Biology subjects

Gao, Y.

Publications and source records attributed to Gao, Y..

At least 631 records · Page 35Linked to original sources

bioRxiv2019

Distinct gut metagenomics and metaproteomics signatures in prediabetics and treatment-naïve type 2 diabetics

BackgroundThe gut microbiota plays important roles in modulating host metabolism. Previous studies have demonstrated differences in the gut microbiome of T2D and prediabetic individuals compared to healthy individuals, with distinct disease-related microbial profiles being reported in groups of different age and ethnicity. However, confounding factors such as anti-diabetic medication hamper identification of the gut microbial changes in disease development.\n\nMethodWe used a combination of in-depth metagenomics and metaproteomics analyses of faecal samples from treatment-naive type 2 diabetic (TN-T2D, n=77), pre-diabetic (Pre-DM, n=80), and normal glucose tolerant (NGT, n=97) individuals to investigate compositional and functional changes of the gut microbiota and the faecal content of microbial and host proteins in Pre-DM and treatment-naive T2D individuals to elucidate possible host-microbial interplays characterising different disease stages.\n\nFindingsWe observed distinct differences characterizing the gut microbiota of these three groups and validated several key features in an independent TN-T2D cohort. We also demonstrated that the content of several human antimicrobial peptides and pancreatic enzymes differed in faecal samples between three groups, such as reduced faecal level of antimicrobial peptides and pancreatic enzymes in TN-T2D.\n\nInterpretationOur findings suggest a complex, disease stage-dependent interplay between the gut microbiota and the host and emphasize the value of metaproteomics to gain further insight into interplays between the gut microbiota and the host.\n\nFundingNational Key Research and Development Program of China, No. 2017YFC0909703, Shenzhen Municipal Government of China, No. JCYJ20170817145809215, and National Natural Science Foundation of China, No. 31601073.

microbiology↗

bioRxiv2019

Adaptive laboratory evolution of Escherichia coli under acid stress

The ability of Escherichia coli to tolerate acid stress is important for its survival and colonization in the human digestive tract. Here, we performed adaptive laboratory evolution of the laboratory strain E. coli K-12 MG1655 at pH 5.5 in glucose minimal medium. By 800 generations, six independent populations under evolution reached 18.0% higher growth rates than their starting strain at pH 5.5, while maintaining comparable growth rates to the starting strain at pH 7. We characterized the evolved strains to find that: (1) whole genome sequencing of isolated clones from each evolved population revealed mutations in rpoC appearing in 5 of 6 sequenced clones; (2) gene expression profiles revealed different strategies to mitigate acid stress, that are related to amino acid metabolism and energy production and conversion. Thus, a combination of adaptive laboratory evolution, genome resequencing, and expression profiling reveals, on a genome-scale, the strategies that E. coli deploys to mitigate acid stress.

microbiology↗

bioRxiv2019

Global analysis of epigenetic heterogeneity identifies divergent drivers of esophageal squamous cell carcinoma

Epigenetic landscapes can shape physiologic and disease phenotypes. We used integrative, high resolution multi-omics methods to characterize the oncogenic drivers of esophageal squamous cell carcinoma (ESCC). We found 98% of CpGs are hypomethylated across the ESCC genome and two-thirds occur in long non-coding (lnc)RNA regions. DNA methylation and epigenetic heterogeneity both coincide with chromosomal topological alterations. Gene body methylation, polycomb repressive complex occupancy, and CTCF binding sites associate with cancer-specific gene regulation. Epigenetically-mediated activation of non-canonical WNT signaling and the lncRNA ESCCAL-1 were validated as potential ESCC driver alterations. Gene-specific cancer driver roles of epigenetic alterations and heterogeneity are identified.

cell biology↗

bioRxiv2019

A Novel L-Serine Exporter and Its Positive Regulator in Corynebacterium glutamicum

Exporters play an essential role in the fermentative production of amino acids. In Corynebacterium glutamicum, ThrE, which can export O_SCPCAPLC_SCPCAP-threonine and O_SCPCAPLC_SCPCAP-serine, is the only identified O_SCPCAPLC_SCPCAP-serine exporter so far. In this study, a novel O_SCPCAPLC_SCPCAP-serine exporter NCgl0580 was identified and characterized in C. glutamicum {Delta}SSAAI (SSAAI), and named as SerE (encoded by serE). Deletion of serE in SSAAI led to a 56.5% decrease in O_SCPCAPLC_SCPCAP-serine titer, whereas overexpression of serE compensated for the lack of serE with respect to O_SCPCAPLC_SCPCAP-serine titer. A fusion protein with SerE and enhanced green fluorescent protein (EGFP) was constructed to confirm that SerE localized at the plasma membrane. The function of SerE was studied by peptide feeding approaches, and the results showed that SerE is a novel exporter for O_SCPCAPLC_SCPCAP-serine and O_SCPCAPLC_SCPCAP-threonine in C. glutamicum. Subsequently, the interaction of a known O_SCPCAPLC_SCPCAP-serine exporter ThrE and SerE was studied, and the results suggested that SerE is more important than ThrE in O_SCPCAPLC_SCPCAP-serine export in SSAAI. Probe plasmid and electrophoretic mobility shift assays (EMSA) revealed NCgl0581 as the transcriptional regulator of SerE. Comparative transcriptomics between SSAAI and the NCgl0581 deletion strain showed that NCgl0581 regulated the transcription of 115 genes in C. glutamicum, among which the transcriptional level of NCgl0580 decreased 280-fold in a NCgl0581 deletion strain, indicating that NCgl0581 is a positive regulator of SerE. Thus, this study provides a novel target for O_SCPCAPLC_SCPCAP-serine and O_SCPCAPLC_SCPCAP-threonine export engineering as well as a novel global transcriptional regulator NCgl0581 in C. glutamicum.\n\nImportanceExporters are gaining increasing attention for improving industrial production of amino acids. This study identified a novel exporter NCgl0580 for O_SCPCAPLC_SCPCAP-serine and O_SCPCAPLC_SCPCAP-threonine in C. glutamicum, and its positive regulator (NCgl0581), which was shown to be a novel global transcriptional regulator in C. glutamicum. This study provides a new target for engineering efflux of O_SCPCAPLC_SCPCAP-serine and O_SCPCAPLC_SCPCAP-threonine, expands the exporter and transcriptional regulator family, and enriches our understanding of amino acid transport system in C. glutamicum.

bioengineering↗

bioRxiv2019

Clinical manifestations and phenotypic analysis of new ANK1 gene mutations in 12 Chinese children with hereditary spherocytosis

ObjectiveTo summarize the clinical features and laboratory examination of ANK1 gene in 12 children with hereditary spherocytosis in China, and to determine the genetic mutations in those children.\n\nMethodsThe clinical data of children and their parents were collected and analyzed. The sequence of related genes was analyzed by second-generation sequencing technology. The suspected pathogenic mutations were detected by Sanger sequencing\n\nResultsNew mutations in the coding region of ANK1 was detected in 12 patients, which caused amino acid changes in the gene encoding, causing structural changes or loss of function.\n\nConclusionANK1 (c.1914_c.1918delTTTG), ANK1 (c.399T>G), ANK1 (c.1564delC), ANK1 (c.4439dupA ), ANK1 (c.4510_4513del), ANK1 (c.2961delC), ANK1 (c.2142dupT), ANK1 (c.2858+1G>C), ANK1 (c.3235delG), ANK1 (c.4739A>G), ANK1 (c.2638-2 A>G), ANK1 (c. 4739A>G) mutations in the coding region of the gene are the cause of suspicious disease in these 12 Chinese children. At the same time, second-generation gene sequencing technology is an effective means of confirming HS. Different types of mutations (P=0.388)and different mutation areas (P=0.660)had no significant effect on the severity of anemia. The 12 gene mutation sites in this study have not been included in the human genome database, dbSNP (v138) and ExAC databases. The new ANK1 gene mutations found in HS children can provide further exploration of the genetic etiology of HS in Chinese population.

genetics↗

bioRxiv2019

ML277 specifically enhances pore opening of KCNQ1 with VSD at the activated state by modulating VSD-pore coupling

In response to membrane depolarization, the KCNQ1 potassium channel opens at the intermediate (IO) and activated (AO) states that correspond to the stepwise activation of the voltage sensing domain (VSD) to the intermediate (I) and activated (A) states. In the heart, KCNQ1 associates with the auxiliary subunit KCNE1 to form the IKs channel that regulates heart rhythm. More than 300 of loss-of-function KCNQ1 mutations cause long QT syndrome (LQTS). KCNE1 suppresses the IO state so that the IKs channel opens only to the AO state. Thus, enhancing AO state presents a potential therapy for anti-LQTS. Here, we systematically tested modulations of KCNQ1 channels by a KCNQ1 activator, ML277. It enhances the current amplitude, slows down activation, deactivation and inactivation kinetics, shifts the voltage dependence of activation to more positive voltages, decreases the Rb+/K+ permeability ratio, and selectively increases currents of mutant KCNQ1 channels that open only to the AO state. All these observations are consistent with the mechanism that ML277 specifically potentiates the AO state. On the other hand, ML277 does not affect the VSD activation, suggesting that it potentiates the AO state by enhancing the electromechanical (E-M) coupling when the VSD moves to the activated state. Our results suggest that ML277 provides a unique tool to investigate the gating mechanism of KCNQ1 and IKs channels. The specificity of ML277 to increase the AO state of native IKs currents also suggests a new strategy for anti-LQTS therapy.

biophysics↗

bioRxiv2019

The Escherichia coli Transcriptome Consists of Independently Regulated Modules

Underlying cellular responses is a transcriptional regulatory network (TRN) that modulates gene expression. A useful description of the TRN would decompose the transcriptome into targeted effects of individual transcriptional regulators. Here, we applied unsupervised learning to a compendium of high-quality Escherichia coli RNA-seq datasets to identify 70 statistically independent signals that modulate the expression of specific gene sets. We show that 50 of these transcriptomic signals represent the effects of currently characterized transcriptional regulators. Condition-specific activation of signals was validated by exposure of E. coli to new environmental conditions. The resulting decomposition of the transcriptome provided: (1) a mechanistic, systems-level, network-based explanation of responses to environmental and genetic perturbations, (2) a guide to gene and regulator function discovery, and (3) a basis for characterizing transcriptomic differences in multiple strains. Taken together, our results show that signal summation forms an underlying principle that describes the composition of a model prokaryotic transcriptome.

systems biology↗

bioRxiv2019

Sing cell RNA-seq reveals cellular diversity and developmental characteristics of human infant retina

Retina, located in the innermost layer of the eye of human, holds the decisive role in visual perception. Dissecting the heterogeneity of retina is essential for understanding the mechanism of vision formation and even the development of central nervous system (CNS). Here, we performed single cell RNA-seq, analyzed 57,832 cells from human infant donors, resulting in 20 distinct clusters representing major cell types in retina: rod photoreceptors, cone photoreceptors, bipolar cells, horizontal cells, amacrine cells, Muller glia cells and microglia. We next constructed extensive networks of intercellular communication and identified ligand-receptor interactions playing crucial roles in regulating neural cell development and immune homeostasis in retina. Though re-clustering, we identified known subtypes in cone PRs and additional unreported subpopulations and corresponding markers in rod PRs as well as bipolar cells. Additionally, we linked inherited retinal disease to certain cell subtypes or subpopulations through enrichment analysis. Intriguingly, we found that status and functions of photoreceptors changed drastically between early and late retina. Overall, our study offers the first retinal cell atlas in human infants, dissecting the heterogeneity of retina and identifying the key molecules in the developmental process, which provides an important resource that will pave the way for retina development mechanism research and regenerative medicine concerning retinal biology.

cell biology↗

bioRxiv2019

Single cell RNA sequencing reveals cellular diversity of trisomy 21 retina

Retina is a crucial tissue for the capturing and processing of light stimulus. Characterization of the retina at single cell level is essential for the understanding of its biological functions. A variety of abnormalities in terms of morphology and function were reported in T21 retina. To evaluate the effects of chromosome aneuploidy on retina development, we characterized single cell transcriptional profiles of a T21 fetus and performed comprehensive bioinformatic analyses. Our data revealed the diversity and heterogeneity of cellular compositions in T21 retina. In total, we identified seven major cell types, and detected several subtypes within each cell type, followed by the detection of corresponding molecular markers including previously reported ones and a series of novel markers. Our analyses identified extensive communication networks between distinct cellular types, among which a few ligand-receptor interactions were associated with the development of retina and immunoregulatory interactions. Taken together, our data provided the first single cell transcriptome profile for human T21 retina which facilitates our understanding on the dosage effects of chromosome 21 on the development of retina.

cell biology↗

bioRxiv2019

Early urine proteome changes in an implanted bone cancer rat model

In this study, Walker 256 cells were implanted into rat tibiae. Urine samples were then collected on days 3, 5, 7, and 13 and were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). With label-free quantification, 25 proteins were found to change significantly in the urine of the tumor group mice compared with the proteins in the urine of the control group mice; this was even the case when there were no significant lesions identified in the Computed Tomography(CT) examination. Among these differentially proteins, 7 were reported to be associated with tumor bone metastasis. GO analysis shows that the differential proteins on day 3 were involved in several responses, including the acute phase response, the adaptive immune response and the innate immune response. The differentially proteins on day 7 were involved in the mineral absorption pathway. The differentially proteins on day 13 were involved in vitamin D binding and calcium ion binding. These processes may be associated with bone metastasis. Our results demonstrate that urine could sensitively reflect the changes in the early stage of implanted bone cancer; this provides valuable clues for future studies of urine biomarkers for tumor bone metastasis.

cancer biology↗

bioRxiv2019

Urine proteome changes in rats with approximately ten tumor cells subcutaneous inoculation.

Biomarkers are changes associated with the disease. Without homeostatic control, urine accumulates very early changes and is an ideal biomarker source. Usually, we performed urinary biomarker studies involving at least thousands of tumor cells. But no tumor starts from a thousand tumor cells. Can we observe any urine proteome changes in rats with approximately ten tumor cells subcutaneous inoculation? Here, we serially diluted Walker-256 carcinosarcoma cells to a concentration of 102/mL and subcutaneously inoculated 0.1 mL of these cells into nine rats. Urine proteomes on days 0, 13 and 21 were profiled by LC-MS/MS analysis and studied with unsupervised clustering analysis. Samples at three time points were almost clustered together, indicating a good consistency in these nine rats. Differential proteins on days 13 and 21 were mainly associated with cell adhesion, autophagic cell death, changes in extracellular matrix organization, angiogenesis, and the pentose phosphate pathway. All of these enriched functional processes were reported to contribute to tumor progression and could not be enriched through random allocation analysis. Our results indicated that 1) the urine proteome reflects changes associated with cancer even with approximately ten tumor cells in the body and that 2) the urine proteome reflects pathophysiological changes in the body with extremely high sensitivity and provides potential for a very early screening process of clinical patients.

biochemistry↗

bioRxiv2019

Dynamic changes in the urine proteome in two ovarian cancer rat models

Ovarian cancer is the most lethal gynecological malignancy in women, and it is likely to metastasize and has a poor prognosis. The early and reliable diagnosis and monitoring of ovarian cancer is very important. Without a homeostasis mechanism, urine can reflect early systemic changes in the body and has a great potential to be used for the early detection of cancer. This study tested whether early changes could be detected in two ovarian cancer rat models. Two rat models were established by either intraperitoneal (i.p.) or orthotopic (o.t.) injection of NuTu-19 ovarian cancer cells in female Fischer344 rats. Urine samples from ovarian cancer rats were collected at five time points during cancer development, and urinary proteins from the rats were profiled by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Compared with pre-injection samples, 49 differential proteins that have human orthologues were significantly changed in the orthotopically injected model. Among them, 24 of the differential proteins have previously been reported to be associated with ovarian cancer, six of which were reported to be biomarkers of ovarian cancer. On the 7th day after orthotopic injection, four differential proteins (APOA1, OX2G, CHMP5, HEXB) were identified before obvious metastases appeared. In the intraperitoneal injection model, 76 differential proteins were changed during the course of ovarian cancer development. The results show that urine proteins could enable the early detection and monitoring of ovarian cancer progression and could lay a foundation for further exploration of the biomarkers of ovarian cancer.

biochemistry↗

bioRxiv2019

FGF/MAPK signaling pathway regulates the genome-wide occupancy of Polycomb Repressive Complex 2 in murine embryonic stem cells

The recruitment of Polycomb repressive complex 2 (PRC2) to gene promoters is critical for its function in repressing gene expression in murine embryonic stem cells (mESCs). However, previous studies have demonstrated although the expression of early lineage-specific genes is largely repressed, the genome-wide PRC2 occupancy is unexpectedly reduced in naive mESCs. In this study, we provide evidence to show the FGF/ERK signaling determines the global PRC2 occupancy through regulating the expression of PRC2-recruting factor JARID2 in naive mESCs. At the transcriptional level, the de-repression of bivalent genes is predominantly determined by the presence of cell signaling-associated transcription factors but not the status of PRC2 occupancy at gene promoters. Hence, this study not only reveals a key molecular mechanism by which the FGF/ERK signaling in regulating the PRC2 occupancy in mESCs, but also elucidates a fundamental question regarding the functional roles of transcription factors and Polycomb-mediated epigenetic mechanisms in transcriptional regulation.

genetics↗

bioRxiv2019

Volumetric two-photon imaging in live cells and embryos via axially gradient excitation

Two-photon microscopy(TPM) that features subcellular resolution, intrinsic optical sectioning ability, and deep penetration in sample is a powerful tool of bioimaging. However, the process of layer-by-layer scanning to form a 3D image inherently limits the volumetric imaging speed and significantly increases the phototoxicity. Here we develop a gradient TPM technique that enables rapid volumetric imaging by only acquiring two 2D images. By sequentially exciting the specimen with two axially elongated two-photon beams with complementary gradient intensities, the axial positions of fluorophores can be decoded from the intensity ratio of the paired images. We achieve an axial localization accuracy of 0.728 {+/-} 0.657 m, which is sufficient for rapid 3D subcellular imaging. We demonstrate the flexibility of the gradient TPM on a variety of sparsely labelled samples, including bead phantoms, mouse brain tissues, live macrophages and live nematode embryos. The results show that, compared with conventional TPM, the 3D imaging speed increases 6 folds while the photobleaching and photodamage are extremely reduced.

bioengineering↗

bioRxiv2019

Genetic Basis of Alternative Polyadenylation is an Emerging Molecular Phenotype for Human Traits and Diseases

Genome-wide association studies have identified thousands of non-coding variants that are statistically associated with human traits and diseases. However, functional interpretation of these variants remains a major challenge. Here, we describe the first atlas of human 3-UTR alternative polyadenylation (APA) Quantitative Trait Loci (3QTLs), i.e. [~]0.4 million genetic variants associated with APA of target genes across 46 Genotype-Tissue Expression (GTEx) tissues from 467 individuals. APA occurs in approximately 70% of human genes and substantively impacts cellular proliferation, differentiation and tumorigenesis. Mechanistically, 3QTLs could alter polyA motifs and RNA-binding protein binding sites, leading to thousands of APA changes. Importantly, 3QTLs can be used to interpret [~]16.1% of trait-associated variants and are largely distinct from other QTLs such as eQTLs. The genetic basis of APA (3QTLs) thus represent a novel molecular phenotype to explain a large fraction of non-coding variants and to provide new insights into complex traits and disease etiologies.\n\nHighlightsO_LIThe first atlas of human 3QTLs: [~]0.4 million genetic variants associated with alternative polyadenylation of target genes across 46 tissues from 467 individuals\nC_LIO_LI3QTLs could alter polyA motifs and RNA-binding protein binding sites\nC_LIO_LI3QTLs can be used to interpret [~]16.1% of trait-associated variants\nC_LIO_LIMany disease-associated 3QTLs contribute to phenotype independent of gene expression\nC_LI

bioinformatics↗

bioRxiv2019

Comparison of different orders of Legendre polynomials in random regression model for estimation of genetic parameters and breeding values of milk yield in the Chinese Holstein population

Random regression test-day model has become the most commonly adopted model for routine genetic evaluations for different dairy populations, which allows accurately accounting for genetic and environmental effects at different periods during lactation. The objective of this study was to explore appropriate random regression test-day model for genetic evaluation of milk yield in Chinese Holstein population. Data included 419,567 test-day records from 54,417 cows in the first lactation. Variance components and breeding values were estimated using random regression test-day model with different order (first order to fifth order) of Legendre polynomials, and accounted for homogeneous or heterogeneous residual variance across the lactation. The goodness of fit of the models was evaluated by total residual variance (TRV) and - 2logL. Further, the predictive ability of the models was assessed by Spearmans rank correlation between estimated breeding values for 305d milk yield (EBV305) from the full data set and reduced data set in which the records from the last calving year were masked. The results showed that random regression models using third order Legendre polynomials (LP3) with heterogeneous residual variance achieved the lower TRV and - 2logL value and the highest correlation for EBV305 between full data and reduced data. Heritability estimated by this model was 0.250 for 305d milk yield and ranged from 0.163 to 0.304 for test-day milk yield. We suggest random regression model with Legendre polynomial of order 3 and accounting for heterogeneous residual variances could be an appropriate model to be used for genetic evaluation of milk yield for Chinese Holstein population.

genetics↗

bioRxiv2019

Interacting cells driving the evolution of multicellular life cycles

Evolution of complex multicellular life begun from the emergence of life cycle involving formation of cell clusters. Opportunity for cells to interact within clusters provided them an advantage over unicellular life forms. However, what kind of interactions may lead to the evolution of multicellular life cycles? Here, we combine evolutionary game theory with a model for the emergence of multicellular groups to investigate how cell interactions can influence reproduction modes during the early stages of the evolution of multicellularity. We identify evolutionary optimal life cycles as those which maximize the population growth rate. Among all interactions captured by two-player games, only eight life cycles were found to be evolutionarily optimal. Moreover, the vast majority of games promotes either of two classes of life cycles: (i) splitting into unicellular propagules or (ii) fragmentation into two offspring clusters of equal (or almost equal) size. Our findings indicate that the three most important characteristics, determining whether multicellular life cycles will evolve, are average performance of homogeneous groups, heterogeneous groups, and solitary cells.

evolutionary biology↗

bioRxiv2019

FabriEVEs: A dedicated platform for endogenous viral elements in fishes, amphibians, birds, reptiles and invertebrates

Endogenous viral elements (EVEs) are heritable viral deriving elements present in the genomes of other species. As DNA fossils left by ancient viruses, EVEs were used to infer the characteristics of extinct viruses. EVEs in mammals have been well classified by several databases, however, EVEs in non-mammalian organisms are poorly documented. Here, we report FabriEVEs (http://tfbsbank.co.uk/FabriEVEs), the first dedicated and comprehensive online platform for the collection, classification and annotation of EVEs in fishes, amphibians, birds, reptiles and invertebrates. In total, nearly 1.5 million EVEs from 82 species deriving from class I (dsDNA), II (ssDNA), III (dsRNA), IV (positive ssRNA), V (negative ssRNA), VI (ssRNA-RT) and VII (dsDNA-RT) viruses were recorded in FabriEVEs, accompanying with comprehensive annotation including the species name, location, genomic features, virus family and associated literature. Flexible and powerful query options were provided to pinpoint desired EVEs. Furthermore, FabriEVEs provides free access to all EVEs data in case users need to download them for further analysis. Taken together, our database provided systematic classification and annotation of EVEs in non-mammal species, which paves the way for comparative analysis of EVEs and throws light upon the co-evolution of EVEs and their hosts.

evolutionary biology↗