Biology subjects

Song, L.

Publications and source records attributed to Song, L..

At least 199 records · Page 11Linked to original sources

bioRxiv2019

Over 50000 metagenomically assembled draft genomes for the human oral microbiome reveal new taxa

The oral cavity of each person is home for hundreds of bacterial species. While taxa for oral diseases have been well studied using culture-based as well as amplicon sequencing methods, metagenomic and genomic information remain scarce compared to the fecal microbiome. Here we provide metagenomic shotgun data for 3346 oral metagenomics samples, and together with 808 published samples, assemble 56,213 metagenome-assembled genomes (MAGs). 64% of the 3,589 species-level genome bins contained no publicly available genomes, others with only a handful. The resulting genome collection is representative of samples around the world and across physiological conditions, contained many genomes from Candidate phyla radiation (CPR) which lack monoculture, and enabled discovery of new taxa such as a family within the Acholeplasmataceae order. New biomarkers were identified for rheumatoid arthritis or colorectal cancer, which would be more convenient than fecal samples. The large number of metagenomic samples also allowed assembly of many strains from important oral taxa such as Porphyromonas and Neisseria. Predicted functions enrich in drug metabolism and small molecule synthesis. Thus, these data lay down a genomic framework for future inquiries of the human oral microbiome.

microbiology↗

bioRxiv2019

Significant improvement of reprogramming efficiency by transient overexpression of ZGA inducer Dux but not Dppa2/4

Cloned animal have been reported by somatic cell nuclear transfer (SCNT) for many years. However, the SCNT is extremely inefficient, and zygotic genome activation (ZGA) is required for SCNT and chemical mediated reprogramming. To identify candidate factors that facilitate ZGA in reprogramming, we performed siRNA-repressor and mRNA-inducer screening, which revealed Dux, Dppa2, and Dppa4 as key factors enhancing the ZGA in SCNT. Direct injection of ZGA-inducers had no significant effect on the SCNT blastocyst formation, and even destroyed the ZGA. Through a inducible Dux transgenic mouse model, we demonstrate that transient overexpression of Dux not only improved SCNT efficiency, but also increased the efficiency of chemical reprogramming. Transcriptome profiling revealed that Dux treated SCNT embryos were similar to fertilized embryos. Furthermore, transient overexpression of Dux combined with inactivation of DNA methyltransferases (Dnmts) further promote the overall development of SCNT-derived animals. These findings enhance our understanding of ZGA-regulators in somatic reprogramming.

bioengineering↗

bioRxiv2019

FvLcp1, a type-D fungal LysM protein with Chitin-binding domains, is a secreted protein involved in host recognition and fumonisin production in Fusarium verticillioides - maize kernel interaction

O_LIFusarium verticillioides is one of the key maize ear rot pathogens and produces fumonisins, a group of mycotoxins detrimental to humans and animals. Unfortunately, our understanding on how this fungus interacts with maize kernels to trigger mycotoxin biosynthesis is very limited.\nC_LIO_LIWe performed a systematic computational network-based analysis of large-scale F. verticillioides RNA-seq datasets to identify potential gene subnetwork modules that are associated with virulence and fumonisin regulation.\nC_LIO_LIAmong the highly discriminative subnetwork modules, we identified a putative hub gene FvLCP1, which encodes a putative a type-D fungal LysM protein with a signal peptide, three LysM domains, and two chitin binding domains. FvLcp1 is a unique protein that harbors these domains amongst five representative Fusarium species.\nC_LIO_LIFvLcp1 is a secreted protein important for fumonisin production with LysM domain playing acritical role. Chitin-binding domain was essential for in vitro chitin binding.\nC_LIO_LIUsing rice blast fungus, we learned that FvLcp1 accumulates in appressoria, a key infection structure, suggesting that FvLcp1 could be involved in host recognition and infection. Also, full length FvLcp1 was able to suppress the BAX triggered plant cell death in Nicotiana benthamiana.\nC_LIO_LIThis is the first report where a unique type-D LysM secreted protein with chitin-binding domain in mycotoxigenic fungus F. verticillioides was shown to be potentially involved in suppressing host cell death and promoting fumonisins biosynthesis while the pathogen colonizes maize kernels.\nC_LI

microbiology↗

bioRxiv2019

Culture under normoxic conditions and enhanced virulence of phase II Coxiella burnetii transformed with a RSF1010-based shuttle vector

Coxiella burnetii is a Gram-negative, facultative intracellular microorganism that can cause acute or chronic Q fever in human. It was recognized as an obligate intracellular organism until the revolutionary design of an axenic cystine culture medium (ACCM). Present axenic culture of C. burnetii strictly requires a hypoxic condition (<10% oxygen). Here we investigated the normoxic growth of C. burnetii strains in ACCM-2 with or without tryptophan supplementation. Three C. burnetii strains - Henzerling phase I, Nine Mile phase II and a Nine Mile phase II transformant, were included. The transformant contains a pMMGK plasmid that is composed of a RSF1010 ori, a repABC operon, an eGFP gene and a kanamycin resistance cassette. We found that, under normoxia if staring from an appropriate concentration of fresh age inocula, Nine Mile phase II can grow significantly in ACCM-2 with tryptophan, while the transformant can grow robustly in ACCM-2 with or without tryptophan. In contrast, long-term frozen stocks of phase II and its transformant, and Henzerling phase I of different ages had no growth capability under normoxia under any circumstances. Furthermore, frozen stocks of the transformant consistently caused large splenomegaly in SCID mice, while wild type Nine Mile phase II induced a lesser extent of splenomegaly. Taken together, our data show that normoxic cultivation of phase II C. burnetii can be achieved under certain conditions. Our data suggests that tryptophan and an unknown temperature sensitive signal are involved in the expression of genes for normoxic growth regulated by quorum sensing in C. burnetii.

microbiology↗

bioRxiv2019

Dissecting the first phased dikaryotic genomes of the wheat rust pathogen Puccinia triticina reveals the mechanisms of somatic exchange in nature

Although somatic hybridization (SH) has been proposed as a means of accelerating rust pathogen virulence evolution in the absence of sexual recombination, previous studies are limited to the laboratory and none have revealed how this process happens. Using long-read sequencing, we generated dikaryotic phased genomes and annotations for three Australian field-collected isolates of the wheat leaf rust pathogen (Puccinia triticina; Pt), including a putative asexual hybrid (Pt64) and two putative parental isolates (Pt104 and Pt53; 132-141 Mb,155-176 contigs, N50 of 1.9-2.1 Mb). The genetic dissection based on the high-quality phased genomes including whole-genome alignments, phylogenetic and syntenic analyses along with short-read sequencing of 27 additional Pt isolates convergently demonstrated that Pt64, which rendered several commercial hybrid wheat cultivars susceptible to leaf rust, arose from SH between isolates within the Pt53 and Pt104 lineages. Parentage analysis demonstrated the role of mitotic crossover in the derivation of both nuclei of Pt64. Within HD mating type genes, the distinct specificity regions in Pt64 and the distinct phylogenetic pattern of the remaining admixed isolates suggested high genetic variation in specificity-related regions on the b locus intrinsically associated with the SH. This study not only provided a fundamental platform for investigating genomic variation underlying virulence evolution in one of the most devastating wheat pathogens, but also offered an in-depth understanding of the mechanisms of naturally occurring SH. This asexual mechanism can be broadly exploited by any dikaryotic pathogen to accelerate virulence evolution, and understanding this process is both urgent and crucial for sustainable pathogen control.\n\nImportanceStrategies to manage plant rust pathogens are challenged by the constant emergence of new virulence. Although somatic hybridization has been proposed as a means by which rusts could overcome host resistance rapidly and cause crop loss, there is very little evidence of this process in nature and the mechanisms underlying it are not known. This study generated and analysed the first dikaryotic phased genomes of the wheat leaf rust pathogen, identifying an isolate as a hybrid and for the first time unveiling parasexuality via mitotic crossover in a rust pathogen. The erosion of the resistance of several hybrid wheat cultivars in agriculture by the hybrid rust has important implications for breeding efforts targeting durable resistance and sustained rust control.

microbiology↗

bioRxiv2019

The Urinary Microbiota in Relation to the Reproductive Tract Microbiota

Human urine is traditionally considered to be sterile, and whether the urine harbours distinct microbial communities has been a matter of debate. The potential link between female urine and reproductive tract microbial communities is currently not clear. Here we collected the urine samples from 147 Chinese women of reproductive age, and explored the nature of colonization by 16S rRNA gene amplicon sequencing, real-time qPCR and live bacteria culture. To demonstrate utility intra-individual Spearmans correlation was used to explore the relationship between urine and multi-sites of the reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Types of diverse, Streptococcus-dominated, and Lactobacillus-dominated were the three most common types in the cohort. Detailed comparison of the urinary microbiota to the multi-sites of reproductive tract microbiota demonstrated the urinary microbiota was more similar to the microbiota in the cervix and uterine cavity instead of vagina in the same women. Our data demonstrates the potential connectivity of the microbiota in the female urogenital system and provided insight into the exploration of urethra and genital tract diseases.

microbiology↗

bioRxiv2019

Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies

We characterized two reference samples for NGS technologies: a human triple-negative breast cancer cell line and a matched normal cell line. Leveraging several whole-genome sequencing (WGS) platforms, multiple sequencing replicates, and orthogonal mutation detection bioinformatics pipelines, we minimized the potential biases from sequencing technologies, assays, and informatics. Thus, our \"truth sets\" were defined using evidence from 21 repeats of WGS runs with coverages ranging from 50X to 100X (a total of 140 billion reads). These \"truth sets\" present many relevant variants/mutations including 193 COSMIC mutations and 9,016 germline variants from the ClinVar database, nonsense mutations in BRCA1/2 and missense mutations in TP53 and FGFR1. Independent validation in three orthogonal experiments demonstrated a successful stress test of the truth set. We expect these reference materials and \"truth sets\" to facilitate assay development, qualification, validation, and proficiency testing. In addition, our methods can be extended to establish new fully characterized reference samples for the community.

bioinformatics↗

bioRxiv2019

Pentamycin biosynthesis in Philippine Streptomyces sp. S816: Cytochrome P450-catalysed installation of the C-14 hydroxyl group

Pentamycin is a polyene antibiotic, registered in Switzerland for the treatment of vaginal candidiasis, trichomo-niasis and mixed infections. Chemical instability has hindered its wide-spread application and development as a drug. Here we report the identification of Streptomyces sp. S816, isolated from Philippine mangrove soil, as a pentamycin producer. Genome sequence analysis identified the putative pentamycin biosynthetic gene cluster, which shows a high degree of similarity to the gene cluster responsible for filipin III biosynthesis. The ptnJ gene, which is absent from the filipin III biosynthetic gene cluster, was shown to encode a cytochrome P450 capable of converting filipin III to pentamycin. This confirms that the cluster directs pentamycin biosynthesis, paving the way for biosynthetic engineering approaches to the production of pentamycin analogues. Several other Streptomyces genomes were found to contain ptnJ orthologues clustered with genes encoding polyketide synthases that appear to have similar architectures to those responsible for the assembly of filipin III and pentamycin, suggesting pentamycin production may be common in Streptomyces species.

biochemistry↗

bioRxiv2019

T-cell activation is modulated by the 3D mechanical microenvironment

T cells recognize mechanical forces through a variety of cellular pathways, including mechanical triggering of the T-cell receptor (TCR) and mechanical triggering of the integrin LFA-1. We show here that T cells can recognize forces arising from the rigidity of the microenvironment. We fabricated 3D hydrogels with mechanical stiffness tuned to 4 kPa and 40 kPa and specially engineered be microporous independent of stiffness. We cultured T cells and antigen presenting cells within the matrices and studied activation by flow cytometry and live imaging. We found there was an augmentation of T-cell activation in the context of mechanically stiffer 3D material as compared to the softer material. In contrast, proliferation, activation markers, and migration were all diminished in T cells cultured in the softer material. These results show that T cells can sense their mechanical environment and amplify responses in the context of mechanical stiffness.

immunology↗

bioRxiv2019

Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels

A detailed understanding of abiotic stress tolerance in plants is essential to provide food security in the face of increasingly harsh climatic conditions. Glucosinolates (GLSs) are secondary metabolites found in the Brassicaceae that protect plants from herbivory and pathogen attack. Here we report that in Arabidopsis, aliphatic GLS levels are regulated by the auxin-sensitive Aux/IAA repressors IAA5, IAA6, and IAA19. These proteins act in a transcriptional cascade that maintains expression of GLS levels when plants are exposed to drought conditions. Loss of IAA5/6/19 results in reduced GLS levels and decreased drought tolerance. Further, we show that this phenotype is associated with a defect in stomatal regulation. Application of GLS to the iaa5,6,19 mutants restores stomatal regulation and normal drought tolerance. GLS action is dependent on the receptor kinase GHR1, suggesting that GLS may signal via reactive oxygen species. These results provide a novel connection between auxin signaling, GLS levels and drought response.\n\nOne Sentence SummaryAux/IAA proteins promote drought tolerance by regulating glucosinolate levels.

plant biology↗

bioRxiv2019

Toll-like receptor 2 stimulation augments esophageal epithelial barrier integrity

BackgroundA key concept of the hygiene hypothesis is that the microbiome modulates both epithelial barrier integrity as well as host immune responses. Defective expression of tight junction complex proteins alters this homeostatic process, and plays a role in atopic disorders including eosinophilic esophagitis. We tested the hypothesis that Toll-like receptor 2 (TLR2) stimulation improves esophageal barrier function in a cell-intrinsic manner by upregulation of TJ-protein expression using an in vitro model of human epithelium. MethodsPattern recognition receptor expression was assessed in esophageal epithelial cells from patients with EoE and non-EoE control patients. Functional consequences of TLR2 stimulation were investigated using human esophageal EPC2-hTERT cells in the three-dimensional air-liquid interface culture (ALI) model to evaluate transepithelial electrical resistance (TEER) and FITC-Dextran permeability. Characterization of TLR2-stimulated ALI cultures was performed by histology, immunohistochemistry, western blotting and chromatin immunoprecipitation. ResultsTLR2 stimulation increased TEER (1.28 to 1.31-fold) and decreased paracellular permeability to FITC-Dextran. Notably, TLR2 stimulation-induced increases in TEER were abolished by treatment with anti-TLR2 blocking antibody. Tight junction complex proteins claudin 1 and zonula occludens 1 were increased following TLR2 stimulation, and chromatin immunoprecipitation analysis demonstrated significant increase in histone 4 acetyl binding at the CLDN1 enhancer and promoter following zymosan treatment, implying the occurrence of durable chromatin changes in the esophageal epithelium. ConclusionsOur findings reveal that the TLR2 pathway may play a regulatory role as a mechanism that maintains epithelial barrier homeostasis in the esophagus.

immunology↗

bioRxiv2019

The vagino-cervical microbiome as a woman's life history

The gut microbiome has been the center of attention for human commensal microbiome studies. The vaginal microbiome is also densely populated with bacteria, viruses and fungi, and the presence of microorganisms beyond the cervix is increasingly reported in non-infectious conditions1-3. Due to the over 90% of human sequences in female reproductive tract samples3,4, metagenomic information has been very limited. 16S rRNA gene amplicon sequencing studies have identified community types in the vaginal microbiota, and observed its dynamic changes due to menstrual cycles and sexual behaviors in small cohorts5,6. Here we perform metagenomic shotgun sequencing on cervical samples from 516 women of reproductive age (more than 10-fold of the Human Microbiome Project (HMP)4), and dissect major factors, especially pregnancy and delivery histories and contraception methods on the microbiome composition. Features of other body sites, such as mood fluctuations and facial speckles could potentially be deduced from the vagino-cervical microbiome. Our results offer an unprecedented glimpse into the microbiota in the female reproductive tract and imply disease susceptibilities that may be relieved by behavioural changes.

microbiology↗

bioRxiv2019

PGCN: Disease gene prioritization by disease and gene embedding through graph convolutional neural networks

MotivationProper prioritization of candidate genes is essential to the genome-based diagnostics of a range of genetic diseases. However, it is a highly challenging task involving limited and noisy knowledge of genes, diseases and their associations. While a number of computational methods have been developed for the disease gene prioritization task, their performance is largely limited by manually crafted features, network topology, or pre-defined rules of data fusion. ResultsHere, we propose a novel graph convolutional network-based disease gene prioritization method, PGCN, through the systematic embedding of the heterogeneous network made by genes and diseases, as well as their individual features. The embedding learning model and the association prediction model are trained together in an end-to-end manner. We compared PGCN with five state-of-the-art methods on the Online Mendelian Inheritance in Man (OMIM) dataset for tasks to recover missing associations and discover associations between novel genes and diseases. Results show significant improvements of PGCN over the existing methods. We further demonstrate that our embedding has biological meaning and can capture functional groups of genes. AvailabilityThe main program and the data are available at https://github.com/lykaust15/Disease_gene_prioritization_GCN.

bioinformatics↗

bioRxiv2018

Regulation by HSP70/90 in the different tissues and testis development of male cattle (Cattle-yak and Yak)

HSP70/90 play important role in testis develop and spermatozoa regulation, but the contact of HSP70/90 with infertility in cattle is unclear. Here, we focus on male cattle-yak and yak, which to investigate the expression and localization of HSP70/90 in different tissues, and explore the influence of HSP70/90 to infertility. In our study, a total of 54 cattle (24 cattle-yak and 30 yak) were examined. The HSP90 mRNA of cattle-yak was cloned first and found amino acid variation in HSP90, which led to difference at protein spatial structure compare with yak. To investigate whether the expression of HSP70/90 mRNA and protein are different in cattle-yak and yak, we used real-time quantitative PCR (qRT-PCR) and Western blot (WB) to examine them. We found that the expression level of HSP70/90 mRNA and protein are disparity in different tissues and testis development stages, and obviously high expression was observed in testicle during juvenile and adult, Moreover, it s interestingly in which the HSP70 expression is significant high in yak whereas HSP90 in cattle-yak (P<0.01). On this bases, we detect the location of HSP70/90 in testis by immunohistochemical (IHC) and immunofluorescence (IF), the results demonstrate that HSP70/90 were located in the epithelial cells, spermatogenic cells and mesenchymal cells. In summary, our study proved the expression of HSP70/90 are different in tissues, and the expression of HSP90 is obviously high in testis of cattle-yak, which propose that the infertility of cattle-yak may cause from up-regulating of HSP90.

biochemistry↗

bioRxiv2018

Fine Tuning of Histone Demethylase KDM6A/B Improves the Development of Nuclear Transfer Embryo

Despite the success of the production of animals by somatic cell nuclear transfer (SCNT) in many species, the method is limited by a low efficiency. After zygotic genome activation (ZGA), a large number of endogenous retroviruses (ERVs) are expressed, including the murine endogenous retrovirus-L (MuERVL/MERVL). In this study, we generated a series of MERVL-reporter mouse strains to detect the ZGA event in embryos. We found that the majority of SCNT embryos exhibited ZGA failure, and histone H3 lysine 27 trimethylation (H3K27me3) prevented SCNT reprogramming. Overexpression of the H3K27me3-specific demethylase KDM6A, but not KDM6B, improved the efficiency of SCNT. Conversely, knockdown KDM6B not only facilitate ZGA, but also impede ectopic Xist expression in SCNT reprogramming. Furthermore, the knockdown of KDM6B increased the rate of SCNT-derived Duchenne muscular dystrophy embryonic stem cell establishment, indicate that these results not only provide insight into the mechanisms underlying failures of SCNT, but also may extend the applications of SCNT.

cell biology↗

bioRxiv2018

SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics

MotivationPolygenic risk score (PRS) methods based on genome-wide association studies (GWAS) have a potential for predicting the risk of developing complex diseases and are expected to become more accurate with larger training data sets and innovative statistical methods. The area under the ROC curve (AUC) is often used to evaluate the performance of PRSs, which requires individual genotypic and phenotypic data in an independent GWAS validation dataset. We are motivated to develop methods for approximating AUC of PRSs based on the summary level data of the validation dataset, which will greatly facilitate the development of PRS models for complex diseases.\n\nResultsWe develop statistical methods and an R package SummaryAUC for approximating the AUC and its variance of a PRS when only the summary level data of the validation dataset are available. SummaryAUC can be applied to PRSs with SNPs either genotyped or imputed in the validation dataset. We examined the performance of SummaryAUC using a large-scale GWAS of schizophrenia. SummaryAUC provides accurate approximations to AUCs and their variances. The bias of AUC is typically less than 0.5% in most analyses. SummaryAUC cannot be applied to PRSs that use all SNPs in the genome because it is computationally prohibitive.\n\nAvailabilityhttps://github.com/lsncibb/SummaryAUC\n\nContactJianxin.Shi@nih.gov

bioinformatics↗

bioRxiv2018

IQGAP3 Overexpression Correlates with Poor Prognosis and Radiation Therapy Resistance in Breast Cancer

Background: IQ motif-containing GTPase activating protein 3 (IQGAP3), the latest found protein of IQGAP family, may act as a crucial factor in the process of cancer development and progression; however, its clinical value in breast cancer remains unestablished so far. Our team explored the correlation between IQGAP3 expression profile and the clinicopathological features in breast cancer. Methods: IQGAP3 levels in breast cancer cell lines and tumor tissues were detected by real-time PCR and western blotting and compared to the normal control groups. Protein expression of IQGAP3 was evaluated immunohistochemically in specimens (archived paraffin embedded) of 257 breast cancer patients. We also analyze the association between IQGAP3 expression and the clinical characters and prognosis. The relationship between IQGAP3 expression and sensitivity to radiation therapy was determined by subgroup analysis. Results: There was significant upregulation of IQGAP3 in breast cancer cell lines and human tumor tissues at both the mRNA and protein level compared to the normal ones. In addition, 110/257 (42.8%) of archived paraffin embedded breast cancer specimens had high protein expression of IQGAP3. High expression of IQGAP3 was significantly related to clinical stage (P=0.001), T category (P=0.002), N category (P=0.001), locoregional recurrence(P=0.002), distant metastasis (P=0.001), and vital status (P=0.001). Univariate and multivariate statistical analysis showed that IQGAP3 was an independent prognostic factor of the whole cohort breast cancer patients (P=0.003, P=0.001). Subgroup analysis revealed IQGAP3 expression correlates with radiation therapy resistance and was also an independent predictor for radiation therapy outcome. Conclusions: Our findings suggest that high IQGAP3 expression predicts poor prognosis and radiation therapy resistance in breast cancer. In addition, IQGAP3 may be a reliable novel biomarker to provide personalized prognostication and identify patients who can profit from more aggressive RT regimen for improving the survival of breast cancer patients.

cancer biology↗

bioRxiv2018

Dominant negative FADD/MORT1 inhibits the development of intestinal intraepithelial lymphocytes with a marked defect on CD8αα+TCRγδ+ T cells

Intestinal intraepithelial lymphocytes are considered to be distinct from thymus-derived cells and are thought to derive locally from cryptopatch (CP) precursors. Although the development and homing of IELs have been studied in some details, the factors controlling their homeostasis are incompletely understood. Here, we demonstrate that FADD, a classic adaptor protein required for death-receptor-induced apoptosis, is a critical regulator of the intestinal IEL development. The mice with a dominant negative mutant of FADD (FADD-DN) display a defective localized intestinal IELs with a marked defect on CD8+TCR{gamma}{delta}+ T cells. Since Lin- LPLs have been identified as precursors CP cells for CD8+ development, we analyzed lamina propria lymphocytes (LPLs) and found the massive accumulation of IL-7R-lin- LPLs in FADD-DN mice. IL-7 plays a differentiation inducing role in the development of intestinal IELs and its receptor IL-7R is a transcriptional target of Notch1. The level of Notch1 expression also showed very low in Lin- LPLs cells from FADD-DN mice compared with normal mice, indicating a possible molecular mechanism of FADD in the early IEL development. In addition, loss of {gamma}{delta} T-IELs induced by FADD-DN results in a worsening inflammation in murine DSS-induced colitis model, suggesting a protective role of FADD in the intestinal homeostasis.

immunology↗