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Genomics, Proteomics & Bioinformatics

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https://www.readbyqxmd.com/read/29462670/microvesicles-as-emerging-biomarkers-and-therapeutic-targets-in-cardiometabolic-diseases
#1
REVIEW
Yan Chen, Guangping Li, Ming-Lin Liu
Microvesicles (MVs, also known as microparticles) are small vesicles that originate from plasma membrane of almost all eukaryotic cells during apoptosis or activation. MVs can serve as extracellular vehicles to transport bioactive molecules from their parental cells to recipient target cells, thereby serving as novel mediators for intercellular communication. Importantly, more and more evidence indicates that MVs could play important roles in early pathogenesis and subsequent progression of cardiovascular and metabolic diseases...
February 17, 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29247874/a-novel-nonlinear-parameter-estimation-method-of-soft-tissues
#2
Qianqian Tong, Zhiyong Yuan, Mianlun Zheng, Xiangyun Liao, Weixu Zhu, Guian Zhang
The elastic parameters of soft tissues are important for medical diagnosis and virtual surgery simulation. In this study, we propose a novel nonlinear parameter estimation method for soft tissues. Firstly, an in-house data acquisition platform was used to obtain external forces and their corresponding deformation values. To provide highly precise data for estimating nonlinear parameters, the measured forces were corrected using the constructed weighted combination forecasting model based on a support vector machine (WCFM_SVM)...
December 13, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29247873/the-ability-of-different-imputation-methods-to-preserve-the-significant-genes-and-pathways-in-cancer
#3
Rosa Aghdam, Taban Baghfalaki, Pegah Khosravi, Elnaz Saberi Ansari
Deciphering important genes and pathways from incomplete gene expression data could facilitate a better understanding of cancer. Different imputation methods can be applied to estimate the missing values. In our study, we evaluated various imputation methods for their performance in preserving significant genes and pathways. In the first step, 5% genes are considered in random for two types of ignorable and non-ignorable missingness mechanisms with various missing rates. Next, 10 well-known imputation methods were applied to the complete datasets...
December 13, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29247872/proteomic-analysis-shows-constitutive-secretion-of-mif-and-p53-associated-activity-of-cox-2-lung-fibroblasts
#4
Mandar Dave, Abul B M M K Islam, Roderick V Jensen, Agueda Rostagno, Jorge Ghiso, Ashok R Amin
The differential expression of two closely-associated cyclooxygenase isozymes, COX-1 and COX-2, exhibited functions beyond eicosanoid metabolism. We hypothesized that COX-1 or COX-2 knockout lung fibroblasts may display altered protein profiles which may allow us to further differentiate the functional roles of these isozymes at the molecular level. Proteomic analysis shows constitutive production of macrophage migration inhibitory factor (MIF) in lung fibroblasts derived from COX-2-/- but not wild-type (WT) or COX-1-/- mice...
December 13, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29246520/a-stack-based-ensemble-framework-for-detecting-cancer-microrna-biomarkers
#5
Sriparna Saha, Sayantan Mitra, Ravi Kant Yadav
MicroRNA (miRNA) plays vital roles in biological processes like RNA slicing and regulation of gene expression. Studies have revealed that there might be possible links between oncogenesis and expression profiles of some miRNAs, due to their differential expression between normal and tumour tissues. However, the automatic classification of miRNAs into different categories by considering the similarity of their expression values has rarely been addressed. This article proposes a solution framework for solving some real-life classification problems related to cancer, miRNA, and mRNA expression datasets...
December 12, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29246519/hybrid-method-based-on-information-gain-and-support-vector-machine-for-gene-selection-in-cancer-classification
#6
Lingyun Gao, Mingquan Ye, Xiaojie Lu, Daobin Huang
It remains a great challenge to achieve sufficient cancer classification accuracy with the entire set of informative genes, due to the high dimensions, small sample size, and big noise of gene expression data. We thus proposed a hybrid gene selection method, Information Gain-Support Vector Machine (IG-SVM) in this study. IG was initially employed to filter irrelevant and redundant genes. Then, further removal of redundant genes was performed using SVM to eliminate the noise in the datasets more effectively...
December 12, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29246518/interactome-analysis-of-microtubule-targeting-agents-reveals-cytotoxicity-bases-in-normal-cells
#7
Andrés Julián Gutiérrez-Escobar, Gina Méndez-Callejas
Cancer causes millions of deaths annually and microtubule-targeting agents (MTAs) are the most commonly-used anti-cancer drugs. However, the high toxicity of MTAs on normal cells raises great concern. Due to the non-selectivity of MTA targets, we analyzed the interaction network in a non-cancerous human cell. Subnetworks of fourteen MTAs were reconstructed and the merged network was compared against a randomized network to evaluate the functional richness. We found that 71.4% of the MTA interactome nodes is shared, which affects cellular processes such as apoptosis, cell differentiation, cell cycle control, stress response, and regulation of energy metabolism...
December 12, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29133277/orthognc-a-software-for-accurate-identification-of-orthologs-based-on-gene-neighborhood-conservation
#8
Soheil Jahangiri-Tazehkand, Limsoon Wong, Changiz Eslahchi
Orthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthology relations. In closely-related species, gene neighborhood information can be used to resolve many ambiguities in orthology inference. Here we present OrthoGNC, a software for accurately predicting pairwise orthology relations based on gene neighborhood conservation...
November 11, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29017968/author-s-reply-comments-on-vitamin-pharmacogenomics-new-insight-into-individual-differences-in-diseases-and-drug-responses
#9
LETTER
Wei Zhang
No abstract text is available yet for this article.
October 7, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29017966/comments-on-vitamin-pharmacogenomics-new-insight-into-individual-differences-in-diseases-and-drug-responses
#10
LETTER
Tom Greenfield
No abstract text is available yet for this article.
October 7, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29037489/latent-hiv-1-tar-regulates-7sk-responsive-p-tefb-target-genes-and-targets-cellular-immune-responses-in-the-absence-of-tat
#11
Sebastian Eilebrecht, Bernd-Joachim Benecke, Arndt G Benecke
The transactivating response element (TAR) structure of the nascent HIV-1 transcript is critically involved in the recruitment of inactive positive transcription elongation factor b (P-TEFb) to the promoter proximal paused RNA polymerase II. The viral transactivator Tat is responsible for subsequent P-TEFb activation in order to start efficient viral transcription elongation. In the absence of the viral transactivator of transcription (Tat), e.g., during latency or in early stages of HIV transcription, TAR mediates an interaction of P-TEFb with its inhibitor hexamethylene bis-acetamide-inducible protein 1 (HEXIM1), keeping P-TEFb in its inactive form...
October 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29031844/alternative-polyadenylation-methods-findings-and-impacts
#12
REVIEW
Wei Chen, Qi Jia, Yifan Song, Haihui Fu, Gang Wei, Ting Ni
Alternative polyadenylation (APA), a phenomenon that RNA molecules with different 3' ends originate from distinct polyadenylation sites of a single gene, is emerging as a mechanism widely used to regulate gene expression. In the present review, we first summarized various methods prevalently adopted in APA study, mainly focused on the next-generation sequencing (NGS)-based techniques specially designed for APA identification, the related bioinformatics methods, and the strategies for APA study in single cells...
October 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29031843/rna-regulations-and-functions-decoded-by-transcriptome-wide-rna-structure-probing
#13
REVIEW
Meiling Piao, Lei Sun, Qiangfeng Cliff Zhang
RNA folds into intricate structures that are crucial for its functions and regulations. To date, a multitude of approaches for probing structures of the whole transcriptome, i.e., RNA structuromes, have been developed. Applications of these approaches to different cell lines and tissues have generated a rich resource for the study of RNA structure-function relationships at a systems biology level. In this review, we first introduce the designs of these methods and their applications to study different RNA structuromes...
October 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29031842/ribosome-profiling-reveals-genome-wide-cellular-translational-regulation-upon-heat-stress-in-escherichia-coli
#14
LETTER
Yanqing Zhang, Zhengtao Xiao, Qin Zou, Jianhuo Fang, Qifan Wang, Xuerui Yang, Ning Gao
Heat shock response is a classical stress-induced regulatory system in bacteria, characterized by extensive transcriptional reprogramming. To compare the impact of heat stress on the transcriptome and translatome in Escherichia coli, we conducted ribosome profiling in parallel with RNA-Seq to investigate the alterations in transcription and translation efficiency when E. coli cells were exposed to a mild heat stress (from 30 °C to 45 °C). While general changes in ribosome footprints correlate with the changes of mRNA transcripts upon heat stress, a number of genes show differential changes at the transcription and translation levels...
October 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29017967/non-coding-rnas-and-their-roles-in-stress-response-in-plants
#15
REVIEW
Jingjing Wang, Xianwen Meng, Oxana B Dobrovolskaya, Yuriy L Orlov, Ming Chen
Eukaryotic genomes encode thousands of non-coding RNAs (ncRNAs), which play crucial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), have emerged as key regulatory molecules in plant stress responses. In this review, we have summarized the current progress on the understanding of plant miRNA and lncRNA identification, characteristics, bioinformatics tools, and resources, and provided examples of mechanisms of miRNA- and lncRNA-mediated plant stress tolerance...
October 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28942262/engineering-novel-molecular-beacon-constructs-to-study-intracellular-rna-dynamics-and-localization
#16
REVIEW
Zhao Ma, Xiaotian Wu, Christopher J Krueger, Antony K Chen
With numerous advancements in novel biochemical techniques, our knowledge of the role of RNAs in the regulation of cellular physiology and pathology has grown significantly over the past several decades. Nevertheless, detailed information regarding RNA processing, trafficking, and localization in living cells has been lacking due to technical limitations in imaging single RNA transcripts in living cells with high spatial and temporal resolution. In this review, we discuss techniques that have shown great promise for single RNA imaging, followed by highlights in our recent work in the development of molecular beacons (MBs), a class of nanoscale oligonucleotide-probes, for detecting individual RNA transcripts in living cells...
October 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28882787/steering-against-wind-a-new-network-of-namirnas-and-enhancers
#17
Ying Liang, Qingping Zou, Wenqiang Yu
MicroRNAs (miRNAs) are a class of endogenous non-coding RNAs with regulatory functions. Traditionally, miRNAs are thought to play a negative regulatory role in the cytoplasm by binding to the 3'UTR of target genes to degrade mRNA or inhibit translation. However, it remains a challenge to interpret the potential function of many miRNAs located in the nucleus. Recently, we reported a new type of miRNAs present in the nucleus, which can activate gene expression by binding to the enhancer, and named them nuclear activating miRNAs (NamiRNAs)...
October 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28813639/exploitation-of-gene-expression-and-cancer-biomarkers-in-paving-the-path-to-era-of-personalized-medicine
#18
REVIEW
Hala Fawzy Mohamed Kamel, Hiba Saeed A Bagader Al-Amodi
Cancer therapy agents have been used extensively as cytotoxic drugs against tissue or organ of a specific type of cancer. With the better understanding of molecular mechanisms underlying carcinogenesis and cellular events during cancer progression and metastasis, it is now possible to use targeted therapy for these molecular events. Targeted therapy is able to identify cancer patients with dissimilar genetic defects at cellular level for the same cancer type and consequently requires individualized approach for treatment...
August 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28811232/cyp2a6-polymorphisms-associate-with-outcomes-of-s-1-plus-oxaliplatin-chemotherapy-in-chinese-gastric-cancer-patients
#19
LETTER
Lin Yang, Shanshan Zou, Chang Shu, Yan Song, Yong-Kun Sun, Wen Zhang, Aiping Zhou, Xinghua Yuan, Yi Yang, Songnian Hu
Gastric carcinoma is a heterogeneous malignant disease involving genetic factors. To identify predictive markers for gastric cancer treatment in Chinese patients, we evaluated the association between polymorphisms of the gene encoding cytochrome P450 2A6 (CYP2A6) and outcomes of S-1 plus oxaliplatin (SOX) chemotherapy treatment. Clinical data on 60 consecutive gastric cancer patients receiving SOX regimen were collected prospectively. We sequenced all exons of CYP2A6 and a total of 22 different polymorphisms were detected in the present study...
August 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28811231/a-step-forward-in-precision-medicine-on-one-belt-one-road
#20
EDITORIAL
Jun Yu
No abstract text is available yet for this article.
August 2017: Genomics, Proteomics & Bioinformatics
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