Omics: a journal of integrative biology

Publications in this journal

• Article: Graphical Identification of Cancer-Associated Gene Subnetworks Based on Small Proteomics Data Sets.

  Karim Mezhoud
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  ABSTRACT: Abstract Proteomics is a rapidly emerging frontier in post-genomics medicine and biology, but the quantitative analysis and validation of proteomic data are in need of further improvements. Before selecting potential candidate proteomic biomarkers, it is important to understand the broader context of how biological processes are regulated under different conditions or in different phenotypes. The enrichment of proteomic data consists of extracting as much biological meaning as possible from curated, pathway-based, functional protein interaction networks. Currently, most of the enrichment tools are intended for microarray data and require parametric data, whereas proteomic data are often nonparametric. In this study, we aimed to select a suite of interactive tools that can enrich proteomic results with a graphical overview. This facilitated diagnosis and interpretation prior to further analysis. From a list of proteins, a network was constructed using a map of the most severely disrupted biological process, and the disease entity was then identified on the basis of clinical data. Taken together, this graphical and interactive method ranks potential proteins via functional analysis in order to improve the choice of biomarkers for validation with the following advantages: 1) It adds neighbor proteins that are not selected by mass spectrometry analysis, but could in fact be key proteins; 2) pinpoints the biological process most often involved; and 3) predicts the most likely disease on the basis of clinical data.
  Omics: a journal of integrative biology 05/2013;
• Article: An NMR Metabolomics Investigation of Perturbations after Treatment with Chinese Herbal Medicine Formula in an Experimental Model of Sepsis.

  Yunzhi Li, Hongbin Liu, Xianzhong Wu, Donghua Li, Jing Huang
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  ABSTRACT: Abstract Sepsis is a leading cause of morbidity and mortality in critically ill patients. OMICS and systems pharmacology approaches offer the promise of new therapeutic candidates for the treatment of patients with sepsis. Qin-Re-Jie-Du (QRJD) and Liang-Xue-Huo-Xue (LXHX) are two traditional Chinese herbal medicine (CHM) formulas with putative effects in sepsis treatment. The present study aimed to assess their efficacy in an experimental model of sepsis in rats (cecal ligation and punctures) and investigate their mechanism of action using a (1)H-NMR metabolomics approach. Rats were randomly divided into four groups (i.e., model group, sham control group, and two CHM treatment groups). Water extracts of QRJD and LXHX were orally administered to the two CHM treatment groups at a dose of 24 g/kg of body weight, once daily for 3 consecutive days. The same volume of 0.9% saline solution was orally administered to the model and sham surgery groups. Plasma samples were collected and measured using 600 MHz (1)H-NMR spectroscopy. As a result, 18 potential metabolite biomarkers involved in multiple metabolic pathways, including increased energy metabolism, fat mobilization, and disrupted amino acid metabolism, were identified in septic rats. The principal component analysis (PCA) and partial least squares discriminant (PLS-DA) plots of the metabolic state correlated well with the mortality and clinical biochemistry results. An analysis of potential biomarkers verified the holistic effects of the two CHM formulas. The Cori cycle was positively regulated in the QRJD-treated formulas treatment group but also inhibited in the LXHX-treated group, which demonstrates the different efficacies of these solutions in septic rats.
  Omics: a journal of integrative biology 04/2013;
• Article: Differential Expression of MicroRNAs in Patients with Glioblastoma after Concomitant Chemoradiotherapy.

  Edmond Changkyun Park, Giwon Kim, Jongsun Jung, Kyoungmin Wang, Sunwoo Lee, Sin-Soo Jeon, Zee Won Lee, Seung Il Kim, Soohyun Kim, Young-Taek Oh, Ju-Hyun Shin, Hong-Seok Jang, Byung-Ock Choi, Gun-Hwa Kim
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  ABSTRACT: Abstract Glioblastoma multiforme (GBM) is the most aggressive primary brain tumor, and notorious for resistance to chemoradiotherapy. MicroRNAs (miRNAs) are significantly involved in the initiation and progression of numerous cancers; however, the role of miRNAs in recurrence of tumors remains unknown. Here we tried to identify novel miRNAs that are differentially expressed in recurrent GBM. Tissue samples were obtained from patients with primary and recurrent GBM treated with chemoradiotherapy, and the expression changes of miRNAs were measured by microarray. A total of 318 miRNAs were expressed in the GBM patients. The expression of 43 miRNAs were significantly altered at least 2-fold in primary and recurrent GBMs. Bioinformatic analysis revealed that the differentially expressed miRNAs and their putative target genes were mainly involved in cell death, cellular development, and cellular growth and proliferation, which are the key regulators for stem cells. Pathway analysis supported that the miRNAs may regulate signaling associated with induction and maintenance of cancer and stem cell, such as p53, ErbB1, Notch, Wnt, and TGF-β signaling pathways. These data suggest that, in recurrent GBM, growth factor and anti-apoptotic signalings for cancer cell growth and proliferation are regulated by miRNAs. Our findings will aid future research in understanding the pathophysiology of recurrent GBM and identifying diagnostic markers and/or therapeutic targets for recurrence of GBM.
  Omics: a journal of integrative biology 04/2013;
• Article: Comparative Metabolomics Analysis of Docosahexaenoic Acid Fermentation Processes by Schizochytrium sp. under Different Oxygen Availability Conditions.

  Juan Li, Lu-Jing Ren, Guan-Nan Sun, Liang Qu, He Huang
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  ABSTRACT: Abstract The intracellular metabolic profile characterization of Schizochytrium sp. throughout docosahexaenoic acid fermentation was investigated using gas chromatography-mass spectrometry (GC-MS). Metabolite profiles originating from Schizochytrium sp. under normal and limited oxygen supply conditions were distinctive and distinguished by principal components analysis (PCA). A total of more than 60 intracellular metabolites were detected and quantified with the levels of some metabolites involved in central carbon metabolism varying throughout both processes. Both fermentation processes were differentiated into three main phases by principal components analysis. Potential biomarkers responsible for distinguishing the different fermentation phases were identified as glutamic acid, proline, glycine, alanine, and glucose. In addition, alanine, glutamic acid, glucose, inositol, ornithine, and galactose were found to make great contribution for dry cell weight and fatty acid composition during normal and limited oxygen supply fermentations. Furthermore, significantly higher levels of succinate and several amino acids in cells of limited oxygen supply fermentation revealed that they might play important roles in resisting oxygen deficiency and increasing DHA synthesis during the lipid accumulation. These findings provide novel insights into the metabolomic characteristics during docosahexaenoic acid fermentation processes by Schizochytrium sp.
  Omics: a journal of integrative biology 04/2013;
• Article: The Interleukin 10 -819C/T Polymorphism and Cancer Risk: A HuGE Review and Meta-Analysis of 73 Studies Including 15,942 Cases and 22,336 Controls.

  Zhibin Yu, Qing Liu, Chen Huang, Minghua Wu, Guiyuan Li
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  ABSTRACT: Abstract The aim of the present work was to perform a meta-analysis to evaluate the association between the interleukin 10 (IL-10) -819C/T (rs1800871) polymorphism and cancer risk. A total of 73 studies, including 15,942 cancer cases and 22,336 controls, were identified in this meta-analysis. The odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using the random-effects model. Overall, no significant association was identified between the IL-10 -819C/T polymorphism and cancer risk. In the subgroup analyses, the T allele and TT genotype were associated with a moderately reduced cancer risk in the Asian population (T allele vs. C allele: OR=0.93, 95%CI: 0.87, 0.99; TT vs. CC: OR=0.86, 95%CI: 0.76, 0.98; TT vs. CT/CC: OR=0.90, 95%CI: 0.82, 0.98). Individuals who were homozygous for the T allele (TT) were found to be associated with significantly reduced gastric cancer risk in the Asian population. The heterozygous variant (CT) and the dominant model (TT/CT vs. CC) were associated with an increased risk for cervical and ovarian cancer. However, the IL-10 -819C/T polymorphism was not significantly associated with breast cancer, colorectal cancer, lung cancer, hepatocellular carcinoma, prostate cancer, lymphoma, or melanoma. The depressed cancer risk of the TT genotype occurred in the studies of hospital-based case-control studies and the studies recruited less than 500 subjects, but no statistically significant results were found in the stratified analyses using genotyping method. The results suggest that the IL-10 -819TT genotype may be a protective factor for cancer in Asians, especially gastric cancer. In contrast, the CT genotype and the dominant model could be risk factors for cervical and ovarian cancer. The importance of stratifying by ethnicity, cancer type, study design, and sample size needs to be standardized in future studies, together with considering the association between the IL-10 -819C/T polymorphism and cancer risk. Furthermore, the linkage of -819C/T with other polymorphisms of the IL-10 gene may help explain the variability in findings.
  Omics: a journal of integrative biology 04/2013; 17(4):200-14.
• Article: Crowd-funded micro-grants for genomics and "big data": an actionable idea connecting small (artisan) science, infrastructure science, and citizen philanthropy.

  Vural Ozdemir, Kamal F Badr, Edward S Dove, Laszlo Endrenyi, Christy Jo Geraci, Peter J Hotez, Djims Milius, Maria Neves-Pereira, Tikki Pang, Charles N Rotimi, Ramzi Sabra, Christineh N Sarkissian, Sanjeeva Srivastava, Hesther Tims, Nathalie K Zgheib, Ilona Kickbusch
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  ABSTRACT: Abstract Biomedical science in the 21(st) century is embedded in, and draws from, a digital commons and "Big Data" created by high-throughput Omics technologies such as genomics. Classic Edisonian metaphors of science and scientists (i.e., "the lone genius" or other narrow definitions of expertise) are ill equipped to harness the vast promises of the 21(st) century digital commons. Moreover, in medicine and life sciences, experts often under-appreciate the important contributions made by citizen scholars and lead users of innovations to design innovative products and co-create new knowledge. We believe there are a large number of users waiting to be mobilized so as to engage with Big Data as citizen scientists-only if some funding were available. Yet many of these scholars may not meet the meta-criteria used to judge expertise, such as a track record in obtaining large research grants or a traditional academic curriculum vitae. This innovation research article describes a novel idea and action framework: micro-grants, each worth $1000, for genomics and Big Data. Though a relatively small amount at first glance, this far exceeds the annual income of the "bottom one billion"-the 1.4 billion people living below the extreme poverty level defined by the World Bank ($1.25/day). We describe two types of micro-grants. Type 1 micro-grants can be awarded through established funding agencies and philanthropies that create micro-granting programs to fund a broad and highly diverse array of small artisan labs and citizen scholars to connect genomics and Big Data with new models of discovery such as open user innovation. Type 2 micro-grants can be funded by existing or new science observatories and citizen think tanks through crowd-funding mechanisms described herein. Type 2 micro-grants would also facilitate global health diplomacy by co-creating crowd-funded micro-granting programs across nation-states in regions facing political and financial instability, while sharing similar disease burdens, therapeutics, and diagnostic needs. We report the creation of ten Type 2 micro-grants for citizen science and artisan labs to be administered by the nonprofit Data-Enabled Life Sciences Alliance International (DELSA Global, Seattle). Our hope is that these micro-grants will spur novel forms of disruptive innovation and genomics translation by artisan scientists and citizen scholars alike. We conclude with a neglected voice from the global health frontlines, the American University of Iraq in Sulaimani, and suggest that many similar global regions are now poised for micro-grant enabled collective innovation to harness the 21(st) century digital commons.
  Omics: a journal of integrative biology 04/2013; 17(4):161-72.
• Article: Proteomics Analysis of Hepatoprotective Effects for Scoparone Using MALDI-TOF/TOF Mass Spectrometry with Bioinformatics.

  Aihua Zhang, Hui Sun, Gelin Wu, Wenjun Sun, Ye Yuan, Xijun Wang
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  ABSTRACT: Abstract Scoparone is an active ingredient of Yinchenhao (Artemisia annua L.), a well-known Chinese medicinal plant, and has been utilized in prevention and therapy of liver damage. However, the molecular drug targets associated with the pharmacological effects of scoparone are largely unknown. In the present article, we extend the previous research on Yinchenhao through a study of its active ingredient and thus the putative targets of scoparone. We employed two-dimensional gel electrophoresis, and all proteins expressed were identified by MALDI-TOF/TOF MS and database research. Protein-interacting networks and pathways were also mapped and evaluated. The possible protein network associated with scoparone was constructed, and contribution of these proteins to the protective effect of scoparone against the carbon tetrachloride-induced acute liver injury in rats are discussed herein. Hepatoprotective effects of scoparone on liver injury in rats were associated with regulated expression of six proteins which were closely related in our protein-protein interaction network, and appear to be involved in antioxidation and signal transduction, energy production, immunity, metabolism, and chaperoning. These observations collectively provide new insights on the molecular mechanisms of scoparone action against hepatic damage in rats.
  Omics: a journal of integrative biology 03/2013;
• Article: In Search of Actionable Targets for Agrigenomics and Microalgal Biofuel Production: Sequence-Structural Diversity Studies on Algal and Higher Plants with a Focus on GPAT Protein.

  Namrata Misra, Prasanna Kumar Panda
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  ABSTRACT: Abstract The triacylglycerol (TAG) pathway provides several targets for genetic engineering to optimize microalgal lipid productivity. GPAT (glycerol-3-phosphate acyltransferase) is a crucial enzyme that catalyzes the initial step of TAG biosynthesis. Despite many recent biochemical studies, a comprehensive sequence-structure analysis of GPAT across diverse lipid-yielding organisms is lacking. Hence, we performed a comparative genomic analysis of plastid-located GPAT proteins from 7 microalgae and 3 higher plants species. The close evolutionary relationship observed between red algae/diatoms and green algae/plant lineages in the phylogenetic tree were further corroborated by motif and gene structure analysis. The predicted molecular weight, amino acid composition, Instability Index, and hydropathicity profile gave an overall representation of the biochemical features of GPAT protein across the species under study. Furthermore, homology models of GPAT from Chlamydomonas reinhardtii, Arabidopsis thaliana, and Glycine max provided deep insights into the protein architecture and substrate binding sites. Despite low sequence identity found between algal and plant GPATs, the developed models exhibited strikingly conserved topology consisting of 14α helices and 9β sheets arranged in two domains. However, subtle variations in amino acids of fatty acyl binding site were identified that might influence the substrate selectivity of GPAT. Together, the results will provide useful resources to understand the functional and evolutionary relationship of GPAT and potentially benefit in development of engineered enzyme for augmenting algal biofuel production.
  Omics: a journal of integrative biology 03/2013;
• Article: Tubulin Beta Chain, Filamin A Alpha Isoform 1, and Cytochrome b-c1 Complex Subunit 1 As Serological Diagnostic Biomarkers of Esophageal Squamous Cell Carcinoma: A Proteomics Study.

  Nai-Jun Fan, Chun-Fang Gao, Xiu-Li Wang
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  ABSTRACT: Abstract Despite the major advances in diagnosis and treatment, esophageal squamous cell carcinoma (ESCC) remains a major life-threatening disease. Early diagnosis is critical for guiding the therapeutic management of ESCC. This case-control study focused on the proteomic analysis of serum of healthy volunteers and ESCC patients using the ClinProt profiling technology based on mass spectrometry. A total of 80 healthy volunteers and 119 ESCC patients were enrolled. We identified a pattern of proteins/peptides (including m/z 1867, 2700, and 2094) and differentiated ESCC patients from healthy volunteers with sensitivity and specificity close to 100%. Using mass spectrometry (LTQ orbitrap XL), tubulin beta chain, filamin A alpha isoform 1, and cytochrome b-c1 complex subunit 1 were identified as the three differentially expressed proteins/peptides in the patient serum. These three dysregulated proteins/peptides could be involved in the pathogenesis of ESCC and may serve as putative serological diagnostic biomarkers of ESCC. We suggest that further proteomics and multi-omics research are warranted to identify novel post-genomics diagnostics that can in the future pave the way for personalized medicine for patients with ESCC, a cancer for which we currently lack an integrated battery of diagnostics in the field of oncology.
  Omics: a journal of integrative biology 03/2013;
• Article: Systemic Inflammation Is Associated with Differential Gene Expression and Airway Neutrophilia in Asthma.

  Juan-Juan Fu, Katherine J Baines, Lisa G Wood, Peter G Gibson
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  ABSTRACT: Abstract Systemic inflammation is reported to be associated with neutrophilic airway inflammation in asthma, but mechanisms underlying this finding are not well understood. This study aimed to examine the molecular mechanisms of the airway neutrophilia that are associated with systemic inflammation in asthma. Fifty stable nonsmoking adults with asthma had plasma high sensitivity C-reactive protein (hsCRP) and interleukin 6 (IL-6) assayed. Subjects with an elevation of both hsCRP and IL-6 were grouped as asthmatics with systemic inflammation, and those with both hsCRP and IL-6 within the normal ranges were grouped as asthmatics without systemic inflammation. Clinical characteristics and sputum inflammatory cell counts were compared between the two groups. Gene expression profiles from sputum were analyzed and altered expression of four genes (CCL8, IL8RA, SELL, and PI3) was confirmed using quantitative PCR. Asthmatics with systemic inflammation (n=18, 36%) had a higher BMI, greater history of cigarette smoking, lower FVC% predicted, and increased sputum neutrophils compared to those without systemic inflammation (n=16, 32%). Microarray analysis identified 449 genes that were significantly altered in sputum between the two groups. Altered genes were involved in IL-1, TNF-α/nuclear factor-κB, and Kit receptor pathways, and were related to innate immune response, defense and inflammatory response, in particular neutrophilic inflammation. Systemic inflammation was associated with airway neutrophilia in asthma, and was related to a group of differentially expressed genes in the lung involving multiple cytokine pathways. Our findings suggest that targeting systemic inflammation might provide a novel therapeutic strategy for neutrophilic asthma.
  Omics: a journal of integrative biology 02/2013;
• Article: Alternative Polyadenylation in Glioblastoma Multiforme and Changes in Predicted RNA Binding Protein Profiles.

  Jiaofang Shao, Jing Zhang, Zengming Zhang, Huawei Jiang, Xiaoyan Lou, Bingding Huang, Gregory Foltz, Qing Lan, Qiang Huang, Biaoyang Lin
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  ABSTRACT: Abstract Alternative polyadenylation (APA) is widely present in the human genome and plays a key role in carcinogenesis. We conducted a comprehensive analysis of the APA products in glioblastoma multiforme (GBM, one of the most lethal brain tumors) and normal brain tissues and further developed a computational pipeline, RNAelements ( http://sysbio.zju.edu.cn/RNAelements/ ), using covariance model from known RNA binding protein (RBP) targets acquired by RNA Immunoprecipitation (RIP) analysis. We identified 4530 APA isoforms for 2733 genes in GBM, and found that 182 APA isoforms from 148 genes showed significant differential expression between normal and GBM brain tissues. We then focused on three genes with long and short APA isoforms that show inconsistent expression changes between normal and GBM brain tissues. These were myocyte enhancer factor 2D, heat shock factor binding protein 1, and polyhomeotic homolog 1 (Drosophila). Using the RNAelements program, we found that RBP binding sites were enriched in the alternative regions between the first and the last polyadenylation sites, which would result in the short APA forms escaping regulation from those RNA binding proteins. To the best of our knowledge, this report is the first comprehensive APA isoform dataset for GBM and normal brain tissues. Additionally, we demonstrated a putative novel APA-mediated mechanism for controlling RNA stability and translation for APA isoforms. These observations collectively lay a foundation for novel diagnostics and molecular mechanisms that can inform future therapeutic interventions for GBM.
  Omics: a journal of integrative biology 02/2013;
• Article: "Omics" of HER2-Positive Breast Cancer.

  Valentina Bravatà, Francesco Paolo Cammarata, Giusi Irma Forte, Luigi Minafra
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  ABSTRACT: Abstract HER2/neu amplification/overexpression is the only somatic mutation widely considered to be a marker of disease outcome and response to treatment in breast cancer. Pathologists have made large efforts to achieve accuracy in characterizing HER2/neu status. The introduction of transtuzumab contributed to development of additional measures to identify sensitive and resistant subclasses of HER2/neu-positive tumors. In this article, we describe the latest advances in HER2/neu status diagnostic assessment and the most relevant research emerging from "Omics" (genomics, epigenetics, transcriptomics, and proteomics) studies on HER2/neu-positive breast cancer. A large quantity of biomarkers from different studies highlighted HER2/neu-positive specific proliferation, cell cycle arrest, and apoptosis mechanisms, as well as immunological and metabolic behavior. Major driver genes of tumor progression have had a candidate status (GRB7, MYC, CCND1, EGFR, etc.), even though the main role for HER2/neu is largely recognized. Nonetheless, existing omics data and HER2/neu-positive molecular profiles seem to suggest that few proteogenomic alterations in HER2, EGFR, and PI3K networks could significantly affect the effectiveness of transtuzumab. The systematic search of molecular alterations in and across these pathways can help to select the most appropriate drug for a given patient based on in-depth understanding of complexity in tumor biology.
  Omics: a journal of integrative biology 02/2013;
• Article: Metabolomic Analysis Reveals Key Metabolites Related to the Rapid Adaptation of Saccharomyce cerevisiae to Multiple Inhibitors of Furfural, Acetic Acid, and Phenol.

  Xin Wang, Bing-Zhi Li, Ming-Zhu Ding, Wei-Wen Zhang, Ying-Jin Yuan
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  ABSTRACT: Abstract During hydrolysis of lignocellulosic biomass, a broad range of inhibitors are generated, which interfere with yeast growth and bioethanol production. In order to improve the strain tolerance to multiple inhibitors-acetic acid, furfural, and phenol (three representative lignocellulose-derived inhibitors) and uncover the underlying tolerant mechanism, an adaptation experiment was performed in which the industrial Saccharomyces cerevisiae was cultivated repeatedly in a medium containing multiple inhibitors. The adaptation occurred quickly, accompanied with distinct increase in growth rate, glucose utilization rate, furfural metabolism rate, and ethanol yield, only after the first transfer. A similar rapid adaptation was also observed for the lab strains of BY4742 and BY4743. The metabolomic analysis was employed to investigate the responses of the industrial S. cereviaise to three inhibitors during the adaptation. The results showed that higher levels of 2-furoic acid, 2, 3-butanediol, intermediates in glycolytic pathway, and amino acids derived from glycolysis, were discovered in the adapted strains, suggesting that enhanced metabolic activity in these pathways may relate to resistance against inhibitors. Additionally, through single-gene knockouts, several genes related to alanine metabolism, GABA shunt, and glycerol metabolism were verified to be crucial for the resistance to multiple inhibitors. This study provides new insights into the tolerance mechanism against multiple inhibitors, and guides for the improvement of tolerant ethanologenic yeast strains for lignocellulose-bioethanol fermentation.
  Omics: a journal of integrative biology 02/2013;
• Article: Phosphoserines of the Carboxy Terminal Domain of RNA Polymerase II Are Involved in the Interaction with Transcription-Associated Proteins (TAPs).

  Subramanian Vidyalakshmi, Viraraghavan Ramamurthy
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  ABSTRACT: Abstract Generation of productive transcripts of protein coding genes in eukaryotes is a complex, multistep process centrally controlled by the RNA polymerase II (Pol II) complex. The carboxy terminal domain (CTD) of the largest subunit of the enzyme is designed to be modified by differential phosphorylation, and plays a key role in orchestrating the multiple events of the process by interacting with a host of transcription-associated proteins (TAPs) at different stages. We analyzed, in silico, the role of serine phosphorylation of CTD in relation to molecular interaction between different TAPs and a representative part of the CTD repeat structure. Using molecular docking, we investigated eight different proteins involved in capping, elongation, splicing, 3' end cleavage, or polyadenylation functions during the transcription process. Among the different phosphorylated forms of CTD, the form found to have the most affinity for a particular protein was also the form that is predominant during that process, the only exception being the equally high affinity of S2PCTD to Spt4, although S5PCTD is the known active form during elongation. The unique phosphoserine of the CTD forms associated with the TAPs was an important participant in the association between both the molecules. These studies have also identified other residues of TAPs interacting with CTD which in previous studies have not been recognized as being functionally significant. These findings add to an emerging body of literature on the regulatory aspects of genomics and proteomics and thus, might catalyze future applications for discovery and translational omics science.
  Omics: a journal of integrative biology 02/2013;
• Article: Lipidomics and in Vitro Azole Resistance in Candida albicans.

  Ashutosh Singh, Kaushal Kumar Mahto, Rajendra Prasad
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  ABSTRACT: Abstract We have shown earlier that fluconazole (FLC) stress induces global changes in the lipidome of Candida albicans in clinically adapted isolates. However, several laboratories have developed adapted in vitro FLC resistant strains of C. albicans to study azole resistance mechanisms. This study aimed to identify the lipid changes associated with FLC resistance in these in vitro adapted isolates. Using comparative lipidomics and principal component and discriminant analyses, we observed gradual changes in several lipid classes and molecular species upon FLC exposure of in vitro resistant C. albicans strains. Although the lipid imprint of FLC in vitro resistant isolates was very distinct from that of clinical isolates of C. albicans, the overall changes in lipid class compositions were similar in both cases. For example, an increased sterol content and depleted sphingolipid levels were the salient features of FLC resistance in both conditions. Taken together, it appears that the overall cellular lipid homeostasis is a critical factor in the observed FLC resistance and in handling FLC stress in both clinical and laboratory situations. The new observations reported herein have implications for more efficacious antifungal drug development as well as understanding host-infectious agent interactions in postgenomics microbiology practice.
  Omics: a journal of integrative biology 02/2013; 17(2):84-93.
• Article: GeneExpressionSignature: an R package for discovering functional connections using gene expression signatures.

  Fei Li, Yang Cao, Lu Han, Xiuliang Cui, Dafei Xie, Shengqi Wang, Xiaochen Bo
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  ABSTRACT: Abstract Comparisons of gene expression signatures provide a way to explore functional connections among biological events in global aspects of cell response. GeneExpressionSignature is an R package developed for the large-scale analysis of gene expression signatures. The package implements two rank-merging algorithms and two similarity-scoring algorithms. The functions of GeneExpressionSignature provide a flexible solution for gene expression signature-based studies and hold great potential in biomedical research applications, such as drug repurposing. GeneExpressionSignature is released under GPL v2 within the Bioconductor project and is freely available at http://www.bioconductor.org/packages/release/bioc/html/GeneExpressionSignature.html .
  Omics: a journal of integrative biology 02/2013; 17(2):116-8.
• Article: Emerging Trends in Genomic Approaches for Microbial Bioprospecting.

  K B Akondi, V V Lakshmi
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  ABSTRACT: Abstract Microorganisms constitute two out of the three domains of life on earth. They exhibit vast biodiversity and metabolic versatility. This enables the microorganisms to inhabit and thrive in even the most extreme environmental conditions, making them all pervading. The magnitude of biodiversity observed among microorganisms substantially supersedes that exhibited by the eukaryotes. These characteristics make the microbial world a very lucrative and inexhaustible resource for prospecting novel bioactive molecules. Despite their vast potential, over 99% of the microbial world still remains to be explored. The primary reason for this is that the culture-dependent methods used in the laboratories are grossly insufficient, as they support the growth of under 1% of the microorganisms found in nature. This limitation necessitated the development of techniques to circumvent culture dependency and gain access to the outstanding majority of the microorganisms. The development of culture-independent techniques has essentially reshaped the study of microbial diversity and community dynamics. Application of genomic and metagenomic approaches is contributing substantially towards characterization of the real microbial diversity. The amenability of these techniques to high throughput has opened the doors to explore the vast number of "uncultivable" microbial forms in substantially lesser time. The present article provides an update on the recent technological advances and emerging trends in exploring microbial community.
  Omics: a journal of integrative biology 01/2013;
• Article: Screening for Drug-Induced Hepatotoxicity in Primary Mouse Hepatocytes Using Acetaminophen, Amiodarone, and Cyclosporin A as Model Compounds: An Omics-Guided Approach.

  Anke Van Summeren, Johan Renes, Daneida Lizarraga, Freek G Bouwman, Jean-Paul Noben, Joost H M van Delft, Jos C S Kleinjans, Edwin C M Mariman
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  ABSTRACT: Abstract Drug-induced hepatotoxicity is a leading cause of attrition for candidate pharmaceuticals in development. New preclinical screening methods are crucial to predict drug toxicity prior to human studies. Of all in vitro hepatotoxicity models, primary human hepatocytes are considered as 'the gold standard.' However, their use is hindered by limited availability and inter-individual variation. These barriers may be overcome by using primary mouse hepatocytes. We used differential in gel electrophoresis (DIGE) to study large-scale protein expression of primary mouse hepatocytes. These hepatocytes were exposed to three well-defined hepatotoxicants: acetaminophen, amiodarone, and cyclosporin A. Each hepatotoxicant induces a different hepatotoxic phenotype. Based on the DIGE results, the mRNA expression levels of deregulated proteins from cyclosporin A-treated cells were also analyzed. We were able to distinguish cyclosporin A from controls, as well as acetaminophen and amiodarone-treated samples. Cyclosporin A induced endoplasmic reticulum (ER) stress and altered the ER-Golgi transport. Moreover, liver carboxylesterase and bile salt sulfotransferase were differentially expressed. These proteins were associated with a protective adaptive response against cyclosporin A-induced cholestasis. The results of this study are comparable with effects in HepG2 cells. Therefore, we suggest both models can be used to analyze the cholestatic properties of cyclosporin A. Furthermore, this study showed a conserved response between primary mouse hepatocytes and HepG2 cells. These findings collectively lend support for use of omics strategies in preclinical toxicology, and might inform future efforts to better link preclinical and clinical research in rational drug development.
  Omics: a journal of integrative biology 01/2013;