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https://www.readbyqxmd.com/read/28728263/-identification-of-mutations-associated-with-coronary-artery-lesion-susceptibility-in-kawasaki-disease-by-targeted-enrichment-of-genomic-region-sequencing-technique
#1
D Y Zhu, S R Song, L J Xie, F Qiu, J Yang, T T Xiao, M Huang
Objective: To screen and identify the mutations in Kawasaki disease by targeted enrichment of genomic region sequencing technique and investigate susceptibility genes associated with coronary artery lesion. Method: This was a case-control study.A total of 114 patients diagnosed as Kawasaki disease treated in Shanghai Children's Hospital between December 2015 and November 2016 were studied and another 45 healthy children who were physically examined in outpatient department were enrolled as control group. Patients were divided into two groups based on the results of echocardiogram...
July 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/28727761/genome-wide-identification-of-the-potato-wrky-transcription-factor-family
#2
Chao Zhang, Dongdong Wang, Chenghui Yang, Nana Kong, Zheng Shi, Peng Zhao, Yunyou Nan, Tengkun Nie, Ruoqiu Wang, Haoli Ma, Qin Chen
WRKY transcription factors play pivotal roles in regulation of stress responses. This study identified 79 WRKY genes in potato (Solanum tuberosum). Based on multiple sequence alignment and phylogenetic relationships, WRKY genes were classified into three major groups. The majority of WRKY genes belonged to Group II (52 StWRKYs), Group III had 14 and Group I consisted of 13. The phylogenetic tree further classified Group II into five sub-groups. All StWRKY genes except StWRKY79 were mapped on potato chromosomes, with eight tandem duplication gene pairs and seven segmental duplication gene pairs found from StWRKY family genes...
2017: PloS One
https://www.readbyqxmd.com/read/28727728/an-integrative-genomics-approach-identifies-novel-pathways-that-influence-candidaemia-susceptibility
#3
Vasiliki Matzaraki, Mark S Gresnigt, Martin Jaeger, Isis Ricaño-Ponce, Melissa D Johnson, Marije Oosting, Lude Franke, Sebo Withoff, John R Perfect, Leo A B Joosten, Bart Jan Kullberg, Frank L van de Veerdonk, Iris Jonkers, Yang Li, Cisca Wijmenga, Mihai G Netea, Vinod Kumar
Candidaemia is a bloodstream infection caused by Candida species that primarily affects specific groups of at-risk patients. Because only small candidaemia patient cohorts are available, classical genome wide association cannot be used to identify Candida susceptibility genes. Therefore, we have applied an integrative genomics approach to identify novel susceptibility genes and pathways for candidaemia. Candida-induced transcriptome changes in human primary leukocytes were assessed by RNA sequencing. Genetic susceptibility to candidaemia was assessed using the Illumina immunochip platform for genotyping of a cohort of 217 patients...
2017: PloS One
https://www.readbyqxmd.com/read/28726130/transmission-network-characteristics-based-on-env-and-gag-sequences-from-msm-during-acute-hiv-1-infection-in-beijing-china
#4
Zhimin Zhang, Lili Dai, Yan Jiang, Kaidi Feng, Lifeng Liu, Wei Xia, Fengjiao Yu, Jun Yao, Wenge Xing, Lijun Sun, Tong Zhang, Hao Wu, Bin Su, Maofeng Qiu
Molecular epidemiology can be used to identify human immunodeficiency virus (HIV) transmission clusters, usually using pol sequence for analysis. In the present study, we explored appropriate parameters to construct a simple network using HIV env and gag sequences instead of pol sequences for constructing a phylogenetic tree and a genetic transmission subnetwork, which were used to identify individuals with many potential transmission links and to explore the evolutionary dynamics of the virus among men who have sex with men (MSM) in Beijing...
July 19, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28725363/bridging-two-scholarly-islands-enriches-both-coi-dna-barcodes-for-species-identification-versus-human-mitochondrial-variation-for-the-study-of-migrations-and-pathologies
#5
David S Thaler, Mark Y Stoeckle
DNA barcodes for species identification and the analysis of human mitochondrial variation have developed as independent fields even though both are based on sequences from animal mitochondria. This study finds questions within each field that can be addressed by reference to the other. DNA barcodes are based on a 648-bp segment of the mitochondrially encoded cytochrome oxidase I. From most species, this segment is the only sequence available. It is impossible to know whether it fairly represents overall mitochondrial variation...
October 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28725217/metagenomics-the-next-culture-independent-game-changer
#6
REVIEW
Jessica D Forbes, Natalie C Knox, Jennifer Ronholm, Franco Pagotto, Aleisha Reimer
A trend towards the abandonment of obtaining pure culture isolates in frontline laboratories is at a crossroads with the ability of public health agencies to perform their basic mandate of foodborne disease surveillance and response. The implementation of culture-independent diagnostic tests (CIDTs) including nucleic acid and antigen-based assays for acute gastroenteritis is leaving public health agencies without laboratory evidence to link clinical cases to each other and to food or environmental substances...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28724549/identification-of-new-tumor-suppressor-genes-in-triple-negative-breast-cancer
#7
Roberto Rangel, Liliana Guzman-Rojas, Takahiro Kodama, Michiko Kodama, Justin Y Newberg, Neal G Copeland, Nancy A Jenkins
Although genomic sequencing has provided a better understating of the genetic landmarks in triple-negative breast cancer (TNBC), functional validation of candidate cancer genes (CCG) remains unsolved. In this study, we used a transposon mutagenesis strategy based on a two-step Sleeping Beauty (SB) forward genetic screen to identify and validate new tumor suppressors (TS) in this disease. We generated 120 siRNAs targeting 40 SB-identified candidate breast cancer TS genes and used them to downregulate expression of these genes in four human TNBC cell lines...
July 19, 2017: Cancer Research
https://www.readbyqxmd.com/read/28724402/a-dual-colour-fluorescence-in-situ-hybridization-fish-assay-for-identifying-the-zoonotic-malaria-parasite-plasmodium-knowlesi-with-a-potential-application-for-the-specific-diagnosis-of-knowlesi-malaria-in-peripheral-level-laboratories-of-southeast-asia
#8
Jyotsna Shah, Akhila Poruri, Olivia Mark, Urmila Khadilka, Franziska Mohring, Robert W Moon, Ranjan Ramasamy
BACKGROUND: Plasmodium knowlesi is primarily responsible for zoonotic malaria in several Southeast Asian countries. Precise identification of the parasite in the blood of patients presently relies on an expensive and elaborate PCR procedure because microscopic examination of blood and other available field identification techniques lack adequate specificity. Therefore, the use of a simple and inexpensive dual-colour fluorescence in situ hybridization (FISH) assay, analogous to FISH assays recently described for Plasmodium falciparum and Plasmodium vivax, was investigated as a potential tool for identifying P...
July 19, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28724083/identification-of-candidate-genes-responsible-for-stem-pith-production-using-expression-analysis-in-solid-stemmed-wheat
#9
A J Oiestad, J M Martin, J Cook, A C Varella, M J Giroux
The wheat stem sawfly (WSS) is an economically important pest of wheat in the Northern Great Plains. The primary means of WSS control is resistance associated with the single quantitative trait locus (QTL) , which controls most stem solidness variation. The goal of this study was to identify stem solidness candidate genes via RNA-seq. This study made use of 28 single nucleotide polymorphism (SNP) makers derived from expressed sequence tags (ESTs) linked to contained within a 5.13 cM region. Allele specific expression of EST markers was examined in stem tissue for solid and hollow-stemmed pairs of two spring wheat near isogenic lines (NILs) differing for the QTL...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28723071/maleic-anhydride-labeling-based-approach-for-quantitative-proteomics-and-successive-derivatization-of-peptides
#10
Shanshan Tian, Shuzhen Zheng, Yanpu Han, Zhenchang Guo, Guijin Zhai, Xue Bai, Xi-Wen He, Enguo Fan, YuKui Zhang, Kai Zhang
Chemical derivatization is a simple approach for stable-isotope covalent labeling of proteins in quantitative proteomics. Herein we describe the development of a novel maleyl-labeling-based approach for protein quantification. Under optimized conditions, maleic anhydride can serve as a highly-efficient reagent to label the amino groups of tryptic peptides. Furthermore, 'click chemistry'was successfully applied to obtain the second modification of maleylated peptides via thiol-Michael addition reaction. Accurate quantification was further achieved via the first or/and second step stable-isotope labeling in this study...
July 19, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28720323/rapid-divergence-of-histones-in-hydrozoa-cnidaria-and-evolution-of-a-novel-histone-involved-in-dna-damage-response-in-hydra
#11
Puli Chandramouli Reddy, Suyog Ubhe, Neha Sirwani, Rasika Lohokare, Sanjeev Galande
Histones are fundamental components of chromatin in all eukaryotes. Hydra, an emerging model system belonging to the basal metazoan phylum Cnidaria, provides an ideal platform to understand the evolution of core histone components at the base of eumetazoan phyla. Hydra exhibits peculiar properties such as tremendous regenerative capacity, lack of organismal senescence and rarity of malignancy. In light of the role of histone modifications and histone variants in these processes it is important to understand the nature of histones themselves and their variants in hydra...
June 15, 2017: Zoology: Analysis of Complex Systems, ZACS
https://www.readbyqxmd.com/read/28720135/exploring-anti-malarial-potential-of-fda-approved-drugs-an-in-silico-approach
#12
Gayatri Ramakrishnan, Nagasuma Chandra, Narayanaswamy Srinivasan
BACKGROUND: The critically important issue on emergence of drug-resistant malarial parasites is compounded by cross resistance, where resistance to one drug confers resistance to other chemically similar drugs or those that share mode of action. This aspect requires discovery of new anti-malarial compounds or formulation of new combination therapy. The current study attempts to contribute towards accelerating anti-malarial drug development efforts, by exploring the potential of existing FDA-approved drugs to target proteins of Plasmodium falciparum...
July 18, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28720084/sequence-based-identification-of-inositol-monophosphatase-like-histidinol-phosphate-phosphatases-hisn-in-corynebacterium-glutamicum-actinobacteria-and-beyond
#13
Robert Kasimir Kulis-Horn, Christian Rückert, Jörn Kalinowski, Marcus Persicke
BACKGROUND: The eighth step of L-histidine biosynthesis is carried out by an enzyme called histidinol-phosphate phosphatase (HolPase). Three unrelated HolPase families are known so far. Two of them are well studied: HAD-type HolPases known from Gammaproteobacteria like Escherichia coli or Salmonella enterica and PHP-type HolPases known from yeast and Firmicutes like Bacillus subtilis. However, the third family of HolPases, the inositol monophosphatase (IMPase)-like HolPases, present in Actinobacteria like Corynebacterium glutamicum (HisN) and plants, are poorly characterized...
July 18, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28719959/pcr-identification-and-phylogenetic-analysis-of-trichomonas-gallinae-from-domestic-pigeons-in-guangzhou-china
#14
Shen-Ben Qiu, Meng-Na Lv, Xi He, Ya-Biao Weng, Shang-Shu Zou, Xin-Qiu Wang, Rui-Qing Lin
Avian trichomoniasis caused by Trichomonas gallinae is a serious protozoan disease worldwide. The domestic pigeon (Columba livia domestica) is the main host for T. gallinae and plays an important role in the spread of the disease. Based on the internal transcribed spacers of nuclear ribosomal DNA of this parasite, a pair of primers (TgF2/TgR2) was designed and used to develop a PCR assay for the diagnosis of T. gallinae infection in domestic pigeons. This approach allowed the identification of T. gallinae, and no amplicons were produced when using DNA from other common avian pathogens...
June 2017: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/28719340/sequence-comparison-of-phor-gyrb-groel-and-chea-genes-as-phylogenetic-markers-for-distinguishing-bacillus-amyloliquefaciens-and-b-subtilis-and-for-identifying-bacillus-strain-b29
#15
C Yu, J Jin, L-Q Meng, H-H Xia, H-F Yuan, J Wang, D-S Yu, X-Y Zhao, C-Q Sha
Given the close genetic relationship between Bacillus amyloliquefaciens and B. subtilis, distinguishing the two solely based on their physiological and biochemical characteristics and 16S rRNA sequences is difficult. Molecular identification was used to discover suitable genes for distinguishing the two bacteria, and to identify the bio-controlling strain B29, due to molecular identification has been paid more and more attention. The similarity of four genes, cheA, gyrB, groEL and phoR, of the two species was compared by the software BLASTN and MAGA, and phylogenetic tree was constructed...
May 20, 2017: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/28719188/phage-selection-of-cyclic-peptides-for-application-in-research-and-drug-development
#16
Kaycie Deyle, Xu-Dong Kong, Christian Heinis
Cyclic peptides can bind to protein targets with high affinities and selectivities, which makes them an attractive modality for the development of research reagents and therapeutics. Additional properties, including low inherent toxicity, efficient chemical synthesis, and facile modification with labels or immobilization reagents, increase their attractiveness. Cyclic peptide ligands against a wide range of protein targets have been isolated from natural sources such as bacteria, fungi, plants, and animals...
July 18, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28717848/new-identification-of-three-or-more-campylobacter-species-on-the-basis-of-a-degenerate-pcr-rflp-method-targeting-gyrb-gene
#17
Hiroyuki Fukuda, Fumiko Kojima, Shuji Fujimoto
This method was aimed targeting more Campylobacter species than conventional PCR-based identifications. They generally use species-specific primers focusing on clinically common species like C. jejuni, resulting in failure to recognize other species. We made the PCR-based identification more flexible using degenerate primers and DdeI- and MboI-separately used RFLP assay, which were designed on the basis of gyrB nucleotide sequence data of 14 Campylobacter species including C. jejuni, C. coli, and C. fetus. Ninety-four clinical isolates from patients with Campylobacter gastroenteritis and 13 biochemically identified C...
July 17, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28717659/identification-and-characterization-of-variants-and-a-novel-4%C3%A2-bp-deletion-in-the-regulatory-region-of-six6-a-risk-factor-for-primary-open-angle-glaucoma
#18
Mohd Hussain Shah, Noemi Tabanera, Subbaiah Ramasamy Krishnadas, Manju R Pillai, Paola Bovolenta, Periasamy Sundaresan
BACKGROUND: Primary open-angle glaucoma (POAG) is a complex disease of multigenic inheritance and the most common subtype of glaucoma. SIX6 encodes a transcription factor involved in retina, optic nerve, and pituitary development. Previous studies showed a genetic association between the SIX6 locus and POAG, identifying risk alleles. Whether these alleles are present also in the south Indian population is unclear. METHODS: To address this question, the SIX6 gene and an already characterized and highly conserved SIX6 enhancer (Ch14:60974427-60974430) were sequenced in two south Indian cohorts, respectively, composed of 65/65 and 200/200 POAG cases/age-matched controls...
July 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28717203/genome-wide-identification-and-characterization-of-circular-rnas-by-high-throughput-sequencing-in-soybean
#19
Wei Zhao, Yihui Cheng, Chi Zhang, Qingbo You, Xinjie Shen, Wei Guo, Yongqing Jiao
Circular RNAs (circRNAs) arise during pre-mRNA splicing, in which the 3' and 5' ends are linked to each other by a covalent bond. Soybean is an ancient tetraploid, which underwent two whole genome duplications. Most of soybean genes are paralogous genes with multiple copies. Although many circRNAs have been identified in animals and plants, little is known about soybean circRNAs, especially about circRNAs derived from paralogous genes. Here, we used deep sequencing technology coupled with RNase R enrichment strategy and bioinformatic approach to uncover circRNAs in soybean...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717173/liquid-phase-sequence-capture-and-targeted-re-sequencing-revealed-novel-polymorphisms-in-tomato-genes-belonging-to-the-mep-carotenoid-pathway
#20
Irma Terracciano, Concita Cantarella, Carlo Fasano, Teodoro Cardi, Giuseppe Mennella, Nunzio D'Agostino
Tomato (Solanum lycopersicum L.) plants are characterized by having a variety of fruit colours that reflect the composition and accumulation of diverse carotenoids in the berries. Carotenoids are extensively studied for their health-promoting effects and this explains the great attention these pigments received by breeders and researchers worldwide. In this work we applied Agilent's SureSelect liquid-phase sequence capture and Illumina targeted re-sequencing of 34 tomato genes belonging to the methylerythritol phosphate (MEP) carotenoid pathway on a panel of 48 genotypes which differ for carotenoid content calculated as the sum of β-carotene, cis- and trans-lycopene...
July 17, 2017: Scientific Reports
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