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https://www.readbyqxmd.com/read/27905885/mefit-merging-and-filtering-tool-for-illumina-paired-end-reads-for-16s-rrna-amplicon-sequencing
#1
Hardik I Parikh, Vishal N Koparde, Steven P Bradley, Gregory A Buck, Nihar U Sheth
BACKGROUND: Recent advances in next-generation sequencing have revolutionized genomic research. 16S rRNA amplicon sequencing using paired-end sequencing on the MiSeq platform from Illumina, Inc., is being used to characterize the composition and dynamics of extremely complex/diverse microbial communities. For this analysis on the Illumina platform, merging and quality filtering of paired-end reads are essential first steps in data analysis to ensure the accuracy and reliability of downstream analysis...
December 1, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27905110/distinct-molecular-landscapes-between-endometrioid-and-non-endometrioid-uterine-carcinomas
#2
Nathaniel L Jones, Joanne Xiu, Sudeshna Chatterjee-Paer, Alexandre Buckley de Meritens, William M Burke, Ana I Tergas, Jason D Wright, June Y Hou
Endometrial carcinoma (EC) is traditionally characterized as endometrioid and non-endometrioid based on histo-pathologic phenotypes. Molecular-based classifications have been proposed, but are not widely implemented. Herein we examine molecular profiles between EC histologic subtypes. 3133 ECs were submitted between March 2011 and July 2014: 1634 Type I and 1226 Type II. In situ hybridization and immunohistochemistry were used to assess copy number and protein expression of selected genes. Sequenced variants in 47 genes were analyzed using the Illumina TruSeq Amplicon Cancer Panel...
December 1, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27905043/potential-role-of-anammox-in-nitrogen-removal-in-a-freshwater-reservoir-jiulonghu-reservoir-china
#3
Li-Dong Shen, Hai-Xiang Cheng, Xu Liu, Jian-Hui Li, Yan Liu
Currently, the nitrogen removal potential of anaerobic ammonium oxidation (anammox) and its regulating factors in reservoir systems remain uncertain. Here, we provided the molecular and isotopic evidence for anammox in the freshwater sediment of Jiulonghu Reservoir that is located in Quzhou, Zhejiang Province, China. Diverse 16S rRNA gene sequences related to Candidatus Kuenenia and Candidatus Brocadia were detected by using high-throughput (Illumina MiSeq) sequencing of total bacterial 16S rRNA genes, and the Candidatus Brocadia was the most frequently detected anammox bacterial genus...
November 30, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27904880/microbial-community-patterns-associated-with-automated-teller-machine-keypads-in-new-york-city
#4
Holly M Bik, Julia M Maritz, Albert Luong, Hakdong Shin, Maria Gloria Dominguez-Bello, Jane M Carlton
In densely populated urban environments, the distribution of microbes and the drivers of microbial community assemblages are not well understood. In sprawling metropolitan habitats, the "urban microbiome" may represent a mix of human-associated and environmental taxa. Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads...
November 2016: MSphere
https://www.readbyqxmd.com/read/27903268/long-term-outdoor-air-pollution-and-dna-methylation-in-circulating-monocytes-results-from-the-multi-ethnic-study-of-atherosclerosis-mesa
#5
Gloria C Chi, Yongmei Liu, James W MacDonald, R Graham Barr, Kathleen M Donohue, Mark D Hensley, Lifang Hou, Charles E McCall, Lindsay M Reynolds, David S Siscovick, Joel D Kaufman
BACKGROUND: DNA methylation may mediate effects of air pollution on cardiovascular disease. The association between long-term air pollution exposure and DNA methylation in monocytes, which are central to atherosclerosis, has not been studied. We investigated the association between long-term ambient air pollution exposure and DNA methylation (candidate sites and global) in monocytes of adults (aged ≥55). METHODS: One-year average ambient fine particulate matter (PM2...
December 1, 2016: Environmental Health: a Global Access Science Source
https://www.readbyqxmd.com/read/27902961/application-of-next-generation-sequencing-for-the-detection-of-human-viral-pathogens-in-clinical-specimens
#6
Jayme Parker, Jack Chen
BACKGROUND: Next generation sequencing (NGS) is a new technology that can be used for broad detection of infectious pathogens and is rapidly becoming an essential platform in clinical laboratories. It is not known how NGS will displace or enhance gold standard methodologies in infectious disease diagnosis. OBJECTIVES: To investigate the feasibility and application of NGS technology in public health laboratories and compare NGS technology with conventional methods...
November 22, 2016: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/27902365/the-oral-cavities-of-healthy-infants-harbor-high-proportions-of-streptococcus-salivarius-strains-with-phenotypic-and-genotypic-resistance-to-multiple-classes-of-antibiotics
#7
Thaís H Palma, Erika Harth-Chú, Jodie Scott, Rafael N Stipp, Heike Boisvert, Mariana F Salomão, Jéssica D Theobaldo, Rosana F Possobon, Leandro C Nascimento, Jonathan W McCafferty, Lina Faller, Margaret J Duncan, Renata O Mattos-Graner
Emerging antibiotic resistance in the oropharyngeal microbiota, of which Streptococcus salivarius is a prominent species, represents a challenge for treating pediatric populations. In this study, we investigated the role of S. salivarius as a reservoir for antibiotic resistance genes (ARG) in the oral microbiota by analyzing 95 S. salivarius isolates from 22 healthy infants (2 to 16 months of age). Minimum inhibitory concentrations (MIC) of penicillin G, amoxicillin, erythromycin, tetracycline, doxycycline and streptomycin were determined...
October 24, 2016: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/27901321/copy-number-variants-in-a-population-based-investigation-of-klippel-trenaunay-syndrome
#8
Aggeliki Dimopoulos, Robert J Sicko, Denise M Kay, Shannon L Rigler, Ruzong Fan, Paul A Romitti, Marilyn L Browne, Charlotte M Druschel, Michele Caggana, Lawrence C Brody, James L Mills
Klippel-Trenaunay syndrome (KTS) is a rare congenital vascular disorder that is thought to occur sporadically; however, reports of familial occurrence suggest a genetic component. We examined KTS cases to identify novel, potentially causal copy number variants (CNVs). We identified 17 KTS cases from all live-births occurring in New York (1998-2010). Extracted DNA was genotyped using Illumina microarrays and CNVs were called using PennCNV software. CNVs selected for follow-up had ≥10 single nucleotide polymorphisms (SNPs) and minimal overlap with in-house controls or controls from the Database of Genomic Variants...
November 30, 2016: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/27901057/digital-gene-expression-profiling-analysis-of-duodenum-transcriptomes-in-sd-rats-administered-ferrous-sulfate-or-ferrous-glycine-chelate-by-gavage
#9
Zhao Zhuo, Shenglin Fang, Qiaoling Hu, Danping Huang, Jie Feng
The absorption of different iron sources is a trending research topic. Many studies have revealed that organic iron exhibits better bioavailability than inorganic iron, but the concrete underlying mechanism is still unclear. In the present study, we examined the differences in bioavailability of ferrous sulfate and ferrous glycinate in the intestines of SD rats using Illumina sequencing technology. Digital gene expression analysis resulted in the generation of almost 128 million clean reads, with expression data for 17,089 unigenes...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900422/comparative-investigation-of-bacterial-fungal-and-archaeal-community-structures-in-soils-in-a-typical-oilfield-in-jianghan-china
#10
Zhi-Feng Zhou, Ming-Xia Wang, Xiao-Hu Zuo, Yan-Hong Yao
Agricultural soils in oilfields have high risk for polycyclic aromatic hydrocarbon (PAH) pollution. In this study, from the Jianghan Oilfield (Hubei Province, China) with a history of >50 years, 7 soil samples (OS-1 to OS-7) were collected. Subsequently, the bacterial, archaeal, and fungal community structures were investigated by Illumina MiSeq sequencing, and the relationship between microbial community structure and soil PAH content was analyzed. The results indicated that bacterial and archaeal Chao 1 indices showed a significantly negative relationship with soil PAH content, and only the bacterial Shannon index had a significantly negative relationship with soil PAH content...
November 29, 2016: Archives of Environmental Contamination and Toxicology
https://www.readbyqxmd.com/read/27899923/community-metabolome-correlations-of-gut-microbiota-from-child-turcotte-pugh-of-a-and-b-patients
#11
Xiao Wei, Shan Jiang, Xiangna Zhao, Huan Li, Weishi Lin, Boxing Li, Jing Lu, Yansong Sun, Jing Yuan
The gut flora are widely involved in the cometabolism with the host and have evident effects on the metabolic phenotype of host. This study performed a metabolome analysis of the intestinal microbiota specific for liver cirrhosis. The study population included patients with Child-Turcotte-Pugh score of A (AP, n = 5) and B (BP, n = 5), and control subjects (NM, n = 3). Metagenomic DNA from fecal microbiota was extracted followed by metagenomic sequencing through Illumina MiSeq high throughput sequencing of 16S rRNA regions...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27899326/complete-plastid-genome-sequence-of-goosegrass-eleusine-indica-and-comparison-with-other-poaceae
#12
Hui Zhang, Nathan Hall, J Scott McElroy, Elijah K Lowe, Leslie R Goertzen
Eleusine indica, also known as goosegrass, is a serious weed in at least 42 countries. In this paper we report the complete plastid genome sequence of goosegrass obtained by de novo assembly of paired-end and mate-paired reads generated by Illumina sequencing of total genomic DNA. The goosegrass plastome is a circular molecule of 135,151bp in length, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 20,919 bases. The large (LSC) and the small (SSC) single-copy regions span 80,667 bases and 12,646 bases, respectively...
November 26, 2016: Gene
https://www.readbyqxmd.com/read/27898963/justification-for-setting-the-individual-animal-genotype-call-rate-threshold-at-eighty-five-percent
#13
D C Purfield, M McClure, D P Berry
Data quality of SNP arrays impacts the accuracy and precision of downstream data analyses. One such quality control measure often imposed is a threshold on individual animal call rate. Different call rate thresholds have been applied across studies; little is known, however, about the impact of these thresholds on the quality of the genotype data. The objective of the present study was to investigate the effect of different call rate thresholds on the integrity of the genotypes but also to quantify the contribution of different factors to the variability in animal call rate...
November 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27898931/genomic-selection-in-the-german-landrace-population-of-the-bavarian-herdbook
#14
M Gertz, C Edel, I Ruß, J Dodenhoff, K-U Götz, G Thaller
The aim of our study was to compare different validation methods with respect to their impact on validation results and to evaluate the feasibility of genomic selection in the German Landrace population of the Bavarian herdbook. For this purpose, a sample of 337 boars and 1,676 sows was genotyped with the Illumina PorcineSNP60 BeadChip. Conventional BLUP breeding values for fertility, growth, carcass, and quality traits were deregressed and used as phenotypes in genomic BLUP. The resulting genomic breeding values were also blended with information from the full conventional breeding value estimation to include information from nongenotyped parents...
November 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27898889/accuracies-of-genomic-prediction-of-feed-efficiency-traits-using-different-prediction-and-validation-methods-in-an-experimental-nelore-cattle-population
#15
R M O Silva, B O Fragomeni, D A L Lourenco, A F B Magalhães, N Irano, R Carvalheiro, R C Canesin, M E Z Mercadante, A A Boligon, F S Baldi, I Misztal, L G Albuquerque
Animal feeding is the most important economic component of beef production systems. Selection for feed efficiency has not been effective mainly due to difficult and high costs to obtain the phenotypes. The application of genomic selection using SNP can decrease the cost of animal evaluation as well as the generation interval. The objective of this study was to compare methods for genomic evaluation of feed efficiency traits using different cross-validation layouts in an experimental beef cattle population genotyped for a high-density SNP panel (BovineHD BeadChip assay 700k, Illumina Inc...
September 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27898882/genome-scan-for-postmortem-carcass-traits-in-nellore-cattle
#16
G A Fernandes Júnior, R B Costa, G M F de Camargo, R Carvalheiro, G J M Rosa, F Baldi, D A Garcia, D G M Gordo, R Espigolan, L Takada, A F B Magalhães, T Bresolin, F L B Feitosa, L A L Chardulo, H N de Oliveira, L G de Albuquerque
Carcass traits measured after slaughter are economically relevant traits in beef cattle. In general, the slaughter house payment system is based on HCW. Ribeye area (REA) is associated with the amount of the meat in the carcass, and a minimum of backfat thickness (BFT) is necessary to protect the carcass during cooling. The aim of this study was to identify potential genomic regions harboring candidate genes affecting those traits in Nellore cattle. The data set used in the present study consisted of 1,756 Nellore males with phenotype records...
October 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27898835/genomic-prediction-of-barley-hybrid-performance
#17
Norman Philipp, Guozheng Liu, Yusheng Zhao, Sang He, Monika Spiller, Gunther Stiewe, Klaus Pillen, Jochen C Reif, Zuo Li
Hybrid breeding in barley ( L.) offers great opportunities to accelerate the rate of genetic improvement and to boost yield stability. A crucial requirement consists of the efficient selection of superior hybrid combinations. We used comprehensive phenotypic and genomic data from a commercial breeding program with the goal of examining the potential to predict the hybrid performances. The phenotypic data were comprised of replicated grain yield trials for 385 two-way and 408 three-way hybrids evaluated in up to 47 environments...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898825/complete-chloroplast-genome-sequence-of-corroborates-structural-heterogeneity-of-inverted-repeats-in-wild-progenitors-of-cultivated-bananas-and-plantains
#18
Santoshkumar M Shetty, Maria Ulfa Md Shah, Kavyashree Makale, Yusmin Mohd-Yusuf, Norzulaani Khalid, Rofina Yasmin Othman
Complete genome sequencing of cytoplasmically inherited chloroplast DNA provides novel insights into the origins of clonally propagated crops such as banana and plantain ( spp.). This study describes the structural organization of the chloroplast genome of Colla and its phylogenetic relationship with other wild progenitors of the domesticated banana cultivars. The chloroplast genome was sequenced using Illumina HiSeq 2000 platform, followed by a combination of de novo short-read assembly and reference-guided mapping of contigs to generate complete plastome sequence...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898805/characterization-of-three-rice-multiparent-advanced-generation-intercross-magic-populations-for-quantitative-trait-loci-identification
#19
Lijun Meng, Longbiao Guo, Kimberly Ponce, Xiangqian Zhao, Guoyou Ye
Three new rice ( L.) multiparent advanced generation intercross (MAGIC) populations were developed using eight elite rice varieties from different breeding programs. These three populations were two recombinant inbred line (RIL) populations derived from two 4-way crosses, DC1 and DC2, and one RIL population derived from an 8-way cross. These populations were genotyped using an Illumina Infinium rice 6K SNP chip. The potential of the three MAGIC populations in identifying marker-trait associations was demonstrated using the plant height (PH) and heading date (HD) measured in 2014...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898768/transcriptome-and-small-rnaome-dynamics-during-a-resistant-and-susceptible-interaction-between-cucumber-and-downy-mildew
#20
Alyssa Burkhardt, Brad Day
Cucumber ( L.) downy mildew, caused by the obligate oomycete pathogen (Berk. and Curt.) Rostov., is the primary factor limiting cucumber production. Although sources of resistance have been identified, such as plant introduction line PI 197088, the genes and processes involved in mediating resistance are still unknown. In the current study, we conducted a comprehensive transcriptome and small RNAome analysis of a resistant (PI 197088) and susceptible ('Vlaspik') cucumber during a time course of infection using Illumina sequencing...
March 2016: Plant Genome
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