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Publisher: Hindawi   (Total: 298 journals)

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Showing 1 - 200 of 298 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: 29, SJR: 0.259, h-index: 6)
Advances in Agriculture     Open Access   (Followers: 7)
Advances in Artificial Intelligence     Open Access   (Followers: 16)
Advances in Astronomy     Open Access   (Followers: 37, SJR: 0.351, h-index: 17)
Advances in Bioinformatics     Open Access   (Followers: 18, SJR: 0.421, h-index: 8)
Advances in Chemistry     Open Access   (Followers: 15)
Advances in Civil Engineering     Open Access   (Followers: 34, SJR: 0.338, h-index: 8)
Advances in Condensed Matter Physics     Open Access   (Followers: 8, SJR: 0.248, h-index: 10)
Advances in Decision Sciences     Open Access   (Followers: 5, SJR: 0.231, h-index: 6)
Advances in Electrical Engineering     Open Access   (Followers: 20)
Advances in Fuzzy Systems     Open Access   (Followers: 5, SJR: 0.258, h-index: 7)
Advances in Hematology     Open Access   (Followers: 9, SJR: 0.892, h-index: 18)
Advances in High Energy Physics     Open Access   (Followers: 19, SJR: 0.892, h-index: 19)
Advances in Human-Computer Interaction     Open Access   (Followers: 20, SJR: 0.439, h-index: 9)
Advances in Materials Science and Engineering     Open Access   (Followers: 32, SJR: 0.263, h-index: 11)
Advances in Mathematical Physics     Open Access   (Followers: 5, SJR: 0.332, h-index: 10)
Advances in Medicine     Open Access   (Followers: 2)
Advances in Meteorology     Open Access   (Followers: 18, SJR: 0.498, h-index: 10)
Advances in Multimedia     Open Access   (Followers: 2, SJR: 0.191, h-index: 10)
Advances in Nonlinear Optics     Open Access   (Followers: 5)
Advances in Numerical Analysis     Open Access   (Followers: 4)
Advances in Operations Research     Open Access   (Followers: 11, 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 Orthopedic Surgery     Open Access   (Followers: 10)
Advances in Orthopedics     Open Access   (Followers: 9)
Advances in Pharmacological Sciences     Open Access   (Followers: 6, SJR: 0.695, h-index: 13)
Advances in Physical Chemistry     Open Access   (Followers: 11, SJR: 0.297, h-index: 7)
Advances in Power Electronics     Open Access   (Followers: 26, SJR: 0.26, h-index: 6)
Advances in Preventive Medicine     Open Access   (Followers: 6)
Advances in Public Health     Open Access   (Followers: 23)
Advances in Tribology     Open Access   (Followers: 10, SJR: 0.267, h-index: 6)
Advances in Urology     Open Access   (Followers: 10, 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: 4, SJR: 0.991, h-index: 11)
Anesthesiology Research and Practice     Open Access   (Followers: 12, SJR: 0.513, h-index: 12)
Applied and Environmental Soil Science     Open Access   (Followers: 17, 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: 12)
Archaea     Open Access   (Followers: 3, SJR: 1.248, h-index: 27)
Arthritis     Open Access   (Followers: 4)
Autism Research and Treatment     Open Access   (Followers: 28)
Autoimmune Diseases     Open Access   (Followers: 3, SJR: 0.909, h-index: 17)
Behavioural Neurology     Open Access   (Followers: 7, 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: 6, SJR: 0.725, h-index: 59)
Biotechnology Research Intl.     Open Access   (Followers: 2)
Bone Marrow Research     Open Access   (Followers: 2)
Canadian J. of Gastroenterology & Hepatology     Open Access   (Followers: 4, SJR: 0.856, h-index: 53)
Canadian J. of Infectious Diseases and Medical Microbiology     Open Access   (Followers: 4, 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)
Cardiovascular Psychiatry and Neurology     Open Access   (Followers: 4, SJR: 1.091, h-index: 14)
Case Reports in Anesthesiology     Open Access   (Followers: 10)
Case Reports in Cardiology     Open Access   (Followers: 2)
Case Reports in Critical Care     Open Access   (Followers: 9)
Case Reports in Dentistry     Open Access   (Followers: 4)
Case Reports in Dermatological Medicine     Open Access   (Followers: 2)
Case Reports in Emergency Medicine     Open Access   (Followers: 15)
Case Reports in Endocrinology     Open Access   (SJR: 0.326, h-index: 1)
Case Reports in Gastrointestinal Medicine     Open Access   (Followers: 3)
Case Reports in Genetics     Open Access   (Followers: 1)
Case Reports in Hematology     Open Access   (Followers: 3)
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: 3)
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: 11)
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: 7)
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: 9)
Case Reports in Rheumatology     Open Access   (Followers: 4)
Case Reports in Surgery     Open Access   (Followers: 9)
Case Reports in Transplantation     Open Access  
Case Reports in Urology     Open Access   (Followers: 9)
Case Reports in Vascular Medicine     Open Access  
Case Reports in Veterinary Medicine     Open Access   (Followers: 5)
Chemotherapy Research and Practice     Open Access   (Followers: 1)
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)
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: 4, SJR: 0.457, h-index: 18)
Epilepsy Research and Treatment     Open Access   (Followers: 3)
Evidence-based Complementary and Alternative Medicine     Open Access   (Followers: 18, SJR: 0.615, h-index: 50)
Experimental Diabetes Research     Open Access   (Followers: 11, SJR: 1.591, h-index: 30)
Gastroenterology Research and Practice     Open Access   (Followers: 3, SJR: 0.664, h-index: 21)
Genetics Research Intl.     Open Access   (Followers: 1)
Geofluids     Open Access   (Followers: 4, SJR: 0.693, h-index: 38)
Hepatitis Research and Treatment     Open Access   (Followers: 6)
HPB Surgery     Open Access   (Followers: 5, SJR: 0.798, h-index: 22)
Indian J. of Materials Science     Open Access  
Infectious Diseases in Obstetrics and Gynecology     Open Access   (Followers: 7, SJR: 0.976, h-index: 34)
Influenza Research and Treatment     Open Access   (Followers: 2)
Interdisciplinary Perspectives on Infectious Diseases     Open Access   (Followers: 2, SJR: 0.763, h-index: 15)
Intl. J. of Aerospace Engineering     Open Access   (Followers: 66, SJR: 0.241, h-index: 6)
Intl. J. of Agronomy     Open Access   (Followers: 8, SJR: 0.223, h-index: 2)
Intl. J. of Alzheimer's Disease     Open Access   (Followers: 12, SJR: 1.193, h-index: 25)
Intl. J. of Analysis     Open Access  
Intl. J. of Analytical Chemistry     Open Access   (Followers: 22, 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 Bacteriology     Open Access  
Intl. J. of Biodiversity     Open Access   (Followers: 4)
Intl. J. of Biomaterials     Open Access   (Followers: 5, SJR: 0.485, h-index: 10)
Intl. J. of Biomedical Imaging     Open Access   (Followers: 5, SJR: 0.581, h-index: 23)
Intl. J. of Breast Cancer     Open Access   (Followers: 12)
Intl. J. of Cell Biology     Open Access   (Followers: 4, 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: 11, SJR: 0.213, h-index: 12)
Intl. J. of Corrosion     Open Access   (Followers: 11, 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: 3)
Intl. J. of Evolutionary Biology     Open Access   (Followers: 9)
Intl. J. of Family Medicine     Open Access   (Followers: 3)
Intl. J. of Food Science     Open Access   (Followers: 3)
Intl. J. of Forestry Research     Open Access   (Followers: 4)
Intl. J. of Genomics     Open Access   (Followers: 2, SJR: 0.721, h-index: 7)
Intl. J. of Hepatology     Open Access   (Followers: 3)
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: 6)
Intl. J. of Microbiology     Open Access   (Followers: 5, SJR: 1.006, h-index: 18)
Intl. J. of Microwave Science and Technology     Open Access   (Followers: 3, SJR: 0.167, h-index: 5)
Intl. J. of Molecular Imaging     Open Access  
Intl. J. of Navigation and Observation     Open Access   (Followers: 20, SJR: 0.411, h-index: 7)
Intl. J. of Nephrology     Open Access   (Followers: 2, 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: 23, SJR: 0.265, h-index: 11)
Intl. J. of Population Research     Open Access   (Followers: 2)
Intl. J. of Proteomics     Open Access   (Followers: 1)
Intl. J. of Reconfigurable Computing     Open Access   (SJR: 0.182, h-index: 8)
Intl. J. of Reproductive Medicine     Open Access   (Followers: 5)
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: 8)
Intl. J. of Stochastic Analysis     Open Access   (Followers: 4, 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 Vehicular Technology     Open Access   (Followers: 4, SJR: 0.169, h-index: 6)
Intl. J. of Zoology     Open Access   (Followers: 1, SJR: 0.389, h-index: 8)
Intl. Scholarly Research Notices     Open Access   (Followers: 206)
ISRN Astronomy and Astrophysics     Open Access   (Followers: 7)
J. of Addiction     Open Access   (Followers: 12)
J. of Advanced Transportation     Hybrid Journal   (Followers: 11, SJR: 0.911, h-index: 24)
J. of Aging Research     Open Access   (Followers: 7, SJR: 1.259, h-index: 23)
J. of Allergy     Open Access   (Followers: 4)
J. of Amino Acids     Open Access   (Followers: 2)
J. of Analytical Methods in Chemistry     Open Access   (Followers: 1, SJR: 0.296, h-index: 13)
J. of Anthropology     Open Access   (Followers: 24)
J. of Applied Chemistry     Open Access   (Followers: 4)
J. of Applied Mathematics     Open Access   (Followers: 2, SJR: 0.341, h-index: 22)
J. of Biomarkers     Open Access  
J. of Biomedical Education     Open Access   (Followers: 2)
J. of Biophysics     Open Access   (Followers: 5, SJR: 0.22, h-index: 5)
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: 7, 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: 17, SJR: 0.27, h-index: 8)
J. of Complex Analysis     Open Access   (Followers: 3)
J. of Computational Engineering     Open Access   (Followers: 1)

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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  [298 journals]
  • The Transcriptional Network Structure of a Myeloid Cell: A Computational
           Approach

    • Abstract: Understanding the general principles underlying genetic regulation in eukaryotes is an incomplete and challenging endeavor. The lack of experimental information regarding the regulation of the whole set of transcription factors and their targets in different cell types is one of the main reasons to this incompleteness. So far, there is a small set of curated known interactions between transcription factors and their downstream genes. Here, we built a transcription factor network for human monocytic THP-1 myeloid cells based on the experimentally curated FANTOM4 database where nodes are genes and the experimental interactions correspond to links. We present the topological parameters which define the network as well as some global structural features and introduce a relative inuence parameter to quantify the relevance of a transcription factor in the context of induction of a phenotype. Genes like ZHX2, ADNP, or SMAD6 seem to be highly regulated to avoid an avalanche transcription event. We compare these results with those of RegulonDB, a highly curated transcriptional network for the prokaryotic organism E. coli, finding similarities between general hallmarks on both transcriptional programs. We believe that an approach, such as the one shown here, could help to understand the one regulation of transcription in eukaryotic cells.
      PubDate: Sat, 30 Sep 2017 07:02:06 +000
       
  • Genomic Survey, Characterization, and Expression Profile Analysis of the
           SBP Genes in Pineapple (Ananas comosus L.)

    • Abstract: Gene expression is regulated by transcription factors, which play many significant developmental processes. SQUAMOSA promoter-binding proteins (SBP) perform a variety of regulatory functions in leaf, flower, and fruit development, plant architecture, and sporogenesis. 16 SBP genes were identified in pineapple and were divided into four groups on basis of phylogenetic analysis. Five paralogs in pineapple for SBP genes were identified with Ka/Ks ratio varied from 0.20 for AcSBP14 and AcSBP15 to 0.36 for AcSBP6 and AcSBP16, respectively. 16 SBP genes were located on 12 chromosomes out of 25 pineapple chromosomes with highly conserved protein sequence structures. The isoionic points of SBP ranged from 6.05 to 9.57, while molecular weight varied from 22.7 to 121.9 kD. Expression profiles of SBP genes revealed that AcSBP7 and AcSBP15 (leaf), AcSBP13, AcSBP12, AcSBP8, AcSBP16, AcSBP9, and AcSBP11 (sepal), AcSBP6, AcSBP4, and AcSBP10 (stamen), AcSBP14, AcSBP1, and AcSBP5 (fruit) while the rest of genes showed low expression in studied tissues. Four genes, that is, AcSBP11, AcSBP6, AcSBP4, and AcSBP12, were highly expressed at 4°C, while AcSBP16 were upregulated at 45°C. RNA-Seq was validated through qRT-PCR for some genes. Salt stress-induced expression of two genes, that is, AcSBP7 and AcSBP14, while in drought stress, AcSBP12 and AcSBP15 were highly expressed. Our study lays a foundation for further gene function and expression studies of SBP genes in pineapple.
      PubDate: Fri, 29 Sep 2017 03:52:26 +000
       
  • Molecular Crosstalking among Noncoding RNAs: A New Network Layer of Genome
           Regulation in Cancer

    • Abstract: Over the past few years, noncoding RNAs (ncRNAs) have been extensively studied because of the significant biological roles that they play in regulation of cellular mechanisms. ncRNAs are associated to higher eukaryotes complexity; accordingly, their dysfunction results in pathological phenotypes, including cancer. To date, most research efforts have been mainly focused on how ncRNAs could modulate the expression of protein-coding genes in pathological phenotypes. However, recent evidence has shown the existence of an unexpected interplay among ncRNAs that strongly influences cancer development and progression. ncRNAs can interact with and regulate each other through various molecular mechanisms generating a complex network including different species of RNAs (e.g., mRNAs, miRNAs, lncRNAs, and circRNAs). Such a hidden network of RNA-RNA competitive interactions pervades and modulates the physiological functioning of canonical protein-coding pathways involved in proliferation, differentiation, and metastasis in cancer. Moreover, the pivotal role of ncRNAs as keystones of network structural integrity makes them very attractive and promising targets for innovative RNA-based therapeutics. In this review we will discuss: (1) the current knowledge on complex crosstalk among ncRNAs, with a special focus on cancer; and (2) the main issues and criticisms concerning ncRNAs targeting in therapeutics.
      PubDate: Sun, 24 Sep 2017 00:00:00 +000
       
  • The miRNA Pull Out Assay as a Method to Validate the miR-28-5p Targets
           Identified in Other Tumor Contexts in Prostate Cancer

    • Abstract: miR-28-5p is an intragenic miRNA which is underexpressed in several tumor types showing a tumor suppressor (TS) activity. Routinely, the known miR-28-5p targets are validated in specific tumor contexts but it is unclear whether these targets are also being regulated in other tumor types. To this end, we adopted the miRNA pull out assay to capture the miR-28-5p targets in DU-145 prostate cancer (PCa) cells. Firstly, we demonstrated that miR-28-5p acts as a TS-miRNA in PCa, affecting cell proliferation, survival, and apoptosis. Secondly, we evaluated the enrichment of the 10 validated miR-28-5p targets in the pull out sample. We showed that E2F6, TEX-261, MAPK1, MPL, N4BP1, and RAP1B but not BAG1, OTUB1, MAD2L1, and p21 were significantly enriched, suggesting that not all the miR-28-5p targets are regulated by this miRNA in PCa. We then verified whether the miR-28-5p-interacting targets were regulated by this miRNA. We selected E2F6, the most enriched target in the pull out sample, and demonstrated that miR-28-5p downregulated E2F6 at the protein level suggesting that our approach was effective. In general terms, these findings support the miRNA pull out assay as a useful method to identify context-specific miRNA targets.
      PubDate: Wed, 20 Sep 2017 00:00:00 +000
       
  • Identifying Novel Glioma-Associated Noncoding RNAs by Their Expression
           Profiles

    • Abstract: Long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) play a significant role in cancer development as regulators of protein-coding genes. Their dysregulation was in some extent already associated with glioma, the most aggressive primary brain tumours in adults. The correct diagnosis and treatment selection due to high tumour heterogeneity might be difficult and inadequate, resulting in poor prognosis. Studies of expression patterns of noncoding RNAs (ncRNAs) could provide useful insight in glioma molecular development. We used the qPCR approach to screen and investigate the expression of lncRNAs that were previously deregulated in other cancer types. The study showed altered expression levels for numerous lncRNAs across histologically different glioma samples. Validation of few lncRNAs showed association of expression levels with histological subtype and/or malignancy grade. We also observed deregulated and subtype-distinctive expression for four lncRNA-associated miRNAs. Expression of few lncRNAs and miRNA was also associated with patients’ survival, showing potential prognostic value. Several ncRNAs, some already related to glioma and some, to the best of our knowledge, investigated for the first time, might be of greater importance in glioma molecular development and progression. Finding the subtype-specific lncRNA and/or miRNA expression patterns may contribute additional information for a more objective classification.
      PubDate: Tue, 12 Sep 2017 07:35:45 +000
       
  • Tissue- and Cell Type-Specific Expression of the Long Noncoding RNA
           Klhl14-AS in Mouse

    • Abstract: lncRNAs are acquiring increasing relevance as regulators in a wide spectrum of biological processes. The extreme heterogeneity in the mechanisms of action of these molecules, however, makes them very difficult to study, especially regarding their molecular function. A novel lncRNA has been recently identified as the most enriched transcript in mouse developing thyroid. Due to its genomic localization antisense to the protein-encoding Klhl14 gene, we named it Klhl14-AS. In this paper, we highlight that mouse Klhl14-AS produces at least five splicing variants, some of which have not been previously described. Klhl14-AS is expressed with a peculiar pattern, characterized by diverse relative abundance of its isoforms in different mouse tissues. We examine the whole expression level of Klhl14-AS in a panel of adult mouse tissues, showing that it is expressed in the thyroid, lung, kidney, testis, ovary, brain, and spleen, although at different levels. In situ hybridization analysis reveals that, in the context of each organ, Klhl14-AS shows a cell type-specific expression. Interestingly, databases report a similar expression profile for human Klhl14-AS. Our observations suggest that this lncRNA could play cell type-specific roles in several organs and pave the way for functional characterization of this gene in appropriate biological contexts.
      PubDate: Sun, 10 Sep 2017 00:00:00 +000
       
  • MicroRNAs as Biomarkers in Thyroid Carcinoma

    • Abstract: Optimal management of patients with thyroid cancer requires the use of sensitive and specific biomarkers. For early diagnosis and effective follow-up, the currently available cytological and serum biomarkers, thyroglobulin and calcitonin, present severe limitations. Research on microRNA expression in thyroid tumors is providing new insights for the development of novel biomarkers that can be used to diagnose thyroid cancer and optimize its management. In this review, we will examine some of the methods commonly used to detect and quantify microRNA in biospecimens from patients with thyroid tumor, as well as the potential applications of these techniques for developing microRNA-based biomarkers for the diagnosis and prognostic evaluation of thyroid cancers.
      PubDate: Wed, 06 Sep 2017 00:00:00 +000
       
  • Biological Function of MicroRNA193a-3p in Health and Disease

    • Abstract: MicroRNAs (miRNAs) are a class of small noncoding RNAs that act mainly as negative regulators of gene expression. Several studies demonstrated that miRNAs take part in numerous biological processes, such as proliferation, apoptosis, and migration. The dysregulation of miRNAs has been frequently observed in different types of disease, including cancer. Here, we provide a comprehensive review on the human miR-193a-3p by considering its role in both physiological and pathological contexts. Different mechanisms involved in regulating miR-193a-3p expression have been reported, including epigenetic modifications and transcription factors. In physiological contexts, miR-193a-3p seemed able to limit proliferation and cell cycle progression in normal cells. Remarkably, several publications demonstrated that miR-193a-3p acted as a tumor suppressor miRNA in cancer by targeting different genes involved in proliferation, apoptosis, migration, invasion, and metastasis. Furthermore, the downregulation of miR-193a-3p has been observed in many primary tumors and altered levels of circulating miR-193a-3p have been identified in serum or plasma of cancer patients and subjects affected by Parkinson’s disease or by schizophrenia. In a clinical perspective, further studies are needed to explore the antitumor effects of the miR-193a-3p mimics delivery and the relevance of this miRNA detection as a possible diagnostic and prognostic biomarker.
      PubDate: Tue, 05 Sep 2017 00:00:00 +000
       
  • Comparative Proteomic Analysis of Paulownia fortunei Response to
           Phytoplasma Infection with Dimethyl Sulfate Treatment

    • Abstract: Paulownia fortunei is a widely cultivated economic forest tree species that is susceptible to infection with phytoplasma, resulting in Paulownia witches’ broom (PaWB) disease. Diseased P. fortunei is characterized by stunted growth, witches’ broom, shortened internodes, and etiolated and smaller leaves. To understand the molecular mechanism of its pathogenesis, we applied isobaric tags for relative and absolute quantitation (iTRAQ) and liquid chromatography coupled with tandem mass spectrometry approaches to study changes in the proteomes of healthy P. fortunei, PaWB-infected P. fortunei, and PaWB-infected P. fortunei treated with 15 mg·L−1 or 75 mg·L−1 dimethyl sulfate. We identified 2969 proteins and 104 and 32 differentially abundant proteins that were phytoplasma infection responsive and dimethyl sulfate responsive, respectively. Based on our analysis of the different proteomes, 27 PaWB-related proteins were identified. The protein-protein interactions of these 27 proteins were analyzed and classified into four groups (photosynthesis-related, energy-related, ribosome-related, and individual proteins). These PaWB-related proteins may help in developing a deeper understanding of how PaWB affects the morphological characteristics of P. fortunei and further establish the mechanisms involved in the response of P. fortunei to phytoplasma.
      PubDate: Tue, 05 Sep 2017 00:00:00 +000
       
  • Overexpression of Chromosome 21 miRNAs May Affect Mitochondrial Function
           in the Hearts of Down Syndrome Fetuses

    • Abstract: Dosage-dependent upregulation of most of chromosome 21 (Hsa21) genes has been demonstrated in heart tissues of fetuses with Down syndrome (DS). Also miRNAs might play important roles in the cardiac phenotype as they are highly expressed in the heart and regulate cardiac development. Five Hsa21 miRNAs have been well studied in the past: miR-99a-5p, miR-125b-2-5p, let-7c-5p, miR-155-5p, and miR-802-5p but few information is available about their expression in trisomic tissues. In this study, we evaluated the expression of these miRNAs in heart tissues from DS fetuses, showing that miR-99a-5p, miR-155-5p, and let-7c-5p were overexpressed in trisomic hearts. To investigate their role, predicted targets were obtained from different databases and cross-validated using the gene expression profiling dataset we previously generated for fetal hearts. Eighty-five targets of let-7c-5p, 33 of miR-155-5p, and 10 of miR-99a-5p were expressed in fetal heart and downregulated in trisomic hearts. As nuclear encoded mitochondrial genes were found downregulated in trisomic hearts and mitochondrial dysfunction is a hallmark of DS phenotypes, we put special attention to let-7c-5p and miR-155-5p targets downregulated in DS fetal hearts and involved in mitochondrial function. The let-7c-5p predicted target SLC25A4/ANT1 was identified as a possible candidate for both mitochondrial and cardiac anomalies.
      PubDate: Tue, 05 Sep 2017 00:00:00 +000
       
  • Exception to the Rule: Genomic Characterization of Naturally Occurring
           Unusual Vibrio cholerae Strains with a Single Chromosome

    • Abstract: The genetic make-up of most bacteria is encoded in a single chromosome while about 10% have more than one chromosome. Among these, Vibrio cholerae, with two chromosomes, has served as a model system to study various aspects of chromosome maintenance, mainly replication, and faithful partitioning of multipartite genomes. Here, we describe the genomic characterization of strains that are an exception to the two chromosome rules: naturally occurring single-chromosome V. cholerae. Whole genome sequence analyses of NSCV1 and NSCV2 (natural single-chromosome vibrio) revealed that the Chr1 and Chr2 fusion junctions contain prophages, IS elements, and direct repeats, in addition to large-scale chromosomal rearrangements such as inversions, insertions, and long tandem repeats elsewhere in the chromosome compared to prototypical two chromosome V. cholerae genomes. Many of the known cholera virulence factors are absent. The two origins of replication and associated genes are generally intact with synonymous mutations in some genes, as are recA and mismatch repair (MMR) genes dam, mutH, and mutL; MutS function is probably impaired in NSCV2. These strains are ideal tools for studying mechanistic aspects of maintenance of chromosomes with multiple origins and other rearrangements and the biological, functional, and evolutionary significance of multipartite genome architecture in general.
      PubDate: Tue, 29 Aug 2017 00:00:00 +000
       
  • Highly Variable Genomic Landscape of Endogenous Retroviruses in the
           C57BL/6J Inbred Strain, Depending on Individual Mouse, Gender, Organ Type,
           and Organ Location

    • Abstract: Transposable repetitive elements, named the “TREome,” represent ~40% of the mouse genome. We postulate that the germ line genome undergoes temporal and spatial diversification into somatic genomes in conjunction with the TREome activity. C57BL/6J inbred mice were subjected to genomic landscape analyses using a TREome probe from murine leukemia virus-type endogenous retroviruses (MLV-ERVs). None shared the same MLV-ERV landscape within each comparison group: (1) sperm and 18 tissues from one mouse, (2) six brain compartments from two females, (3) spleen and thymus samples from four age groups, (4) three spatial tissue sets from two females, and (5) kidney and liver samples from three females and three males. Interestingly, males had more genomic MLV-ERV copies than females; moreover, only in the males, the kidneys had higher MLV-ERV copies than the livers. Perhaps, the mouse-, gender-, and tissue/cell-dependent MLV-ERV landscapes are linked to the individual-specific and dynamic phenotypes of the C57BL/6J inbred population.
      PubDate: Tue, 29 Aug 2017 00:00:00 +000
       
  • HaVec: An Efficient de Bruijn Graph Construction Algorithm for Genome
           Assembly

    • Abstract: Background. The rapid advancement of sequencing technologies has made it possible to regularly produce millions of high-quality reads from the DNA samples in the sequencing laboratories. To this end, the de Bruijn graph is a popular data structure in the genome assembly literature for efficient representation and processing of data. Due to the number of nodes in a de Bruijn graph, the main barrier here is the memory and runtime. Therefore, this area has received significant attention in contemporary literature. Results. In this paper, we present an approach called HaVec that attempts to achieve a balance between the memory consumption and the running time. HaVec uses a hash table along with an auxiliary vector data structure to store the de Bruijn graph thereby improving the total memory usage and the running time. A critical and noteworthy feature of HaVec is that it exhibits no false positive error. Conclusions. In general, the graph construction procedure takes the major share of the time involved in an assembly process. HaVec can be seen as a significant advancement in this aspect. We anticipate that HaVec will be extremely useful in the de Bruijn graph-based genome assembly.
      PubDate: Sun, 27 Aug 2017 00:00:00 +000
       
  • Common Expression Quantitative Trait Loci Shared by Histone Genes

    • Abstract: A genome-wide association study (GWAS) was conducted to examine expression quantitative trait loci (eQTLs) for histone genes. We examined common eQTLs for multiple histone genes in 373 European lymphoblastoid cell lines (LCLs). A linear regression model was employed to identify single-nucleotide polymorphisms (SNPs) associated with expression of the histone genes, and the number of eQTLs was determined by linkage disequilibrium analysis. Additional associations of the identified eQTLs with other genes were also examined. We identified 31 eQTLs for 29 histone genes through genome-wide analysis using 29 histone genes (). Among them, 12 eQTLs were associated with the expression of multiple histone genes. Transcriptome-wide association analysis using the identified eQTLs showed their associations with additional 80 genes (). In particular, expression of RPPH1, SCARNA2, and SCARNA7 genes was associated with 26, 25, and 23 eQTLs, respectively. This study suggests that histone genes shared 12 common eQTLs that might regulate cell cycle-dependent transcription of histone and other genes. Further investigations are needed to elucidate the transcriptional mechanisms of these genes.
      PubDate: Sun, 27 Aug 2017 00:00:00 +000
       
  • Haplotypes for Type, Degree, and Rate of Marbling in Cattle Are Syntenic
           with Human Muscular Dystrophy

    • Abstract: Traditional analyses of a QTL on Bota 19 implicate a surfeit of candidates, but each is of marginal significance in explaining the deposition of healthy, low melting temperature fat within marbled muscle of Wagyu cattle. As an alternative approach, we have used genomic, multigenerational segregation to identify 14 conserved, ancestral 20 Mb haplotypes. These determine the degree and rate of marbling in Wagyu and other breeds of cattle. The melting temperature of intramuscular fat is highly heritable and traceable by haplotyping. Fortunately, for the production of healthy beef, some of these haplotypes are sufficiently penetrant to be expressed in heterozygous crossbreds, thereby allowing selection of sires which will improve the healthiness of beef produced under even harsh climatic conditions. The region of Bota 19 is syntenic to a region of Hosa 17 known to be important in muscle metabolism and in determining susceptibility to a form of human muscular dystrophy.
      PubDate: Thu, 17 Aug 2017 00:00:00 +000
       
  • Comparative Genomic In Situ Hybridization and the Possible Role of
           Retroelements in the Karyotypic Evolution of Three Akodontini Species

    • Abstract: South American Akodontini rodents are characterized by a large number of chromosome rearrangements. Among them, the genus Akodon has been extensively analyzed with classical and molecular cytogenetics, which allowed the identification of a large number of intra- and interspecific chromosomal variation due to Robertsonian rearrangements, pericentric inversions, and heterochromatin additions/deletions. In order to shed some light on the cause of these rearrangements, we comparatively analyzed the karyotypes of three Akodontini species, Akodon cursor (2n = 14, FN = 19), A. montensis (2n = 24, FN = 42), and Necromys lasiurus (2n = 34, FN = 34), after GTG- and CBG-banding. The karyotypes differed by Robertsonian rearrangements, pericentric inversions, centromere repositioning, and heterochromatin variation. Genome comparisons were performed through interspecific fluorescent in situ hybridization (FISH) with total genomic DNAs of each species as probes (GISH). Our results revealed considerable conservation of the euchromatic portions among the three karyotypes suggesting that they mostly differ in their heterochromatic regions. FISH was also performed to assess the distribution of telomeric sequences, long and short interspersed repetitive elements (LINE-1 and B1 SINE) and of the endogenous retrovirus mysTR in the genomes of the three species. The results led us to infer that transposable elements have played an important role in the enormous chromosome variation found in Akodontini.
      PubDate: Wed, 16 Aug 2017 07:04:52 +000
       
  • Aquatic Plant Genomics: Advances, Applications, and Prospects

    • Abstract: Genomics is a discipline in genetics that studies the genome composition of organisms and the precise structure of genes and their expression and regulation. Genomics research has resolved many problems where other biological methods have failed. Here, we summarize advances in aquatic plant genomics with a focus on molecular markers, the genes related to photosynthesis and stress tolerance, comparative study of genomes and genome/transcriptome sequencing technology.
      PubDate: Wed, 16 Aug 2017 03:36:32 +000
       
  • Serum and Brain Metabolomic Variations Reveal Perturbation of Sleep
           Deprivation on Rats and Ameliorate Effect of Total Ginsenoside Treatment

    • Abstract: Sleep loss or sleep deprivation (SD) refers to shorter sleep than average baseline need, and SD has been a serious problem of modern societies which affects health and well-being. Panax ginseng is a well-known traditional Chinese medicine (TCM). Our previous study has demonstrated that total ginsenosides (GS), the extracts from Panax ginseng, could effectively improve cognition and behavior on SD rats. However, little is known about its metabolomic study. In this study, serum and brain metabolomic method based on gas chromatography coupled with mass spectrometry (GC/MS) was employed to evaluate the efficacy and study the mechanism of GS on a rat model of SD. With pattern recognition analysis of serum and brain tissue metabolite profile, a clear separation of the model group and control group was acquired for serum and brain tissue samples; the MGS (model + GS) group showed a tendency of recovering when compared to control group, which was consistent with behavioral and biochemical parameters. 39 and 40 potential biomarkers of brain tissues and serum samples, respectively, were identified and employed to explore the possible mechanism. Our work revealed that GS has significant protective effects on SD, and metabolomics is a useful tool for evaluating efficacy and elucidating mechanism in TCM.
      PubDate: Wed, 16 Aug 2017 00:00:00 +000
       
  • miRNA Expression Profile and Effect of Wenxin Granule in Rats with
           Ligation-Induced Myocardial Infarction

    • Abstract: Wenxin Granule (WXKL) is a traditional Chinese medicine used for treatment of myocardial infarction (MI) and arrhythmias. However, the genomic pathological mechanisms of MI and mechanisms of WXKL are largely unknown. This study aims to investigate a comprehensive miRNA expression profile, and the predicted correlation pathways to be targeted by differentially expressed miRNAs in MI, and mechanisms of WXKL from a gene level. MI rat model was established by a coronary artery ligation surgery. miRNA expression microarrays were performed and the data were deposited in Gene Expression Omnibus (GEO number GSE95855). And, pathway analysis was performed by using the DIANA-miRPath v3.0 online tool. The expressions of miR-1, miR-133, Cx43, and Cx45 were detected by quantitative real-time PCR. It was found that 35 differentially expressed miRNAs and 23 predicted pathways, including miR-1, miR-133, and gap junction pathway, are involved in the pathogenesis of MI. And, WXKL increased the expressions of miR-1 and miR-133, while also increased the mRNA levels of Cx43 and Cx45, and, especially, recovered the Cx43/Cx45 ratio near to normal level. The results suggest that regulatory effects on miR-1, miR-133, Cx43, and Cx45 might be a possible mechanism of WXKL in the treatment of MI at the gene level.
      PubDate: Tue, 15 Aug 2017 00:00:00 +000
       
  • MicroRNA Profiling in Cartilage Ageing

    • Abstract: Osteoarthritis (OA) is the most common age-related joint disorder in man. MicroRNAs (miRNA), a class of small noncoding RNAs, are potential therapeutic targets for regulating molecular mechanisms in both disease and ageing. Whilst there is an increasing amount of research on the roles of miRNAs in ageing, there has been scant research on age-related changes in miRNA in a cartilage. We undertook a microarray study on young and old human cartilages. Findings were validated in an independent cohort. Contrasts between these samples identified twenty differentially expressed miRNAs in a cartilage from old donors, derived from an OA environment which clustered based on OA severity. We identified a number of recognised and novel miRNAs changing in cartilage ageing and OA including miR-126: a potential new candidate with a role in OA pathogenesis. These analyses represent important candidates that have the potential as cartilage ageing and OA biomarkers and therapeutic targets.
      PubDate: Mon, 14 Aug 2017 00:00:00 +000
       
  • The Role of miRNAs as Biomarkers for Pregnancy Outcomes: A Comprehensive
           Review

    • Abstract: Several studies showed that altered expression of the miRNA-ome in maternal circulation or in placental tissue may reflect not only gestational disorders, such as preeclampsia, spontaneous abortion, preterm birth, low birth weight, or macrosomia, but also prenatal exposure to environmental pollutants. Generally, the relationships between environmental exposure, changes in miRNA expression, and gestational disorders are explored separately, producing conflicting findings. However, validation of tissue-accessible biomarkers for the monitoring of adverse pregnancy outcomes needs a systematic methodological approach that takes also into account early-life environmental exposure. To achieve this goal, exposure to xenochemicals, endogenous agents, and diet should be assessed. This study has the aim to provide a comprehensive review on the role of miRNAs as potential biomarkers for adverse pregnancy outcomes and prenatal environmental exposure.
      PubDate: Sun, 13 Aug 2017 00:00:00 +000
       
  • Transcriptome Analysis of Two Different Developmental Stages of Paeonia
           lactiflora Seeds

    • Abstract: Paeonia lactiflora is a herbaceous flower in the family Paeoniaceae with both hypocotyl and epicotyl dormant seeds. We used high-throughput transcriptome sequencing on two different developmental stages of P. lactiflora seeds to identify seed dormancy and germination-related genes. We performed de novo assembly and annotated a total of 123,577 unigenes, which encoded 24,688 putative proteins with 47 GO categories. A total of 10,714 unigenes were annotated in the KEGG database, and 258 pathways were involved in the annotations. A total of 1795 genes were differentially expressed in the functional enrichment analysis. The key genes for seed germination and dormancy, such as GAI1 and ARF, were confirmed by quantitative reverse transcription-polymerase chain reaction analysis. This is the first report of sequencing the P. lactiflora seed transcriptome. Our results provide fundamental frame work and technical support for further selective breeding and cultivation of Paeonia. Our transcriptomic data also serves as the basis for future genetics and genomics research on Paeonia and its closely related species.
      PubDate: Mon, 07 Aug 2017 07:19:12 +000
       
  • Mapping QTL for Root and Shoot Morphological Traits in a Durum
           Wheat × T. dicoccum Segregating Population at Seedling Stage

    • Abstract: A segregating population of 136 recombinant inbred lines derived from a cross between the durum wheat cv. “Simeto” and the T. dicoccum accession “Molise Colli” was grown in soil and evaluated for a number of shoot and root morphological traits. A total of 17 quantitative trait loci (QTL) were identified for shoot dry weight, number of culms, and plant height and for root dry weight, volume, length, surface area, and number of forks and tips, on chromosomes 1B, 2A, 3A, 4B, 5B, 6A, 6B, and 7B. LODs were 2.1 to 21.6, with percent of explained phenotypic variability between 0.07 and 52. Three QTL were mapped to chromosome 4B, one of which corresponds to the Rht-B1 locus and has a large impact on both shoot and root traits (LOD 21.6). Other QTL that have specific effects on root morphological traits were also identified. Moreover, meta-QTL analysis was performed to compare the QTL identified in the “Simeto” × “Molise Colli” segregating population with those described in previous studies in wheat, with three novel QTL defined. Due to the complexity of phenotyping for root traits, further studies will be helpful to validate these regions as targets for breeding programs for optimization of root function for field performance.
      PubDate: Sun, 06 Aug 2017 00:00:00 +000
       
  • A Pilot Genome-Wide Association Study in Postmenopausal Mexican-Mestizo
           Women Implicates the RMND1/CCDC170 Locus Is Associated with Bone Mineral
           Density

    • Abstract: To identify genetic variants influencing bone mineral density (BMD) in the Mexican-Mestizo population, we performed a GWAS for femoral neck (FN) and lumbar spine (LS) in Mexican-Mestizo postmenopausal women. In the discovery sample, 300,000 SNPs were genotyped in a cohort of 411 postmenopausal women and seven SNPs were analyzed in the replication cohort (). The combined results of a meta-analysis from the discovery and replication samples identified two loci, RMND1 (rs6904364, ) and CCDC170 (rs17081341, ), associated with FN BMD. We also compared our results with those of the Genetic Factors for Osteoporosis (GEFOS) Consortium meta-analysis. The comparison revealed two loci previously reported in the GEFOS meta-analysis: SOX6 (rs7128738) and PKDCC (rs11887431) associated with FN and LS BMD, respectively, in our study population. Interestingly, rs17081341 rare in Caucasians (minor allele frequency 
      PubDate: Thu, 03 Aug 2017 00:00:00 +000
       
  • A New Network-Based Strategy for Predicting the Potential miRNA-mRNA
           Interactions in Tumorigenesis

    • Abstract: MicroRNA (miRNA) plays an important role in the degradation and inhibition of mRNAs and is a kind of essential drug targets for cancer therapy. To facilitate the clinical cancer research, we proposed a network-based strategy to identify the cancer-related miRNAs and to predict their targeted genes based on the gene expression profiles. The strategy was validated by using the data sets of acute myeloid leukemia (AML), breast invasive carcinoma (BRCA), and kidney renal clear cell carcinoma (KIRC). The results showed that in the top 20 miRNAs ranked by their degrees, 90.0% (18/20), 70.0% (14/20), and 70.0% (14/20) miRNAs were found to be associated with the cancers for AML, BRCA, and KIRC, respectively. The KEGG pathways and GO terms enriched with the genes that were predicted as the targets of the cancer-related miRNAs were significantly associated with the biological processes of cancers. In addition, several genes, which were predicted to be regulated by more than three miRNAs, were identified to be the potential drug targets annotated by using the human protein atlas database. Our results demonstrated that the proposed strategy can be helpful for predicting the miRNA-mRNA interactions in tumorigenesis and identifying the cancer-related miRNAs as the potential drug targets.
      PubDate: Wed, 02 Aug 2017 00:00:00 +000
       
  • Uncover the Underlying Mechanism of Drug-Induced Myopathy by Using Systems
           Biology Approaches

    • Abstract: Drug-induced myopathy (DIM) is a rare side effect; however, the consequence could be fatal. There are few reports to systematically assess the underlying mechanism of DIM. In this study, we curated the comprehensive DIM drug list based on structured labeling products (SPLs) and carried out the analysis based on chemical structure space, drug protein interaction, side effect space, and transcriptomic profiling space. Some key features are enriched from each of analysis. Specifically, the similarity of DIM drugs is more significant than random chance, which shows that the chemical structure could distinguish the DIM-positive drugs from negatives. The cytochrome P450 (CYP) was identified to be shared by DIM drugs, which indicated the important role of metabolism in DIM. Three pathways including pathways in cancer, MAPK signaling pathway, and GnRH signaling pathway enriched based on transcriptomic analysis may explain the underlying mechanism of DIM. Although the DIM is the current focus of the study, the proposed approaches could be applied to other toxicity assessments and facilitate the safety evaluation.
      PubDate: Mon, 31 Jul 2017 00:00:00 +000
       
  • Genome-Wide Identification and Transcriptional Expression Analysis of
           Cucumber Superoxide Dismutase (SOD) Family in Response to Various Abiotic
           Stresses

    • Abstract: Superoxide dismutase (SOD) proteins are widely present in the plant kingdom and play important roles in different biological processes. However, little is known about the SOD genes in cucumber. In this study, night SOD genes were identified from cucumber (Cucumis sativus) using bioinformatics-based methods, including 5 Cu/ZnSODs, 3 FeSODs, and 1 MnSOD. Gene structure and motif analysis indicated that most of the SOD genes have relatively conserved exon/intron arrangement and motif composition. Phylogenetic analyses with SODs from cucumber and several other species revealed that these SOD proteins can be traced back to two ancestral SODs before the divergence of monocot and dicot plants. Many cis-elements related to stress responses and plant hormones were found in the promoter sequence of each CsSOD gene. Gene expression analysis revealed that most of the CsSOD genes are expressed in almost all the tested tissues. qRT-PCR analysis of 8 selected CsSOD genes showed that these genes could respond to heat, cold, osmotic, and salt stresses. Our results provide a basis for further functional research on SOD gene family in cucumber and facilitate their potential applications in the genetic improvement of cucumber.
      PubDate: Thu, 20 Jul 2017 00:00:00 +000
       
  • Differential MicroRNA Analyses of Burkholderia pseudomallei- and
           Francisella tularensis-Exposed hPBMCs Reveal Potential Biomarkers

    • Abstract: Increasing evidence that microRNAs (miRNAs) play important roles in the immune response against infectious agents suggests that miRNA might be exploitable as signatures of exposure to specific infectious agents. In order to identify potential early miRNA biomarkers of bacterial infections, human peripheral blood mononuclear cells (hPBMCs) were exposed to two select agents, Burkholderia pseudomallei K96243 and Francisella tularensis SHU S4, as well as to the nonpathogenic control Escherichia coli DH5α. RNA samples were harvested at three early time points, 30, 60, and 120 minutes postexposure, then sequenced. RNAseq analyses identified 87 miRNAs to be differentially expressed (DE) in a linear fashion. Of these, 31 miRNAs were tested using the miScript miRNA qPCR assay. Through RNAseq identification and qPCR validation, we identified differentially expressed miRNA species that may be involved in the early response to bacterial infections. Based upon its upregulation at early time points postexposure in two different individuals, hsa-mir-30c-5p is a miRNA species that could be studied further as a potential biomarker for exposure to these gram-negative intracellular pathogens. Gene ontology functional analyses demonstrated that programmed cell death is the first ranking biological process associated with miRNAs that are upregulated in F. tularensis-exposed hPBMCs.
      PubDate: Sun, 16 Jul 2017 00:00:00 +000
       
  • Transcriptome-Based Modeling Reveals that Oxidative Stress Induces
           Modulation of the AtfA-Dependent Signaling Networks in Aspergillus
           nidulans

    • Abstract: To better understand the molecular functions of the master stress-response regulator AtfA in Aspergillus nidulans, transcriptomic analyses of the atfA null mutant and the appropriate control strains exposed to menadione sodium bisulfite- (MSB-), t-butylhydroperoxide- and diamide-induced oxidative stresses were performed. Several elements of oxidative stress response were differentially expressed. Many of them, including the downregulation of the mitotic cell cycle, as the MSB stress-specific upregulation of FeS cluster assembly and the MSB stress-specific downregulation of nitrate reduction, tricarboxylic acid cycle, and ER to Golgi vesicle-mediated transport, showed AtfA dependence. To elucidate the potential global regulatory role of AtfA governing expression of a high number of genes with very versatile biological functions, we devised a model based on the comprehensive transcriptomic data. Our model suggests that an important function of AtfA is to modulate the transduction of stress signals. Although it may regulate directly only a limited number of genes, these include elements of the signaling network, for example, members of the two-component signal transduction systems. AtfA acts in a stress-specific manner, which may increase further the number and diversity of AtfA-dependent genes. Our model sheds light on the versatility of the physiological functions of AtfA and its orthologs in fungi.
      PubDate: Sun, 09 Jul 2017 00:00:00 +000
       
  • Blood Transcriptional Signatures for Disease Progression in a Rat Model of
           Osteoarthritis

    • Abstract: Biomarkers of osteoarthritis (OA) that can accurately diagnose the disease at the earliest stage would significantly support efforts to develop treatments for prevention and early intervention. We have sought to determine the time course of alterations in peripheral blood gene expression profile associated with the development of OA. Blood samples were collected from a tail vein of individual rats with monosodium iodoacetate- (MIA-) induced OA (2, 14, 21, and 28 days after the treatment). We used whole-genome microarrays to reveal OA-related transcriptional alterations of 72 transcripts. Three main groups of coexpressed genes revealed diverse time-dependent profiles of up- and downregulation. Functional links that connect expression of the gradually downregulated genes to the G13 signaling pathway were indicated. The mRNA abundance levels of the identified transcripts were further analyzed in publicly available gene expression dataset obtained from a GARP study cohort of OA patients. We revealed three-gene signature differentially expressed in both rat and human blood (TNK2, KCTD2, and WDR37). The alterations in expression of the selected transcripts in peripheral blood samples of the patients indicate heterogeneity of the OA profiles potentially related to disease progress and severity of clinical symptoms. Our study identifies several potential stage-specific biomarkers of OA progression.
      PubDate: Mon, 03 Jul 2017 00:00:00 +000
       
 
 
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