Biology subjects

Zheng, X.

Publications and source records attributed to Zheng, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2018

Insufficient fumarase contributes to generating reactive oxygen species in Dahl salt sensitive rats

Dahl SS rats exhibit greater levels of renal medullary oxidative stress and lower levels of fumarase activities. Fumarase insufficiencies can increase reactive oxygen species (ROS), the mechanism of which, however, is not clear. A proteomic analysis indicated fumarase knockdown in HK-2 cells resulted in changes in the expression or activity of NADPH oxidase, mitochondrial respiratory chain complex I and III, ATP synthase subunits, and -oxoglutarate dehydrogenase, all of which are sites of ROS formation. Meantime, the activities of key antioxidant enzymes such as G6PD, 6PGD, GR, GPx and GST increased significantly too. The apparent activation of antioxidant defense appeared insufficient as glutathione precursors, glutathione and GSH/GSSG ratio were decreased. SS rats exhibited changes in redox metabolism similar to HK-2 cells with fumarase knockdown. Supplementation with fumarate and malate, the substrate and product of fumarase, increased and decreased, respectively, blood pressure and the levels of H2O2 and MDA in kidney tissues of SS rats. These results indicate fumarase insufficiencies cause a wide range of changes at several sites of ROS production and antioxidant mechanisms.

molecular biology↗

bioRxiv2018

Lactobacillus acidophilus disrupts collaborative multispecies bile acid metabolism

Bile acids are metabolic links between hosts and their gut microbiomes, yet little is known about the roles they play in microbe-to-microbe interactions. Here we present a study designed to investigate the effect that a common probiotic, Lactobacillus acidophilus, has on microbial interactions that lead to formation of secondary bile acids. A model microbial consortium was built from three human gut isolates, Clostridium scindens, Collinsella aerofaciens, and Blautia obeum, and cultured under different bile acid and probiotic treatments. A multi-omics platform that included mass spectrometry-based metabolomics and activity-based proteomic probes was used to produce two major results. The first, was that an uncommon secondary bile acid - ursocholate - was produced by a multi-species chemical synthesis pathway. This result highlights a new microbe-to-microbe interaction mediated by bile acids. The second finding was that the probiotic strain, L. acidophilus, quenched the observed interactions and effectively halted consortial synthesis of ursocholate. Little is known about the role that ursocholate plays in human health and development. However, we did discover that a decrease in ursocholate abundance corresponded with successful weight loss in patients after gastric bypass surgery versus those who did not lose weight after surgery. Hence, this study uncovered basic knowledge that may aid future designs of custom probiotic therapies to combat obesity.

microbiology↗

bioRxiv2018

A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 nucleases in rice

Targeting specificity has been an essential issue for applying genome editing systems in functional genomics, precise medicine and plant breeding. Understanding the scope of off-target mutations in Cas9 or Cpf1-edited crops is critical for research and regulation. In plants, only limited studies had used whole-genome sequencing (WGS) to test off-target effects of Cas9. However, the cause of numerous discovered mutations is still controversial. Furthermore, WGS based off-target analysis of Cpf1 has not been reported in any higher organism to date. Here, we conducted a WGS analysis of 34 plants edited by Cas9 and 15 plants edited by Cpf1 in T0 and T1 generations along with 20 diverse control plants in rice, a major food crop with a genome size of ~380 Mb. The sequencing depth ranged from 45X to 105X with reads mapping rate above 96%. Our results clearly show that most mutations in edited plants were created by tissue culture process, which caused ~102 to 148 single nucleotide variations (SNVs) and ~32 to 83 insertions/deletions (indels) per plant. Among 12 Cas9 single guide RNAs (sgRNAs) and 3 Cpf1 CRISPR RNAs (crRNAs) assessed by WGS, only one Cas9 sgRNA resulted in off-target mutations in T0 lines at sites predicted by computer programs. Moreover, we cannot find evidence for bona fide off-target mutations due to continued expression of Cas9 or Cpf1 with guide RNAs in T1 generation. Taken together, our comprehensive and rigorous analysis of WGS big data across multiple sample types suggests both Cas9 and Cpf1 nucleases are very specific in generating targeted DNA modifications and off-targeting can be avoided by designing guide RNAs with high specificity.

molecular biology↗

bioRxiv2018

Kynurenine 3-monooxygenase (KMO) is a critical regulator of renal ischemia-reperfusion injury

Acute kidney injury (AKI) following ischemia-reperfusion injury (IRI) has a high mortality and lacks specific therapies. Here, we report that mice lacking kynurenine 3-monooxygenase (KMO) activity (Kmonull mice) are protected against AKI after renal IRI. This advances our previous work showing that KMO blockade protects against acute lung injury and AKI in experimental multiple organ failure caused by acute pancreatitis. We show that KMO is highly expressed in the kidney and exerts major metabolic control over the biologically-active kynurenine metabolites 3-hydroxykynurenine, kynurenic acid and downstream metabolites. In experimental AKI induced by unilateral kidney IRI, Kmonull mice had preserved renal function, reduced renal tubular cell injury, and fewer infiltrating neutrophils compared to wild-type (Kmowt) control mice. Together, these data confirm that flux through KMO contributes to AKI after IRI, and supports the rationale for KMO inhibition as a therapeutic strategy to protect against AKI during critical illness.

pathology↗

bioRxiv2018

Sex- and Context-dependent Effects of Oxytocin on Social Reward Processing

We interact socially and form bonds with others because such experiences are rewarding. However, an insecure attachment style or social anxiety can reduce these rewarding effects. The neuropeptide oxytocin (OXT) may facilitate social interactions either by increasing their rewarding experience or by attenuating anxiety, although effects can be sex- and attachment-style dependent. In this study, 64 pairs of same-sex friends completed a social sharing paradigm in a double-blind, placebo-controlled, between-subject design with one friend inside an MRI scanner and the other in a remote behavioral testing room. In this way we could examine whether intranasal-OXT differentially modulated the emotional impact of social sharing and associated neural processing. Additionally, we investigated if OXT effects were modulated by sex and attachment style. Results showed that in women, but not men, OXT increased ratings for sharing stimuli with their friend but not with a stranger, particularly in the friend in the scanner. Corresponding neuroimaging results showed that OXT decreased both amygdala and insula activity as well as their functional connectivity in women when they shared with friends but had the opposite effect in men. On the other hand, OXT did not enhance responses in brain reward circuitry. In the PLC treated group amygdala responses in women when they shared pictures with their friend were positively associated with attachment anxiety and OXT uncoupled this. Our findings demonstrate that OXT facilitates the impact of sharing positive experiences with others in women, but not men, and that this is associated with differential effects on the amygdala and insula and their functional connections. Furthermore, OXT particularly reduced increased amygdala responses during sharing in individuals with higher attachment anxiety. Thus, OXT effects in this context may be due more to reduced anxiety when sharing with a friend than to enhanced social reward.

neuroscience↗

bioRxiv2018

Direct Imaging of the circular chromosome of a live bacterium

New assays for quantitative imaging1-6 and sequencing7-11 have yielded great progress towards understanding the organizational principles of chromosomes. Yet, even for the well-studied model bacterium Escherichia coli, many basic questions remain unresolved regarding chromosomal (sub-)structure2,11, its mechanics1,2,12 and dynamics13,14, and the link between structure and function1,15,16. Here we resolve the spatial organization of the circular chromosome of bacteria by directly imaging the chromosome in live E. coli cells with a broadened cell shape. The chromosome was observed to exhibit a torus topology with a 4.2 m toroidal length and 0.4 m bundle thickness. On average, the DNA density along the chromosome shows dense right and left arms that branch from a lower-density origin of replication, and are connected at the terminus of replication by an ultrathin flexible string of DNA. At the single-cell level, the DNA density along the torus is found to be strikingly heterogeneous, with blob-like Mbp-size domains that undergo major dynamic rearrangements, splitting and merging at a minute timescale. We show that prominent domain boundaries at the terminus and origin of replication are induced by MatP proteins, while weaker transient domain boundaries are facilitated by the global transcription regulators HU and Fis. These findings provide an architectural basis for the understanding of the spatial organization of bacterial genomes.

microbiology↗

bioRxiv2018

Long Noncoding RNA-Maternally Expressed Gene 3 Contributes to Hypoxic Pulmonary Hypertension

The expression and function of long noncoding RNAs (lncRNAs) in the development of hypoxic pulmonary hypertension, especially in the proliferation of pulmonary artery smooth muscle cells (PASMCs) are largely unknown. Here, we characterized the expression of lncRNA-maternally expressed gene 3 (lncRNA-MEG3) was significantly increased and primarily located in the cytoplasm of PASMCs by hypoxia. LncRNA-MEG3 knockdown by lung-specific delivery of small interfering RNAs (siRNAs) significantly prevented the development of hypoxic pulmonary hypertension in vivo. Silencing of lncRNA-MEG3 by siRNAs and gapmers attenuated PASMC responses to hypoxia in vitro. Mechanically, we found that lncRNA-MEG3 acts as a molecular sponge of microRNA-328 (miR-328); upon hypoxia, lncRNA-MEG3 interacts and sequesters miR-328, leading to the upregulation of insulin-like growth factor 1 receptor (IGF1R). Additionally, higher expression of lncRNA-MEG3 and IGF1R, and lower expression of miR-328 were observed in PASMCs of iPAH patients. These data provide insight into the contribution of lncRNA-MEG3 in hypoxia pulmonary hypertension. Upregulation of lncRNA-MEG3 sequesters cytoplasmic miR-328, eventually leading to the expression of IGF1R, revealing a regulatory mechanism by lncRNAs in hypoxia-induced PASMC proliferation.

molecular biology↗

bioRxiv2017

Lamins organize the global three-dimensional genome from the nuclear periphery

Lamins are structural components of the nuclear lamina (NL) that regulate genome organization and gene expression, but the mechanism remains unclear. Using Hi-C, we show that lamins maintain proper interactions among the topologically associated chromatin domains (TADs) but not their overall architecture. Combining Hi-C with fluorescence in situ hybridization (FISH) and analyses of lamina-associated domains (LADs), we reveal that lamin loss causes expansion or detachment of specific LADs in mouse ES cells. The detached LADs disrupt 3D interactions of both LADs and interior chromatin. 4C and epigenome analyses further demonstrate that lamins maintain the active and repressive chromatin domains among different TADs. By combining these studies with transcriptome analyses, we found a significant correlation between transcription changes and the changes of active and inactive chromatin domain interactions. These findings provide a foundation to further study how the nuclear periphery impacts genome organization and transcription in development and NL-associated diseases.\n\nHighlightsO_LILamin loss does not affect the overall TAD structure but alters TAD-TAD interactions\nC_LIO_LILamin null ES cells exhibit decondensation or detachment of specific LAD regions\nC_LIO_LIExpansion and detachment of LADs can alter genome-wide 3D chromatin interactions\nC_LIO_LIAltered chromatin domain interactions are correlated with altered transcription\nC_LI

genomics↗

bioRxiv2017

Cholecystokinin release triggered by presynaptic NMDA receptors produces LTP and sound-sound associative memory formation

Memory is stored in neural networks via changes in synaptic strength mediated in part by NMDA-dependent long-term potentiation (LTP). There is evidence that entorhinal cortex enables neocortical neuroplasticity through cholecystokinin (CCK)-containing neocortical projections. Here we show that a CCKB antagonist blocks high-frequency stimulation (HFS)-induced LTP in the auditory cortex, whereas local infusion of CCK induces LTP. CCK-/- mice lacked neocortical LTP and showed deficits in a cue-cue associative learning paradigm; administration of CCK rescued associative learning. HFS of CCK-containing entorhino-neocortical projection neurons in anesthetized mice enabled cue-cue associative learning. Furthermore, when one cue was pre-conditioned to footshock, the mouse showed a freezing response to the other cue, indicating that the mice had formed an association. HFS-induced neocortical LTP was completely blocked by either NMDA antagonist or CCK-BR antagonist, while application of either NMDA or CCK induced LTP after low-frequency stimulation (LFS). Moreover, in the presence of CCK LTP was still induced, even after blockade of NMDA receptors. Local application of NMDA induced CCK release in the neocortex. To identify how NMDA receptor switches LTP, a stimulation protocol of 25 pulse-pairs was adopted to replace HFS; NMDA-dependent LTP was induced with the inter-pulse intervals between 10 and 100 ms, but not with those of 5 and 200 ms. LTP-mediated plasticity was linked to localization of the NMDA receptor subunit NR2a on cortical CCK terminals originating in the entorhinal cortex. These novel findings suggest that presynaptic NMDA receptors on CCK terminals control the release of CCK, which enables neocortical LTP and formation of cue-cue associative memory.\n\nOne Sentence SummaryPresynaptic NMDA receptors switches the release of CCK from entorhinal neurons, which enables neocortical LTP and formation of sound-sound associative memory.

neuroscience↗

bioRxiv2017

CscoreTool: Fast Hi-C Compartment Analysis at High Resolution

SummaryThe chromosome conformation capture (Hi-C) has revealed that the eukaryotic genome can be partitioned into A and B compartments that have distinctive chromatin and transcription features. Current Principle Component Analyses (PCA)-based method for the prediction of A/B compartment prediction from Hi-C data requires substantial CPU time and memory. We report the development of a method, CscoreTool, that enables fast and memory-efficient determination of A/B compartments at high resolution even in dataset with low sequencing depth.\n\nAvailabilitygithub.com/scoutzxb/CscoreTool\n\nContactxzheng@carnegiescience.edu

bioinformatics↗

bioRxiv2017

Hsf1 phosphorylation generates cell-to-cell variation in Hsp90 levels and promotes phenotypic plasticity

Clonal populations of cells exhibit cell-to-cell variation in the transcription of individual genes. In addition to this \"noise\" in gene expression, heterogeneity in the proteome and the proteostasis network expands the phenotypic diversity of a population. Heat shock transcription factor (Hsf1) regulates chaperone gene expression, thereby coupling transcriptional noise to proteostasis. Here we show that cell-to-cell variation in Hsf1 activity is an important determinant of phenotypic plasticity. Budding yeast cells with high Hsf1 activity were enriched for the ability to acquire resistance to an antifungal drug, and this enrichment depended on Hsp90 - a known \"phenotypic capacitor\" and canonical Hsf1 target. We show that Hsf1 phosphorylation promotes cell-to-cell variation, and this variation - rather than absolute Hsf1 activity - promotes antifungal resistance. We propose that Hsf1 phosphorylation enables differential tuning of the proteostasis network in individual cells, allowing populations to access a wide range of phenotypic states.

systems biology↗

bioRxiv2017

Hsf1 and Hsp70 constitute a two-component feedback loop that regulates the yeast heat shock response

Models for regulation of the eukaryotic heat shock response typically invoke a negative feedback loop consisting of the transcriptional activator Hsf1 and a molecular chaperone encoded by an Hsf1 target gene. Previously, we identified Hsp70 as the chaperone responsible for Hsf1 repression in Saccharomyces cerevisiae and constructed a mathematical model based on Hsp70-mediated negative feedback that recapitulated the dynamic activity of Hsf1 during heat shock. The model was based on two assumptions: dissociation of Hsp70 activates Hsf1, and transcriptional induction of Hsp70 deactivates Hsf1. Here we validated these assumptions. First, we severed the feedback loop by uncoupling Hsp70 expression from Hsf1 regulation. As predicted by the model, Hsf1 was unable to efficiently deactivate in the absence of Hsp70 transcriptional induction. Next we mapped a discrete Hsp70 binding site on Hsf1 to a motif in the C-terminal activation domain known as conserved element 2 (CE2). Removal of CE2 resulted in increased Hsf1 activity under non-heat shock conditions and delayed deactivation kinetics. In addition, we uncovered a role for the N-terminal domain of Hsf1 in negatively regulating DNA binding. These results reveal the quantitative control mechanisms underlying the feedback loop charged with maintaining cytosolic proteostasis.

biochemistry↗

bioRxiv2017

Gene markers for exon capture and phylogenomics in ray-finned fishes

Gene capture coupled with the next generation sequencing has become one of the favorable methods in subsampling genomes for phylogenomic studies. Many target gene markers have been developed in plants, sharks, frogs, reptiles and others, but few have been reported in the ray-finned fishes. Here, we identified a suite of \"single-copy\" protein coding sequence (CDS) markers through comparing eight fish genomes, and tested them empirically in 83 species (33 families and 11 orders) of ray-finned fishes. Sorting through the markers according to their completeness and phylogenetic decisiveness in taxa tested resulted in a selection of 4,434 markers, which were proven to be useful in reconstructing phylogenies of the ray-finned fishes at different taxonomic level. We also proposed a strategy of refining baits (probes) design a posteriori based on empirical data. The markers that we have developed may fill a gap in the tool kit of phylogenomic study in vertebrates.

evolutionary biology↗

bioRxiv2017

Genome-Wide SNPs Reveal the Drivers of Gene Flow In An Urban Population of the Asian Tiger Mosquito, Aedes albopictus

Aedes albopictus is a highly invasive disease vector with an expanding worldwide distribution. Genetic assays using low to medium resolution markers have found little evidence of spatial genetic structure even at broad geographic scales, suggesting frequent passive movement along human transportation networks. Here we analysed genetic structure of Ae. albopictus collected from 12 sample sites in Guangzhou, China, using thousands of genome-wide single nucleotide polymorphisms (SNPs). We found evidence for passive gene flow, with distance from shipping terminals being the strongest predictor of genetic distance among mosquitoes. As further evidence of passive dispersal, we found multiple pairs of full-siblings distributed between two sample sites 3.7 km apart. After accounting for geographical variability, we also found evidence for isolation by distance, previously undetectable in Ae. albopictus. These findings demonstrate how large SNP datasets and spatially-explicit hypothesis testing can be used to decipher processes at finer geographic scales than formerly possible. Our approach can be used to help predict new invasion pathways of Ae. albopictus and to refine strategies for vector control that involve the transformation or suppression of mosquito populations.\n\nAuthor SummaryAedes albopictus, the Asian Tiger Mosquito, is a highly invasive disease vector with a growing global distribution. Designing strategies to prevent invasion and to control Ae. albopictus populations in invaded regions requires knowledge of how Ae. albopictus disperses. Studies comparing Ae. albopictus populations have found little evidence of genetic structure even between distant populations, suggesting that dispersal along human transportation networks is common. However, a more specific understanding of dispersal processes has been unavailable due to an absence of studies using high-resolution genetic markers. Here we present a study using high-resolution markers, which investigates genetic structure among 152 Ae. albopictus from Guangzhou, China. We found that human transportation networks, particularly shipping terminals, had an influence on genetic structure. We also found genetic distance was correlated with geographical distance, the first such observation in this species. This study demonstrates how high-resolution markers can be used to investigate ecological processes that may otherwise escape detection. We conclude that strategies for controlling Ae. albopictus will have to consider both passive reinvasion along human transportation networks and active reinvasion from neighbouring regions.

ecology↗

bioRxiv2017

In vivo Imaging β-cell Function Reveals Two Waves of β-cell Maturation

The insulin-secreting cells generated from stem cells in vitro are less glucose responsive than primary {beta}-cells. To search for the missing ingredients that are needed for {beta}-cell maturation, we have longitudinally monitored function of every {beta}-cell in Tg (ins:Rcamp1.07) zebrafish embryos with a newly-invented two-photon light-sheet microscope. We have shown that {beta}-cell maturation begins from the islet mantle and propagates to the islet core during the hatching period, coordinated by the islet vascularization. Lower concentration of glucose is optimal to initiate {beta}-cell maturation, while increased glucose delivery to every cell through microcirculation is required for functional boosting of the {beta}-cells. Both the initiation and the boosting of {beta}-cell maturation demands activation of calcineurin/NFAT by glucose. Calcineurin activator combined with glucose promotes mouse neonatal {beta}-cells cultured in vitro to mature to a functional state similar to adult {beta}-cells, suggesting a new strategy for improving stem cell-derived {beta}-like cell function in vitro.

developmental biology↗

bioRxiv2017

A pipeline for interrogating and engineering single-subunit oligosaccharyltransferases

Asparagine-linked (N-linked) protein glycosylation is one of the most abundant types of post-translational modification, occurring in all domains of life. The central enzyme in N-linked glycosylation is the oligosaccharyltransferase (OST), which catalyzes the covalent attachment of preassembled glycans to specific asparagine residues in target proteins. Whereas in higher eukaryotes the OST is comprised of eight different membrane proteins of which the catalytic subunit is STT3, in kinetoplastids and prokaryotes the OST is a monomeric enzyme bearing homology to STT3. Given their relative simplicity, these single-subunit OSTs (ssOSTs) have emerged as important targets for mechanistic dissection of poorly understood aspects of N-glycosylation and at the same time hold great potential for the biosynthesis of custom glycoproteins. To take advantage of this utility, this chapter describes a multipronged approach for studying and engineering ssOSTs that integrates in vivo screening technology with in vitro characterization methods, thereby creating a versatile and readily-adaptable pipeline for virtually any ssOST of interest.\n\nAbbreviations

synthetic biology↗

bioRxiv2017

Gelsolin regulates proliferation, apoptosis and invasion in NK/T-cell lymphoma cells through the PI3K/Akt signaling pathway

The expression of gelsolin (GSN) is abnormal in many cancers, including extranodal nasal-type natural killer/T-cell lymphoma (NKTCL). However, the biological function of GSN and its mechanism in NKTCL remain unclear. We found GSN overexpression significantly suppressed cell proliferation, colony formationand invasion and promoted apoptosis of YTS cells. Moreover, the upregulation of GSN significantly decreased the protein levels of PI3K and p-AKT. Interestingly, blocking the PI3K/AKT signaling pathway significantly inhibited cell proliferation and invasion and promoted apoptosis of YTS cells. In conclusion, our findings indicate that GSN can suppress cell proliferation and invasion and promote apoptosis of YTS cells, which is likely to be mediated at least partially through inhibition of the PI3K/AKT signaling pathway.

cancer biology↗

bioRxiv2017

Characterization Of Imprinted Genes In Rice Reveals Post-Fertilization Regulation And Conservation At Some Loci Of Imprinting In Plant Species

Genomic imprinting is an epigenetic phenomenon by which certain genes display monoallelic expression in a parent-of-origin-dependent manner. Hundreds of imprinted genes have been identified from several plant species. Here we identified, with a high level of confidence, 208 imprinted candidates from rice. Imprinted genes of rice showed limited association to the transposable elements, which is contrast to the findings in Arabidopsis. Generally, imprinting of rice is conserved within species, but intraspecific variations were confirmed here. Imprinting between cultivated rice and wild rice are likely similar. The imprinted genes of rice do not show significant selective signatures overall, which suggests that domestication imposes limited evolutionary effects on genomic imprinting of rice. Though the conservation of imprinting in plants is limited, here we prove that some loci tend to be imprinted in different species. In addition, our results suggest that differential epigenetic regulation between parental alleles can be established either prior to or post-fertilization. The imprinted 24-nt small RNAs, but not the 21-nt ones, likely involve the regulation of imprinting in an opposite parental-allele targeting manner. Together, our findings suggest that regulation of imprinting can be very diverse, and genomic imprinting as well as imprinted genes have essential evolutionary and biological significance.

plant biology↗