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International Journal of Genomics

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https://www.readbyqxmd.com/read/29333433/vitamin-d-receptor-gene-polymorphisms-influence-t1d-susceptibility-among-pakistanis
#1
Maryam Mukhtar, Andleeb Batool, Abdul Wajid, Iram Qayyum
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29318138/enriching-genomic-resources-and-transcriptional-profile-analysis-of-miscanthus-sinensis-under-drought-stress-based-on-rna-sequencing
#2
Gang Nie, Linkai Huang, Xiao Ma, Zhongjie Ji, Yajie Zhang, Lu Tang, Xinquan Zhang
Miscanthus × giganteus is wildly cultivated as a potential biofuel feedstock around the world; however, the narrow genetic basis and sterile characteristics have become a limitation for its utilization. As a progenitor of M. × giganteus, M. sinensis is widely distributed around East Asia providing well abiotic stress tolerance. To enrich the M. sinensis genomic databases and resources, we sequenced and annotated the transcriptome of M. sinensis by using an Illumina HiSeq 2000 platform. Approximately 316 million high-quality trimmed reads were generated from 349 million raw reads, and a total of 114,747 unigenes were obtained after de novo assembly...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29318137/huoxuejiedu-formula-alleviates-diabetic-retinopathy-in-rats-by-inhibiting-socs3-stat3-and-timp1-a2m-pathways
#3
Hongliang Wang, Wei Xing, Shijie Tang, Zhenglin Wang, Tiantian Lv, Yan Wu, Shuzhen Guo, Chun Li, Jing Han, Ruixin Zhu, Wei Wang
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29250532/insights-on-genomic-and-molecular-alterations-in-multiple-myeloma-and-their-incorporation-towards-risk-adapted-treatment-strategy-concise-clinical-review
#4
REVIEW
Taiga Nishihori, Kenneth Shain
Although recent advances in novel treatment approaches and therapeutics have shifted the treatment landscape of multiple myeloma, it remains an incurable plasma cell malignancy. Growing knowledge of the genome and expressed genomic information characterizing the biologic behavior of multiple myeloma continues to accumulate. However, translation and incorporation of vast molecular understanding of complex tumor biology to deliver personalized and precision treatment to cure multiple myeloma have not been successful to date...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29234674/microrna-in-glioblastoma-an-overview
#5
REVIEW
Barbara Banelli, Alessandra Forlani, Giorgio Allemanni, Anna Morabito, Maria Pia Pistillo, Massimo Romani
Glioblastoma is the most aggressive brain tumor and, even with the current multimodal therapy, is an invariably lethal cancer with a life expectancy that depends on the tumor subtype but, even in the most favorable cases, rarely exceeds 2 years. Epigenetic factors play an important role in gliomagenesis, are strong predictors of outcome, and are important determinants for the resistance to radio- and chemotherapy. The latest addition to the epigenetic machinery is the noncoding RNA (ncRNA), that is, RNA molecules that are not translated into a protein and that exert their function by base pairing with other nucleic acids in a reversible and nonmutational mode...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29201893/evidence-of-the-complexity-of-gene-expression-analysis-in-fish-wild-populations
#6
Mbaye Tine
The present work examines the induction of the band 3 anion transport protein, mitogen-activated protein kinase, and lactate dehydrogenase, respectively related to osmolyte transport, cell volume regulation, and energy production in the gills of two tilapia strains exposed to either freshwater or hypersaline water. Overall, genes showed similar expression patterns between strains. However, a wild population survey across a range of natural habitats and salinities did not reveal the expected patterns. Although significant, the correlations between gene expression and salinity were slightly ambiguous and did not show any link with phenotypic differences in life history traits previously reported between the same populations...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29181384/identification-and-characterization-of-the-diverse-stress-responsive-r2r3-rmyb-transcription-factor-from-hibiscus-sabdariffa-l
#7
Bahaeldeen Babikar Mohamed, Beenish Aftab, Muhammad Bilal Sarwar, Bushra Rashid, Zarnab Ahmad, Sameera Hassan, Tayyab Husnain
Various regulatory proteins play a fundamental role to manage the healthy plant growth under stress conditions. Differential display reverse transcriptase PCR and random amplification of cDNA ends (RACE) was used to explore the osmotic stress-responsive transcripts. We identified and characterized the salt stress-responsive R2R3 type RMYB transcription factor from Hibiscus sabdariffa which has an open reading frame of 690 bp, encoding 229 long chain amino acids. In silico analysis confirmed the conserved R2 and R3 domain as well as an NLS-1 localization site...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29147648/molecular-crosstalking-among-noncoding-rnas-a-new-network-layer-of-genome-regulation-in-cancer
#8
REVIEW
Marco Ragusa, Cristina Barbagallo, Duilia Brex, Angela Caponnetto, Matilde Cirnigliaro, Rosalia Battaglia, Davide Barbagallo, Cinzia Di Pietro, Michele Purrello
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29138748/identifying-novel-glioma-associated-noncoding-rnas-by-their-expression-profiles
#9
Alenka Matjašič, Mojca Tajnik, Emanuela Boštjančič, Mara Popović, Boštjan Matos, Damjan Glavač
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29119102/the-transcriptional-network-structure-of-a-myeloid-cell-a-computational-approach
#10
Jesús Espinal-Enríquez, Daniel González-Terán, Enrique Hernández-Lemus
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29104869/genomic-survey-characterization-and-expression-profile-analysis-of-the-sbp-genes-in-pineapple-ananas-comosus-l
#11
Hina Ali, Yanhui Liu, Syed Muhammad Azam, Zia Ur Rahman, S V G N Priyadarshani, Weimin Li, Xinyu Huang, Bingyan Hu, Junjie Xiong, Umair Ali, Yuan Qin
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29085832/the-mirna-pull-out-assay-as-a-method-to-validate-the-mir-28-5p-targets-identified-in-other-tumor-contexts-in-prostate-cancer
#12
Milena Rizzo, Gabriele Berti, Francesco Russo, Monica Evangelista, Marco Pellegrini, Giuseppe Rainaldi
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29082235/tissue-and-cell-type-specific-expression-of-the-long-noncoding-rna-klhl14-as-in-mouse
#13
Sara Carmela Credendino, Nicole Lewin, Miriane de Oliveira, Swaraj Basu, Barbara D'Andrea, Elena Amendola, Luigi Di Guida, Antonio Nardone, Remo Sanges, Mario De Felice, Gabriella De Vita
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29057256/overexpression-of-chromosome-21-mirnas-may-affect-mitochondrial-function-in-the-hearts-of-down-syndrome-fetuses
#14
Antonella Izzo, Rosanna Manco, Tiziana de Cristofaro, Ferdinando Bonfiglio, Rita Cicatiello, Nunzia Mollo, Marco De Martino, Rita Genesio, Mariastella Zannini, Anna Conti, Lucio Nitsch
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29038787/comparative-proteomic-analysis-of-paulownia-fortunei-response-to-phytoplasma-infection-with-dimethyl-sulfate-treatment
#15
Zhen Wei, Zhe Wang, Xiaoyu Li, Zhenli Zhao, Minjie Deng, Yanpeng Dong, Xibing Cao, Guoqiang Fan
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29038786/micrornas-as-biomarkers-in-thyroid-carcinoma
#16
REVIEW
Marilena Celano, Francesca Rosignolo, Valentina Maggisano, Valeria Pecce, Michelangelo Iannone, Diego Russo, Stefania Bulotta
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/29038785/biological-function-of-microrna193a-3p-in-health-and-disease
#17
REVIEW
Ilaria Grossi, Alessandro Salvi, Edoardo Abeni, Eleonora Marchina, Giuseppina De Petro
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28951866/exception-to-the-rule-genomic-characterization-of-naturally-occurring-unusual-vibrio-cholerae-strains-with-a-single-chromosome
#18
Gary Xie, Shannon L Johnson, Karen W Davenport, Mathumathi Rajavel, Torsten Waldminghaus, John C Detter, Patrick S Chain, Shanmuga Sozhamannan
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28951865/highly-variable-genomic-landscape-of-endogenous-retroviruses-in-the-c57bl-6j-inbred-strain-depending-on-individual-mouse-gender-organ-type-and-organ-location
#19
Kang-Hoon Lee, Debora Lim, David Greenhalgh, Kiho Cho
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28929106/common-expression-quantitative-trait-loci-shared-by-histone-genes
#20
Hanseol Kim, Yujin Suh, Chaeyoung Lee
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...
2017: International Journal of Genomics
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