Jie Ping

Association between adverse clinical outcome in human disease caused by novel influenza A H7N9 virus and sustained viral shedding and emergence of antiviral resistance

BACKGROUNDnOn March 30, a novel influenza A subtype H7N9 virus (A/H7N9) was detected in patients with severe respiratory disease in eastern China. Virological factors associated with a poor clinical outcome for this virus remain unclear. We quantified the viral load and analysed antiviral resistance mutations in specimens from patients with A/H7N9.nnnMETHODSnWe studied 14 patients with A/H7N9 disease admitted to the Shanghai Public Health Clinical Centre (SPHCC), China, between April 4, and April 20, 2013, who were given antiviral treatment (oseltamivir or peramivir) for less than 2 days before admission. We investigated the viral load in throat, stool, serum, and urine specimens obtained sequentially from these patients. We also sequenced viral RNA from these specimens to study the mutations associated with resistance to neuraminidase inhibitors and their association with disease outcome.nnnFINDINGSnAll patients developed pneumonia, seven of them required mechanical ventilation, and three of them further deteriorated to become dependent on extracorporeal membrane oxygenation (ECMO), two of whom died. Antiviral treatment was associated with a reduction of viral load in throat swab specimens in 11 surviving patients. Three patients with persistently high viral load in the throat in spite of antiviral therapy became ECMO dependent. An Arg292Lys mutation in the virus neuraminidase (NA) gene known to confer resistance to both zanamivir and oseltamivir was identified in two of these patients, both also received corticosteroid treatment. In one of them, wild-type sequence Arg292 was noted 2 days after start of antiviral treatment, and the resistant mutant Lys292 dominated 9 days after start of treatment.nnnINTERPRETATIONnReduction of viral load following antiviral treatment correlated with improved outcome. Emergence of NA Arg292Lys mutation in two patients who also received corticosteroid treatment led to treatment failure and a poor clinical outcome. The emergence of antiviral resistance in A/H7N9 viruses, especially in patients receiving corticosteroid therapy, is concerning, needs to be closely monitored, and considered in pandemic preparedness planning.nnnFUNDINGnNational Megaprojects of China for Infectious Diseases, Shanghai Municipal Health and Family Planning Commission, the National Key Basic Research Program of China, Ministry of Science and Technology, and National Natural Science Foundation of China.

A comparative analysis of liver transcriptome suggests divergent liver function among human, mouse and rat

The human liver plays a vital role in meeting the bodys metabolic needs and maintaining homeostasis. To address the molecular mechanisms of liver function, we integrated multiple gene expression datasets from microarray, MPSS, SAGE and EST platforms to generate a transcriptome atlas of the normal human liver. Our results show that 17396 genes are expressed in the human liver. 238 genes were identified as liver enrichment genes, involved in the functions of immune response and metabolic processes, from the MPSS and EST datasets. A comparative analysis of liver transcriptomes was performed in humans, mice and rats with microarray datasets shows that the expression profile of homologous genes remains significantly different between mouse/rat and human, suggesting a functional variance and regulation bias of genes expressed in the livers. The integrated liver transcriptome data should provide a valuable resource for the in-depth understanding of human liver biology and liver disease.

Molecular Dynamics Studies on the Conformational Transitions of Adenylate Kinase: A Computational Evidence for the Conformational Selection Mechanism

Escherichia coli adenylate kinase (ADK) is a monomeric phosphotransferase enzyme that catalyzes reversible transfer of phosphoryl group from ATP to AMP with a large-scale domain motion. The detailed mechanism for this conformational transition remains unknown. In the current study, we performed long time-scale molecular dynamics simulations on both open and closed states of ADK. Based on the structural analyses of the simulation trajectories, we detected over 20 times conformational transitions between the open and closed states of ADK and identified two novel conformations as intermediate states in the catalytic processes. With these findings, we proposed a possible mechanism for the large-scale domain motion of Escherichia coli ADK and its catalytic process: (1) the substrate free ADK adopted an open conformation; (2) ATP bound with LID domain closure; (3) AMP bound with NMP domain closure; (4) phosphoryl transfer occurred with ATP, and AMP converted into two ADPs, and no conformational transition was detected in the enzyme; (5) LID domain opened with one ADP released; (6) another ADP released with NMP domain open. As both open and closed states sampled a wide range of conformation transitions, our simulation strongly supported the conformational selection mechanism for Escherichia coli ADK.

Negatively cooperative binding properties of human cytochrome P450 2E1 with monocyclic substrates.

Human CYP2E1 accounts for almost 2% of total CYP enzymes in the liver cells, and plays a crucial role in the metabolism of small molecular weight compounds. This enzyme is associated with the nearly 6% metabolisms of the currently clinical drugs. However, it is found that CYP2E1 has a non-hyperbolic kinetic profile that can not be explained by the common Michaelis-Menten mechanism. Further studies show that the non-hyperbolic kinetic behaviors are associated with multiple substrate binding, which is also known as the cooperative binding properties. However, the detailed mechanism for the cooperative binding is not clear by now. In this paper, we summarized the experimental and theoretical studies on the cooperative binding mechanism. Based on the structural analysis, a second substrate binding site is confirmed in human CYP2E1, which is located neither in the region near Leu103, Leu210 and Phe478, nor far from the active site. Additionally, two important residues Thr303 and Phe478 are also identified to be the key factors in the cooperative binding on the short-range and long-range effects, respectively. The former plays a crucial role in the positioning of substrates and in proton delivery to the active site; the latter is located between the substrate access channel and the active site, and exhibits directly effects on substrate access or on substrate positioning in the active site. All these points can provide useful information for the cooperative binding in human CYP2E1, revealing the detailed mechanism for the non-hyperbolic kinetic behaviors.

Revealing parasite influence in metabolic pathways in Apicomplexa infected patients

BackgroundAs an obligate intracellular parasite, Apicomplexa interacts with the host in the special living environment, competing for energy and nutrients from the host cells by manipulating the host metabolism. Previous studies of host-parasite interaction mainly focused on using cellular and biochemical methods to investigate molecular functions in metabolic pathways of parasite infected hosts. Computational approaches taking advantage of high-throughput biological data and topology of metabolic pathways have a great potential in revealing the details and mechanism of parasites-to-host interactions. A new analytical method was designed in this work to study host-parasite interactions in human cells infected with Plasmodium falciparum and Cryptosporidium parvum.ResultsWe introduced a new method that analyzes the host metabolic pathways in divided parts: host specific subpathways and host-parasite common subpathways. Upon analysis on gene expression data from cells infected by Plasmodium falciparum or Cryptosporidium parvum, we found: (i) six host-parasite common subpathways and four host specific subpathways were significantly altered in plasmodium infected human cells; (ii) plasmodium utilized fatty acid biosynthesis and elongation, and Pantothenate and CoA biosynthesis to obtain nutrients from host environment; (iii) in Cryptosporidium parvum infected cells, most of the host-parasite common enzymes were down-regulated, whereas the host specific enzymes up-regulated; (iv) the down-regulation of common subpathways in host cells might be caused by competition for the substrates and up-regulation of host specific subpathways may be stimulated by parasite infection.ConclusionResults demonstrated a significantly coordinated expression pattern between the two groups of subpathways. The method helped expose the impact of parasite infection on host cell metabolism, which was previously concealed in the pathway enrichment analysis. Our approach revealed detailed subpathways and metabolic information are important to the symbiosis in two kinds of the apicomplex parasites, and highlighted its significance in research and understanding of parasite-host interactions.

Human gene expression sensitivity according to large scale meta-analysis.

BackgroundGenes show different sensitivities in expression corresponding to various biological conditions. Systematical study of this concept is required because of its important implications in microarray analysis etc. J.H. Ohn et al. first studied this gene property with yeast transcriptional profiling data.ResultsHere we propose a calculation framework for gene expression sensitivity analysis. We also compared the functions, centralities and transcriptional regulations of the sensitive and robust genes. We found that the robust genes tended to be involved in essential cellular processes. Oppositely, the sensitive genes perform their functions diversely. Moreover while genes from both groups show similar geometric centrality by coupling them onto integrated protein networks, the robust genes have higher vertex degree and betweenness than that of the sensitive genes. An interesting fact was also found that, not alike the sensitive genes, the robust genes shared less transcription factors as their regulators.ConclusionOur study reveals different propensities of gene expression to external perturbations, demonstrates different roles of sensitive genes and robust genes in the cell and proposes the necessity of combining the gene expression sensitivity in the microarray analysis.

The domain landscape of virus-host interactomes.

Viral infections result in millions of deaths in the world today. A thorough analysis of virus-host interactomes may reveal insights into viral infection and pathogenic strategies. In this study, we presented a landscape of virus-host interactomes based on protein domain interaction. Compared to the analysis at protein level, this domain-domain interactome provided a unique abstraction of protein-protein interactome. Through comparisons among DNA, RNA, and retrotranscribing viruses, we identified a core of human domains, that viruses used to hijack the cellular machinery and evade the immune system, which might be promising antiviral drug targets. We showed that viruses preferentially interacted with host hub and bottleneck domains, and the degree and betweenness centrality among three categories of viruses are significantly different. Further analysis at functional level highlighted that different viruses perturbed the host cellular molecular network by common and unique strategies. Most importantly, we creatively proposed a viral disease network among viral domains, human domains and the corresponding diseases, which uncovered several unknown virus-disease relationships that needed further verification. Overall, it is expected that the findings will help to deeply understand the viral infection and contribute to the development of antiviral therapy.

GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction

BackgroundIn the post-genomic era, the development of high-throughput gene expression detection technology provides huge amounts of experimental data, which challenges the traditional pipelines for data processing and analyzing in scientific researches.ResultsIn our work, we integrated gene expression information from Gene Expression Omnibus (GEO), biomedical ontology from Medical Subject Headings (MeSH) and signaling pathway knowledge from sigPathway entries to develop a context mining tool for gene expression analysis – GEOGLE. GEOGLE offers a rapid and convenient way for searching relevant experimental datasets, pathways and biological terms according to multiple types of queries: including biomedical vocabularies, GDS IDs, gene IDs, pathway names and signature list. Moreover, GEOGLE summarizes the signature genes from a subset of GDSes and estimates the correlation between gene expression and the phenotypic distinction with an integrated p value.ConclusionThis approach performing global searching of expression data may expand the traditional way of collecting heterogeneous gene expression experiment data. GEOGLE is a novel tool that provides researchers a quantitative way to understand the correlation between gene expression and phenotypic distinction through meta-analysis of gene expression datasets from different experiments, as well as the biological meaning behind. The web site and user guide of GEOGLE are available at: http://omics.biosino.org:14000/kweb/workflow.jsp?id=00020

Computational studies on the substrate interactions of influenza A virus PB2 subunit.

Influenza virus, which spreads around the world in seasonal epidemics and leads to large numbers of deaths every year, has several ribonucleoproteins in the central core of the viral particle. These viral ribonucleoproteins can specifically bind the conserved 3′ and 5′ caps of the viral RNAs with responsibility for replication and transcription of the viral RNA in the nucleus of infected cells. A fundamental question of most importance is that how the cap-binding proteins in the influenza virus discriminates between capped RNAs and non-capped ones. To get an answer, we performed molecular dynamics simulations and free energy calculations on the influenza A virus PB2 subunit, an important component of the RNP complexes, with a cap analog m7GTP. Our calculations showed that some key residues in the active site, such as Arg355, His357, Glu361 as well as Gln406, could offer significant hydrogen bonding and hydrophobic interactions with the guanine ring of the cap analog m7GTP to form an aromatic sandwich mechanism for the cap recognition and positioning in the active site. Subsequently, we applied this idea to a virtual screening procedure and identified 5 potential candidates that might be inhibitors against the PB2 subunit. Interestingly, 2 candidates Cpd1 and Cpd2 have been already reported to have inhibitory activities to the influenza virus cap-binding proteins. Further calculation also showed that they had comparatively higher binding affinities to the PB2 subunit than that of m7GTP. We believed that our findings could give an atomic insight into the deeper understanding of the cap recognition and binding mechanism, providing useful information for searching or designing novel drugs against influenza viruses.

EcoBrowser: a web-based tool for visualizing transcriptome data of Escherichia coli

BackgroundEscherichia coli has been extensively studied as a prokaryotic model organism whose whole genome was determined in 1997. However, it is difficult to identify all the gene products involved in diverse functions by using whole genome sequencesalone. The high-resolution transcriptome mapping using tiling arrays has proved effective to improve the annotation of transcript units and discover new transcripts of ncRNAs. While abundant tiling array data have been generated, the lack of appropriate visualization tools to accommodate and integrate multiple sources of data has emerged.FindingsEcoBrowser is a web-based tool for visualizing genome annotations and transcriptome data of E. coli. Important tiling array data of E. coli from different experimental platforms are collected and processed for query. An AJAX based genome browser is embedded for visualization. Thus, genome annotations can be compared with transcript profiling and genome occupancy profiling from independent experiments, which will be helpful in discovering new transcripts including novel mRNAs and ncRNAs, generating a detailed description of the transcription unit architecture, further providing clues for investigation of prokaryotic transcriptional regulation that has proved to be far more complex than previously thought.ConclusionsWith the help of EcoBrowser, users can get a systemic view both from the vertical and parallel sides, as well as inspirations for the design of new experiments which will expand our understanding of the regulation mechanism.