journal
MENU ▼
Read by QxMD icon Read
search

International Journal of Genomics

journal
https://www.readbyqxmd.com/read/29147648/molecular-crosstalking-among-noncoding-rnas-a-new-network-layer-of-genome-regulation-in-cancer
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/28929105/havec-an-efficient-de-bruijn-graph-construction-algorithm-for-genome-assembly
#14
Md Mahfuzer Rahman, Ratul Sharker, Sajib Biswas, M Sohel Rahman
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28913347/haplotypes-for-type-degree-and-rate-of-marbling-in-cattle-are-syntenic-with-human-muscular-dystrophy
#15
Sally S Lloyd, Edward J Steele, Jose L Valenzuela, Roger L Dawkins
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28900619/aquatic-plant-genomics-advances-applications-and-prospects
#16
REVIEW
Shiqi Hu, Gaojie Li, Jingjing Yang, Hongwei Hou
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.
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28900618/comparative-genomic-in-situ-hybridization-and-the-possible-role-of-retroelements-in-the-karyotypic-evolution-of-three-akodontini-species
#17
Naiara Pereira Araújo, Gustavo Campos Silva Kuhn, Flávia Nunes Vieira, Thaís Queiroz Morcatty, Adriano Pereira Paglia, Marta Svartman
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28900617/serum-and-brain-metabolomic-variations-reveal-perturbation-of-sleep-deprivation-on-rats-and-ameliorate-effect-of-total-ginsenoside-treatment
#18
Xiao-Jun Gou, Fang Cen, Zi-Quan Fan, Ying Xu, Hong-Yi Shen, Ming-Mei Zhou
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...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28894747/mirna-expression-profile-and-effect-of-wenxin-granule-in-rats-with-ligation-induced-myocardial-infarction
#19
Aiming Wu, Lixia Lou, Jianying Zhai, Dongmei Zhang, Limin Chai, Bo Nie, Haiyan Zhu, Yonghong Gao, Hongcai Shang, Mingjing Zhao
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)...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28890892/microrna-profiling-in-cartilage-ageing
#20
Panagiotis Balaskas, Katarzyna Goljanek-Whysall, Peter Clegg, Yongxiang Fang, Andy Cremers, Pieter Emans, Tim Welting, Mandy Peffers
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...
2017: International Journal of Genomics
journal
journal
47642
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"