transcriptional regulation and histone marks associated with enhancers are broadly unchanged upon CTCF depletion. Our results suggest CTCF-independent mechanisms in maintenance of chromatin organization.

genomics↗