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https://www.readbyqxmd.com/read/28749454/the-association-of-low-penetrance-variants-in-dna-repair-genes-with-colorectal-cancer-a-systematic-review-and-meta-analysis
#1
Nikhil Aggarwal, Neil D Donald, Salim Malik, Subothini S Selvendran, Mark Jw McPhail, Kevin J Monahan
OBJECTIVES: Approximately 35% of colorectal cancer (CRC) risk is attributable to heritable factors known hereditary syndromes, accounting for 6%. The remainder may be due to lower penetrance polymorphisms particularly of DNA repair genes. DNA repair pathways, including base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), direct reversal repair (DRR), and double-strand break repair are complex, evolutionarily conserved, and critical in carcinogenesis. Germline mutations in these genes are associated with high-penetrance CRC syndromes such as Lynch syndrome...
July 27, 2017: Clinical and Translational Gastroenterology
https://www.readbyqxmd.com/read/28749132/universal-ratiometric-photoelectrochemical-bioassay-with-target-nucleotide-transduction-amplification-and-electron-transfer-tunneling-distance-regulation-strategies-for-ultrasensitive-determination-of-microrna-in-cells
#2
Yingning Zheng, Wenbin Liang, Chengyi Xiong, Ying Zhuo, Yaqin Chai, Ruo Yuan
A universal ratiometric photoelectrochemical (PEC) bioassay, which could be readily expanded for untrasensitive determination of various targets in complex biological matrix, was established by coupling a target-nucleotide transduction-amplification with DNA nanomachine mediated electron-transfer tunneling distance regulation strategies. With the help of target-nucleotide transduction-amplification strategy, the one input target signal could be transducted to corresponding multiple output DNA signals by nucleotide specific recognition technology, simultaneously leading to an efficient signal amplification for target...
July 27, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28749108/snp-and-haplotype-analysis-of-vascular-endothelial-growth-factor-vegf-gene-in-lung-cancer-patients-of-kashmir
#3
Niyaz A Naikoo, Dil Afroze, Roohi Rasool, Sonaullah Shah, A G Ahangar, Imtiyaz A Bhat, Iqbal Qasim, Mushtaq A Siddiqi, Zafar A Shah
Vascular endothelial growth factor (VEGF) is a major mediator of angiogenesis involving tumor growth and metastasis. In this large case-control study, we investigated whether functional polymorphisms (+405C>G, +936C>T) in the VEGF gene are associated with the risk of lung cancer. The study investigates the association between variants of VEGF gene and lung cancer. We performed single nucleotide polymorphism (SNP), haplotype and linkage disequilibrium studies on 100 patients and 128 healthy controls with 2 SNPs in the VEGF gene...
July 27, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28748773/differentiation-between-wild-type-and-vaccines-strains-of-varicella-zoster-virus-vzv-based-on-four-single-nucleotide-polymorphisms
#4
L Jin, S Xu, P A C Maple, W Xu, K E Brown
Varicella-zoster virus (VZV) infection (chickenpox) results in latency and subsequent reactivation manifests as shingles. Effective attenuated vaccines (vOka) are available for prevention of both illnesses. In this study, an amplicon-based sequencing method capable of differentiating between VZV wild-type (wt) strains and vOka vaccine is described. A total of 44 vesicular fluid specimens collected from 43 patients (16 from China and 27 from the UK) with either chickenpox or shingles were investigated, of which 10 had received previous vaccination...
July 27, 2017: Epidemiology and Infection
https://www.readbyqxmd.com/read/28748635/copy-number-changes-identified-using-whole-exome-sequencing-in-nonsyndromic-cleft-lip-and-palate-in-a-honduran-population
#5
Yi Cai, Karynne E Patterson, Frederic Reinier, Sarah E Keesecker, Elizabeth Blue, Michael Bamshad, Joseph Haddad
BACKGROUND: The majority of cleft lip with or without cleft palate cases appear as an isolated, nonsyndromic entity (NSCLP). With the advent of next generation sequencing, whole exome sequencing (WES) has been used to identify single nucleotide variants and insertion/deletions which cause or increase the risk of NSCLP. However, to our knowledge, there are no published studies using WES in NSCLP to investigate copy number changes (CNCs), which are a major component of human genetic variation...
July 27, 2017: Birth defects research
https://www.readbyqxmd.com/read/28748554/estimation-of-inbreeding-depression-on-female-fertility-in-the-finnish-ayrshire-population
#6
K Martikainen, A M Tyrisevä, K Matilainen, J Pösö, P Uimari
Single nucleotide polymorphism (SNP) data enable the estimation of inbreeding at the genome level. In this study, we estimated inbreeding levels for 19,075 Finnish Ayrshire cows genotyped with a low-density SNP panel (8K). The genotypes were imputed to 50K density, and after quality control, 39,144 SNPs remained for the analysis. Inbreeding coefficients were estimated for each animal based on the percentage of homozygous SNPs (FPH ), runs of homozygosity (FROH ) and pedigree (FPED ). Phenotypic records were available for 13,712 animals including non-return rate (NRR), number of inseminations (AIS) and interval from first to last insemination (IFL) for heifers and up to three parities for cows, as well as interval from calving to first insemination (ICF) for cows...
July 27, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28748134/genomic-characterization-reconfirms-the-taxonomic-status-of-lactobacillus-parakefiri
#7
Yasuhiro Tanizawa, Hisami Kobayashi, Eli Kaminuma, Mitsuo Sakamoto, Moriya Ohkuma, Yasukazu Nakamura, Masanori Arita, Masanori Tohno
Whole-genome sequencing was performed for Lactobacillus parakefiri JCM 8573(T) to confirm its hitherto controversial taxonomic position. Here, we report its first reliable reference genome. Genome-wide metrics, such as average nucleotide identity and digital DNA-DNA hybridization, and phylogenomic analysis based on multiple genes supported its taxonomic status as a distinct species in the genus Lactobacillus. The availability of a reliable genome sequence will aid future investigations on the industrial applications of L...
2017: Bioscience of Microbiota, Food and Health
https://www.readbyqxmd.com/read/28747977/use-of-c57bl-6n-mice-on-the-variety-of-immunological-researches
#8
REVIEW
Hyun Keun Song, Dae Youn Hwang
Inbred mice are an essential animal strain for research as they can improve the reproducibility and reliability of study results. The establishment of new inbred lines is continuing, and new inbred lines are being used in many research fields. C57BL/6 is a mouse laboratory animal that has been developed and used as an inbred strain since early stage of mouse strain development, and, in the 1950s, C57BL/6 was separated into substrains by the Jackson Laboratory (C57BL/6J) and the National Institutes of Health (C57BL/6N)...
June 2017: Laboratory Animal Research
https://www.readbyqxmd.com/read/28747922/identification-of-major-quantitative-trait-loci-for-seed-oil-content-in-soybeans-by-combining-linkage-and-genome-wide-association-mapping
#9
Yongce Cao, Shuguang Li, Zili Wang, Fangguo Chang, Jiejie Kong, Junyi Gai, Tuanjie Zhao
Soybean oil is the most widely produced vegetable oil in the world and its content in soybean seed is an important quality trait in breeding programs. More than 100 quantitative trait loci (QTLs) for soybean oil content have been identified. However, most of them are genotype specific and/or environment sensitive. Here, we used both a linkage and association mapping methodology to dissect the genetic basis of seed oil content of Chinese soybean cultivars in various environments in the Jiang-Huai River Valley...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28747921/unreduced-megagametophyte-production-in-lemon-occurs-via-three-meiotic-mechanisms-predominantly-second-division-restitution
#10
Houssem Rouiss, José Cuenca, Luis Navarro, Patrick Ollitrault, Pablo Aleza
Unreduced (2n) gametes have played a pivotal role in polyploid plant evolution and are useful for sexual polyploid breeding in various species, particularly for developing new seedless citrus varieties. The underlying mechanisms of 2n gamete formation were recently revealed for Citrus reticulata but remain poorly understood for other citrus species, including lemon (C. limon [L.] Burm. f.). Here, we investigated the frequency and causal meiotic mechanisms of 2n megagametophyte production in lemon. We genotyped 48progeny plants of two lemon genotypes, "Eureka Frost" and "Fino", using 16 Simple Sequence Repeat (SSR) and 18 Single Nucleotide Polymorphism (SNP) markers to determine the genetic origin of the progenies and the underlying mechanisms for 2n gamete formation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28747902/in-silico-taxonomic-classification-of-373-genomes-reveals-species-misidentification-and-new-genospecies-within-the-genus-pseudomonas
#11
Phuong N Tran, Michael A Savka, Han Ming Gan
The genus Pseudomonas has one of the largest diversity of species within the Bacteria kingdom. To date, its taxonomy is still being revised and updated. Due to the non-standardized procedure and ambiguous thresholds at species level, largely based on 16S rRNA gene or conventional biochemical assay, species identification of publicly available Pseudomonas genomes remains questionable. In this study, we performed a large-scale analysis of all Pseudomonas genomes with species designation (excluding the well-defined P...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28747736/association-of-ubash3a-gene-polymorphism-and-atopic-dermatitis-in-the-chinese-han-population
#12
Y Li, H Cheng, F-L Xiao, B Liang, F-S Zhou, P Li, X-D Zheng, L-D Sun, S Yang, X-J Zhang
Genome-wide association studies have revealed a large number of genetic-risk loci for many autoimmune diseases. One clear finding emerging from the published genetic studies of autoimmunity is that different autoimmune diseases share susceptibility loci. Recent evidence has demonstrated that UBASH3A gene was associated with multiple autoimmune diseases. The aim of this study was to explore the association between UBASH3A single-nucleotide polymorphisms (SNPs) and atopic dermatitis (AD) in a Chinese Han population...
July 27, 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28747730/epidemiology-and-characterization-of-avian-infectious-bronchitis-virus-strains-circulating-in-southern-china-during-the-period-from-2013-2015
#13
Keyu Feng, Feng Wang, Yu Xue, Qingfeng Zhou, Feng Chen, Yingzuo Bi, Qingmei Xie
Two hundred and six strains of avian infectious bronchitis virus (IBV) were isolated from chickens showing signs of disease in southern China during the period from 2013-2015. The nucleotide and amino acid sequences from the isolated field strains were compared to 42 published references. Nucleotide homologies ranged from 63.1-99.9% and amino acid homologies ranging from 60.2-100%. At least seven IBV genotypes were co-circulating in commercial chicken farms in southern China. The IBV isolates were genetically diverse and underwent continuing evolution...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747720/mitochondrial-genomes-of-two-bombycoidea-insects-and-implications-for-their-phylogeny
#14
Zhao-Zhe Xin, Yu Liu, Xiao-Yu Zhu, Ying Wang, Hua-Bin Zhang, Dai-Zhen Zhang, Chun-Lin Zhou, Bo-Ping Tang, Qiu-Ning Liu
The mitochondrial genome (mt genome) provides important information for understanding molecular evolution and phylogenetics. As such, the two complete mt genomes of Ampelophaga rubiginosa and Rondotia menciana were sequenced and annotated. The two circular genomes of A. rubiginosa and R. menciana are 15,282 and 15,636 bp long, respectively, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region. The nucleotide composition of the A. rubiginosa mt genome is A + T rich (81...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747718/predicting-the-functional-consequences-of-non-synonymous-single-nucleotide-polymorphisms-in-il8-gene
#15
Tikam Chand Dakal, Deepak Kala, Gourav Dhiman, Vinod Yadav, Andrey Krokhotin, Nikolay V Dokholyan
Here we report an in-silico approach for identification, characterization and validation of deleterious non-synonymous SNPs (nsSNPs) in the interleukin-8 gene using three steps. In first step, sequence homology-based genetic analysis of a set of 50 coding SNPs associated with 41 rsIDs using SIFT (Sorting Intolerant from Tolerant) and PROVEAN (Protein Variation Effect Analyzer) identified 23 nsSNPs to be putatively damaging/deleterious in at least one of the two tools used. Subsequently, structure-homology based PolyPhen-2 (Polymorphism Phenotyping) analysis predicted 9 of 23 nsSNPs (K4T, E31A, E31K, S41Y, I55N, P59L, P59S, L70P and V88D) to be damaging...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747695/compounds-that-enhance-the-tailing-activity-of-moloney-murine-leukemia-virus-reverse-transcriptase
#16
Yoshiyuki Ohtsubo, Yuji Nagata, Masataka Tsuda
In a previous study, we showed that MMLV-RT has a strong terminal transferase activity, and that the C-, G-, and T-tailing activities are enhanced by dGMP, dCMP, and dAMP, respectively. In this study, to achieve faster reaction and higher tailing efficiency, we screened other compounds for the ability to enhance the tailing activities of MMLV-RT, and determined the corresponding optimal concentrations. The C-, G-, and T-tailing activities were enhanced by guanine, cytosine, and adenine, respectively, and by derivatives thereof, suggesting a transient Watson-Click base pairing between an enhancer molecule and the nucleotide to be incorporated...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747664/mutations-targeting-the-coagulation-pathway-are-enriched-in-brain-metastases
#17
Cristina Richichi, Lorenzo Fornasari, Giorgio E M Melloni, Paola Brescia, Monica Patanè, Massimiliano Del Bene, Dana A M Mustafa, Johan M Kros, Bianca Pollo, Giancarlo Pruneri, Angela Sciandivasci, Elisabetta Munzone, Francesco DiMeco, Pier Giuseppe Pelicci, Laura Riva, Giuliana Pelicci
Brain metastases (BMs) are the most common malignancy of the central nervous system. Recently it has been demonstrated that plasminogen activator inhibitor serpins promote brain metastatic colonization, suggesting that mutations in serpins or other members of the coagulation cascade can provide critical advantages during BM formation. We performed whole-exome sequencing on matched samples of breast cancer and BMs and found mutations in the coagulation pathway genes in 5 out of 10 BM samples. We then investigated the mutational status of 33 genes belonging to the coagulation cascade in a panel of 29 BMs and we identified 56 Single Nucleotide Variants (SNVs)...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747581/protein-tyrosine-phosphatase-nonreceptor-type-22-ptpn22-gene-single-nucleotide-polymorphisms-and-its-interaction-with-t2dm-on-pulmonary-tuberculosis-in-chinese-uygur-population
#18
Xian-Hua Wang, Ai-Guo Ma, Xiu-Xia Han, Lei Chen, Hui Liang, Aishan-Litifu, Abudumijit-Ablez, Feng Xue
AIMS: To investigate the association of several single nucleotide polymorphisms (SNPs) within Protein tyrosine phosphatase nonreceptor type 22 (PTPN22) gene and additional gene- gene and gene- type 2 diabetes mellitus (T2DM) interaction with pulmonary tuberculosis (PTB) risk in Chinese Uygur population. METHODS: A total of 722 participants (186 males, 536 females) were selected, including 360 PTB patients and 362 control participants. Generalized multifactor dimensionality reduction (GMDR) was used to screen the best interaction combination among SNPs and T2DM...
July 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28747530/sequence-intrinsic-somatic-mutation-mechanisms-contribute-to-affinity-maturation-of-vrc01-class-hiv-1-broadly-neutralizing-antibodies
#19
Joyce K Hwang, Chong Wang, Zhou Du, Robin M Meyers, Thomas B Kepler, Donna Neuberg, Peter D Kwong, John R Mascola, M Gordon Joyce, Mattia Bonsignori, Barton F Haynes, Leng-Siew Yeap, Frederick W Alt
Variable regions of Ig chains provide the antigen recognition portion of B-cell receptors and derivative antibodies. Ig heavy-chain variable region exons are assembled developmentally from V, D, J gene segments. Each variable region contains three antigen-contacting complementarity-determining regions (CDRs), with CDR1 and CDR2 encoded by the V segment and CDR3 encoded by the V(D)J junction region. Antigen-stimulated germinal center (GC) B cells undergo somatic hypermutation (SHM) of V(D)J exons followed by selection for SHMs that increase antigen-binding affinity...
July 26, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28747474/male-female-relatedness-at-specific-snp-linkage-groups-influences-cryptic-female-choice-in-chinook-salmon-oncorhynchus-tshawytscha
#20
Cornelia Geßner, Sheri L Johnson, Paul Fisher, Shannon Clarke, Kim Rutherford, Jane Symonds, Neil J Gemmell
In a range of taxa, the relatedness between mates influences both pre- and post-mating processes of sexual selection. However, relatively little is known about the genetic loci facilitating such a bias, with the exception of the major histocompatibility complex. Here, we performed tightly controlled replicated in vitro fertilization trials to explore the impact of relatedness on two possible mechanisms of cryptic female choice (CFC) in Chinook salmon (Oncorhynchus tshawytscha). We tested (i) whether relatedness of mates, assessed using 682 single nucleotide polymorphisms (SNPs) on 29 SNP-linkage groups (LGs), biases a male's sperm velocity in ovarian fluid (a parameter previously shown to predict male fertilization success), and (ii) whether relatedness of mates governs fertilization success via other mechanisms, probably via sperm-egg interactions...
July 26, 2017: Proceedings. Biological Sciences
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