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Frontiers in Genetics

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https://www.readbyqxmd.com/read/28210267/mir-30-family-potentially-targeting-pi3k-siah2-predicted-interaction-network-represents-a-novel-putative-theranostic-panel-in-non-small-cell-lung-cancer
#1
Lawrence W C Chan, Fengfeng Wang, Fei Meng, Lili Wang, Sze Chuen Cesar Wong, Joseph S K Au, Sijun Yang, William C S Cho
Non-small cell lung cancer (NSCLC) comprises about 84% of all lung cancers. Many treatment options are available but the survival rate is still very low due to drug resistance. It has been found that phosphoinositide-3-kinase (PI3K) affects sensitivity to tyrosine kinase inhibitors (TKIs), including gefitinib and erlotinib. Expression level of seven in absentia homolog 2 (SIAH2), an E3 ubiquitin-protein ligase, is upregulated in NSCLC and correlated with tumor grade. However, the relationship between PI3K and SIAH2 remains unclear and therefore it is not known whether they can act as treatment co-targets and theranostic dual markers for overcoming TKI resistance...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28197171/genome-wide-microrna-binding-site-variation-between-extinct-wild-aurochs-and-modern-cattle-identifies-candidate-microrna-regulated-domestication-genes
#2
Martin Braud, David A Magee, Stephen D E Park, Tad S Sonstegard, Sinead M Waters, David E MacHugh, Charles Spillane
The domestication of cattle from the now-extinct wild aurochs (Bos primigenius) involved selection for physiological and behavioral traits, with underlying genetic factors that remain largely unknown. Non-coding microRNAs have emerged as key regulators of the spatio-temporal expression of target genes controlling mammalian growth and development, including in livestock species. During the domestication process, selection of mutational changes in miRNAs and/or miRNA binding sites could have provided a mechanism to generate some of the traits that differentiate domesticated cattle from wild aurochs...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28194159/role-of-ucp1-gene-variants-in-interethnic-differences-in-the-development-of-cardio-metabolic-diseases
#3
Andreas D Flouris, Yulii V Shidlovskii, Alexander V Shaposhnikov, Levon Yepiskoposyan, Liliya Nadolnik, Lidia Karabon, Anna Kowalska, Andres E Carrillo, George S Metsios, Paraskevi Sakellariou
Cardio-metabolic diseases (CMDs) comprise a cluster of risk factors that contribute to chronic pathological conditions with adverse consequences for cardiovascular function and metabolic processes. A wide range of CMD prevalence rates among different ethnic groups has been documented. In view of accumulated evidence, there is a trend toward increasing CMD prevalence rates in Eastern Europe and Western Asia. Numerous studies have revealed an association between uncoupling protein 1 (UCP1) gene variants and CMDs...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28194158/role-and-regulation-of-acc-deaminase-gene-in-sinorhizobium-meliloti-is-it-a-symbiotic-rhizospheric-or-endophytic-gene
#4
Alice Checcucci, Elisa Azzarello, Marco Bazzicalupo, Anna De Carlo, Giovanni Emiliani, Stefano Mancuso, Giulia Spini, Carlo Viti, Alessio Mengoni
Plant-associated bacteria exhibit a number of different strategies and specific genes allow bacteria to communicate and metabolically interact with plant tissues. Among the genes found in the genomes of plant-associated bacteria, the gene encoding the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS) is one of the most diffused. This gene is supposed to be involved in the cleaving of plant-produced ACC, the precursor of the plant stress-hormone ethylene toning down the plant response to infection...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28179914/cell-cycle-and-cell-size-dependent-gene-expression-reveals-distinct-subpopulations-at-single-cell-level
#5
Soheila Dolatabadi, Julián Candia, Nina Akrap, Christoffer Vannas, Tajana Tesan Tomic, Wolfgang Losert, Göran Landberg, Pierre Åman, Anders Ståhlberg
Cell proliferation includes a series of events that is tightly regulated by several checkpoints and layers of control mechanisms. Most studies have been performed on large cell populations, but detailed understanding of cell dynamics and heterogeneity requires single-cell analysis. Here, we used quantitative real-time PCR, profiling the expression of 93 genes in single-cells from three different cell lines. Individual unsynchronized cells from three different cell lines were collected in different cell cycle phases (G0/G1 - S - G2/M) with variable cell sizes...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28174593/glucose-driven-changes-in-beta-cell-identity-are-important-for-function-and-possibly-autoimmune-vulnerability-during-the-progression-of-type-1-diabetes
#6
Gordon C Weir, Susan Bonner-Weir
This commentary explores the hypothesis that when autoimmunity leads to a fall of beta cell mass during the progression of type 1 diabetes (T1D), rising glucose levels cause major changes in beta cell identity. This then leads to profound changes in secretory function and less well-understood changes in beta cell susceptibility to autoimmune destruction, which may influence of rate of progression of beta cell killing.
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28167955/corrigendum-enhancement-of-rna-directed-dna-methylation-of-a-transgene-by-simultaneously-downregulating-a-ros1-ortholog-using-a-virus-vector-in-nicotiana-benthamiana
#7
Shungo Otagaki, Megumi Kasai, Chikara Masuta, Akira Kanazawa
[This corrects the article on p. 44 in vol. 4, PMID: 23565118.].
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28119737/corrigendum-reference-cells-and-ploidy-in-the-comet-assay
#8
Gunnar Brunborg, Andrew Collins, Anne Graupner, Kristine B Gutzkow, Ann-Karin Olsen
[This corrects the article on p. 61 in vol. 6, PMID: 25774164.].
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28123396/mirnas-in-%C3%AE-cell-development-identity-and-disease
#9
REVIEW
Aida Martinez-Sanchez, Guy A Rutter, Mathieu Latreille
Pancreatic β-cells regulate glucose metabolism by secreting insulin, which in turn stimulates the utilization or storage of the sugar by peripheral tissues. Insulin insufficiency and a prolonged period of insulin resistance are usually the core components of type 2 diabetes (T2D). Although, decreased insulin levels in T2D have long been attributed to a decrease in β-cell function and/or mass, this model has recently been refined with the recognition that a loss of β-cell "identity" and dedifferentiation also contribute to the decline in insulin production...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/28119736/recent-positive-selection-in-genes-of-the-mammalian-epidermal-differentiation-complex-locus
#10
Zane A Goodwin, Cristina de Guzman Strong
The epidermal differentiation complex (EDC) is the most rapidly evolving locus in the human genome compared to that of the chimpanzee. Yet the EDC genes that are undergoing positive selection across mammals and in humans are not known. We sought to identify the positively selected genetic variants and determine the evolutionary events of the EDC using mammalian-wide and clade-specific branch- and branch-site likelihood ratio tests and a genetic algorithm (GA) branch test. Significant non-synonymous substitutions were found in filaggrin, SPRR4, LELP1, and S100A2 genes across 14 mammals...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/28119735/extending-the-r-library-proper-to-enable-power-calculations-for-isoform-level-analysis-with-ebseq
#11
Amadou Gaye
RNA-Sequencing (RNA-Seq) has become a routine technology for investigating gene expression differences in comparative transcriptomic studies. Differential expression (DE) analysis of the isoforms of genes is just emerging now that expression (read counts) can be estimated with higher accuracy at the isoform level. Estimating the statistical power that can be achieved with a specific number of repeats is a key step in RNA-Seq analysis. The R library proper was developed to provide realistic empirical power analysis...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/28119734/advances-in-gut-microbiome-research-opening-new-strategies-to-cope-with-a-western-lifestyle
#12
REVIEW
Gina P Rodriguez-Castaño, Alejandro Caro-Quintero, Alejandro Reyes, Fernando Lizcano
The "westernization" of global eating and lifestyle habits is associated with the growing rate of chronic diseases, mainly cardiovascular diseases, cancer, type 2 diabetes mellitus, and respiratory diseases. The primary prevention approach is to make nutritional and behavioral changes, however, there is another important determinant of our health that only recently has been considered and is the presence of beneficial microorganisms and their products in our gastrointestinal tract. Microorganisms living in our body can alter the fate of food, drugs, hormones, and xenobiotics, and recent studies point to the use of microorganisms that can counteract the harmful effects of certain compounds introduced or produced endogenously in our body...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/28111590/a-theory-for-the-origin-of-human-menopause
#13
Mike Takahashi, Rama S Singh, John Stone
A complete and compelling evolutionary explanation for the origin of human menopause is wanting. Menopause onset is defined clinically as the final menses, confirmed after 1 year without menstruation. The theory proposed herein explains at multiple levels - ultimately genetic but involving (1) behavioral, (2) life history, and (3) social changes - the origin and evolution of menopause in women. Individuals in Lower Paleolithic human populations were characterized by short lifespans with diminished late-age survival and fertility, similar to contemporary chimpanzees, and thence were subject to three changes...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/28096806/a-systems-approach-implicates-a-brain-mitochondrial-oxidative-homeostasis-co-expression-network-in-genetic-vulnerability-to-alcohol-withdrawal
#14
Nicole A R Walter, DeAunne L Denmark, Laura B Kozell, Kari J Buck
Genetic factors significantly affect vulnerability to alcohol dependence (alcoholism). We previously identified quantitative trait loci on distal mouse chromosome 1 with large effects on predisposition to alcohol physiological dependence and associated withdrawal following both chronic and acute alcohol exposure in mice (Alcdp1 and Alcw1, respectively). We fine-mapped these loci to a 1.1-1.7 Mb interval syntenic with human 1q23.2-23.3. Alcw1/Alcdp1 interval genes show remarkable genetic variation among mice derived from the C57BL/6J and DBA/2J strains, the two most widely studied genetic animal models for alcohol-related traits...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/28083017/distribution-of-hydrogenases-in-cyanobacteria-a-phylum-wide-genomic-survey
#15
Vincenzo Puggioni, Sébastien Tempel, Amel Latifi
Microbial Molecular hydrogen (H2) cycling plays an important role in several ecological niches. Hydrogenases (H2ases), enzymes involved in H2 metabolism, are of great interest for investigating microbial communities, and producing BioH2. To obtain an overall picture of the genetic ability of Cyanobacteria to produce H2ases, we conducted a phylum wide analysis of the distribution of the genes encoding these enzymes in 130 cyanobacterial genomes. The concomitant presence of the H2ase and genes involved in the maturation process, and that of well-conserved catalytic sites in the enzymes were the three minimal criteria used to classify a strain as being able to produce a functional H2ase...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/28083016/genomic-selection-in-the-era-of-next-generation-sequencing-for-complex-traits-in-plant-breeding
#16
REVIEW
Javaid A Bhat, Sajad Ali, Romesh K Salgotra, Zahoor A Mir, Sutapa Dutta, Vasudha Jadon, Anshika Tyagi, Muntazir Mushtaq, Neelu Jain, Pradeep K Singh, Gyanendra P Singh, K V Prabhu
Genomic selection (GS) is a promising approach exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. In plant breeding, it provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost-benefit balance was an important consideration for GS to work in crop plants. Availability of genome-wide high-throughput, cost-effective and flexible markers, having low ascertainment bias, suitable for large population size as well for both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/28083015/comparison-of-multiple-methods-for-determination-of-fcgr3a-b-genomic-copy-numbers-in-hapmap-asian-populations-with-two-public-databases
#17
Yuan-Yuan Qi, Xu-Jie Zhou, Ding-Fang Bu, Ping Hou, Ji-Cheng Lv, Hong Zhang
Low FCGR3 copy numbers (CNs) has been associated with susceptibility to several systemic autoimmune diseases. However, inconsistent associations were reported and errors caused by shaky methods were suggested to be the major causes. In large scale case control association studies, robust copy number determination method is thus warranted, which was the main focus of the current study. In the present study, FCGR3 CNs of 90 HapMap Asians were firstly checked using four assays including paralog ratio test combined with restriction enzyme digest variant ratio (PRT-REDVR), real-time quantitative (qPCR) using TaqMan assay, real-time qPCR using SYBR Green dye and short tenden repeat (STR)...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/28083014/genotyping-by-sequencing-uncovers-the-introgression-alien-segments-associated-with-sclerotinia-basal-stalk-rot-resistance-from-wild-species-i-helianthus-argophyllus-and-h-petiolaris
#18
Lili Qi, Yunming Long, Zahirul I Talukder, Gerald J Seiler, Charles C Block, Thomas J Gulya
Basal stalk rot (BSR), caused by Sclerotinia sclerotiorum, is a devastating disease in sunflower worldwide. The progress of breeding for Sclerotinia BSR resistance has been hampered due to the lack of effective sources of resistance for cultivated sunflower. Our objective was to transfer BSR resistance from wild annual Helianthus species into cultivated sunflower and identify the introgressed alien segments associated with BSR resistance using a genotyping-by-sequencing (GBS) approach. The initial crosses were made between the nuclear male sterile HA 89 with the BSR resistant plants selected from wild Helianthus argophyllus and H...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/28066501/adipose-bone-marrow-and-synovial-joint-derived-mesenchymal-stem-cells-for-cartilage-repair
#19
REVIEW
Christopher R Fellows, Csaba Matta, Roza Zakany, Ilyas M Khan, Ali Mobasheri
Current cell-based repair strategies have proven unsuccessful for treating cartilage defects and osteoarthritic lesions, consequently advances in innovative therapeutics are required and mesenchymal stem cell-based (MSC) therapies are an expanding area of investigation. MSCs are capable of differentiating into multiple cell lineages and exerting paracrine effects. Due to their easy isolation, expansion, and low immunogenicity, MSCs are an attractive option for regenerative medicine for joint repair. Recent studies have identified several MSC tissue reservoirs including in adipose tissue, bone marrow, cartilage, periosteum, and muscle...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/28018425/the-decay-of-disease-association-with-declining-linkage-disequilibrium-a-fine-mapping-theorem
#20
Mehdi Maadooliat, Naveen K Bansal, Jiblal Upadhya, Manzur R Farazi, Xiang Li, Max M He, Scott J Hebbring, Zhan Ye, Steven J Schrodi
Several important and fundamental aspects of disease genetics models have yet to be described. One such property is the relationship of disease association statistics at a marker site closely linked to a disease causing site. A complete description of this two-locus system is of particular importance to experimental efforts to fine map association signals for complex diseases. Here, we present a simple relationship between disease association statistics and the decline of linkage disequilibrium from a causal site...
2016: Frontiers in Genetics
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