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functional annotation

Cheng Jin, Jianjiang Feng, Lei Wang, Heng Yu, Jiang Liu, Jiwen Lu, Jie Zhou
In this paper, we present an approach for left atrial appendage (LAA) multi-phase fast segmentation and quantitative assisted diagnosis of atrial fibrillation (AF) based on 4D-CT data. We take full advantage of the temporal dimension information to segment the living, flailed LAA based on a parametric max-flow method and graph-cut approach to build 3-D model of each phase. To assist the diagnosis of AF, we calculate the volumes of 3-D models, and then generate a "volume-phase" curve to calculate the important dynamic metrics: ejection fraction, filling flux, and emptying flux of the LAA's blood by volume...
March 9, 2018: Computers in Biology and Medicine
Lokesh K Narnoliya, Rajender S Sangwan, Sudhir P Singh
Rose-scented geranium (Pelargonium sp.) is widely known as aromatic and medicinal herb, accumulating specialized metabolites of high economic importance, such as essential oils, ascorbic acid, and tartaric acid. Ascorbic acid and tartaric acid are multifunctional metabolites of human value to be used as vital antioxidants and flavor enhancing agents in food products. No information is available related to the structural and functional properties of the enzymes involved in ascorbic acid and tartaric acid biosynthesis in rose-scented geranium...
March 15, 2018: Molecular Biology Reports
Long Chen, Yifeng Jiang, Zhen Du
Although previous studies have demonstrated that dental pulp stem cells (DPSCs) from mature and immature teeth exhibit potential for multi-directional differentiation, the molecular and biological difference between the DPSCs from mature and immature permanent teeth has not been fully investigated. In the present study, 500 differentially expressed genes from dental pulp cells (DPCs) in mature and immature permanent teeth were obtained from the Gene Expression Omnibus online database. Based on bioinformatics analysis using the Database for Annotation, Visualization and Integrated Discovery, these genes were divided into a number of subgroups associated with immunity, inflammation and cell signaling...
April 2018: Experimental and Therapeutic Medicine
Graziela de Sá Machado Araújo, Ronaldo da Silva Francisco Junior, Cristina Dos Santos Ferreira, Pedro Thyago Mozer Rodrigues, Douglas Terra Machado, Thais Louvain de Souza, Jozimara Teixeira de Souza, Cleiton Figueiredo Osorio da Silva, Antônio Francisco Alves da Silva, Claudia Caixeta Franco Andrade, Alan Tardin da Silva, Victor Ramos, Ana Beatriz Garcia, Filipe Brum Machado, Enrique Medina-Acosta
A hallmark of imprinted genes in mammals is the occurrence of parent-of-origin-dependent asymmetry of DNA cytosine methylation (5m C) of alleles at CpG islands (CGIs) in their promoter regions. This 5m CpG asymmetry between the parental alleles creates allele-specific imprinted differentially methylated regions (iDMRs). iDMRs are often coupled to the transcriptional repression of the methylated allele and the activation of the unmethylated allele in a tissue-specific, developmental-stage-specific and/or isoform-specific fashion...
2018: Frontiers in Genetics
Shefali Setia Verma, Navya Josyula, Anurag Verma, Xinyuan Zhang, Yogasudha Veturi, Frederick E Dewey, Dustin N Hartzel, Daniel R Lavage, Joe Leader, Marylyn D Ritchie, Sarah A Pendergrass
The DrugBank database consists of ~800 genes that are well characterized drug targets. This list of genes is a useful resource for association testing. For example, loss of function (LOF) genetic variation has the potential to mimic the effect of drugs, and high impact variation in these genes can impact downstream traits. Identifying novel associations between genetic variation in these genes and a range of diseases can also uncover new uses for the drugs that target these genes. Phenome Wide Association Studies (PheWAS) have been successful in identifying genetic associations across hundreds of thousands of diseases...
March 15, 2018: Scientific Reports
Soumya Luthra, Uma Chandran, Brenda Diergaarde, Michael Becich, Adrian V Lee, Carola A Neumann
Increased reactive species (RS; reactive oxygen and nitrogen species) are a byproduct of both enzymatic and non-enzymatic systems, and critical in cancer development, including breast tumorigenesis. To investigate the role of RS-related genes in breast cancer, expression levels of the most common annotated genes involved in regulating cellular RS levels and proteins that are substrates of RS in specific subtypes of breast cancer 9 were evaluated using public data bases. Based on the premise that increased RS promote tumor formation, and breast cancer subtypes vary in aggressiveness, we hypothesized that specific RS gene expression signatures are associated with breast cancer aggressiveness and patient survival...
March 12, 2018: Free Radical Biology & Medicine
Tong Liu, Dong-Wei Tian, Li-Juan Zou, Fang-Yu Liu, Qi-Yan Can, Jin-Kui Yang, Jian-Ping Xu, Xiao-Wei Huang, Jia-Qin Xi, Ming-Liang Zhu, Ming-He Mo, Ke-Qin Zhang
Ammonia is one of the fungistatic factors in soil that can suppress conidial germination, but the molecular mechanism underlying the suppression is unknown. In this study, the proteomes of fungistatic conidia, fresh conidia and germinated conidia of Arthrobotrys oligospora ATCC24927 were determined and quantified. The protein expression profile of fungistatic conidia was significantly different from those in the other two conditions. 281 proteins were down expressed in fungistatic conidia and characterized by GO annotation...
March 12, 2018: International Journal of Biochemistry & Cell Biology
Qian-Wen Deng, Xiang-Dong Luo, Ya-Ling Chen, Yi Zhou, Fan-Tao Zhang, Biao-Lin Hu, Jian-Kun Xie
BACKGROUND: Low phosphorus availability is a major factor restricting rice growth. Dongxiang wild rice (Oryza rufipogon Griff.) has many useful genes lacking in cultivated rice, including stress resistance to phosphorus deficiency, cold, salt and drought, which is considered to be a precious germplasm resource for rice breeding. However, the molecular mechanism of regulation of phosphorus deficiency tolerance is not clear. RESULTS: In this study, cDNA libraries were constructed from the leaf and root tissues of phosphorus stressed and untreated Dongxiang wild rice seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in phosphorus stress response...
March 15, 2018: Biological Research
Konstantinos C Tsolis, Evridiki-Pandora Tsare, Georgia Orfanoudaki, Tobias Busche, Katerina Kanaki, Reshmi Ramakrishnan, Frederic Rousseau, Joost Schymkowitz, Christian Rückert, Jörn Kalinowski, Jozef Anné, Spyridoula Karamanou, Maria I Klapa, Anastassios Economou
BACKGROUND: Members of the genus Streptomyces are Gram-positive bacteria that are used as important cell factories to produce secondary metabolites and secrete heterologous proteins. They possess some of the largest bacterial genomes and thus proteomes. Understanding their complex proteomes and metabolic regulation will improve any genetic engineering approach. RESULTS: Here, we performed a comprehensive annotation of the subcellular localization of the proteome of Streptomyces lividans TK24 and developed the Subcellular Topology of Polypeptides in Streptomyces database (SToPSdb) to make this information widely accessible...
March 15, 2018: Microbial Cell Factories
Feng Shen, Qing Guo, Qi Hu, Ailiang Zeng, Weining Wu, Wei Yan, Yongping You
Nuclear factor κB (NF-κB) exhibits an important role in inflammation and tumorigenesis. The key regulatory protein of the pathway, RELB Proto-Oncogene, NF-KB Subunit (relB), is overexpressed and associated with the pathogenesis of a variety of malignant tumors. However, the molecular features and clinical signature of relB expression in gliomas remains to be elucidated. The present study obtained the raw sequencing data of 325 glioma samples of all grades from the Chinese Glioma Genome Atlas (CGGA) database and human glioma cell line (LN229) from the Chinese Academy of Sciences cell bank...
April 2018: Oncology Letters
Lishuang Shen, Marcella Attimonelli, Renkui Bai, Marie T Lott, Douglas C Wallace, Marni J Falk, Xiaowu Gai
Accurate mitochondrial DNA (mtDNA) variant annotation is essential for the clinical diagnosis of diverse human diseases. Substantial challenges to this process include the inconsistency in mtDNA nomenclatures, the existence of multiple reference genomes, and a lack of reference population frequency data. Clinicians need a simple bioinformatics tool that is user-friendly, and bioinformaticians need a powerful informatics resource for programmatic usage. Here, we report the development and functionality of the MSeqDR mtDNA Variant Tool set (mvTool), a one-stop mtDNA variant annotation and analysis web service...
March 14, 2018: Human Mutation
Hongfang Li, Yuzhi Zhen, Yunshuang Geng, Junyan Feng, Jun Wang, Hongsong Zhang
BACKGROUND The aim of this study was to identify some key genes related to the pathogenesis of thoracic aortic aneurysm (TAA) and gain more insights to the molecular mechanism of TAA. MATERIAL AND METHODS The expression profile of GSE9106 was downloaded from the Gene Expression Omnibus (GEO) database. The data contained 58 TAA peripheral blood samples and 36 normal peripheral blood samples. The differently expressed genes (DEGs) between the TAA samples and the normal samples were identified via limma package of R...
March 14, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Meixia Pang, Weiwei Luo, Beide Fu, Xiaomu Yu, Ying Zhou, Jingou Tong
Feed efficiency is an economically crucial trait for cultured animals, however, progress has been scarcely made in the genetic analyses of feed conversion efficiency (FCE) in fish because of the difficulties in measurement of trait phenotypes. In the present investigation, we present the first application of RNA sequencing (RNA-Seq) combined with differentially expressed genes (DEGs) analysis for identification of functional determinants related to FCE at the gene level in an aquaculture fish, crucian carp ( Carassius auratus )...
March 14, 2018: International Journal of Molecular Sciences
Xiaochen Lin, Katie Kei-Hang Chan, Yen-Tsung Huang, Xi Luo, Liming Liang, James Wilson, Adolfo Correa, Daniel Levy, Simin Liu
PURPOSE: Leisure-time physical activity (LTPA) is a well-established modifiable lifestyle determinant for multiple cardio-metabolic outcomes. However, current understanding of the genetic architecture that may determine LTPA remains very limited. Therefore, we aimed to examine the role of genetic factors in affecting LTPA, which has yet to be investigated comprehensively and in-depth. METHODS: We conducted a genome-wide analysis using 1000 Genomes Project imputed data from the Women's Health Initiative (n=11,865), the Jackson Heart Study (n=3,015) and the Framingham Heart Study (n=7,339)...
March 13, 2018: Medicine and Science in Sports and Exercise
Yi Xiong, Xiaolei Zhu, Hao Dai, Dong-Qing Wei
The increasing number of protein structures with uncharacterized function necessitates the development of in silico prediction methods for functional annotations on proteins. In this chapter, different kinds of computational approaches are briefly introduced to predict DNA-binding residues on surface of DNA-binding proteins, and the merits and limitations of these methods are mainly discussed. This chapter focuses on the structure-based approaches and mainly discusses the framework of machine learning methods in application to DNA-binding prediction task...
2018: Methods in Molecular Biology
Yuchen Yang, Wuxia Guo, Xu Shen, Jianfang Li, Shuhuan Yang, Sufang Chen, Ziwen He, Renchao Zhou, Suhua Shi
Alternative splicing (AS), which produces multiple mRNA transcripts from a single gene, plays crucial roles in plant growth, development and environmental stress responses. Functional significances of conserved AS events among congeneric species have not been well characterized. In this study, we performed transcriptome sequencing to characterize AS events in four common species of Sonneratia, a mangrove genus excellently adaptive to intertidal zones. 7,248 to 12,623 AS events were identified in approximately 25% to 35% expressed genes in the roots of the four species...
March 13, 2018: Scientific Reports
Cécile Molinier, Céline M O Reisser, Peter Fields, Adeline Ségard, Yan Galimov, Christoph R Haag
Daphnia reproduce by cyclic-parthenogenesis, where phases of asexual reproduction are intermitted by sexual production of diapause stages. This life cycle, together with environmental sex determination, allow the comparison of gene expression between genetically identical males and females. We investigated gene expression differences between males and females in four genotypes of Daphnia magna and compared the results with published data on sex-biased gene expression in two other Daphnia species, each representing one of the major phylogenetic clades within the genus...
March 13, 2018: G3: Genes—Genomes—Genetics
Chengxin Zhang, Wei Zheng, Peter L Freddolino, Yang Zhang
Homology-based transferal remains the major approach to computational protein function annotations, but it becomes increasingly unreliable when the sequence identity between query and template decreases below 30%. We propose a novel pipeline, MetaGO, to deduce Gene Ontology attributes of proteins by combining sequence homology-based annotation with low-resolution structure prediction and comparison, and partner's-homology based protein-protein network mapping. The pipeline was tested on a large-scale set of 1000 non-redundant proteins from the CAFA3 experiment...
March 10, 2018: Journal of Molecular Biology
Tadashige Nozaki, Yuka Sasaki, Itsuko Fukuda, Mayu Isumi, Keitaro Nakamoto, Takae Onodera, Mitsuko Masutani
Poly (ADP-ribose) polymerase family, member 1 (Parp1) has pleiotropic and disparate functions in multiple cellular signaling pathways through post-translational protein modification. It contributes to the regulation of various cellular processes, including DNA damage repair, cell death, and cell differentiation, genetically or epigenetically. Meanwhile, the functions of Parp1 in intercellular signaling remain to be established. To examine the functions of Parp1 in intercellular signaling, we examined microRNA (miRNA) regulation in exosomes derived from Parp1-deficient (Parp1-/- ) embryonic stem (ES) cells...
March 10, 2018: Biochemical and Biophysical Research Communications
Yara Suliman, Frank Becker, Klaus Wimmers
Poor fertility of breeding stallions is a recognised problem in the equine industry. The aim of the present study was to detect molecular pathways using two groups of stallions that differed in pregnancy rates as well as in the proportion of normal and motile spermatozoa. RNA was isolated from spermatozoa of each stallion and microarray data were analysed to obtain a list of genes for which transcript abundance differed between the groups (P ≤0.05, fold change ≥1.2). In all, there were 437 differentially expressed (DE) genes between the two groups (P ≤ 0...
March 14, 2018: Reproduction, Fertility, and Development
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