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Frontiers in Genetics

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https://www.readbyqxmd.com/read/27920798/evolutionary-and-functional-features-of-copy-number-variation-in-the-cattle-genome
#1
Brittney N Keel, Amanda K Lindholm-Perry, Warren M Snelling
Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27920797/genome-wide-association-study-for-identifying-loci-that-affect-fillet-yield-carcass-and-body-weight-traits-in-rainbow-trout-oncorhynchus-mykiss
#2
Dianelys Gonzalez-Pena, Guangtu Gao, Matthew Baranski, Thomas Moen, Beth M Cleveland, P Brett Kenney, Roger L Vallejo, Yniv Palti, Timothy D Leeds
Fillet yield (FY, %) is an economically-important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has received little attention in breeding programs because it is difficult to measure on a large number of fish and cannot be directly measured on breeding candidates. The recent development of a high-density SNP array for rainbow trout has provided the needed tool for studying the underlying genetic architecture of this trait. A genome-wide association study (GWAS) was conducted for FY, body weight at 10 (BW10) and 13 (BW13) months post-hatching, head-off carcass weight (CAR), and fillet weight (FW) in a pedigreed rainbow trout population selectively bred for improved growth performance...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27917194/a-network-approach-of-gene-co-expression-in-the-zea-mays-aspergillus-flavus-pathosystem-to-map-host-pathogen-interaction-pathways
#3
Bryan M Musungu, Deepak Bhatnagar, Robert L Brown, Gary A Payne, Greg OBrian, Ahmad M Fakhoury, Matt Geisler
A gene co-expression network (GEN) was generated using a dual RNA-seq study with the fungal pathogen Aspergillus flavus and its plant host Zea mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network revealed a high degree of connectivity in many of the previously recognized pathways in Z. mays such as jasmonic acid, ethylene, and reactive oxygen species (ROS). For the pathogen A. flavus, a link between aflatoxin production and vesicular transport was identified within the network...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27917193/dna-damage-response-and-autophagy-a-meaningful-partnership
#4
REVIEW
Aristides G Eliopoulos, Sophia Havaki, Vassilis G Gorgoulis
Autophagy and the DNA damage response (DDR) are biological processes essential for cellular and organismal homeostasis. Herein, we summarize and discuss emerging evidence linking DDR to autophagy. We highlight published data suggesting that autophagy is activated by DNA damage and is required for several functional outcomes of DDR signaling, including repair of DNA lesions, senescence, cell death, and cytokine secretion. Uncovering the mechanisms by which autophagy and DDR are intertwined provides novel insight into the pathobiology of conditions associated with accumulation of DNA damage, including cancer and aging, and novel concepts for the development of improved therapeutic strategies against these pathologies...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27917192/mining-centuries-old-in-situ-conserved-turkish-wheat-landraces-for-grain-yield-and-stripe-rust-resistance-genes
#5
Deepmala Sehgal, Susanne Dreisigacker, Savaş Belen, Ümran Küçüközdemir, Zafer Mert, Emel Özer, Alexey Morgounov
Wheat landraces in Turkey are an important genetic resource for wheat improvement. An exhaustive 5-year (2009-2014) effort made by the International Winter Wheat Improvement Programme (IWWIP), a cooperative program between the Ministry of Food, Agriculture and Livestock of Turkey, the International Center for Maize and Wheat Improvement (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA), led to the collection and documentation of around 2000 landrace populations from 55 provinces throughout Turkey...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27909446/functional-toxicogenomic-profiling-expands-insight-into-modulators-of-formaldehyde-toxicity-in-yeast
#6
Matthew North, Brandon D Gaytán, Carlos Romero, Vanessa Y De La Rosa, Alex Loguinov, Martyn T Smith, Luoping Zhang, Chris D Vulpe
Formaldehyde (FA) is a commercially important chemical with numerous and diverse uses. Accordingly, occupational and environmental exposure to FA is prevalent worldwide. Various adverse effects, including nasopharyngeal, sinonasal, and lymphohematopoietic cancers, have been linked to FA exposure, prompting designation of FA as a human carcinogen by U.S. and international scientific entities. Although the mechanism(s) of FA toxicity have been well studied, additional insight is needed in regard to the genetic requirements for FA tolerance...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27899935/editorial-advances-in-genomics-and-epigenomics-of-social-insects
#7
EDITORIAL
Greg J Hunt, Juergen R Gadau
No abstract text is available yet for this article.
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27895664/application-of-genomic-technologies-to-the-breeding-of-trees
#8
REVIEW
Maria L Badenes, Angel Fernández I Martí, Gabino Ríos, María J Rubio-Cabetas
The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27895663/mir-30a-5p-overexpression-may-overcome-egfr-inhibitor-resistance-through-regulating-pi3k-akt-signaling-pathway-in-non-small-cell-lung-cancer-cell-lines
#9
Fei Meng, Fengfeng Wang, Lili Wang, S C Cesar Wong, William C S Cho, Lawrence W C Chan
Lung cancer is one of the most common deadly diseases worldwide, most of which is non-small cell lung cancer (NSCLC). The epidermal growth factor receptor (EGFR) mutant NSCLCs frequently respond to the EGFR tyrosine kinase inhibitors (EGFR-TKIs) treatment, such as Gefitinib and Erlotinib, but the development of acquired resistance limits the utility. Multiple resistance mechanisms have been explored, e.g., the activation of alternative tyrosine kinase receptors (TKRs) sharing similar downstream pathways to EGFR...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27895662/muscle-enriched-micrornas-isolated-from-whole-blood-are-regulated-by-exercise-and-are-potential-biomarkers-of-cardiorespiratory-fitness
#10
Joshua Denham, Priscilla R Prestes
MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression post-transcriptionally. Evidence indicating miRNAs influence exercise-induced health and performance adaptations is mounting. Circulating miRNAs are responsible for intercellular communication and could serve as biomarkers for disease and exercise-related traits. Such biomarkers would contribute to exercise screening, monitoring, and the development of personalized exercise prescription. Accordingly, we investigated the impact of long-term strenuous aerobic exercise training and a single bout of maximal aerobic exercise on five muscle-enriched miRNAs implicated in exercise adaptations (miR-1, miR-133a, miR-181a, miR-486, and miR-494)...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27895661/the-genome-conformation-as-an-integrator-of-multi-omic-data-the-example-of-damage-spreading-in-cancer
#11
Fabio Tordini, Marco Aldinucci, Luciano Milanesi, Pietro Liò, Ivan Merelli
Publicly available multi-omic databases, in particular if associated with medical annotations, are rich resources with the potential to lead a rapid transition from high-throughput molecular biology experiments to better clinical outcomes for patients. In this work, we propose a model for multi-omic data integration (i.e., genetic variations, gene expression, genome conformation, and epigenetic patterns), which exploits a multi-layer network approach to analyse, visualize, and obtain insights from such biological information, in order to use achieved results at a macroscopic level...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27877193/a-combined-linkage-and-exome-sequencing-analysis-for-electrocardiogram-parameters-in-the-erasmus-rucphen-family-study
#12
Claudia T Silva, Irina V Zorkoltseva, Najaf Amin, Ayşe Demirkan, Elisabeth M van Leeuwen, Jan A Kors, Marten van den Berg, Bruno H Stricker, André G Uitterlinden, Anatoly V Kirichenko, Jacqueline C M Witteman, Rob Willemsen, Ben A Oostra, Tatiana I Axenovich, Cornelia M van Duijn, Aaron Isaacs
Electrocardiogram (ECG) measurements play a key role in the diagnosis and prediction of cardiac arrhythmias and sudden cardiac death. ECG parameters, such as the PR, QRS, and QT intervals, are known to be heritable and genome-wide association studies of these phenotypes have been successful in identifying common variants; however, a large proportion of the genetic variability of these traits remains to be elucidated. The aim of this study was to discover loci potentially harboring rare variants utilizing variance component linkage analysis in 1547 individuals from a large family-based study, the Erasmus Rucphen Family Study (ERF)...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27877192/pure-and-confounded-effects-of-causal-snps-on-longevity-insights-for-proper-interpretation-of-research-findings-in-gwas-of-populations-with-different-genetic-structures
#13
Anatoliy I Yashin, Ilya Zhbannikov, Liubov Arbeeva, Konstantin G Arbeev, Deqing Wu, Igor Akushevich, Arseniy Yashkin, Mikhail Kovtun, Alexander M Kulminski, Eric Stallard, Irina Kulminskaya, Svetlana Ukraintseva
This paper shows that the effects of causal SNPs on lifespan, estimated through GWAS, may be confounded and the genetic structure of the study population may be responsible for this effect. Simulation experiments show that levels of linkage disequilibrium (LD) and other parameters of the population structure describing connections between two causal SNPs may substantially influence separate estimates of the effect of the causal SNPs on lifespan. This study suggests that differences in LD levels between two causal SNP loci within two study populations may contribute to the failure to replicate previous GWAS findings...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27857721/circulating-plasma-micrornas-as-diagnostic-markers-for-nsclc
#14
REVIEW
Jinpao Hou, Fei Meng, Lawrence W C Chan, William C S Cho, S C Cesar Wong
Lung cancer is the most common cause of cancer deaths all over the world, in which non-small cell lung cancer (NSCLC) accounts for ~85% of cases. It is well known that microRNAs (miRNAs) play a critical role in various cellular processes, mediating post-transcriptional silencing either by mRNA degradation through binding the 3' UTR of target mRNA or by translational inhibition of the protein. In the past decade, miRNAs have also been increasingly identified in biological fluids such as human serum or plasma known as circulating or cell-free miRNAs, and may function as non-invasive diagnostic markers for various cancer types including NSCLC...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27853466/editorial-small-non-coding-rnas-in-streptococci
#15
EDITORIAL
Mohamed A Zorgani, Emilie Camiade, Roland Quentin, Marie-Frédérique Lartigue
No abstract text is available yet for this article.
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27853465/epigenetic-dna-methylation-profiling-with-msre-a-quantitative-ngs-approach-using-a-parkinson-s-disease-test-case
#16
Adam G Marsh, Matthew T Cottrell, Morton F Goldman
Epigenetics is a rapidly developing field focused on deciphering chemical fingerprints that accumulate on human genomes over time. As the nascent idea of precision medicine expands to encompass epigenetic signatures of diagnostic and prognostic relevance, there is a need for methodologies that provide high-throughput DNA methylation profiling measurements. Here we report a novel quantification methodology for computationally reconstructing site-specific CpG methylation status from next generation sequencing (NGS) data using methyl-sensitive restriction endonucleases (MSRE)...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27833639/expression-of-concern-enhancement-of-rna-directed-dna-methylation-of-a-transgene-by-simultaneously-downregulating-a-ros1-ortholog-using-a-virus-vector-in-nicotiana-benthamiana
#17
COMMENT
https://www.readbyqxmd.com/read/27826318/epigenetic-inheritance-across-the-landscape
#18
REVIEW
Amy V Whipple, Liza M Holeski
The study of epigenomic variation at the landscape-level in plants may add important insight to studies of adaptive variation. A major goal of landscape genomic studies is to identify genomic regions contributing to adaptive variation across the landscape. Heritable variation in epigenetic marks, resulting in transgenerational plasticity, can influence fitness-related traits. Epigenetic marks are influenced by the genome, the environment, and their interaction, and can be inherited independently of the genome...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27826317/dna-damage-from-chronic-inflammation-to-age-related-deterioration
#19
REVIEW
Anna Ioannidou, Evi Goulielmaki, George A Garinis
To lessen the "wear and tear" of existence, cells have evolved mechanisms that continuously sense DNA lesions, repair DNA damage and restore the compromised genome back to its native form. Besides genome maintenance pathways, multicellular organisms may also employ adaptive and innate immune mechanisms to guard themselves against bacteria or viruses. Recent evidence points to reciprocal interactions between DNA repair, DNA damage responses and aspects of immunity; both self-maintenance and defense responses share a battery of common players and signaling pathways aimed at safeguarding our bodily functions over time...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27826316/ltdna-evidence-on-trial
#20
Paul Roberts
Adopting the interpretative/hermeneutical method typical of much legal scholarship, this article considers two sets of issues pertaining to LTDNA profiles as evidence in criminal proceedings. The section titled Expert Evidence as Forensic Epistemic Warrant addresses some rather large questions about the epistemic status and probative value of expert testimony in general. It sketches a theoretical model of expert evidence, highlighting five essential criteria: (1) expert competence; (2) disciplinary domain; (3) methodological validity; (4) materiality; and (5) legal admissibility...
2016: Frontiers in Genetics
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