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Publisher: Hindawi   (Total: 330 journals)

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Showing 1 - 200 of 330 Journals sorted alphabetically
Abstract and Applied Analysis     Open Access   (Followers: 3, SJR: 0.343, CiteScore: 1)
Active and Passive Electronic Components     Open Access   (Followers: 7, SJR: 0.136, CiteScore: 0)
Advances in Acoustics and Vibration     Open Access   (Followers: 33, SJR: 0.147, CiteScore: 0)
Advances in Aerospace Engineering     Open Access   (Followers: 52)
Advances in Agriculture     Open Access   (Followers: 8)
Advances in Artificial Intelligence     Open Access   (Followers: 15)
Advances in Astronomy     Open Access   (Followers: 36, SJR: 0.257, CiteScore: 1)
Advances in Bioinformatics     Open Access   (Followers: 17, SJR: 0.565, CiteScore: 2)
Advances in Biology     Open Access   (Followers: 8)
Advances in Chemistry     Open Access   (Followers: 21)
Advances in Civil Engineering     Open Access   (Followers: 38, SJR: 0.539, CiteScore: 1)
Advances in Computer Engineering     Open Access   (Followers: 4)
Advances in Condensed Matter Physics     Open Access   (Followers: 10, SJR: 0.315, CiteScore: 1)
Advances in Decision Sciences     Open Access   (Followers: 3, SJR: 0.303, CiteScore: 1)
Advances in Electrical Engineering     Open Access   (Followers: 26)
Advances in Electronics     Open Access   (Followers: 65)
Advances in Emergency Medicine     Open Access   (Followers: 11)
Advances in Endocrinology     Open Access   (Followers: 5)
Advances in Environmental Chemistry     Open Access   (Followers: 5)
Advances in Epidemiology     Open Access   (Followers: 8)
Advances in Fuzzy Systems     Open Access   (Followers: 5, SJR: 0.161, CiteScore: 1)
Advances in Geology     Open Access   (Followers: 14)
Advances in Geriatrics     Open Access   (Followers: 5)
Advances in Hematology     Open Access   (Followers: 11, SJR: 0.661, CiteScore: 2)
Advances in Hepatology     Open Access   (Followers: 2)
Advances in High Energy Physics     Open Access   (Followers: 19, SJR: 0.866, CiteScore: 2)
Advances in Human-Computer Interaction     Open Access   (Followers: 20, SJR: 0.186, CiteScore: 1)
Advances in Materials Science and Engineering     Open Access   (Followers: 30, SJR: 0.315, CiteScore: 1)
Advances in Mathematical Physics     Open Access   (Followers: 4, SJR: 0.218, CiteScore: 1)
Advances in Medicine     Open Access   (Followers: 2)
Advances in Meteorology     Open Access   (Followers: 20, SJR: 0.48, CiteScore: 1)
Advances in Multimedia     Open Access   (Followers: 1, SJR: 0.173, CiteScore: 1)
Advances in Nonlinear Optics     Open Access   (Followers: 6)
Advances in Numerical Analysis     Open Access   (Followers: 5)
Advances in Nursing     Open Access   (Followers: 26)
Advances in Operations Research     Open Access   (Followers: 12, SJR: 0.205, CiteScore: 1)
Advances in Optical Technologies     Open Access   (Followers: 3, SJR: 0.214, CiteScore: 1)
Advances in Optics     Open Access   (Followers: 3)
Advances in OptoElectronics     Open Access   (Followers: 6, SJR: 0.141, CiteScore: 0)
Advances in Orthopedics     Open Access   (Followers: 8, SJR: 0.922, CiteScore: 2)
Advances in Pharmacological Sciences     Open Access   (Followers: 7, SJR: 0.591, CiteScore: 2)
Advances in Physical Chemistry     Open Access   (Followers: 9, SJR: 0.179, CiteScore: 1)
Advances in Power Electronics     Open Access   (Followers: 29, SJR: 0.184, CiteScore: 0)
Advances in Preventive Medicine     Open Access   (Followers: 5)
Advances in Public Health     Open Access   (Followers: 23)
Advances in Software Engineering     Open Access   (Followers: 10)
Advances in Statistics     Open Access   (Followers: 4)
Advances in Toxicology     Open Access   (Followers: 2)
Advances in Tribology     Open Access   (Followers: 12, SJR: 0.265, CiteScore: 1)
Advances in Urology     Open Access   (Followers: 9, SJR: 0.51, CiteScore: 1)
Advances in Virology     Open Access   (Followers: 7, SJR: 0.838, CiteScore: 2)
AIDS Research and Treatment     Open Access   (Followers: 3, SJR: 0.758, CiteScore: 2)
Analytical Cellular Pathology     Open Access   (Followers: 2, SJR: 0.886, CiteScore: 2)
Anatomy Research Intl.     Open Access   (Followers: 2)
Anemia     Open Access   (Followers: 5, SJR: 0.669, CiteScore: 2)
Anesthesiology Research and Practice     Open Access   (Followers: 14, SJR: 0.501, CiteScore: 1)
Applied and Environmental Soil Science     Open Access   (Followers: 16, SJR: 0.451, CiteScore: 1)
Applied Bionics and Biomechanics     Open Access   (Followers: 8, SJR: 0.288, CiteScore: 1)
Applied Computational Intelligence and Soft Computing     Open Access   (Followers: 11)
Archaea     Open Access   (Followers: 3, SJR: 0.852, CiteScore: 2)
Arthritis     Open Access   (Followers: 5, SJR: 0.454, CiteScore: 1)
Autism Research and Treatment     Open Access   (Followers: 25)
Autoimmune Diseases     Open Access   (Followers: 3, SJR: 0.805, CiteScore: 2)
Behavioural Neurology     Open Access   (Followers: 9, SJR: 0.786, CiteScore: 2)
Biochemistry Research Intl.     Open Access   (Followers: 6, SJR: 0.437, CiteScore: 2)
Bioinorganic Chemistry and Applications     Open Access   (Followers: 10, SJR: 0.419, CiteScore: 2)
BioMed Research Intl.     Open Access   (Followers: 4, SJR: 0.935, CiteScore: 3)
Biotechnology Research Intl.     Open Access   (Followers: 1)
Bone Marrow Research     Open Access   (Followers: 2, SJR: 0.531, CiteScore: 1)
Canadian J. of Gastroenterology & Hepatology     Open Access   (Followers: 5, SJR: 0.867, CiteScore: 1)
Canadian J. of Infectious Diseases and Medical Microbiology     Open Access   (Followers: 5, SJR: 0.548, CiteScore: 1)
Canadian Respiratory J.     Open Access   (Followers: 1, SJR: 0.474, CiteScore: 1)
Cardiology Research and Practice     Open Access   (Followers: 8, SJR: 1.237, CiteScore: 4)
Case Reports in Anesthesiology     Open Access   (Followers: 10)
Case Reports in Cardiology     Open Access   (Followers: 3, SJR: 0.219, CiteScore: 0)
Case Reports in Critical Care     Open Access   (Followers: 8)
Case Reports in Dentistry     Open Access   (Followers: 5, SJR: 0.229, CiteScore: 0)
Case Reports in Dermatological Medicine     Open Access   (Followers: 2)
Case Reports in Emergency Medicine     Open Access   (Followers: 14)
Case Reports in Endocrinology     Open Access   (Followers: 1, SJR: 0.209, CiteScore: 1)
Case Reports in Gastrointestinal Medicine     Open Access   (Followers: 2)
Case Reports in Genetics     Open Access   (Followers: 1)
Case Reports in Hematology     Open Access   (Followers: 5)
Case Reports in Hepatology     Open Access   (Followers: 1)
Case Reports in Immunology     Open Access   (Followers: 4)
Case Reports in Infectious Diseases     Open Access   (Followers: 5)
Case Reports in Medicine     Open Access   (Followers: 2)
Case Reports in Nephrology     Open Access   (Followers: 4)
Case Reports in Neurological Medicine     Open Access   (Followers: 1)
Case Reports in Obstetrics and Gynecology     Open Access   (Followers: 10)
Case Reports in Oncological Medicine     Open Access   (Followers: 2, SJR: 0.204, CiteScore: 1)
Case Reports in Ophthalmological Medicine     Open Access   (Followers: 3)
Case Reports in Orthopedics     Open Access   (Followers: 5)
Case Reports in Otolaryngology     Open Access   (Followers: 6)
Case Reports in Pathology     Open Access   (Followers: 5)
Case Reports in Pediatrics     Open Access   (Followers: 6)
Case Reports in Psychiatry     Open Access   (Followers: 12)
Case Reports in Pulmonology     Open Access   (Followers: 3)
Case Reports in Radiology     Open Access   (Followers: 8)
Case Reports in Rheumatology     Open Access   (Followers: 5)
Case Reports in Surgery     Open Access   (Followers: 11)
Case Reports in Transplantation     Open Access  
Case Reports in Urology     Open Access   (Followers: 8)
Case Reports in Vascular Medicine     Open Access  
Case Reports in Veterinary Medicine     Open Access   (Followers: 6)
Child Development Research     Open Access   (Followers: 17, SJR: 0.144, CiteScore: 0)
Chinese J. of Engineering     Open Access   (Followers: 2, SJR: 0.114, CiteScore: 0)
Chinese J. of Mathematics     Open Access  
Cholesterol     Open Access   (Followers: 1, SJR: 0.424, CiteScore: 1)
Chromatography Research Intl.     Open Access   (Followers: 6)
Complexity     Hybrid Journal   (Followers: 6, SJR: 0.531, CiteScore: 2)
Computational and Mathematical Methods in Medicine     Open Access   (Followers: 2, SJR: 0.403, CiteScore: 1)
Computational Intelligence and Neuroscience     Open Access   (Followers: 10, SJR: 0.326, CiteScore: 1)
Contrast Media & Molecular Imaging     Open Access   (Followers: 3, SJR: 0.842, CiteScore: 3)
Critical Care Research and Practice     Open Access   (Followers: 10, SJR: 0.499, CiteScore: 1)
Current Gerontology and Geriatrics Research     Open Access   (Followers: 9, SJR: 0.512, CiteScore: 2)
Depression Research and Treatment     Open Access   (Followers: 13, SJR: 0.816, CiteScore: 2)
Dermatology Research and Practice     Open Access   (Followers: 3, SJR: 0.806, CiteScore: 2)
Diagnostic and Therapeutic Endoscopy     Open Access   (SJR: 0.201, CiteScore: 1)
Discrete Dynamics in Nature and Society     Open Access   (Followers: 5, SJR: 0.279, CiteScore: 1)
Disease Markers     Open Access   (Followers: 1, SJR: 0.9, CiteScore: 2)
Education Research Intl.     Open Access   (Followers: 19)
Emergency Medicine Intl.     Open Access   (Followers: 7, SJR: 0.298, CiteScore: 1)
Enzyme Research     Open Access   (Followers: 3, SJR: 0.653, CiteScore: 3)
Evidence-based Complementary and Alternative Medicine     Open Access   (Followers: 20, SJR: 0.683, CiteScore: 2)
Game Theory     Open Access   (Followers: 1)
Gastroenterology Research and Practice     Open Access   (Followers: 2, SJR: 0.768, CiteScore: 2)
Genetics Research Intl.     Open Access   (Followers: 1, SJR: 0.61, CiteScore: 2)
Geofluids     Open Access   (Followers: 4, SJR: 0.952, CiteScore: 2)
Hepatitis Research and Treatment     Open Access   (Followers: 6, SJR: 0.389, CiteScore: 2)
HPB Surgery     Open Access   (Followers: 5, SJR: 0.824, CiteScore: 2)
Infectious Diseases in Obstetrics and Gynecology     Open Access   (Followers: 5, SJR: 1.27, CiteScore: 2)
Interdisciplinary Perspectives on Infectious Diseases     Open Access   (Followers: 1, SJR: 0.627, CiteScore: 2)
Intl. J. of Aerospace Engineering     Open Access   (Followers: 73, SJR: 0.232, CiteScore: 1)
Intl. J. of Agronomy     Open Access   (Followers: 5, SJR: 0.311, CiteScore: 1)
Intl. J. of Alzheimer's Disease     Open Access   (Followers: 11, SJR: 0.787, CiteScore: 3)
Intl. J. of Analysis     Open Access  
Intl. J. of Analytical Chemistry     Open Access   (Followers: 20, SJR: 0.285, CiteScore: 1)
Intl. J. of Antennas and Propagation     Open Access   (Followers: 11, SJR: 0.233, CiteScore: 1)
Intl. J. of Atmospheric Sciences     Open Access   (Followers: 21)
Intl. J. of Biodiversity     Open Access   (Followers: 4)
Intl. J. of Biomaterials     Open Access   (Followers: 4, SJR: 0.511, CiteScore: 2)
Intl. J. of Biomedical Imaging     Open Access   (Followers: 3, SJR: 0.501, CiteScore: 2)
Intl. J. of Breast Cancer     Open Access   (Followers: 13, SJR: 1.025, CiteScore: 2)
Intl. J. of Cell Biology     Open Access   (Followers: 3, SJR: 1.887, CiteScore: 4)
Intl. J. of Chemical Engineering     Open Access   (Followers: 7, SJR: 0.327, CiteScore: 1)
Intl. J. of Chronic Diseases     Open Access   (Followers: 1)
Intl. J. of Computer Games Technology     Open Access   (Followers: 9, SJR: 0.287, CiteScore: 2)
Intl. J. of Corrosion     Open Access   (Followers: 10, SJR: 0.194, CiteScore: 1)
Intl. J. of Dentistry     Open Access   (Followers: 6, SJR: 0.649, CiteScore: 2)
Intl. J. of Differential Equations     Open Access   (Followers: 7, SJR: 0.191, CiteScore: 0)
Intl. J. of Digital Multimedia Broadcasting     Open Access   (Followers: 5, SJR: 0.296, CiteScore: 2)
Intl. J. of Electrochemistry     Open Access   (Followers: 8)
Intl. J. of Endocrinology     Open Access   (Followers: 4, SJR: 1.012, CiteScore: 3)
Intl. J. of Engineering Mathematics     Open Access   (Followers: 5)
Intl. J. of Food Science     Open Access   (Followers: 3, SJR: 0.44, CiteScore: 2)
Intl. J. of Forestry Research     Open Access   (Followers: 3, SJR: 0.373, CiteScore: 1)
Intl. J. of Genomics     Open Access   (Followers: 2, SJR: 0.868, CiteScore: 3)
Intl. J. of Geophysics     Open Access   (Followers: 4, SJR: 0.182, CiteScore: 1)
Intl. J. of Hepatology     Open Access   (Followers: 4, SJR: 0.874, CiteScore: 2)
Intl. J. of Hypertension     Open Access   (Followers: 6, SJR: 0.578, CiteScore: 1)
Intl. J. of Inflammation     Open Access   (SJR: 1.264, CiteScore: 3)
Intl. J. of Inorganic Chemistry     Open Access   (Followers: 3)
Intl. J. of Manufacturing Engineering     Open Access   (Followers: 2)
Intl. J. of Mathematics and Mathematical Sciences     Open Access   (Followers: 3, SJR: 0.177, CiteScore: 0)
Intl. J. of Medicinal Chemistry     Open Access   (Followers: 6, SJR: 0.31, CiteScore: 1)
Intl. J. of Metals     Open Access   (Followers: 4)
Intl. J. of Microbiology     Open Access   (Followers: 4, SJR: 0.662, CiteScore: 2)
Intl. J. of Microwave Science and Technology     Open Access   (Followers: 3, SJR: 0.136, CiteScore: 1)
Intl. J. of Navigation and Observation     Open Access   (Followers: 20, SJR: 0.267, CiteScore: 2)
Intl. J. of Nephrology     Open Access   (Followers: 1, SJR: 0.697, CiteScore: 1)
Intl. J. of Optics     Open Access   (Followers: 7, SJR: 0.231, CiteScore: 1)
Intl. J. of Otolaryngology     Open Access   (Followers: 3)
Intl. J. of Partial Differential Equations     Open Access   (Followers: 2)
Intl. J. of Pediatrics     Open Access   (Followers: 6)
Intl. J. of Peptides     Open Access   (Followers: 4, SJR: 0.46, CiteScore: 1)
Intl. J. of Photoenergy     Open Access   (Followers: 2, SJR: 0.341, CiteScore: 1)
Intl. J. of Plant Genomics     Open Access   (Followers: 4, SJR: 0.583, CiteScore: 1)
Intl. J. of Polymer Science     Open Access   (Followers: 24, SJR: 0.298, CiteScore: 1)
Intl. J. of Population Research     Open Access   (Followers: 2)
Intl. J. of Reconfigurable Computing     Open Access   (SJR: 0.123, CiteScore: 1)
Intl. J. of Reproductive Medicine     Open Access   (Followers: 4)
Intl. J. of Rheumatology     Open Access   (Followers: 4, SJR: 0.645, CiteScore: 2)
Intl. J. of Rotating Machinery     Open Access   (Followers: 2, SJR: 0.193, CiteScore: 1)
Intl. J. of Spectroscopy     Open Access   (Followers: 6)
Intl. J. of Stochastic Analysis     Open Access   (Followers: 3, SJR: 0.279, CiteScore: 1)
Intl. J. of Surgical Oncology     Open Access   (Followers: 1, SJR: 0.573, CiteScore: 2)
Intl. J. of Telemedicine and Applications     Open Access   (Followers: 4, SJR: 0.403, CiteScore: 2)
Intl. J. of Vascular Medicine     Open Access   (SJR: 0.782, CiteScore: 2)
Intl. J. of Zoology     Open Access   (Followers: 2, SJR: 0.209, CiteScore: 1)
Intl. Scholarly Research Notices     Open Access   (Followers: 196)
ISRN Astronomy and Astrophysics     Open Access   (Followers: 6)
J. of Addiction     Open Access   (Followers: 12)
J. of Advanced Transportation     Hybrid Journal   (Followers: 13, SJR: 0.581, CiteScore: 1)
J. of Aerodynamics     Open Access   (Followers: 5)
J. of Aging Research     Open Access   (Followers: 6, SJR: 0.573, CiteScore: 2)
J. of Amino Acids     Open Access   (Followers: 2, SJR: 0.474, CiteScore: 2)
J. of Analytical Methods in Chemistry     Open Access   (Followers: 1, SJR: 0.323, CiteScore: 1)
J. of Anthropology     Open Access   (Followers: 19)
J. of Applied Chemistry     Open Access   (Followers: 5)

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Journal Cover
International Journal of Genomics
Journal Prestige (SJR): 0.868
Citation Impact (citeScore): 3
Number of Followers: 2  

  This is an Open Access Journal Open Access journal
ISSN (Print) 2314-436X - ISSN (Online) 2314-4378
Published by Hindawi Homepage  [330 journals]
  • Transcriptome and Expression Profiling Analysis of Recalcitrant Tea
           (Camellia sinensis L.) Seeds Sensitive to Dehydration

    • Abstract: The tea plant (Camellia sinensis (L.) O. Kuntze) is an economically important woody perennial nonalcoholic health beverage crop. Tea seeds are categorized as recalcitrant and are sensitive to dehydration treatment. However, the molecular basis of this phenomenon has not been investigated. Thus, we analyzed the genome-wide expression profiles of three dehydration stages using RNA-Seq and digital gene expression (DGE) technologies. We performed de novo assembly and obtained a total of 91,925 nonredundant unigenes, of which 58,472 were extensively annotated. By a hierarchical clustering of differentially expressed genes (DEGs), we found that 8929 DEGs were downregulated and 5875 DEGs were upregulated during dehydration treatment. A series of genes related to ABA biosynthesis and signal transduction, transcription factor, antioxidant enzyme, LEA protein, and proline metabolism that have been reported to function in dehydration process were found to be downregulated. Additionally, the expression profiles of 12 selected genes related to tea seed dehydration treatment were confirmed by qRT-PCR analysis. To our knowledge, this is the first genome-wide study elucidating the possible molecular mechanisms of sensitivity of recalcitrant tea seeds to dehydration. The results obtained in this study contribute to the preservation of tea seeds as genetic resources and can also be used to explore the mechanism of dehydration sensitivity of other recalcitrant seeds.
      PubDate: Tue, 05 Jun 2018 06:21:18 +000
       
  • Nonredundant, Highly Connected MicroRNAs Control Functionality in Breast
           Cancer Networks

    • Abstract: Alterations to transcriptional regulation are an important factor in breast cancer. Noncoding RNA, such as microRNA (miR), have very influential roles in the transcriptional regulation of genes. Transcriptional regulation can be successfully modeled and analyzed using complex network theory. Particularly, interactions between two distinct classes of biological elements, such as miR and genes, can be approached through the bipartite network formalism. Based on bipartite network properties, it is possible to identify highly influential miRs in the network, such as those that have a large number of connections indicating regulation of a large set of genes. Some miRs in a network are nonredundant, which indicates that they are solely responsible of the regulation of a particular set of genes, which in turn may be associated to a particular biological process. We hypothesize that highly influential, nonredundant miRs, which we call Commodore miRs (Cdre-miRs), have an important role on the control of biological functions through transcriptional networks. In this work, we analyze the regulation of gene expression by miRs in healthy and cancerous breast tissue using bipartite miR-gene networks inferred from the Cancer Genome Atlas (TCGA) expression data. We observe differences in the degree, clustering coefficient and redundancy distributions for miRs and genes in the network, indicating differences in the way that these elements interact with each other. Furthermore, we identify a small set of five Cdre-miRs in the breast cancer network: miR-190b, miR-let7i, miR-292-b, miR-511, and miR-141. The neighborhood of genes controlled by each of these miRs is involved in particular biological functions such as dynein structure-associated processes, immune response, angiogenesis, cytokine activity, and cell motility. We propose that these Cdre-miRs are important control elements of biological functions deregulated in breast cancer.
      PubDate: Tue, 29 May 2018 00:00:00 +000
       
  • Overexpression of a New Zinc Finger Protein Transcription Factor OsCTZFP8
           Improves Cold Tolerance in Rice

    • Abstract: Cold stress is one of the most important abiotic stresses in rice. C2H2 zinc finger proteins play important roles in response to abiotic stresses in plants. In the present study, we isolated and functionally characterized a new C2H2 zinc finger protein transcription factor OsCTZFP8 in rice. OsCTZFP8 encodes a C2H2 zinc finger protein, which contains a typical zinc finger motif, as well as a potential nuclear localization signal (NLS) and a leucine-rich region (L-box). Expression of OsCTZFP8 was differentially induced by several abiotic stresses and was strongly induced by cold stress. Subcellular localization assay and yeast one-hybrid analysis revealed that OsCTZFP8 was a nuclear protein and has transactivation activity. To characterize the function of OsCTZFP8 in rice, the full-length cDNA of OsCTZFP8 was isolated and transgenic rice with overexpression of OsCTZFP8 driven by the maize ubiquitin promoter was generated using Agrobacterium-mediated transformation. Among 46 independent transgenic lines, 6 single-copy homozygous overexpressing lines were selected by Southern blot analysis and Basta resistance segregation assay in both T1 and T2 generations. Transgenic rice overexpressing OsCTZFP8 exhibited cold tolerant phenotypes with significantly higher pollen fertilities and seed setting rates than nontransgenic control plants. In addition, yield per plant of OsCTZFP8-expressing lines was significantly () higher than that of nontransgenic control plants under cold treatments. These results demonstrate that OsCTZFP8 was a C2H2 zinc finger transcription factor that plays an important role in cold tolerance in rice.
      PubDate: Wed, 23 May 2018 06:02:35 +000
       
  • Advancing Genomics for Drug Development and Safety Evaluation

    • PubDate: Wed, 23 May 2018 00:00:00 +000
       
  • Insights into the Genome Sequence of Chromobacterium amazonense Isolated
           from a Tropical Freshwater Lake

    • Abstract: Members of the genus Chromobacterium have been isolated from geographically diverse ecosystems and exhibit considerable metabolic flexibility, as well as biotechnological and pathogenic properties in some species. This study reports the draft assembly and detailed sequence analysis of Chromobacterium amazonense strain 56AF. The de novo-assembled genome is 4,556,707 bp in size and contains 4294 protein-coding and 95 RNA genes, including 88 tRNA, six rRNA, and one tmRNA operon. A repertoire of genes implicated in virulence, for example, hemolysin, hemolytic enterotoxins, colicin V, lytic proteins, and Nudix hydrolases, is present. The genome also contains a collection of genes of biotechnological interest, including esterases, lipase, auxins, chitinases, phytoene synthase and phytoene desaturase, polyhydroxyalkanoates, violacein, plastocyanin/azurin, and detoxifying compounds. Importantly, unlike other Chromobacterium species, the 56AF genome contains genes for pore-forming toxin alpha-hemolysin, a type IV secretion system, among others. The analysis of the C. amazonense strain 56AF genome reveals the versatility, adaptability, and biotechnological potential of this bacterium. This study provides molecular information that may pave the way for further comparative genomics and functional studies involving Chromobacterium-related isolates and improves our understanding of the global genomic diversity of Chromobacterium species.
      PubDate: Sun, 20 May 2018 06:25:59 +000
       
  • Whole-Exome Sequencing Identifies One De Novo Variant in the FGD6 Gene in
           a Thai Family with Autism Spectrum Disorder

    • Abstract: Autism spectrum disorder (ASD) has a strong genetic basis, although the genetics of autism is complex and it is unclear. Genetic testing such as microarray or sequencing was widely used to identify autism markers, but they are unsuccessful in several cases. The objective of this study is to identify causative variants of autism in two Thai families by using whole-exome sequencing technique. Whole-exome sequencing was performed with autism-affected children from two unrelated families. Each sample was sequenced on SOLiD 5500xl Genetic Analyzer system followed by combined bioinformatics pipeline including annotation and filtering process to identify candidate variants. Candidate variants were validated, and the segregation study with other family members was performed using Sanger sequencing. This study identified a possible causative variant for ASD, c.2951G>A, in the FGD6 gene. We demonstrated the potential for ASD genetic variants associated with ASD using whole-exome sequencing and a bioinformatics filtering procedure. These techniques could be useful in identifying possible causative ASD variants, especially in cases in which variants cannot be identified by other techniques.
      PubDate: Thu, 17 May 2018 00:00:00 +000
       
  • Genome-Wide Expression Profiles of Hemp (Cannabis sativa L.) in Response
           to Drought Stress

    • Abstract: Drought is the main environmental factor impairing hemp growth and yield. In order to decipher the molecular responses of hemp to drought stress, transcriptome changes of drought-stressed hemp (DS1 and DS2), compared to well-watered control hemp (CK1 and CK2), were studied with RNA-Seq technology. RNA-Seq generated 9.83, 11.30, 11.66, and 11.31 M clean reads in the CK1, CK2, DS1, and DS2 libraries, respectively. A total of 1292 differentially expressed genes (DEGs), including 409 (31.66%) upregulated and 883 (68.34%) downregulated genes, were identified. The expression patterns of 12 selected genes were validated by qRT-PCR, and the results were accordant with Illumina analysis. Gene Ontology (GO) and KEGG analysis illuminated particular important biological processes and pathways, which enriched many candidate genes such as NAC, B3, peroxidase, expansin, and inositol oxygenase that may play important roles in hemp tolerance to drought. Eleven KEGG pathways were significantly influenced, the most influenced being the plant hormone signal transduction pathway with 15 differentially expressed genes. A similar expression pattern of genes involved in the abscisic acid (ABA) pathway under drought, and ABA induction, suggested that ABA is important in the drought stress response of hemp. These findings provide useful insights into the drought stress regulatory mechanism in hemp.
      PubDate: Tue, 15 May 2018 00:00:00 +000
       
  • Comparative Genomics Analysis of Plasmid pPV989-94 from a Clinical Isolate
           of Pantoea vagans PV989

    • Abstract: Pantoea vagans, a gram-negative bacterium from the genus Pantoea and family Enterobacteriaceae, is present in various natural environments and considered to be plant endophytes. We isolated the Pantoea vagans PV989 strain from the clinic and sequenced its whole genome. Besides a chromosome DNA molecule, it also harboured three large plasmids. A comparative genomics analysis was performed for the smallest plasmid, pPV989-94. It can be divided into four regions, including three conservative regions related to replication (R1), transfer conjugation (R2), and transfer leading (R3), and one variable region (R4). Further analysis showed that pPV989-94 is most similar to plasmids LA637P2 and pEA68 of Erwinia amylovora strains isolated from fruit trees. These three plasmids share three conservative regions (R1, R2, and R3). Interestingly, a fragment (R4) in R4, mediated by phage integrase and phage integrase family site-specific recombinase and encoding 9 genes related to glycometabolism, resistance, and DNA repair, was unique in pPV989-94. Homologues of R4 were found in other plasmids or chromosomes, suggesting that horizontal gene transfer (HGT) occurred among different bacteria of various species or genera. The acquired functional genes may play important roles in the adaptation of bacteria to different hosts or environmental conditions.
      PubDate: Thu, 10 May 2018 07:11:58 +000
       
  • The Challenges and Opportunities in the Clinical Application of Noncoding
           RNAs: The Road Map for miRNAs and piRNAs in Cancer Diagnostics and
           Prognostics

    • Abstract: Discoveries on nonprotein-coding RNAs have induced a paradigm shift in our overall understanding of gene expression and regulation. We now understand that coding and noncoding RNA machinery work in concert to maintain overall homeostasis. Based on their length, noncoding RNAs are broadly classified into two groups—long (>200 nt) and small noncoding RNAs (
      PubDate: Mon, 30 Apr 2018 00:00:00 +000
       
  • Genome-Wide Identification, Phylogeny, and Expression Analysis of ARF
           Genes Involved in Vegetative Organs Development in Switchgrass

    • Abstract: Auxin response factors (ARFs) have been reported to play vital roles during plant growth and development. In order to reveal specific functions related to vegetative organs in grasses, an in-depth study of the ARF gene family was carried out in switchgrass (Panicum virgatum L.), a warm-season C4 perennial grass that is mostly used as bioenergy and animal feedstock. A total of 47 putative ARF genes (PvARFs) were identified in the switchgrass genome (2n = 4x = 36), 42 of which were anchored to the seven pairs of chromosomes and found to be unevenly distributed. Sixteen PvARFs were predicted to be potential targets of small RNAs (microRNA160 and 167). Phylogenetically speaking, PvARFs were divided into seven distinct subgroups based on the phylogeny, exon/intron arrangement, and conserved motif distribution. Moreover, 15 pairs of PvARFs have different temporal-spatial expression profiles in vegetative organs (2nd, 3rd, and 4th internode and leaves), which implies that different PvARFs have specific functions in switchgrass growth and development. In addition, at least 14 pairs of PvARFs respond to naphthylacetic acid (NAA) treatment, which might be helpful for us to study on auxin response in switchgrass. The comprehensive analysis, described here, will facilitate the future functional analysis of ARF genes in grasses.
      PubDate: Sun, 29 Apr 2018 00:00:00 +000
       
  • Characterization of Transcription Termination-Associated RNAs: New
           

    • Abstract: Next-generation sequencing has uncovered novel classes of small RNAs (sRNAs) in eukaryotes, in addition to the well-known miRNAs, siRNAs, and piRNAs. In particular, sRNA species arise from transcription start sites (TSSs) and the transcription termination sites (TTSs) of genes. However, a detailed characterization of these new classes of sRNAs is still lacking. Here, we present a comprehensive study of sRNAs derived from TTSs of expressed genes (TTSa-RNAs) in human cell lines and primary tissues. Taking advantage of sRNA-sequencing, we show that TTSa-RNAs are present in the nuclei of human cells, are loaded onto both AGO1 and AGO2, and their biogenesis does not require DICER and AGO2 endonucleolytic activity. TTSa-RNAs display a strong bias against a G residue in the first position at 5 end, a known feature of AGO-bound sRNAs, and a peculiar oligoA tail at 3 end. AGO-bound TTSa-RNAs derive from genes involved in cell cycle progression regulation and DNA integrity checkpoints. Finally, we provide evidence that TTSa-RNAs can be detected by sRNA-Seq in primary human tissue, and their expression increases in tumor samples as compared to nontumor tissues, suggesting that in the future, TTSa-RNAs might be explored as biomarker for diagnosis or prognosis of human malignancies.
      PubDate: Thu, 26 Apr 2018 00:00:00 +000
       
  • The YABBY Genes of Leaf and Leaf-Like Organ Polarity in Leafless Plant
           Monotropa hypopitys

    • Abstract: Monotropa hypopitys is a mycoheterotrophic, nonphotosynthetic plant acquiring nutrients from the roots of autotrophic trees through mycorrhizal symbiosis, and, similar to other extant plants, forming asymmetrical lateral organs during development. The members of the YABBY family of transcription factors are important players in the establishment of leaf and leaf-like organ polarity in plants. This is the first report on the identification of YABBY genes in a mycoheterotrophic plant devoid of aboveground vegetative organs. Seven M. hypopitys YABBY members were identified and classified into four clades. By structural analysis of putative encoded proteins, we confirmed the presence of YABBY-defining conserved domains and identified novel clade-specific motifs. Transcriptomic and qRT-PCR analyses of different tissues revealed MhyYABBY transcriptional patterns, which were similar to those of orthologous YABBY genes from other angiosperms. These data should contribute to the understanding of the role of the YABBY genes in the regulation of developmental and physiological processes in achlorophyllous leafless plants.
      PubDate: Tue, 24 Apr 2018 00:00:00 +000
       
  • Gene Variation of Endoplasmic Reticulum Aminopeptidases 1 and 2, and Risk
           of Blood Pressure Progression and Incident Hypertension among 17,255
           Initially Healthy Women

    • Abstract: Recent studies have demonstrated the importance of endoplasmic reticulum aminopeptidase (ERAP) in blood pressure (BP) homeostasis. To date, no large prospective, genetic–epidemiological data are available on genetic variation within ERAP and hypertension risk. The association of 45 genetic variants of ERAP1 and ERAP2 was investigated in 17,255 Caucasian female participants from the Women’s Genome Health Study. All subjects were free of hypertension at baseline. During an 18-year follow-up period, 10,216 incident hypertensive cases were identified. Multivariable linear, logistic, and Cox regression analyses were performed to assess the relationship of genotypes with baseline BP levels, BP progression at 48 months, and incident hypertension assuming an additive genetic model. Linear regression analyses showed associations of four tSNPs (ERAP1: rs27524; ERAP2: rs3733904, rs4869315, and rs2549782; all ) with baseline systolic BP levels. Three tSNPs (ERAP1: rs27851, rs27429, and rs34736, all ) were associated with baseline diastolic BP levels. Multivariable logistic regression analysis showed that ERAP1 rs27772 was associated with BP progression at 48 months (). Multivariable Cox regression analysis showed an association of three tSNPs (ERAP1: rs469783 and rs10050860; ERAP2: rs2927615; all ) with risk of incident hypertension. Analyses of dbGaP for genotype–phenotype association and GTEx Portal for gene expression quantitative trait loci revealed five tSNPs with differential association of BP and nine tSNPs with lower ERAP1 and ERAP2 mRNA expression levels, respectively. The present study suggests that ERAP1 and ERAP2 gene variation may be useful for risk assessment of BP progression and the development of hypertension.
      PubDate: Thu, 19 Apr 2018 05:27:16 +000
       
  • Identification of Novel Causal FBN1 Mutations in Pedigrees of Marfan
           Syndrome

    • Abstract: Marfan syndrome (MFS) is an autosomal dominant genetic disorder of the connective tissue, typically characteristic of cardiovascular manifestations, valve prolapse, left ventricle enlargement, and cardiac failure. Fibrillin-1 (FBN1) is the causative gene in the pathogenesis of MFS. Patients with different FBN1 mutations often present more considerable phenotypic variation. In the present study, three affected MFS pedigrees were collected for genetic analysis. Using next-generation sequencing (NGS) technologies, 3 novel frameshift pathogenic mutations which are cosegregated with affected subjects in 3 pedigrees were identified. These novel mutations provide important diagnostic and therapeutic insights for precision medicine in MFS, especially regarding the lethal cardiovascular events.
      PubDate: Tue, 17 Apr 2018 00:00:00 +000
       
  • The Progress of Methylation Regulation in Gene Expression of Cervical
           Cancer

    • Abstract: Cervical cancer is one of the most common gynecological tumors in females, which is closely related to high-rate HPV infection. Methylation alteration is a type of epigenetic decoration that regulates the expression of genes without changing the DNA sequence, and it is essential for the progression of cervical cancer in pathogenesis while reflecting the prognosis and therapeutic sensitivity in clinical practice. Hydroxymethylation has been discovered in recent years, thus making 5-hmC, the more stable marker, attract more attention in the field of methylation research. As markers of methylation, 5-hmC and 5-mC together with 5-foC and 5-caC draw the outline of the reversible cycle, and 6-mA takes part in the methylation of RNA, especially mRNA. Furthermore, methylation modification participates in ncRNA regulation and histone decoration. In this review, we focus on recent advances in the understanding of methylation regulation in the process of cervical cancer, as well as HPV and CIN, to identify the significant impact on the prospect of overcoming cervical cancer.
      PubDate: Mon, 16 Apr 2018 09:14:06 +000
       
  • Genome-Wide Identification and Characterization of Fox Genes in the
           Honeybee, Apis cerana, and Comparative Analysis with Other Bee Fox Genes

    • Abstract: The forkhead box (Fox) gene family, one of the most important families of transcription factors, participates in various biological processes. However, Fox genes in Hymenoptera are still poorly known. In this study, 14 Fox genes were identified in the genome of Apis cerana. In addition, 16 (Apis mellifera), 13 (Apis dorsata), 16 (Apis florea), 17 (Bombus terrestris), 16 (Bombus impatiens), and 18 (Megachile rotundata) Fox genes were identified in their genomes, respectively. Phylogenetic analyses suggest that FoxA is absent in the genome of A. dorsata genome. Similarly, FoxG is missing in the genomes A. cerana and A. dorsata. Temporal expression profiles obtained by quantitative real-time PCR revealed that Fox genes have distinct expression patterns in A. cerana, especially for three genes ACSNU03719T0 (AcFoxN4), ACSNU05765T0 (AcFoxB), and ACSNU07465T0 (AcFoxL2), which displayed high expression at the egg stage. Tissue expression patterns showed that FoxJ1 is significantly higher in the antennae of A. cerana and A. mellifera compared to other tissues. These results may facilitate a better understanding of the potential physiological functions of the Fox gene family in A. cerana and provide valuable information for a comprehensive functional analysis of the Fox gene family in Hymenopterans.
      PubDate: Mon, 16 Apr 2018 00:00:00 +000
       
  • Whole-Genome Sequencing and Comparative Genome Analysis Provided Insight
           into the Predatory Features and Genetic Diversity of Two Bdellovibrio
           Species Isolated from Soil

    • Abstract: Bdellovibrio spp. are predatory bacteria with great potential as antimicrobial agents. Studies have shown that members of the genus Bdellovibrio exhibit peculiar characteristics that influence their ecological adaptations. In this study, whole genomes of two different Bdellovibrio spp. designated SKB1291214 and SSB218315 isolated from soil were sequenced. The core genes shared by all the Bdellovibrio spp. considered for the pangenome analysis including the epibiotic B. exovorus were 795. The number of unique genes identified in Bdellovibrio spp. SKB1291214, SSB218315, W, and B. exovorus JJS was 1343, 113, 857, and 1572, respectively. These unique genes encode hydrolytic, chemotaxis, and transporter proteins which might be useful for predation in the Bdellovibrio strains. Furthermore, the two Bdellovibrio strains exhibited differences based on the % GC content, amino acid identity, and 16S rRNA gene sequence. The 16S rRNA gene sequence of Bdellovibrio sp. SKB1291214 shared 99% identity with that of an uncultured Bdellovibrio sp. clone 12L 106 (a pairwise distance of 0.008) and 95–97% identity (a pairwise distance of 0.043) with that of other culturable terrestrial Bdellovibrio spp., including strain SSB218315. In Bdellovibrio sp. SKB1291214, 174 bp sequence was inserted at the host interaction (hit) locus region usually attributed to prey attachment, invasion, and development of host independent Bdellovibrio phenotypes. Also, a gene equivalent to Bd0108 in B. bacteriovorus HD100 was not conserved in Bdellovibrio sp. SKB1291214. The results of this study provided information on the genetic characteristics and diversity of the genus Bdellovibrio that can contribute to their successful applications as a biocontrol agent.
      PubDate: Tue, 10 Apr 2018 07:01:38 +000
       
  • Genomics Approach of the Natural Product Pharmacology for High Impact
           Diseases

    • PubDate: Sun, 08 Apr 2018 00:00:00 +000
       
  • The Influence of Metabolic Syndrome and Sex on the DNA Methylome in
           Schizophrenia

    • Abstract: Introduction. The mechanism by which metabolic syndrome occurs in schizophrenia is not completely known; however, previous work suggests that changes in DNA methylation may be involved which is further influenced by sex. Within this study, the DNA methylome was profiled to identify altered methylation associated with metabolic syndrome in a schizophrenia population on atypical antipsychotics. Methods. Peripheral blood from schizophrenia subjects was utilized for DNA methylation analyses. Discovery analyses () were performed using an epigenome-wide analysis on the Illumina HumanMethylation450K BeadChip based on metabolic syndrome diagnosis. A secondary discovery analysis was conducted based on sex. The top hits from the discovery analyses were assessed in an additional validation set () using site-specific methylation pyrosequencing. Results. A significant increase in CDH22 gene methylation in subjects with metabolic syndrome was identified in the overall sample. Additionally, differential methylation was found within the MAP3K13 gene in females and the CCDC8 gene within males. Significant differences in methylation were again observed for the CDH22 and MAP3K13 genes, but not CCDC8, in the validation sample set. Conclusions. This study provides preliminary evidence that DNA methylation may be associated with metabolic syndrome and sex in schizophrenia.
      PubDate: Tue, 03 Apr 2018 00:00:00 +000
       
  • Transcriptomic Profiling of Fruit Development in Black Raspberry Rubus
           coreanus

    • Abstract: The wild Rubus species R. coreanus, which is widely distributed in southwest China, shows great promise as a genetic resource for breeding. One of its outstanding properties is adaptation to high temperature and humidity. To facilitate its use in selection and breeding programs, we assembled de novo 179,738,287 R. coreanus reads (125 bp in length) generated by RNA sequencing from fruits at three representative developmental stages. We also used the recently released draft genome of R. occidentalis to perform reference-guided assembly. We inferred a final 95,845-transcript reference for R. coreanus. Of these genetic resources, 66,597 (69.5%) were annotated. Based on these results, we carried out a comprehensive analysis of differentially expressed genes. Flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, and cutin, suberin, and wax biosynthesis pathways were significantly enriched throughout the ripening process. We identified 23 transcripts involved in the flavonoid biosynthesis pathway whose expression perfectly paralleled changes in the metabolites. Additionally, we identified 119 nucleotide-binding site leucine-rich repeat (NBS-LRR) protein-coding genes, involved in pathogen resistance, of which 74 were in the completely conserved domain. These results provide, for the first time, genome-wide genetic information for understanding developmental regulation of R. coreanus fruits. They have the potential for use in breeding through functional genetic approaches in the near future.
      PubDate: Sun, 01 Apr 2018 00:00:00 +000
       
  • Expression Characterization of Six Genes Possibly Involved in Gonad
           Development for Stellate Sturgeon Individuals (Acipenser stellatus, Pallas
           1771)

    • Abstract: Nowadays, in sturgeon’s aquaculture, there is a necessity for sex identification at early stages in order to increase the efficiency of this commercial activity. The basis for a correct identification is studying the different factors that influence the gonad development. The research has been directed towards molecular methods that have been employed with various degrees of success in identifying genes with different expression patterns between male and female sturgeons during their development stages. For the purpose of understanding the sexual development of 4-year-old stellate sturgeon (Acipenser stellatus) individuals, we have selected six genes (foxl2, cyp17a1, ar, dmrt1, sox9, and star). We analysed the gene expression of the selected genes for gonads, anal fin, liver, body kidney, and white muscle. The cyp17a1, ar, dmrt1, and sox9 genes have a significant higher expression in male gonads than in female gonads, while the data shows no significant differences in the expression of the investigated genes in the other organs. We investigate these genes to shed light on aquaculture sturgeon sexual development.
      PubDate: Thu, 29 Mar 2018 00:00:00 +000
       
  • Whole Genome Sequencing of Greater Amberjack (Seriola dumerili) for SNP
           Identification on Aligned Scaffolds and Genome Structural Variation
           Analysis Using Parallel Resequencing

    • Abstract: Greater amberjack (Seriola dumerili) is distributed in tropical and temperate waters worldwide and is an important aquaculture fish. We carried out de novo sequencing of the greater amberjack genome to construct a reference genome sequence to identify single nucleotide polymorphisms (SNPs) for breeding amberjack by marker-assisted or gene-assisted selection as well as to identify functional genes for biological traits. We obtained 200 times coverage and constructed a high-quality genome assembly using next generation sequencing technology. The assembled sequences were aligned onto a yellowtail (Seriola quinqueradiata) radiation hybrid (RH) physical map by sequence homology. A total of 215 of the longest amberjack sequences, with a total length of 622.8 Mbp (92% of the total length of the genome scaffolds), were lined up on the yellowtail RH map. We resequenced the whole genomes of 20 greater amberjacks and mapped the resulting sequences onto the reference genome sequence. About 186,000 nonredundant SNPs were successfully ordered on the reference genome. Further, we found differences in the genome structural variations between two greater amberjack populations using BreakDancer. We also analyzed the greater amberjack transcriptome and mapped the annotated sequences onto the reference genome sequence.
      PubDate: Wed, 28 Mar 2018 00:00:00 +000
       
  • Endometriosis Malignant Transformation: Epigenetics as a Probable
           Mechanism in Ovarian Tumorigenesis

    • Abstract: Endometriosis, defined as the presence of ectopic endometrial glands and stroma outside the uterine cavity, is a chronic, hormone-dependent gynecologic disease affecting millions of women across the world, with symptoms including chronic pelvic pain, dysmenorrhea, dyspareunia, dysuria, and subfertility. In addition, there is well-established evidence that, although endometriosis is considered benign, it is associated with an increased risk of malignant transformation, with the involvement of various mechanisms of development. More and more evidence reveals an important contribution of epigenetic modification not only in endometriosis but also in mechanisms of endometriosis malignant transformation, including DNA methylation and demethylation, histone modifications, and miRNA aberrant expressions. In this present review, we mainly summarize the research progress about the current knowledge regarding the epigenetic modifications of the relations between endometriosis malignant transformation and ovarian cancer in an effort to identify some risk factors probably associated with ectopic endometrium transformation.
      PubDate: Tue, 27 Mar 2018 00:00:00 +000
       
  • Differential Expression Profiling of Long Noncoding RNA and mRNA during
           Osteoblast Differentiation in Mouse

    • Abstract: Long noncoding RNAs (lncRNAs) are emerging as an important controller affecting metabolic tissue development, signaling, and function. However, little is known about the function and profile of lncRNAs in osteoblastic differentiation in mice. Here, we analyzed the RNA-sequencing (RNA-Seq) datasets obtained for 18 days in two-day intervals from neonatal mouse calvarial pre-osteoblast-like cells. Over the course of osteoblast differentiation, 4058 mRNAs and 3948 lncRNAs were differentially expressed, and they were grouped into 12 clusters according to the expression pattern by fuzzy c-means clustering. Using weighted gene coexpression network analysis, we identified 9 modules related to the early differentiation stage (days 2–8) and 7 modules related to the late differentiation stage (days 10–18). Gene ontology and KEGG pathway enrichment analysis revealed that the mRNA and lncRNA upregulated in the late differentiation stage are highly associated with osteogenesis. We also identified 72 mRNA and 89 lncRNAs as potential markers including several novel markers for osteoblast differentiation and activation. Our findings provide a valuable resource for mouse lncRNA study and improves our understanding of the biology of osteoblastic differentiation in mice.
      PubDate: Thu, 22 Mar 2018 08:02:44 +000
       
  • Systems Pharmacology-Based Approach of Connecting Disease Genes in
           Genome-Wide Association Studies with Traditional Chinese Medicine

    • Abstract: Traditional Chinese medicine (TCM) originated in ancient China has been practiced over thousands of years for treating various symptoms and diseases. However, the molecular mechanisms of TCM in treating these diseases remain unknown. In this study, we employ a systems pharmacology-based approach for connecting GWAS diseases with TCM for potential drug repurposing and repositioning. We studied 102 TCM components and their target genes by analyzing microarray gene expression experiments. We constructed disease-gene networks from 2558 GWAS studies. We applied a systems pharmacology approach to prioritize disease-target genes. Using this bioinformatics approach, we analyzed 14,713 GWAS disease-TCM-target gene pairs and identified 115 disease-gene pairs with value 
      PubDate: Thu, 22 Mar 2018 00:00:00 +000
       
  • Relationship of SNP rs2645429 in Farnesyl-Diphosphate Farnesyltransferase
           1 Gene Promoter with Susceptibility to Lung Cancer

    • Abstract: Background and Purpose. The mevalonate pathway is one of the major metabolic pathways that use acetyl-CoA to produce sterols and isoprenoids. These compounds can be effective in the growth and development of tumors. One of the enzymes involved in the mevalonate pathway is FDFT1. Different variants of this gene are involved in the risk of suffering various diseases. The present study examined the relationship between FDFT1 rs2645429 polymorphism and the risk of nonsmall cell lung cancer (NSCLC) in a population from southern Iran. Method. The genotypes of rs2645429 polymorphism of FDFT1 gene were examined in 95 samples: 34 patients with NSCLC and 61 healthy individuals by RFLP method. Results. The results of this study indicated that C allele of this polymorphism was effectively associated with the risk of NSCLC in the Iranian population ( value = 0.023; OR = 2.71; 95% CI = 1.12–6.59) and CC genotype has significant relation with susceptibility to NSCLC ( value = 0.029; OR = 3.02; 95% CI = 1.09–8.39). This polymorphism is located in the promoter region FDFT1 gene, and CC genotype may increase the activity of this promoter. This study also found a significant relationship between C allele and metastatic status. C allele was more common in NSCLC patients. (). Conclusion. C allele of FDFT1 rs2645429 polymorphism gene can be a risk factor for NSCLC, whereas T allele probably has a low protective role.
      PubDate: Thu, 22 Mar 2018 00:00:00 +000
       
  • Calibrating Transcriptional Activity Using Constitutive Synthetic
           Promoters in Mutants for Global Regulators in Escherichia coli

    • Abstract: The engineering of synthetic circuits in cells relies on the use of well-characterized biological parts that would perform predicted functions under the situation considered, and many efforts have been taken to set biological standards that could define the basic features of these parts. However, since most synthetic biology projects usually require a particular cellular chassis and set of growth conditions, defining standards in the field is not a simple task as gene expression measurements could be affected severely by genetic background and culture conditions. In this study, we addressed promoter parameterization in bacteria in different genetic backgrounds and growth conditions. We found that a small set of constitutive promoters of different strengths controlling a short-lived GFP reporter placed in a low-copy number plasmid produces remarkably reproducible results that allow for the calibration of promoter activity over different genetic backgrounds and physiological conditions, thus providing a simple way to set standards of promoter activity in bacteria. Based on these results, we proposed the utilization of synthetic constitutive promoters as tools for calibration for the standardization of biological parts, in a way similar to the use of DNA and protein ladders in molecular biology as references for comparison with samples of interest.
      PubDate: Wed, 21 Mar 2018 00:00:00 +000
       
  • Data Mining Mycobacterium tuberculosis Pathogenic Gene Transcription
           Factors and Their Regulatory Network Nodes

    • Abstract: Tuberculosis (TB) is one of the deadliest infectious diseases worldwide. In Mycobacterium tuberculosis, changes in gene expression are highly variable and involve many genes, so traditional single-gene screening of M. tuberculosis targets has been unable to meet the needs of clinical diagnosis. In this study, using the National Center for Biotechnology Information (NCBI) GEO Datasets, whole blood gene expression profile data were obtained in patients with active pulmonary tuberculosis. Linear model-experience Bayesian statistics using the Limma package in R combined with t-tests were applied for nonspecific filtration of the expression profile data, and the differentially expressed human genes were determined. Using DAVID and KEGG, the functional analysis of differentially expressed genes (GO analysis) and the analysis of signaling pathways were performed. Based on the differentially expressed gene, the transcriptional regulatory element databases (TRED) were integrated to construct the M. tuberculosis pathogenic gene regulatory network, and the correlation of the network genes with disease was analyzed with the DAVID online annotation tool. It was predicted that IL-6, JUN, and TP53, along with transcription factors SRC, TNF, and MAPK14, could regulate the immune response, with their function being extracellular region activity and protein binding during infection with M. tuberculosis.
      PubDate: Wed, 14 Mar 2018 00:00:00 +000
       
  • Clustering Pattern and Functional Effect of SNPs in Human miRNA Seed
           Regions

    • Abstract: miRNAs are a class of noncoding RNAs important in posttranscriptional repressors and involved in the regulation of almost every biological process by base paring with target genes through sequence in their seed regions. Genetic variations in the seed regions have vital effects on gene expression, phenotypic variation, and disease susceptibility in humans. The distribution pattern of genetic variation in miRNA seed regions might be related to miRNA function and is worth paying more attention to. We here employed computational analyses to explore the clustering pattern and functional effect of SNPs in human miRNA seed regions. A total of 1879 SNPs were mapped to 1226 human miRNA seed regions. We found that miRNAs with SNPs in their seed region are significantly enriched in miRNA clusters. We also found that SNPs in clustered miRNA seed regions have a lower functional effect than have SNPs in nonclustered miRNA seed regions. Additionally, we found that clustered miRNAs with SNPs in seed regions are involved in more pathways. Overall, our results demonstrate that SNPs in clustered miRNA seed regions can take part in more intricate and complex gene-regulating networks with lower functional cost by functional complementarity. Moreover, our results also broaden current knowledge on the genetic variation in human miRNA seed regions.
      PubDate: Tue, 06 Mar 2018 08:56:51 +000
       
  • Classification of Complete Proteomes of Different Organisms and Protein
           Sets Based on Their Protein Distributions in Terms of Some Key Attributes
           of Proteins

    • Abstract: The existence of complete genome sequences makes it important to develop different approaches for classification of large-scale data sets and to make extraction of biological insights easier. Here, we propose an approach for classification of complete proteomes/protein sets based on protein distributions on some basic attributes. We demonstrate the usefulness of this approach by determining protein distributions in terms of two attributes: protein lengths and protein intrinsic disorder contents (ID). The protein distributions based on L and ID are surveyed for representative proteome organisms and protein sets from the three domains of life. The two-dimensional maps (designated as fingerprints here) from the protein distribution densities in the LD space defined by ln(L) and ID are then constructed. The fingerprints for different organisms and protein sets are found to be distinct with each other, and they can therefore be used for comparative studies. As a test case, phylogenetic trees have been constructed based on the protein distribution densities in the fingerprints of proteomes of organisms without performing any protein sequence comparison and alignments. The phylogenetic trees generated are biologically meaningful, demonstrating that the protein distributions in the LD space may serve as unique phylogenetic signals of the organisms at the proteome level.
      PubDate: Sun, 04 Mar 2018 00:00:00 +000
       
 
 
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