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Wanhua Hu, Xiaodong Lin, Huihe Zhang, Na Zhao
BACKGROUND ABCA2 has been genetically linked to Alzheimer's disease (AD) risk, but its mRNA expression and epigenetics in AD have not been investigated. MATERIAL AND METHODS To explore the diagnosis value of ABCA2 mRNA expression in AD, 2 datasets GES15222 and GSE33000 containing expression profile of brain cortex tissues and 2 datasets GSE63063 (Cohort 1) and GSE63063 (Cohort 2) containing expression profile of blood were downloaded from the NCBI GEO database and analyzed by receiver operating characteristic curve (ROC) analyses and logistic regression...
December 10, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Alexander W Murphey, William B Clinkscales, Samuel L Oyer
Importance: A review of the role of masseteric nerve transfer is needed to guide its use in facial reanimation. Objective: To systematically review the available literature, and, when applicable, analyze the combined outcomes of masseteric nerve transfer to better define its role in reanimation and to guide further research. Data Sources: Two independent researchers conducted the review using PubMed-NCBI and Scopus literature databases for studies on masseteric nerve transfer for facial nerve paralysis...
December 7, 2017: JAMA Facial Plastic Surgery
Barbara Robbertse, Pooja K Strope, Priscila Chaverri, Romina Gazis, Stacy Ciufo, Michael Domrachev, Conrad L Schoch
January 1, 2017: Database: the Journal of Biological Databases and Curation
Robin C Willenbring, Yasuhiro Ikeda, Larry R Pease, Aaron J Johnson
BACKGROUND: Deleterious mutations in PRF1 result in lethal, childhood disease, familial hemophagocytic lymphohistiocytosis type 2 (FHL 2). However, not all mutations in PRF1 are deleterious and result in FHL 2. Currently, these nondeleterious mutations are being investigated in the onset of numerous disorders, such as lymphomas and diabetes. Yet, there is still an overwhelmingly large amount of PRF1 mutations that are not associated with disease. METHODS: We conducted a post hoc analysis of the PRF1 mutations in the coding region using the recently published Exome Aggregation Consortium genomes, Leiden Open Variation Database, NCBI SNP database, and primary literature to better understand PRF1 variation in the human population...
December 7, 2017: Molecular Genetics & Genomic Medicine
Kopal Singhal, Sujata Mohanty
Multiple toxin-antitoxin (TA) systems are housed in different locations within the bacterial genome and are known to be associated with various cellular processes and stress-related adaptation. In endosymbionts, although, the TA system has scarce occurrence but studies have highlighted its presence in enhancing host-symbiont interactions. Wolbachia, an obligate endosymbiont, has recently been proposed as a biocontrol agent which may be helpful in controlling vector-borne diseases. There are reports suggesting the role of TA system in inducing cytoplasmic incompatibility in case of Wolbachia, however, the underlying mechanism is still not known...
December 6, 2017: Molecular Genetics and Genomics: MGG
Pingchuan Li, Bill Biligetu, Bruce E Coulman, Michael Schellenberg, Yong-Bi Fu
Crested wheatgrass [Agropyron cristatum L. (Gaertn.)] is an important cool-season forage grass widely used for early spring grazing. However, the genomic resources for this non-model plant are still lacking. Our goal was to generate the first set of next generation sequencing data using the genotyping-by-sequencing technique. A total of 272 crested wheatgrass plants representing seven breeding lines, five cultivars and five geographically diverse accessions were sequenced with an Illumina MiSeq instrument. These sequence datasets were processed using different bioinformatics tools to generate contigs for diploid and tetraploid plants and SNPs for diploid plants...
December 2017: Data in Brief
Silvana Rocio Ferreira, Alicia Beatriz Motta
BACKGROUND: The endometrium is one of the most important female reproductive organs. Polycystic ovarian syndrome (PCOS) is a reproductive and endocrine pathology that affect women of reproductive age. PCOS negatively affects the endometrium, leading to implantation failure and proliferative aberrations. METHODS: We conducted a search at the database using the following key words: endometrial steroid receptors, endometrium, uterine function, endometrium and PCOS, implantation window, implantation and PCOS, implantation markers, inflammation, oxidative stress...
December 5, 2017: Current Medicinal Chemistry
Vasanthakumar Ponesakki, Sayan Paul, Dinesh Kumar Sudalai Mani, Veeraragavan Rajendiran, Paulkumar Kanniah, Sudhakar Sivasubramaniam
In annelid worms, the nerve cord serves as a crucial organ to control the sensory and behavioral physiology. The inadequate genome resource of earthworms has prioritized the comprehensive analysis of their transcriptome dataset to monitor the genes express in the nerve cord and predict their role in the neurotransmission and sensory perception of the species. The present study focuses on identifying the potential transcripts and predicting their functional features by annotating the transcriptome dataset of nerve cord tissues prepared by Gong et al...
December 2017: Genomics Data
Zhai Yue, Jian-Ying Huang, Park Hyun, Fang Ji, Zhao-Liang Fei, Jiang Tao
PURPOSE: To investigate the expression of human β-defensin(HBD) in human dental pulp tissue and to explore the regulation of HBD in pulp inflammation and the relationship among HBD family members. METHODS: The gene expression of HBD in human dental pulp tissue was assessed in NCBI GEO profiles and was verified by RT-PCR. Human dental pulp cells were stimulated with TNF-α, IL-1α, IL-1β and IL-6 in different combinations and the expression of HBD2 was analyzed by qPCR...
August 2017: Shanghai Kou Qiang Yi Xue, Shanghai Journal of Stomatology
Jenny R Onley, Samiha Ahsan, Robert A Sanford, Frank E Löffler
The versatile soil bacterium Anaeromyxobacter dehalogenans lacks the hallmark denitrification genes nirS and nirK (NO2-→NO), and couples growth to NO3- reduction to NH4+ (respiratory ammonification) and to N2O reduction to N2A. dehalogenans also grows by reducing Fe(III) to Fe(II), which chemically reacts with NO2- to form N2O (i.e., chemodenitrification). Following the addition of 100 μmoles of NO3- or NO2- to Fe(III)-grown, axenic cultures of A. dehalogenans, 54 (±7) μmoles and 113 (±2) μmoles N2O-N, respectively, were produced and subsequently consumed...
December 1, 2017: Applied and Environmental Microbiology
Garima Awasthi, Anjani Kumari, Aditya Bhushan Pant, Prachi Srivastava
Chemical substances not showing any importance in existence of biological systems and causing serious health hazards may be designated as Xenobiotic compound. Elimination or degradation of these unwanted substances is a major issue of concern for current time research. Process of biodegradation is a very important aspect of current research as discussed in current manuscript. Current study focuses on the detailed mining of data for the construction of microbial consortia for wide range of xenobiotics compounds...
November 28, 2017: Microbial Pathogenesis
Zhenchao Zhang, Shuai Wang, Charles Li, Liheng Liu
The apicomplexan protozoans Eimeria spp. cause coccidioses, the most common intestinal diseases in chickens. Coccidiosis is associated with significant animal welfare issues and has a high economic impact on the poultry industry. Lack of a full understanding of immunogenic molecules and their precise functions involved in the Eimeria life cycles may limit development of effective vaccines and drug therapies. In this study, immunoproteomic approaches were used to define the antigenic protein repertoire from the total proteins of unsporulated Eimeria tenella oocysts...
2017: Parasite: Journal de la Société Française de Parasitologie
Ilene Karsch-Mizrachi, Toshihisa Takagi, Guy Cochrane
For more than 30 years, the International Nucleotide Sequence Database Collaboration (INSDC; has been committed to capturing, preserving and providing access to comprehensive public domain nucleotide sequence and associated metadata which enables discovery in biomedicine, biodiversity and biological sciences. Since 1987, the DNA Data Bank of Japan (DDBJ) at the National Institute for Genetics in Mishima, Japan; the European Nucleotide Archive (ENA) at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK; and GenBank at National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health in Bethesda, Maryland, USA have worked collaboratively to enable access to nucleotide sequence data in standardized formats for the worldwide scientific community...
November 28, 2017: Nucleic Acids Research
Mark F Richardson, Fernando Sequeira, Daniel Selechnik, Miguel Carneiro, Marcelo Vallinoto, Jack G Reid, Andrea J West, Michael R Crossland, Richard Shine, Lee A Rollins
Background: Cane toads (Rhinella marina) are an iconic invasive species introduced to four continents and well utilized for studies of rapid evolution in introduced environments. Despite the long introduction history of this species, its profound ecological impacts and its utility for demonstrating evolutionary principles, genetic information is sparse. Here we produce a de novo transcriptome spanning multiple tissues and life stages to enable investigation of the genetic basis of previously identified rapid phenotypic change over the introduced range...
November 27, 2017: GigaScience
Zhuang-Li Tang, Shuang Wang, Chen Tu, Tian Wang, Cheng-Wen Ma, Yan Liu, Sheng-Xiang Xiao, Xiao-Peng Wang
AIMS: To identify potential novel gene mutations in Chinese patients with dyschromatosis symmetrica hereditaria (DSH). METHODS: We enrolled 8 Chinese patients with familial DSH, 5 Chinese patients with sporadic DSH, and 100 randomly selected healthy individuals in this study. The genome of each participant was extracted from peripheral blood samples. Sanger sequencing was performed after polymerase chain reaction. Comparison between the outcomes and the NCBI database was made, thus novel mutations were identified...
November 29, 2017: Genetic Testing and Molecular Biomarkers
Therése Bengtsson, Inger Åhman, Outi Manninen, Lars Reitan, Therese Christerson, Jens Due Jensen, Lene Krusell, Ahmed Jahoor, Jihad Orabi
The powdery mildew fungus, Blumeria graminis f. sp. hordei is a worldwide threat to barley (Hordeum vulgare L. ssp. vulgare) production. One way to control the disease is by the development and deployment of resistant cultivars. A genome-wide association study was performed in a Nordic spring barley panel consisting of 169 genotypes, to identify marker-trait associations significant for powdery mildew. Powdery mildew was scored during three years (2012-2014) in four different locations within the Nordic region...
2017: Frontiers in Plant Science
Mitsuharu Sato, Kentaro Miyazaki
Horizontal gene transfer (HGT) is a ubiquitous genetic event in bacterial evolution, but it seldom occurs for genes involved in highly complex supramolecules (or biosystems), which consist of many gene products. The ribosome is one such supramolecule, but several bacteria harbor dissimilar and/or chimeric 16S rRNAs in their genomes, suggesting the occurrence of HGT of this gene. However, we know little about whether the genes actually experience HGT and, if so, the frequency of such a transfer. This is primarily because the methods currently employed for phylogenetic analysis (e...
2017: Frontiers in Microbiology
Anna Kaznadzey, Pavel Shelyakin, Mikhail S Gelfand
BACKGROUND: Bacterial carbohydrate metabolism is extremely diverse, since carbohydrates serve as a major energy source and are involved in a variety of cellular processes. Bacterial genes belonging to same metabolic pathway are often co-localized in the chromosome, but it is not a strict rule. Gene co-localization in linked to co-evolution and co-regulation. This study focuses on a large-scale analysis of bacterial genomic loci related to the carbohydrate metabolism. RESULTS: We demonstrate that only 53% of 148,000 studied genes from over six hundred bacterial genomes are co-localized in bacterial genomes with other carbohydrate metabolism genes, which points to a significant role of singleton genes...
November 25, 2017: Biology Direct
Laise de Azevedo Gomes, Leopoldo Augusto Moraes, Délia Cristina Figueira Aguiar, Hilma Lúcia Tavares Dias, Ana Silvia Sardinha Ribeiro, Henrique Piram do Couto Rocha, Márcio Roberto Teixeira Nunes, Evonnildo Costa Gonçalves
This study aimed to identify and characterize genetically species of the genus Hepatozoon detected in Hydrochoerus hydrochaeris (capybaras) and Pecari tajacu (collared peccaries) from two localities from the Eastern Amazon. Blood samples from 196 free-living H. hydrochaeris from Marajó Island and 109 P. tajacu kept in captivity in Belém, Pará, were collected and analyzed for the presence of Hepatozoon spp. Partial sequences of the 18S rRNA gene were obtained and analyzed in comparison to others available in the NCBI database...
November 11, 2017: Ticks and Tick-borne Diseases
Pio Maria Furneri, Virginia Fuochi, Rosario Pignatello
BACKGROUND: The class of fluoroquinolone antibiotics, due to its core chemical modifications, is considered as wide-spectrum antibacterial drugs with useful pharmacokinetic and pharmacodynamic properties. However, because of their poor solubility in water, they are used as salts (lactates or hydrochlorides). Fluoroquinolones, bacterial membranes and eukaryotic cell membranes interactions are well known and their permeation properties are well investigated. In fact, they are concentrated inside the cells and intracellular compartments...
November 21, 2017: Current Pharmaceutical Design
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