Biology subjects

Liang, X.

Publications and source records attributed to Liang, X..

12 recordsLinked to original sources

bioRxiv2018

Antigen-specific T-cell receptor signatures of cytomegalovirus infection

Cytomegalovirus (CMV) is a prevalent human pathogen. The virus cannot be eliminated from the body, but is kept in check by CMV-specific T cells. Patients with an insufficient T-cell response, such as transplant recipients, are at high risk of developing CMV disease. However, the CMV-specific T-cell repertoire is complex, and is not yet clear which T cells protect best against virus reactivation and disease. Here we present a highly resolved characterization of CMV-specific CD8+ T cells based on enrichment by specific peptide stimulation and mRNA sequencing of their T-cell receptor {beta} chains (TCR{beta}). Our analysis included recently identified T-cell epitopes restricted through HLA-C, whose presentation is resistant to viral immunomodulation, and well-studied HLA-B-restricted epitopes. In 8 healthy virus carriers, we identified a total of 1052 CMV-specific TCR{beta} chains. HLA-C-restricted, CMV-specific TCR{beta} clonotypes the ex vivo T-cell response, and contributed the highest-frequency clonotype of the entire repertoire in 2 of 8 donors. We analyzed sharing and similarity of CMV-specific TCR{beta} sequences and identified 63 public or related sequences belonging to 17 public TCR{beta} families. In our cohort and in an independent cohort of 352 donors, the cumulative frequency of these public TCR{beta} family members was a highly discriminatory indicator of carrying both CMV infection and the relevant HLA type. Based on these findings, we propose CMV-specific TCR{beta} signatures as a biomarker for an antiviral T-cell response to identify patients in need of treatment and to guide future development of immunotherapy.

immunology↗

bioRxiv2018

Morning and Evening Circadian Pacemakers Independently Drive Premotor Centers via a Specific Dopamine Relay

Many animals exhibit morning and evening peaks of locomotor behavior. In Drosophila, previous studies identified two corresponding circadian neural oscillators: M (morning) cells which exhixbit a morning neural activity peak, and E (evening) cells which exhibit a corresponding evening peak of activity. Yet we know little of how these distinct circadian oscillators produce specific outputs that regulate pre-motor circuits to precisely control behavioral episodes. Here we show that the Ring Neurons of the Ellipsoid Body (EB-RNs), a defined pre-motor center, display a spontaneous in vivo neural activity rhythm, with peaks in the morning and in the evening. The two EB-RN activity peaks coincide with the major bouts of locomotor activity and result from independent activation by M and E cells, respectively. Further, M and E cells regulate EB-RNs via two identified dopaminergic neurons PPM3-EB, which project to the EB and which are normally co-active with EB-RNs. Blocking the dopaminergic modulation onto EB-RNs prevents the daily two-peak pattern of neural activity in the EB-RN and greatly impairs circadian locomotor activity. These in vivo findings establish the fundamental elements of a circadian neuronal output pathway: distinct circadian oscillators independently drive a common pre-motor center through the agency of specific dopaminergic interneurons.

neuroscience↗

bioRxiv2018

Impact of Microbial Iron Oxide Reduction on the Transport of Diffusible Tracers and Non-diffusible Nanoparticles in Soils

AbstractIn situ bioremediation to achieve immobilization of toxic metals and radionuclides or detoxification of chlorinated solvents relies on electron donor additions. This practice promotes microbial Fe(III)-oxide mineral reduction that could change soil pore structure, release soil colloids, alter matrix surface properties, and cause the formation of secondary (i.e., reduced) Fe-mineral phases. These processes in turn may impact rates of bioremediation, groundwater quality, and ultimately contaminant fate. Continuous flow columns packed with water-stable soil aggregates high in Fe-oxides were infused with artificial groundwater containing acetate as electron donor and operated for 20 or 60 days inside an anoxic chamber. Soluble Fe(II) and soil colloids were detected in the effluent within one week after initiation of the acetate addition, demonstrating Fe(III)-bioreduction and colloid formation. Br-, 2,6-difluorobenzoate (DFBA), and silica-shelled silver nanoparticles (SSSNP) were selected as diffusible tracer, low-diffusible tracer, and non-diffusible nanoparticles, respectively, to perform transport experiments before and after the active 20-day bioreduction phase, with an aim of assessing the changes in soil structure and surface chemical properties resulting from Fe(III)-bioreduction. The transport of diffusible Br- was not influenced by the Fe(III)-bioreduction as evidenced by identical breakthrough curves before and after the introduction of acetate. Low-diffusible DFBA showed earlier breakthrough and less tailing after the bioreduction, suggesting alterations in flow paths and surface chemical properties of the soils. Similarly, non-diffusible SSSNP exhibited early breakthrough and enhanced transport after the bioreduction phase. Unexpectedly, the bioreduction caused complete retention of SSSNP in the soil columns when the acetate injection was extended from 20 days to 60 days, though no changes were observed for Br- and DFBA during the extended bioreduction period. The large change in the transport of SSSNP was attributed to the enhancement of soil aggregate breakdown and soil colloid release causing mechanical straining of SSSNP and the exposure of iron oxide surfaces previously unavailable within aggregate interiors favorable to the attachment of SSSNP. These results demonstrate that microbial activity can affect soil properties and transport behaviors of diffusivity-varying solutes and colloids in a time dependent fashion, a finding with implication for interpreting the data generated from soil column experiments under continuous flow.\n\nHighlightsO_LIFe(III)-bioreduction causes time-dependent aggregate breakdown and colloid release.\nC_LIO_LIShort-term bioreduction alters soil aggregate surface chemistry and tracer transport.\nC_LIO_LIElectron donor amendment enhances transport of nanoparticle tracer.\nC_LI

microbiology↗

bioRxiv2018

Sequencing of Panax notoginseng genome reveals genes involved in disease resistance and ginsenoside biosynthesis

Panax notoginseng is a traditional Chinese herb with high medicinal and economic value. There has been considerable research on the pharmacological activities of ginsenosides contained in Panax spp.; however, very little is known about the ginsenoside biosynthetic pathway. We reported the first de novo genome of 2.36 Gb of sequences from P. notoginseng with 35,451 protein-encoding genes. Compared to other plants, we found notable gene family contraction of disease-resistance genes in P. notoginseng, but notable expansion for several ATP-binding cassette (ABC) transporter subfamilies, such as the Gpdr subfamily, indicating that ABCs might be an additional mechanism for the plant to cope with biotic stress. Combining eight transcriptomes of roots and aerial parts, we identified several key genes, their transcription factor binding sites and all their family members involved in the synthesis pathway of ginsenosides in P. notoginseng, including dammarenediol synthase, CYP716 and UGT71. The complete genome analysis of P. notoginseng, the first in genus Panax, will serve as an important reference sequence for improving breeding and cultivation of this important nutraceutical and medicinal but vulnerable plant species.

genomics↗

bioRxiv2018

Reliable Multiplex Sequencing with Rare Index Mis-Assignment on DNB-Based NGS Platform

BackgroundMassively-parallel-sequencing, coupled with sample multiplexing, has made genetic tests broadly affordable. However, intractable index mis-assignments (commonly exceeds 1%) were repeatedly reported on some widely used sequencing platforms.\n\nResultsHere, we investigated this quality issue on BGI sequencers using three library preparation methods: whole genome sequencing (WGS) with PCR, PCR-free WGS, and two-step targeted PCR. BGIs sequencers utilize a unique DNB technology which uses rolling circle replication for DNA-nanoball preparation; this linear amplification is PCR free and can avoid error accumulation. We demonstrated that single index mis-assignment from free indexed oligos occurs at a rate of one in 36 million reads, suggesting virtually no index hopping during DNB creation and arraying. Furthermore, the DNB-based NGS libraries have achieved an unprecedentedly low sample-to-sample mis-assignment rate of 0.0001% to 0.0004% under recommended procedures.\n\nConclusionsSingle indexing with DNB technology provides a simple but effective method for sensitive genetic assays with large sample numbers.

genomics↗

bioRxiv2018

A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection

Respiratory viruses are highly infectious; however, the variation of individuals physiologic responses to viral exposure is poorly understood. Most studies examining molecular predictors of response focus on late stage predictors, typically near the time of peak symptoms. To determine whether pre- or early post-exposure factors could predict response, we conducted a community-based analysis to identify predictors of resilience or susceptibility to several respiratory viruses (H1N1, H3N2, Rhinovirus, and RSV) using peripheral blood gene expression profiles collected from healthy subjects prior to viral exposure, as well as up to 24 hours following exposure. This analysis revealed that it is possible to construct models predictive of symptoms using profiles even prior to viral exposure. Analysis of predictive gene features revealed little overlap among models; however, in aggregate, these genes were enriched for common pathways. Heme Metabolism, the most significantly enriched pathway, was associated with higher risk of developing symptoms following viral exposure.

immunology↗

bioRxiv2018

Loss of E2F7 confers resistance to poly-ADP-ribose polymerase (PARP) inhibitors in BRCA2-deficient cells

BRCA proteins are essential for Homologous Recombination DNA repair, and their germline or somatic inactivation is frequently observed in human tumors. Understanding the molecular mechanisms underlying the response to chemotherapy of BRCA-deficient tumors is paramount for developing improved personalized cancer therapies. While PARP inhibitors have been recently approved for treatment of BRCA-mutant breast and ovarian cancers, resistance to these novel drugs remains a major clinical problem. Several mechanisms of chemoresistance in BRCA2-deficient cells have been identified. Rather than restoring normal recombination, these mechanisms result in stabilization of stalled replication forks, which normally are subjected to degradation in BRCA2-mutated cells. Here, we show that the transcriptional repressor E2F7 controls chemoresistance in BRCA2-deficient cells. We found that E2F7 depletion restores PARP inhibitor and cisplatin resistance in BRCA2-depleted cells. Moreover, we show that the mechanism underlying this activity involves increased expression of RAD51, a target for E2F7-mediated transcriptional repression, which enhances both Homologous Recombination DNA repair, and replication fork stability in BRCA2-deficient cells. Our work describes a new mechanism of chemotherapy resistance in BRCA2-deficient cells, and identifies E2F7 as a novel biomarker for tumor response to PARP inhibitor therapy.

cancer biology↗

bioRxiv2018

A mechanosensitive RhoA pathway that protects epithelia against acute tensile stress.

Adherens junctions are tensile structures that couple epithelial cells together. Junctional tension can arise from cell-intrinsic application of contractility or from the cell-extrinsic forces of tissue movement. In all these circumstances, it is essential that epithelial integrity be preserved despite the application of tensile stress. In this study, we identify junctional RhoA as a mechanosensitive signaling pathway that responds to epithelial stress. The junctional specificity of this response is mediated by the heterotrimeric protein G12, which is recruited by E-cadherin and, in turn, recruits p114 RhoGEF to activate RhoA. Further, we identify Myosin VI as a key mechanosensor, based on its intrinsic capacity to anchor E-cadherin to F-actin when exposed to tensile load. Tension-activated RhoA signaling was necessary to preserve epithelial integrity, which otherwise undergoes fracture when monolayer stress is acutely increased by calyculin. Paradoxically, this homeostatic RhoA signaling pathway increases junctional actomyosin, a contractile response that might be expected to itself promote fracture. Simulations of a vertex-based model revealed that the protective effect of RhoA signaling can be explained through increased yield limit at multicellular vertices, where experiments showed p114 RhoGEF was necessary to increase E-cadherin and promote actin assembly and organization.

cell biology↗

bioRxiv2018

Structural and histone binding studies of the chromo barrel domain of TIP60

TIP60 consists of an N-terminal chromo barrel domain (TIP60-CB) and a C-terminal acetyltransferase domain and acetylates histone and non-histone proteins within diverse cellular processes. Whereas the TIP60-CB is thought to recognize histone tails, molecular details of this interaction remain unclear. Here we attempted a quantitative analysis of the interaction between the TIP60-CB and histone peptides, but did not observe any binding through either fluorescence polarization or isothermal titration calorimetry. We solved a crystal structure of the TIP60-CB alone. Analysis of the crystal structure demonstrates a putative peptide binding site that may be occluded by the basic side chain of a residue in a unique {beta} hairpin between the two N-terminal strands of the {beta} barrel.

biochemistry↗

bioRxiv2017

Chlorinated electron acceptor availability selects for specific Dehalococcoides populations in dechlorinating enrichment cultures and in groundwater

Individual Dehalococcoides mccartyi (Dhc) strains differ primarily from one another by the number and identity of the reductive dehalogenase homologous catalytic subunit A (rdhA) genes contained within their respective genomes. While thousands of rdhA genes have been sequenced, the activity of the corresponding proteins have been identified in only a handful of cases. Most effort has focused on identifying the enzymes that dechlorinate substrates including trichloroethene (TCE), cis-dichloroethene (cDCE) and vinyl chloride (VC) relevant to groundwater remediation. The associated rdhA genes, namely tceA, bvcA, and vcrA, along with the D. mccartyi 16S rRNA gene are often used to track growth and dechlorinating activity in DNA extracted from field samples. In this study, we augmented the typical suite of three characterized rdhA genes to include an additional 12 uncharacterized rdhA sequences identified in the metagenome in the mixed Dhc-containing culture KB-1 to track population shifts within the culture and at two bioaugmented field sites. Quantitative PCR assays were developed for the 15 selected D. mccartyi rdhA genes and evaluated using 11 different sub-cultures of KB-1, each enriched on different chlorinated ethenes and ethanes. The proportion of rdhA gene copies relative to Dhc 16S gene copies indicated the presence of multiple distinct Dhc populations in each culture. The specific electron acceptor amended to each culture had a major influence on the distribution of D. mccartyi populations and their associated rdhA genes. We also surveyed the abundance of rdhA genes in samples obtained from two bioaugmented field sites. Growth of the dominant D. mccartyi population in the KB-1 inoculum was detected in the UK site samples. At both field sites, the measurement of relative rdhA abundances revaled significant D. mccartyi population shifts over time as dechlorination progressed from TCE through cDCE to VC and ethene, indicating that the selective pressure of the most abundant chlorinated electron acceptor that was observed in lab cultures was also occurring in the populations in the field. Understanding driving forces behind D. mccartyi population selection and activity is improving predictability of remediation performance at chlorinated solvent contaminated sites.

microbiology↗

bioRxiv2017

Integration of multiple data sources for gene network inference using genetic perturbation data

BackgroundThe inference of gene regulatory networks is of great interest and has various applications. The recent advances in high-throughout biological data collection have facilitated the construction and understanding of gene regulatory networks in many model organisms. However, the inference of gene networks from large-scale human genomic data can be challenging. Generally, it is difficult to identify the correct regulators for each gene in the large search space, given that the high dimensional gene expression data only provides a small number of observations for each gene.\n\nResultsWe present a Bayesian approach integrating external data sources with knockdown data from human cell lines to infer gene regulatory networks. In particular, we assemble multiple data sources including gene expression data, genome-wide binding data, gene ontology, known pathways and use a supervised learning framework to compute prior probabilities of regulatory relationships. We show that our integrated method improves the accuracy of inferred gene networks. We apply our method to two different human cell lines, which illustrates the general scope of our method.\n\nConclusionsWe present a flexible and systematic framework for external data integration that improves the accuracy of human gene network inference while retaining efficiency. Integrating various data sources of biological information also provides a systematic way to build on knowledge from existing literature.

systems biology↗

bioRxiv2017

Pleiotropic Chemoreceptors Facilitate The Maintenance Of Signal-Receptor Coupling In Pheromonal Communication

Optimal mating decisions depend on stable signaling systems because any independent changes in either the signal or its perception could carry a fitness cost. However, since the perception and production of specific mating signals are often mediated by different tissues and cell types, the genetic and cellular mechanisms that drive and maintain their coupling on the evolutionary and physiological timescales remain unknown for most animal species. Here, we show that in Drosophila melanogaster, sensory perception and synthesis of an inhibitory mating pheromone is regulated by the action of Gr8a, a member of the Gustatory receptor gene family. Particularly, Gr8a acts as a pheromone chemoreceptor in the sensory system of males and females, and, independently regulates pheromone synthesis in the male fat body and oenocytes. These data provide a relatively simple molecular explanation for how genetic coupling allows for the robust and stable flow of social information at the population level.

genetics↗