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Publisher: Hindawi   (Total: 281 journals)

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Showing 1 - 200 of 281 Journals sorted alphabetically
Abstract and Applied Analysis     Open Access   (Followers: 3, SJR: 0.512, h-index: 32)
Active and Passive Electronic Components     Open Access   (Followers: 7, SJR: 0.157, h-index: 15)
Advances in Acoustics and Vibration     Open Access   (Followers: 33, SJR: 0.259, h-index: 6)
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: 35, SJR: 0.351, h-index: 17)
Advances in Bioinformatics     Open Access   (Followers: 17, SJR: 0.421, h-index: 8)
Advances in Chemistry     Open Access   (Followers: 20)
Advances in Civil Engineering     Open Access   (Followers: 37, SJR: 0.338, h-index: 8)
Advances in Condensed Matter Physics     Open Access   (Followers: 10, SJR: 0.248, h-index: 10)
Advances in Decision Sciences     Open Access   (Followers: 3, SJR: 0.231, h-index: 6)
Advances in Electronics     Open Access   (Followers: 63)
Advances in Fuzzy Systems     Open Access   (Followers: 5, SJR: 0.258, h-index: 7)
Advances in Hematology     Open Access   (Followers: 10, SJR: 0.892, h-index: 18)
Advances in High Energy Physics     Open Access   (Followers: 18, SJR: 0.892, h-index: 19)
Advances in Human-Computer Interaction     Open Access   (Followers: 19, SJR: 0.439, h-index: 9)
Advances in Materials Science and Engineering     Open Access   (Followers: 30, SJR: 0.263, h-index: 11)
Advances in Mathematical Physics     Open Access   (Followers: 3, SJR: 0.332, h-index: 10)
Advances in Medicine     Open Access   (Followers: 2)
Advances in Meteorology     Open Access   (Followers: 19, SJR: 0.498, h-index: 10)
Advances in Multimedia     Open Access   (Followers: 1, SJR: 0.191, h-index: 10)
Advances in Nonlinear Optics     Open Access   (Followers: 6)
Advances in Numerical Analysis     Open Access   (Followers: 4)
Advances in Nursing     Open Access   (Followers: 27)
Advances in Operations Research     Open Access   (Followers: 12, SJR: 0.343, h-index: 7)
Advances in Optical Technologies     Open Access   (Followers: 3, SJR: 0.283, h-index: 16)
Advances in OptoElectronics     Open Access   (Followers: 5, SJR: 0.973, h-index: 16)
Advances in Orthopedics     Open Access   (Followers: 8)
Advances in Pharmacological Sciences     Open Access   (Followers: 7, SJR: 0.695, h-index: 13)
Advances in Physical Chemistry     Open Access   (Followers: 9, SJR: 0.297, h-index: 7)
Advances in Power Electronics     Open Access   (Followers: 29, SJR: 0.26, h-index: 6)
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 Tribology     Open Access   (Followers: 12, SJR: 0.267, h-index: 6)
Advances in Urology     Open Access   (Followers: 9, SJR: 0.629, h-index: 16)
Advances in Virology     Open Access   (Followers: 7, SJR: 1.04, h-index: 12)
AIDS Research and Treatment     Open Access   (Followers: 3, SJR: 1.125, h-index: 14)
Analytical Cellular Pathology     Open Access   (Followers: 2, SJR: 0.334, h-index: 12)
Anatomy Research Intl.     Open Access   (Followers: 2)
Anemia     Open Access   (Followers: 5, SJR: 0.991, h-index: 11)
Anesthesiology Research and Practice     Open Access   (Followers: 13, SJR: 0.513, h-index: 12)
Applied and Environmental Soil Science     Open Access   (Followers: 16, SJR: 0.53, h-index: 9)
Applied Bionics and Biomechanics     Open Access   (Followers: 8, SJR: 0.23, h-index: 13)
Applied Computational Intelligence and Soft Computing     Open Access   (Followers: 11)
Archaea     Open Access   (Followers: 3, SJR: 1.248, h-index: 27)
Arthritis     Open Access   (Followers: 5)
Autism Research and Treatment     Open Access   (Followers: 25)
Autoimmune Diseases     Open Access   (Followers: 3, SJR: 0.909, h-index: 17)
Behavioural Neurology     Open Access   (Followers: 9, SJR: 0.696, h-index: 34)
Biochemistry Research Intl.     Open Access   (Followers: 6, SJR: 1.085, h-index: 17)
Bioinorganic Chemistry and Applications     Open Access   (Followers: 9, SJR: 0.286, h-index: 19)
BioMed Research Intl.     Open Access   (Followers: 4, SJR: 0.725, h-index: 59)
Biotechnology Research Intl.     Open Access   (Followers: 1)
Bone Marrow Research     Open Access   (Followers: 2)
Canadian J. of Gastroenterology & Hepatology     Open Access   (Followers: 5, SJR: 0.856, h-index: 53)
Canadian J. of Infectious Diseases and Medical Microbiology     Open Access   (Followers: 5, SJR: 0.409, h-index: 25)
Canadian Respiratory J.     Open Access   (Followers: 1, SJR: 0.503, h-index: 42)
Cardiology Research and Practice     Open Access   (Followers: 8, SJR: 0.941, h-index: 17)
Case Reports in Anesthesiology     Open Access   (Followers: 10)
Case Reports in Cardiology     Open Access   (Followers: 3)
Case Reports in Critical Care     Open Access   (Followers: 8)
Case Reports in Dentistry     Open Access   (Followers: 5)
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: 0.326, h-index: 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)
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: 16)
Chinese J. of Engineering     Open Access   (Followers: 2)
Chinese J. of Mathematics     Open Access  
Cholesterol     Open Access   (Followers: 1, SJR: 0.906, h-index: 12)
Chromatography Research Intl.     Open Access   (Followers: 6)
Complexity     Hybrid Journal   (Followers: 6, SJR: 0.526, h-index: 27)
Computational and Mathematical Methods in Medicine     Open Access   (Followers: 2, SJR: 0.415, h-index: 22)
Computational Intelligence and Neuroscience     Open Access   (Followers: 10, SJR: 0.232, h-index: 30)
Contrast Media & Molecular Imaging     Open Access   (Followers: 3, SJR: 0.932, h-index: 34)
Critical Care Research and Practice     Open Access   (Followers: 10, SJR: 0.916, h-index: 14)
Current Gerontology and Geriatrics Research     Open Access   (Followers: 9, SJR: 0.8, h-index: 12)
Depression Research and Treatment     Open Access   (Followers: 13, SJR: 0.77, h-index: 11)
Dermatology Research and Practice     Open Access   (Followers: 3, SJR: 0.576, h-index: 15)
Diagnostic and Therapeutic Endoscopy     Open Access   (SJR: 0.651, h-index: 18)
Discrete Dynamics in Nature and Society     Open Access   (Followers: 5, SJR: 0.323, h-index: 24)
Disease Markers     Open Access   (Followers: 1, SJR: 0.774, h-index: 49)
Education Research Intl.     Open Access   (Followers: 19)
Emergency Medicine Intl.     Open Access   (Followers: 7)
Enzyme Research     Open Access   (Followers: 3, SJR: 0.457, h-index: 18)
Evidence-based Complementary and Alternative Medicine     Open Access   (Followers: 20, SJR: 0.615, h-index: 50)
Experimental Diabetes Research     Open Access   (Followers: 14, SJR: 1.591, h-index: 30)
Gastroenterology Research and Practice     Open Access   (Followers: 2, SJR: 0.664, h-index: 21)
Genetics Research Intl.     Open Access   (Followers: 1)
Geofluids     Open Access   (Followers: 4, SJR: 0.693, h-index: 38)
HPB Surgery     Open Access   (Followers: 4, SJR: 0.798, h-index: 22)
Infectious Diseases in Obstetrics and Gynecology     Open Access   (Followers: 5, SJR: 0.976, h-index: 34)
Interdisciplinary Perspectives on Infectious Diseases     Open Access   (Followers: 1, SJR: 0.763, h-index: 15)
Intl. J. of Aerospace Engineering     Open Access   (Followers: 71, SJR: 0.241, h-index: 6)
Intl. J. of Agronomy     Open Access   (Followers: 5, SJR: 0.223, h-index: 2)
Intl. J. of Alzheimer's Disease     Open Access   (Followers: 11, SJR: 1.193, h-index: 25)
Intl. J. of Analysis     Open Access  
Intl. J. of Analytical Chemistry     Open Access   (Followers: 20, SJR: 0.157, h-index: 2)
Intl. J. of Antennas and Propagation     Open Access   (Followers: 11, SJR: 0.385, h-index: 15)
Intl. J. of Atmospheric Sciences     Open Access   (Followers: 23)
Intl. J. of Biodiversity     Open Access   (Followers: 4)
Intl. J. of Biomaterials     Open Access   (Followers: 4, SJR: 0.485, h-index: 10)
Intl. J. of Biomedical Imaging     Open Access   (Followers: 3, SJR: 0.581, h-index: 23)
Intl. J. of Breast Cancer     Open Access   (Followers: 13)
Intl. J. of Cell Biology     Open Access   (Followers: 3, SJR: 2.658, h-index: 25)
Intl. J. of Chemical Engineering     Open Access   (Followers: 7, SJR: 0.361, h-index: 10)
Intl. J. of Chronic Diseases     Open Access   (Followers: 1)
Intl. J. of Computer Games Technology     Open Access   (Followers: 9, SJR: 0.213, h-index: 12)
Intl. J. of Corrosion     Open Access   (Followers: 10, SJR: 0.19, h-index: 7)
Intl. J. of Dentistry     Open Access   (Followers: 6, SJR: 0.558, h-index: 11)
Intl. J. of Differential Equations     Open Access   (Followers: 7, SJR: 0.363, h-index: 11)
Intl. J. of Digital Multimedia Broadcasting     Open Access   (Followers: 5, SJR: 0.144, h-index: 10)
Intl. J. of Electrochemistry     Open Access   (Followers: 8)
Intl. J. of Endocrinology     Open Access   (Followers: 3, SJR: 0.961, h-index: 24)
Intl. J. of Engineering Mathematics     Open Access   (Followers: 5)
Intl. J. of Food Science     Open Access   (Followers: 3)
Intl. J. of Forestry Research     Open Access   (Followers: 3)
Intl. J. of Genomics     Open Access   (Followers: 2, SJR: 0.721, h-index: 7)
Intl. J. of Hepatology     Open Access   (Followers: 4)
Intl. J. of Hypertension     Open Access   (Followers: 6, SJR: 0.823, h-index: 20)
Intl. J. of Inflammation     Open Access   (SJR: 0.876, h-index: 14)
Intl. J. of Mathematics and Mathematical Sciences     Open Access   (Followers: 3, SJR: 0.346, h-index: 27)
Intl. J. of Medicinal Chemistry     Open Access   (Followers: 5)
Intl. J. of Microbiology     Open Access   (Followers: 4, SJR: 1.006, h-index: 18)
Intl. J. of Navigation and Observation     Open Access   (Followers: 20, SJR: 0.411, h-index: 7)
Intl. J. of Nephrology     Open Access   (Followers: 1, SJR: 0.926, h-index: 14)
Intl. J. of Optics     Open Access   (Followers: 7, SJR: 0.262, h-index: 7)
Intl. J. of Otolaryngology     Open Access   (Followers: 3)
Intl. J. of Pediatrics     Open Access   (Followers: 5)
Intl. J. of Peptides     Open Access   (Followers: 4, SJR: 0.73, h-index: 16)
Intl. J. of Photoenergy     Open Access   (Followers: 2, SJR: 0.348, h-index: 28)
Intl. J. of Plant Genomics     Open Access   (Followers: 4, SJR: 1.578, h-index: 20)
Intl. J. of Polymer Science     Open Access   (Followers: 24, SJR: 0.265, h-index: 11)
Intl. J. of Population Research     Open Access   (Followers: 2)
Intl. J. of Quality, Statistics, and Reliability     Open Access   (Followers: 15, SJR: 0.345, h-index: 4)
Intl. J. of Reconfigurable Computing     Open Access   (SJR: 0.182, h-index: 8)
Intl. J. of Reproductive Medicine     Open Access   (Followers: 4)
Intl. J. of Rheumatology     Open Access   (Followers: 4, SJR: 1.015, h-index: 18)
Intl. J. of Rotating Machinery     Open Access   (Followers: 2, SJR: 0.402, h-index: 19)
Intl. J. of Spectroscopy     Open Access   (Followers: 6)
Intl. J. of Stochastic Analysis     Open Access   (Followers: 3, SJR: 0.234, h-index: 19)
Intl. J. of Surgical Oncology     Open Access   (Followers: 1, SJR: 0.753, h-index: 11)
Intl. J. of Telemedicine and Applications     Open Access   (Followers: 4, SJR: 0.757, h-index: 14)
Intl. J. of Vascular Medicine     Open Access   (SJR: 0.865, h-index: 16)
Intl. J. of Zoology     Open Access   (Followers: 1, SJR: 0.389, h-index: 8)
Intl. Scholarly Research Notices     Open Access   (Followers: 190)
ISRN Astronomy and Astrophysics     Open Access   (Followers: 7)
J. of Addiction     Open Access   (Followers: 12)
J. of Advanced Transportation     Hybrid Journal   (Followers: 12, SJR: 0.911, h-index: 24)
J. of Aging Research     Open Access   (Followers: 6, SJR: 1.259, h-index: 23)
J. of Analytical Methods in Chemistry     Open Access   (Followers: 1, SJR: 0.296, h-index: 13)
J. of Applied Chemistry     Open Access   (Followers: 4)
J. of Applied Mathematics     Open Access   (Followers: 2, SJR: 0.341, h-index: 22)
J. of Biomedical Education     Open Access   (Followers: 3)
J. of Blood Transfusion     Open Access   (Followers: 1)
J. of Botany     Open Access   (Followers: 3, SJR: 0.101, h-index: 2)
J. of Cancer Epidemiology     Open Access   (Followers: 5, SJR: 1.427, h-index: 12)
J. of Chemistry     Open Access   (Followers: 5, SJR: 0.225, h-index: 11)
J. of Combustion     Open Access   (Followers: 22, SJR: 0.27, h-index: 8)
J. of Complex Analysis     Open Access   (Followers: 3)
J. of Composites     Open Access   (Followers: 80)
J. of Computer Networks and Communications     Open Access   (Followers: 4, SJR: 0.257, h-index: 8)
J. of Construction Engineering     Open Access   (Followers: 8)
J. of Control Science and Engineering     Open Access   (Followers: 1, SJR: 0.299, h-index: 9)
J. of Diabetes Research     Open Access   (Followers: 12, SJR: 1.024, h-index: 13)
J. of Drug Delivery     Open Access   (Followers: 6, SJR: 4.523, h-index: 2)
J. of Electrical and Computer Engineering     Open Access   (Followers: 9, SJR: 0.225, h-index: 10)
J. of Energy     Open Access   (Followers: 2)
J. of Engineering     Open Access  
J. of Environmental and Public Health     Open Access   (Followers: 15, SJR: 1.136, h-index: 16)
J. of Food Quality     Hybrid Journal   (Followers: 7, SJR: 0.497, h-index: 30)
J. of Function Spaces     Open Access   (SJR: 0.414, h-index: 10)
J. of Geological Research     Open Access   (Followers: 1)
J. of Healthcare Engineering     Open Access   (Followers: 3, SJR: 0.345, h-index: 10)

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Journal Cover International Journal of Genomics
  [SJR: 0.721]   [H-I: 7]   [2 followers]  Follow
    
  This is an Open Access Journal Open Access journal
   ISSN (Print) 2314-436X - ISSN (Online) 2314-4378
   Published by Hindawi Homepage  [281 journals]
  • 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
       
  • Regulation of Long Noncoding RNAs Responsive to Phytoplasma Infection in
           Paulownia tomentosa

    • Abstract: Paulownia witches’ broom caused by phytoplasma infection affects the production of Paulownia trees worldwide. Emerging evidence showed that long noncoding RNAs (lncRNA) play a protagonist role in regulating the expression of genes in plants. So far, the identification of lncRNAs has been limited to a few model plant species, and their roles in mediating responses to Paulownia tomentosa that free of phytoplasma infection are yet to be characterized. Here, whole-genome identification of lncRNAs, based on strand-specific RNA sequencing, from four Paulownia tomentosa samples, was performed and identified 3689 lncRNAs. These lncRNAs showed low conservation among plant species and some of them were miRNA precursors. Further analysis revealed that the 112 identified lncRNAs were related to phytoplasma infection. We predicted the target genes of these phytoplasma-responsive lncRNAs, and our analysis showed that 51 of the predicted target genes were alternatively spliced. Moreover, we found the expression of the lncRNAs plays vital roles in regulating the genes involved in the reactive oxygen species induced hypersensitive response and effector-triggered immunity in phytoplasma-infected Paulownia. This study indicated that diverse sets of lncRNAs were responsive to Paulownia witches’ broom, and the results will provide a starting point to understand the functions and regulatory mechanisms of Paulownia lncRNAs in the future.
      PubDate: Wed, 21 Feb 2018 00:00:00 +000
       
  • Urinary Metabolomic Study of Chlorogenic Acid in a Rat Model of Chronic
           Sleep Deprivation Using Gas Chromatography-Mass Spectrometry

    • Abstract: The urinary metabolomic study based on gas chromatography-mass spectrometry (GC-MS) had been developed to investigate the possible antidepressant mechanism of chlorogenic acid (CGA) in a rat model of sleep deprivation (SD). According to pattern recognition analysis, there was a clear separation among big platform group (BP), sleep deprivation group (SD), and the CGA (model + CGA), and CGA group was much closer to the BP group by showing a tendency of recovering towards BP group. Thirty-six significantly changed metabolites related to antidepressant by CGA were identified and used to explore the potential mechanism. Combined with the result of the classic behavioral tests and biochemical indices, CGA has significant antidepressant effects in a rat model of SD, suggesting that the mechanism of action of CGA might be involved in regulating the abnormal pathway of nicotinate and nicotinamide metabolism; glyoxylate and dicarboxylate metabolism; glycine, serine, and threonine metabolism; and arginine and proline metabolism. Our results also show that metabolomics analysis based on GC-MS is a useful tool for exploring biomarkers involved in depression and elucidating the potential therapeutic mechanisms of Chinese medicine.
      PubDate: Sun, 11 Feb 2018 00:00:00 +000
       
  • Marker-Assisted Introgression of Saltol QTL Enhances Seedling Stage Salt
           Tolerance in the Rice Variety “Pusa Basmati 1”

    • Abstract: Marker-assisted selection is an unequivocal translational research tool for crop improvement in the genomics era. Pusa Basmati 1 (PB1) is an elite Indian Basmati rice cultivar sensitive to salinity. Here, we report enhanced seedling stage salt tolerance in improved PB1 genotypes developed through marker-assisted transfer of a major QTL, Saltol. A highly salt tolerant line, FL478, was used as the Saltol donor. Parental polymorphism survey using 456 microsatellite (SSR)/QTL-linked markers revealed 14.3% polymorphism between PB1 and FL478. Foreground selection was carried out using three Saltol-linked polymorphic SSR markers RM8094, RM493, and RM10793 and background selection by 62 genome-wide polymorphic SSR markers. In every backcross generation, foreground selection was restricted to the triple heterozygotes of foreground markers, which was followed by phenotypic and background selections. Twenty-four near isogenic lines (NILs), with recurrent parent genome recovery of 96.0–98.4%, were selected after two backcrosses followed by three selfing generations. NILs exhibited agronomic traits similar to those of PB1 and additional improvement in the seedling stage salt tolerance. They are being tested for per se performance under salt-affected locations for release as commercial varieties. These NILs appear promising for enhancing rice production in salinity-affected pockets of Basmati Geographical Indication (GI) areas of India.
      PubDate: Sun, 11 Feb 2018 00:00:00 +000
       
  • Metabolic Pathway Genes Associated with Susceptibility Genes to Coronary
           Artery Disease

    • Abstract: Coronary artery disease (CAD) is one of the leading threats to global health. Previous research has proven that metabolic pathway disorders, such as high blood lipids and diabetes, are one of the risk factors that mostly cause CAD. However, the crosstalk between metabolic pathways and CAD was mostly studied on physiology processes by analyzing a single gene function. A canonical correlation analysis was used to identify the metabolic pathways, which were integrated as a unit to coexpress with CAD susceptibility genes, and to resolve additional metabolic factors that are related to CAD. Seven pathways, including citrate cycle, ubiquinone, terpenoid quinone biosynthesis, and N-glycan biosynthesis, were identified as an integrated unit coexpressed with CAD genes. These pathways could not be revealed as a coexpressed pathway through traditional methods as each single gene has weak correlation. Furthermore, sets of genes in these pathways were candidate markers for diagnosis and detection from patients’ serum.
      PubDate: Sun, 11 Feb 2018 00:00:00 +000
       
  • Identification of Wheat Inflorescence Development-Related Genes Using a
           Comparative Transcriptomics Approach

    • Abstract: Inflorescence represents the highly specialized plant tissue producing the grains. Although key genes regulating flower initiation and development are conserved, the mechanism regulating fertility is still not well explained. To identify genes and gene network underlying inflorescence morphology and fertility of bread wheat, expressed sequence tags (ESTs) from different tissues were analyzed using a comparative transcriptomics approach. Based on statistical comparison of EST frequencies of individual genes in EST pools representing different tissues and verification with RT-PCR and RNA-seq data, 170 genes of 59 gene sets predominantly expressed in the inflorescence were obtained. Nearly one-third of the gene sets displayed differentiated expression profiles in terms of their subgenome orthologs. The identified genes, most of which were predominantly expressed in anthers, encode proteins involved in wheat floral identity determination, anther and pollen development, pollen-pistil interaction, and others. Particularly, 25 annotated gene sets are associated with pollen wall formation, of which 18 encode enzymes or proteins participating in lipid metabolic pathway, including fatty acid ω-hydroxylation, alkane and fatty alcohol biosynthesis, and glycerophospholipid metabolism. We showed that the comparative transcriptomics approach was effective in identifying genes for reproductive development and found that lipid metabolism was particularly active in wheat anthers.
      PubDate: Thu, 08 Feb 2018 10:04:35 +000
       
  • Transcriptome Analysis of the Thymus in Short-Term Calorie-Restricted Mice
           Using RNA-seq

    • Abstract: Calorie restriction (CR), which is a factor that expands lifespan and an important player in immune response, is an effective protective method against cancer development. Thymus, which plays a critical role in the development of the immune system, reacts to nutrition deficiency quickly. RNA-seq-based transcriptome sequencing was performed to thymus tissues of MMTV-TGF-α mice subjected to ad libitum (AL), chronic calorie restriction (CCR), and intermittent calorie restriction (ICR) diets in this study. Three cDNA libraries were sequenced using Illumina HiSeq™ 4000 to produce 100 base pair-end reads. On average, 105 million clean reads were mapped and in total 6091 significantly differentially expressed genes (DEGs) were identified (). These DEGs were clustered into Gene Ontology (GO) categories. The expression pattern revealed by RNA-seq was validated by quantitative real-time PCR (qPCR) analysis of four important genes, which are leptin, ghrelin, Igf1, and adinopectin. RNA-seq data has been deposited in NCBI Gene Expression Omnibus (GEO) database (GSE95371). We report the use of RNA sequencing to find DEGs that are affected by different feeding regimes in the thymus.
      PubDate: Sun, 04 Feb 2018 00:00:00 +000
       
  • Multitarget Effects of Danqi Pill on Global Gene Expression Changes in
           Myocardial Ischemia

    • Abstract: Danqi pill (DQP) is a widely prescribed traditional Chinese medicine (TCM) in the treatment of cardiovascular diseases. The objective of this study is to systematically characterize altered gene expression pattern induced by myocardial ischemia (MI) in a rat model and to investigate the effects of DQP on global gene expression. Global mRNA expression was measured. Differentially expressed genes among the sham group, model group, and DQP group were analyzed. The gene ontology enrichment analysis and pathway analysis of differentially expressed genes were carried out. We quantified 10,813 genes. Compared with the sham group, expressions of 339 genes were upregulated and 177 genes were downregulated in the model group. The upregulated genes were enriched in extracellular matrix organization, response to wounding, and defense response pathways. Downregulated genes were enriched in fatty acid metabolism, pyruvate metabolism, PPAR signaling pathways, and so forth. This indicated that energy metabolic disorders occurred in rats with MI. In the DQP group, expressions of genes in the altered pathways were regulated back towards normal levels. DQP reversed expression of 313 of the 516 differentially expressed genes in the model group. This study provides insight into the multitarget mechanism of TCM in the treatment of complex diseases.
      PubDate: Thu, 01 Feb 2018 03:37:19 +000
       
  • Noncoding RNAs in Health and Disease

    • PubDate: Mon, 22 Jan 2018 00:00:00 +000
       
  • Shiftwork-Mediated Disruptions of Circadian Rhythms and Sleep Homeostasis
           Cause Serious Health Problems

    • Abstract: Shiftwork became common during the last few decades with the growing demands of human life. Despite the social inactivity and irregularity in habits, working in continuous irregular shifts causes serious health issues including sleep disorders, psychiatric disorders, cancer, and metabolic disorders. These health problems arise due to the disruption in circadian clock system, which is associated with alterations in genetic expressions. Alteration in clock controlling genes further affects genes linked with disorders including major depression disorder, bipolar disorder, phase delay and phase advance sleep syndromes, breast cancer, and colon cancer. A diverse research work is needed focusing on broad spectrum changes caused by jet lag in brain and neuronal system. This review is an attempt to motivate the researchers to conduct advanced studies in this area to identify the risk factors and mechanisms. Its goal is extended to make the shift workers aware about the risks associated with shiftwork.
      PubDate: Sun, 21 Jan 2018 00:00:00 +000
       
  • Ensemble Methods with Voting Protocols Exhibit Superior Performance for
           Predicting Cancer Clinical Endpoints and Providing More Complete Coverage
           of Disease-Related Genes

    • Abstract: In genetic data modeling, the use of a limited number of samples for modeling and predicting, especially well below the attribute number, is difficult due to the enormous number of genes detected by a sequencing platform. In addition, many studies commonly use machine learning methods to evaluate genetic datasets to identify potential disease-related genes and drug targets, but to the best of our knowledge, the information associated with the selected gene set was not thoroughly elucidated in previous studies. To identify a relatively stable scheme for modeling limited samples in the gene datasets and reveal the information that they contain, the present study first evaluated the performance of a series of modeling approaches for predicting clinical endpoints of cancer and later integrated the results using various voting protocols. As a result, we proposed a relatively stable scheme that used a set of methods with an ensemble algorithm. Our findings indicated that the ensemble methodologies are more reliable for predicting cancer prognoses than single machine learning algorithms as well as for gene function evaluating. The ensemble methodologies provide a more complete coverage of relevant genes, which can facilitate the exploration of cancer mechanisms and the identification of potential drug targets.
      PubDate: Wed, 10 Jan 2018 00:00:00 +000
       
  • Lingguizhugan Decoction Protects against High-Fat-Diet-Induced
           Nonalcoholic Fatty Liver Disease by Alleviating Oxidative Stress and
           Activating Cholesterol Secretion

    • Abstract: Background. Nonalcoholic fatty liver disease (NAFLD) has become a leading cause of liver transplantation. Lingguizhugan decoction (LGZG), a classical Chinese herbal formula, has beneficial effects on NAFLD animal models. Our study examined the impact of LGZG on hepatic global transcriptome of high-fat-diet-induced NAFLD rats. Methods. Three groups of Wistar rats were included: normal, NAFLD model, and LGZG-treated NAFLD groups. Four weeks for the treatment, liver tissues were harvested for RNA sequencing. Differentially expressed genes (DEGs) and enriched pathways were detected on hepatic global transcriptome profile. Real-time PCR validated the regulatory patterns of LGZG on NAFLD rats. Results. DEGs between the NAFLD model and normal groups indicated the elevated peroxisome proliferator-activated receptor (PPAR) and hedgehog signaling pathways in NAFLD rats. In bile secretion pathway, genes involved in cholesterol secretion were activated by LGZG treatment. Increased expression of antioxidant OSIGN1 and decreased expression of genes (AHR, IRF2BP2, and RASGEF1B) that induce oxidative stress and inflammation were observed in NAFLD rats treated with LGZG. The regulatory patterns of LGZG treatment on these oxidative stress-related genes were confirmed by real-time PCR. Conclusion. Our study revealed a “two-hits-targeting” mechanism of LGZG in the treatment for NAFLD: alleviating oxidative stress and activating cholesterol secretion.
      PubDate: Sun, 31 Dec 2017 00:00:00 +000
       
  • MicroRNA and Putative Target Discoveries in Chrysanthemum Polyploidy
           Breeding

    • Abstract: MicroRNAs (miRNAs), around 22 nucleotides (nt) in length, are a class of endogenous and noncoding RNA molecule that play an essential role in plant development, either by suppressing the transcription of target genes at a transcriptional level or inhibiting translation at a posttranscriptional level. To understand the roles of miRNAs and their target genes in chrysanthemum polyploidy breeding, three sRNA libraries of normal and abnormal embryos after hybridization were performed by RNA-Seq. As a result, a total of 170 miRNAs were identified and there are 41 special miRNAs in cross of paternal chromosome doubling, such as miR169b, miR440, and miR528-5p. miR164c and miR159a were highly expressed in a normal embryo at 18 days after pollination, suggesting the regulatory role at the late stage of embryonic development. miR172c was only detected in the normal embryo at 18 days after pollination, which means that miR172c mainly mediates gene expression in postembryonic development and these genes may promote embryo maturation. Other miRNAs, including miR414, miR2661, and miR5021, may regulate the genes participated in pathways of auxin response and energy metabolism; then they regulate the complex embryonic development together.
      PubDate: Wed, 13 Dec 2017 07:48:49 +000
       
  • Effect of Gegen Qinlian Decoction on Cardiac Gene Expression in Diabetic
           Mice

    • Abstract: The aim of this research is to investigate the therapeutic effect of GGQL decoction on cardiac dysfunction and elucidate the pharmacological mechanisms. db/db mice were divided into DB group or GGQL group, and WT mice were used as control. All mice were accessed by echocardiography. And the total RNA of LV tissue samples was sequenced, then differential expression genes were analyzed. The RNA-seq results were validated by the results of RT-qPCR of 4 genes identified as differentially expressed. The content of pyruvate and ceramide in myocardial tissue was also measured. The results showed that GGQL decoction could significantly improve the diastolic dysfunction, increase the content of pyruvate, and had the trend to reduce the ceramide content. The results of RNA-seq showed that 2958 genes were differentially expressed when comparing the DB group with the WT group. Among them, compared with the DB group, 26 genes were differentially regulated in the GGQL group. The expression results of 4 genes were consistent with the RNA-seq results. Our study reveals that GGQL decoction has a therapeutic effect on diastolic dysfunction of the left ventricular and the effect may be related to its role in promoting myocardial glycolysis and decreasing the content of ceramide.
      PubDate: Tue, 12 Dec 2017 00:00:00 +000
       
  • Circular RNAs: Biogenesis, Function, and a Role as Possible Cancer
           Biomarkers

    • Abstract: Circular RNAs (circRNAs) are a class of noncoding RNAs (ncRNAs) that form covalently closed continuous loop structures, lacking the terminal 5 and 3 ends. CircRNAs are generated in the process of back-splicing and can originate from different genomic regions. Their unique circular structure makes circRNAs more stable than linear RNAs. In addition, they also display insensitivity to ribonuclease activity. Generally, circRNAs function as microRNA (miRNA) sponges and have a regulatory role in transcription and translation. They may be also translated in a cap-independent manner in vivo, to generate specific proteins. In the last decade, next-generation sequencing techniques, especially RNA-seq, have revealed great abundance and also dysregulation of many circRNAs in various diseases, suggesting their involvement in disease development and progression. Regarding their high stability and relatively specific differential expression patterns in tissues and extracellular environment (e.g., body fluids), they are regarded as promising novel biomarkers in cancer. Therefore, we focus this review on describing circRNA biogenesis, function, and involvement in human cancer development and address the potential of circRNAs to be effectively used as novel cancer diagnostic and prognostic biomarkers.
      PubDate: Mon, 04 Dec 2017 00:00:00 +000
       
  • Vitamin D Receptor Gene Polymorphisms Influence T1D Susceptibility among
           Pakistanis

    • Abstract: Background. The vitamin D receptor (VDR) gene regulates insulin secretion from the pancreas and acts as a mediator of the immune response through vitamin D. Polymorphism in VDR causes alterations in the functioning of vitamin D, leading to type 1 diabetes (T1D) predisposition. The aim of the present study was to determine VDR gene polymorphism in association with T1D in Pakistanis. Methods. The association was evaluated by selecting rs2228570 (FokΙ), rs7975232 (ApaΙ), and rs731236 (TaqΙ) polymorphic sites in 102 patients and 100 controls. Genotypes were identified by DNA sequencing and PCR-RFLP. Results. The allelic and genotypic frequencies of FokΙ and ApaI were significantly associated with T1D () development. At the FokΙ site, tryptophan was replaced with arginine due to polymorphism. A novel SNP (GeneBank acc number KT280406) was identified through the sequencing of intron 8, 62 bp downstream from the ApaI polymorphic site, and significantly associated with T1D development. The TaqΙ did not depict any association with T1D at the allelic or genotypic level (). CCGC, CCGG, CCTC, and CCTG haplotypes were significantly associated with disease development (). However, CTGG haplotype was protective towards T1D (). Conclusion. VDR polymorphisms were identified as susceptible regions for T1D development in the Pakistani population.
      PubDate: Sun, 03 Dec 2017 00:00:00 +000
       
  • HuoXueJieDu Formula Alleviates Diabetic Retinopathy in Rats by Inhibiting
           SOCS3-STAT3 and TIMP1-A2M Pathways

    • Abstract: HuoXueJieDu (HXJD) formula exerts protective effects against diabetic retinopathy (DR) in rats, but its underlying mechanism remains unknown. In the present study, the diabetic rats were established using streptozocin. The administration of HXJD was initiated at 20 weeks after diabetes induction and continued for 12 weeks. Whole genome expression profiles in rat retinas were examined using microarray technology. Differential gene expression and pathway enrichment analysis were conducted on the microarray data, with validation through real-time PCR and immunohistochemical staining. The results showed that 170 genes and several IPA canonical pathways related to inflammation, matrix metabolism, and phototransduction were regulated by HXJD. PCR validation of selected genes, including SOCS3, STAT3, TIMP1, and A2M, confirmed the gene expression changes influenced by HXJD. In addition, the immunohistochemical staining results suggested that critical members of the SOCS3-STAT3 pathway were also affected by HXJD. Taken together, these results indicated that SOCS3-STAT3 and TIMP1-A2M pathways might mediate the alleviation of HXJD activities in rats with diabetic retinopathy.
      PubDate: Wed, 29 Nov 2017 00:00:00 +000
       
 
 
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