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Frontiers in Genetics

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https://www.readbyqxmd.com/read/28804494/editorial-population-genetics-of-worldwide-jewish-people
#1
EDITORIAL
Eran Elhaik
No abstract text is available yet for this article.
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28769976/new-insights-into-5hmc-dna-modification-generation-distribution-and-function
#2
REVIEW
Dong-Qiao Shi, Iftikhar Ali, Jun Tang, Wei-Cai Yang
Dynamic DNA modifications, such as methylation/demethylation on cytosine, are major epigenetic mechanisms to modulate gene expression in both eukaryotes and prokaryotes. In addition to the common methylation on the 5th position of the pyrimidine ring of cytosine (5mC), other types of modifications at the same position, such as 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC), are also important. Recently, 5hmC, a product of 5mC demethylation by the Ten-Eleven Translocation family proteins, was shown to regulate many cellular and developmental processes, including the pluripotency of embryonic stem cells, neuron development, and tumorigenesis in mammals...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28751909/simultaneous-methylation-level-assessment-of-hundreds-of-cpg-sites-by-targeted-bisulfite-pcr-sequencing-tbpseq
#3
Kyuheum Jeon, Byungkuk Min, Jung S Park, Yong-Kook Kang
Methylated-DNA sequencing technologies are producing vast amounts of methylome data from cancer samples, from which cancer-associated differentially methylated CpG sites (cDMCs) are continuously identified and filed. The inclusion of as many cDMCs as possible helps improve the accuracy of cancer diagnosis and sometimes identify cancer subtypes. However, the lack of an established method for the analysis of 100s of cDMCs practically impedes their robust use in clinical medicine. Here, we tested the availability of targeted bisulfite-PCR-sequencing (TBPseq) technology for the assessment of methylation levels of a myriad of CpGs scattered over the genome...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28751908/quantifying-gene-regulatory-relationships-with-association-measures-a-comparative-study
#4
Zhi-Ping Liu
In this work, we provide a comparative study of the main available association measures for characterizing gene regulatory strengths. Detecting the association between genes (as well as RNAs, proteins, and other molecules) is very important to decipher their functional relationship from genomic data in bioinformatics. With the availability of more and more high-throughput datasets, the quantification of meaningful relationships by employing association measures will make great sense of the data. There are various quantitative measures have been proposed for identifying molecular associations...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28736571/evaluation-of-quality-assessment-protocols-for-high-throughput-genome-resequencing-data
#5
REVIEW
Matteo Chiara, Giulio Pavesi
Large-scale initiatives aiming to recover the complete sequence of thousands of human genomes are currently being undertaken worldwide, concurring to the generation of a comprehensive catalog of human genetic variation. The ultimate and most ambitious goal of human population scale genomics is the characterization of the so-called human "variome," through the identification of causal mutations or haplotypes. Several research institutions worldwide currently use genotyping assays based on Next-Generation Sequencing (NGS) for diagnostics and clinical screenings, and the widespread application of such technologies promises major revolutions in medical science...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28713423/discovering-the-unexpected-with-the-utilization-of-ngs-in-diagnostics-of-non-syndromic-hearing-loss-disorders-the-family-case-of-ildr1-dependent-hearing-loss-disorder
#6
Jernej Kovač, Gašper Klančar, Katarina Trebušak Podkrajšek, Saba Battelino
Sensorineural hearing loss (SNHL) is a heterogeneous family of hearing disabilities with congenital (including genetic) as well as acquired etiology. Congenital SNHL of genetic etiology is further sub-divided into autosomal dominant, autosomal recessive and X-linked SNHL. More than 60 genes are involved in the etiology of autosomal recessive non-syndromic hearing loss (ARNSHL) commonly manifesting as heterogeneous pre-lingual profound to severe non-progressive clinical phenotype. ILDR1-dependent ARNSHL (DFNB42, OMIM: # 609646) is a very rare sub-type of hearing disability, with unknown prevalence, caused by function-damaging genetic variants in ILDR1 gene reported in families of Middle-Eastern origin...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28713422/computational-analysis-of-lifespan-experiment-reproducibility
#7
Michael Petrascheck, Dana L Miller
Independent reproducibility is essential to the generation of scientific knowledge. Optimizing experimental protocols to ensure reproducibility is an important aspect of scientific work. Genetic or pharmacological lifespan extensions are generally small compared to the inherent variability in mean lifespan even in isogenic populations housed under identical conditions. This variability makes reproducible detection of small but real effects experimentally challenging. In this study, we aimed to determine the reproducibility of C...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28713421/analyses-of-genomic-trna-reveal-presence-of-novel-trnas-in-oryza-sativa
#8
Tapan K Mohanta, Hanhong Bae
Transfer rRNAs are important molecules responsible for the translation event during protein synthesis. tRNAs are widespread found in unicellular to multi-cellular organisms. Analysis of tRNA gene family members in Oryza sativa revealed the presence of 750 tRNA genes distributed unevenly in different chromosomes. The length of O. sativa tRNAs genes were ranged from 66 to 91 nucleotides encoding 52 isoacceptor in total. tRNA(Ser) found in chromosome 8 of O. sativa encoded only 66 nucleotides which is the smallest tRNA of O...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28713420/modeling-the-metabolism-of-arabidopsis-thaliana-application-of-network-decomposition-and-network-reduction-in-the-context-of-petri-nets
#9
Ina Koch, Joachim Nöthen, Enrico Schleiff
Motivation:Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. Nevertheless, the system is not yet fully understood, although many mechanisms are described, and information for many processes exists. However, the combination and interpretation of the large amount of biological data remain a big challenge, not only because data sets for metabolic paths are still incomplete. Moreover, they are often inconsistent, because they are coming from different experiments of various scales, regarding, for example, accuracy and/or significance...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28702050/circulating-micrornas-in-serum-from-cattle-challenged-with-bovine-viral-diarrhea-virus
#10
Tasia M Taxis, Fernando V Bauermann, Julia F Ridpath, Eduardo Casas
Bovine viral diarrhea virus (BVDV) is an RNA virus that is often associated with respiratory disease in cattle. MicroRNAs have been proposed as indicators of exposure to respiratory pathogens. The objective of this study was to identify microRNAs in cattle that had been challenged with a non-cytopathic field strain of BVDV. Five colostrum deprived neonate Holstein calves were inoculated with BVDV (challenged) and 4 were mock challenged (control). Serum from all calves was collected at four different times: prior to challenge (day 0) and at 4, 9, and 16 days post-challenge...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28702049/endurance-exercise-ability-in-the-horse-a-trait-with-complex-polygenic-determinism
#11
Anne Ricard, Céline Robert, Christine Blouin, Fanny Baste, Gwendoline Torquet, Caroline Morgenthaler, Julie Rivière, Nuria Mach, Xavier Mata, Laurent Schibler, Eric Barrey
Endurance horses are able to run at more than 20 km/h for 160 km (in bouts of 30-40 km). This level of performance is based on intense aerobic metabolism, effective body heat dissipation and the ability to endure painful exercise. The known heritabilities of endurance performance and exercise-related physiological traits in Arabian horses suggest that adaptation to extreme endurance exercise is influenced by genetic factors. The objective of the present genome-wide association study (GWAS) was to identify single nucleotide polymorphisms (SNPs) related to endurance racing performance in 597 Arabian horses...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28690636/forks-on-the-run-can-the-stalling-of-dna-replication-promote-epigenetic-changes
#12
REVIEW
Hollie Rowlands, Piriththiv Dhavarasa, Ashley Cheng, Krassimir Yankulov
Built of DNA polymerases and multiple associated factors, the replication fork steadily progresses along the DNA template and faithfully replicates DNA. This model can be found in practically every textbook of genetics, with the more complex situation of chromatinized DNA in eukaryotes often viewed as a variation. However, the replication-coupled disassembly/reassembly of chromatin adds significant complexity to the whole replication process. During the course of eukaryotic DNA replication the forks encounter various conditions and numerous impediments...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28680442/perspectives-and-challenges-in-microbial-communities-metabolic-modeling
#13
Emanuele Bosi, Giovanni Bacci, Alessio Mengoni, Marco Fondi
Bacteria have evolved to efficiently interact each other, forming complex entities known as microbial communities. These "super-organisms" play a central role in maintaining the health of their eukaryotic hosts and in the cycling of elements like carbon and nitrogen. However, despite their crucial importance, the mechanisms that influence the functioning of microbial communities and their relationship with environmental perturbations are obscure. The study of microbial communities was boosted by tremendous advances in sequencing technologies, and in particular by the possibility to determine genomic sequences of bacteria directly from environmental samples...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28680441/the-origins-of-ashkenaz-ashkenazic-jews-and-yiddish
#14
Ranajit Das, Paul Wexler, Mehdi Pirooznia, Eran Elhaik
Recently, the geographical origins of Ashkenazic Jews (AJs) and their native language Yiddish were investigated by applying the Geographic Population Structure (GPS) to a cohort of exclusively Yiddish-speaking and multilingual AJs. GPS localized most AJs along major ancient trade routes in northeastern Turkey adjacent to primeval villages with names that resemble the word "Ashkenaz." These findings were compatible with the hypothesis of an Irano-Turko-Slavic origin for AJs and a Slavic origin for Yiddish and at odds with the Rhineland hypothesis advocating a Levantine origin for AJs and German origins for Yiddish...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28670325/more-is-better-recent-progress-in-multi-omics-data-integration-methods
#15
REVIEW
Sijia Huang, Kumardeep Chaudhary, Lana X Garmire
Multi-omics data integration is one of the major challenges in the era of precision medicine. Considerable work has been done with the advent of high-throughput studies, which have enabled the data access for downstream analyses. To improve the clinical outcome prediction, a gamut of software tools has been developed. This review outlines the progress done in the field of multi-omics integration and comprehensive tools developed so far in this field. Further, we discuss the integration methods to predict patient survival at the end of the review...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28663758/lmna-sequences-of-60-706-unrelated-individuals-reveal-132-novel-missense-variants-in-a-type-lamins-and-suggest-a-link-between-variant-p-g602s-and-type-2-diabetes
#16
Alyssa Florwick, Tejas Dharmaraj, Julie Jurgens, David Valle, Katherine L Wilson
Mutations in LMNA, encoding nuclear intermediate filament proteins lamins A and C, cause multiple diseases ('laminopathies') including muscular dystrophy, dilated cardiomyopathy, familial partial lipodystrophy (FPLD2), insulin resistance syndrome and progeria. To assess the prevalence of LMNA missense mutations ('variants') in a broad, ethnically diverse population, we compared missense alleles found among 60,706 unrelated individuals in the ExAC cohort to those identified in 1,404 individuals in the laminopathy database (UMD-LMNA)...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28663757/genome-wide-analysis-suggests-the-relaxed-purifying-selection-affect-the-evolution-of-wox-genes-in-pyrus-bretschneideri-prunus-persica-prunus-mume-and-fragaria-vesca
#17
Yunpeng Cao, Yahui Han, Dandan Meng, Guohui Li, Dahui Li, Muhammad Abdullah, Qing Jin, Yi Lin, Yongping Cai
WUSCHEL-related homeobox (WOX) family is one of the largest group of transcription factors (TFs) specifically found in plant kingdom. WOX TFs play an important role in plant development processes and evolutionary novelties. Although the roles of WOXs in Arabidopsis and rice have been well-studied, however, little are known about the relationships among the main clades in the molecular evolution of these genes in Rosaceae. Here, we carried out a genome-wide analysis and identified 14, 10, 10, and 9 of WOX genes from four Rosaceae species (Fragaria vesca, Prunus persica, Prunus mume, and Pyrus bretschneideri, respectively)...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28659971/computational-methods-for-characterizing-cancer-mutational-heterogeneity
#18
REVIEW
Fabio Vandin
Advances in DNA sequencing technologies have allowed the characterization of somatic mutations in a large number of cancer genomes at an unprecedented level of detail, revealing the extreme genetic heterogeneity of cancer at two different levels: inter-tumor, with different patients of the same cancer type presenting different collections of somatic mutations, and intra-tumor, with different clones coexisting within the same tumor. Both inter-tumor and intra-tumor heterogeneity have crucial implications for clinical practices...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28659970/effects-of-genotype-by-environment-interaction-on-genetic-gain-and-genetic-parameter-estimates-in-red-tilapia-oreochromis-spp
#19
Nguyen H Nguyen, Azhar Hamzah, Ngo P Thoa
The extent to which genetic gain achieved from selection programs under strictly controlled environments in the nucleus that can be expressed in commercial production systems is not well-documented in aquaculture species. The main aim of this paper was to assess the effects of genotype by environment interaction on genetic response and genetic parameters for four body traits (harvest weight, standard length, body depth, body width) and survival in Red tilapia (Oreochromis spp.). The growth and survival data were recorded on 19,916 individual fish from a pedigreed population undergoing three generations of selection for increased harvest weight in earthen ponds from 2010 to 2012 at the Aquaculture Extension Center, Department of Fisheries, Jitra in Kedah, Malaysia...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28659969/complementary-network-based-approaches-for-exploring-genetic-structure-and-functional-connectivity-in-two-vulnerable-endemic-ground-squirrels
#20
Victoria H Zero, Adi Barocas, Denim M Jochimsen, Agnès Pelletier, Xavier Giroux-Bougard, Daryl R Trumbo, Jessica A Castillo, Diane Evans Mack, Mark A Linnell, Rachel M Pigg, Jessica Hoisington-Lopez, Stephen F Spear, Melanie A Murphy, Lisette P Waits
The persistence of small populations is influenced by genetic structure and functional connectivity. We used two network-based approaches to understand the persistence of the northern Idaho ground squirrel (Urocitellus brunneus) and the southern Idaho ground squirrel (U. endemicus), two congeners of conservation concern. These graph theoretic approaches are conventionally applied to social or transportation networks, but here are used to study population persistence and connectivity. Population graph analyses revealed that local extinction rapidly reduced connectivity for the southern species, while connectivity for the northern species could be maintained following local extinction...
2017: Frontiers in Genetics
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