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https://www.readbyqxmd.com/read/28339832/effects-of-feeding-original-xpc%C3%A2-to-broilers-with-a-live-coccidiosis-vaccine-under-industrial-conditions-part-2-cecal-microbiota-analysis
#1
S H Park, S Roto, H Pavlidis, D McIntyre, K Striplin, L Brammer, S C Ricke
Biological supplements in poultry feed are of continued interest due to the improvements in growth performance, protection from pathogen invasion, and benefits in overall host health. The fermentation metabolites of Diamond V Original XPC™ (XPC) have previously been shown to improve commercial performance and reduce Salmonella in poultry. The current study sought to characterize the cecal microbiota using culture-independent analysis based on 16S rRNA gene in Coccivac-D sprayed broilers supplemented with XPC and/or Salinomycin (SAL)...
March 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339749/multi-generational-genome-wide-association-studies-identify-chromosomal-regions-associated-with-ascites-phenotype
#2
K J Tarrant, S Dey, R Kinney, N B Anthony, D D Rhoads
Ascites is a multi-faceted disease commonly observed in fast growing broilers, which is initiated when the body is insufficiently oxygenated. A series of events follow, including an increase in pulmonary artery pressure, right ventricle hypertrophy, and accumulation of fluid in the abdominal cavity and pericardium. Advances in management practices along with improved selection programs have decreased ascites incidence in modern broilers. However, ascites syndrome remains an economically important disease throughout the world, causing estimated losses of $100 million per year...
February 21, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339495/microrna-expression-profiles-identify-disease-specific-alterations-in-systemic-lupus-erythematosus-and-primary-sj%C3%A3-gren-s-syndrome
#3
Ji-Qing Chen, Gábor Papp, Szilárd Póliska, Krisztina Szabó, Tünde Tarr, Bálint László Bálint, Péter Szodoray, Margit Zeher
The discovery of microRNAs (miRNAs) and their critical role in genetic control opened new avenues in understanding of various biological processes including immune cell lineage commitment, differentiation, proliferation and apoptosis. However, a given miRNA may have hundreds of different mRNA targets and a target might be regulated by multiple miRNAs, thus the characterisation of dysregulated miRNA expression profiles could give a better insight into the development of immunological disturbances in autoimmune diseases...
2017: PloS One
https://www.readbyqxmd.com/read/28339009/identification-of-egflam-spatc1l-and-rnase13-as-novel-susceptibility-loci-for-aortic-aneurysm-in-japanese-individuals-by-exome-wide-association-studies
#4
Yoshiji Yamada, Jun Sakuma, Ichiro Takeuchi, Yoshiki Yasukochi, Kimihiko Kato, Mitsutoshi Oguri, Tetsuo Fujimaki, Hideki Horibe, Masaaki Muramatsu, Motoji Sawabe, Yoshinori Fujiwara, Yu Taniguchi, Shuichi Obuchi, Hisashi Kawai, Shoji Shinkai, Seijiro Mori, Tomio Arai, Masashi Tanaka
We performed an exome-wide association study (EWAS) to identify genetic variants - in particular, low‑frequency or rare variants with a moderate to large effect size - that confer susceptibility to aortic aneurysm with 8,782 Japanese subjects (456 patients with aortic aneurysm, 8,326 control individuals) and with the use of Illumina HumanExome-12 DNA Analysis BeadChip or Infinium Exome-24 BeadChip arrays. The correlation of allele frequencies for 41,432 single nucleotide polymorphisms (SNPs) that passed quality control to aortic aneurysm was examined with Fisher's exact test...
March 21, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28338908/metabolite-profiling-of-barley-flag-leaves-under-drought-and-combined-heat-and-drought-stress-reveals-metabolic-qtls-for-metabolites-associated-with-antioxidant-defense
#5
Sven Eduard Templer, Alexandra Ammon, David Pscheidt, Otilia Ciobotea, Christian Schuy, Christopher McCollum, Uwe Sonnewald, Anja Hanemann, Jutta Förster, Frank Ordon, Maria von Korff, Lars Matthias Voll
Barley (Hordeum vulgare L.) is among the most stress-tolerant crops; however, not much is known about the genetic and environmental control of metabolic adaptation of barley to abiotic stresses. We have subjected a genetically diverse set of 81 barley accessions, consisting of Mediterranean landrace genotypes and German elite breeding lines, to drought and combined heat and drought stress at anthesis. Our aim was to (i) investigate potential differences in morphological, physiological, and metabolic adaptation to the two stress scenarios between the Mediterranean and German barley genotypes and (ii) identify metabolic quantitative trait loci (mQTLs)...
March 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28337567/novel-16s-rdna-primers-revealed-the-diversity-and-habitats-related-community-structure-of-sphingomonads-in-10-different-niches
#6
Yili Huang, Hao Feng, Hang Lu, Yanhua Zeng
It is believed that sphingomonads are ubiquitously distributed in environments. However detailed information about their community structure and their co-relationship with environmental parameters remain unclear. In this study, novel sphingomonads-specific primers based on the 16S rRNA gene were designed to investigate the distribution of sphingomonads in 10 different niches. Both in silico and in-practice tests on pure cultures and environmental samples showed that Sph384f/Sph701r was an efficient primer set...
March 23, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28337392/microsatellite-markers-for-population-studies-of-the-salt-marsh-species-juncus-roemerianus-juncaceae
#7
Hayley R Tumas, Brian M Shamblin, Mark S Woodrey, Campbell J Nairn
PREMISE OF THE STUDY: Juncus roemerianus (Juncaceae) is a foundational species and ecosystem engineer of salt marshes in the Gulf of Mexico. These ecosystems provide coastal flood attenuation, nurseries for important species, and other ecosystem services, but are experiencing significant decline. Nuclear microsatellite markers were developed for J. roemerianus to study genetic diversity and population structure for conservation and restoration efforts. METHODS AND RESULTS: Illumina NextSeq high-throughput sequencing was used to develop a panel of 19 polymorphic microsatellite markers that were tested across individuals from three populations on the Gulf Coast...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337391/an-efficient-field-and-laboratory-workflow-for-plant-phylotranscriptomic-projects
#8
Ya Yang, Michael J Moore, Samuel F Brockington, Alfonso Timoneda, Tao Feng, Hannah E Marx, Joseph F Walker, Stephen A Smith
PREMISE OF THE STUDY: We describe a field and laboratory workflow developed for plant phylotranscriptomic projects that involves cryogenic tissue collection in the field, RNA extraction and quality control, and library preparation. We also make recommendations for sample curation. METHODS AND RESULTS: A total of 216 frozen tissue samples of Caryophyllales and other angiosperm taxa were collected from the field or botanical gardens. RNA was extracted, stranded mRNA libraries were prepared, and libraries were sequenced on Illumina HiSeq platforms...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337389/development-of-microsatellite-markers-using-illumina-miseq-sequencing-to-characterize-ephedra-gerardiana-ephedraceae
#9
Ji De, Weidong Zhu, Tianmeng Liu, Zhe Wang, Yang Zhong
PREMISE OF THE STUDY: Ephedragerardiana (Ephedraceae), occurring in the Himalayan ranges, is an important plant species used in Tibetan medicine. Due to the lack of molecular markers to characterize genetic diversity, knowledge for conservation and uses of E. gerardiana resources is limited; we therefore developed microsatellite markers for use in this species. METHODS AND RESULTS: Using Illumina MiSeq sequencing technology, we developed 29 polymorphic microsatellite loci suitable for E...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28337209/transcriptional-responses-of-chilean-quinoa-chenopodium-quinoa-willd-under-water-deficit-conditions-uncovers-aba-independent-expression-patterns
#10
Andrea Morales, Andres Zurita-Silva, Jonathan Maldonado, Herman Silva
HIGHLIGHTS R49 genotype displayed best performance on selected physiological parameters and highest tolerance to drought.R49 drought over-represented transcripts has exhibited 19% of genes (306 contigs) that presented no homology to published databases.Expression pattern for canonical responses to drought such as ABA biosynthesis and other genes induced in response to drought were assessed by qPCR. Global freshwater shortage is one of the biggest challenges of our time, often associated to misuse, increased consumption demands and the effects of climate change, paralleled with the desertification of vast areas...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28336973/microbial-community-composition-is-related-to-soil-biological-and-chemical-properties-and-bacterial-wilt-outbreak
#11
Rui Wang, Hongchun Zhang, Liguang Sun, Gaofu Qi, Shu Chen, Xiuyun Zhao
Soil microbes play important roles in plant growth and health. Little is known about the differences of soil microbes between healthy and bacterial wilt infected soils with Ralstonia solanacearum. By Illumina-MiSeq sequencing of 16S rRNA and 18S rRNA gene amplicons, we found the soil microbial composition and diversity were distinct between healthy and bacterial wilt infected soils. Soil microbial community varied at different plant growth stages due to changes of root exudates composition and soil pH. Healthy soils exhibited higher microbial diversity than the bacterial wilt infected soils...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28336594/first-report-on-the-complete-genome-sequence-of-lactobacillus-crustorum-mn047-a-potent-probiotic-strain-isolated-from-koumiss-in-china
#12
Lanhua Yi, Xing Guo, Lian Liu, Chunge Shao, Xin Lü
The complete genome sequence of Lactobacillus crustorum deciphered by PacBio RS II and Illumina HiSeq 4000 sequencing was first reported with one chromosome and two plasmids. Sequence analysis of L. crustorum MN047 showed probiotic characteristics.
March 23, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28336094/distinct-succession-patterns-of-abundant-and-rare-bacteria-in-temporal-microcosms-with-pollutants
#13
Shuo Jiao, Yantao Luo, Mingmei Lu, Xiao Xiao, Yanbing Lin, Weimin Chen, Gehong Wei
Elucidating the driving forces behind the temporal dynamics of abundant and rare microbes is essential for understanding the assembly and succession of microbial communities. Here, we explored the successional trajectories and mechanisms of abundant and rare bacteria via soil-enrichment subcultures in response to various pollutants (phenanthrene, n-octadecane, and CdCl2) using time-series Illumina sequencing datasets. The results reveal different successional patterns of abundant and rare sub-communities in eighty pollutant-degrading consortia and two original soil samples...
March 21, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28335817/gene-expression-differences-between-paxgene-and-tempus-blood-rna-tubes-are-highly-reproducible-between-independent-samples-and-biobanks
#14
Anne Heidi Skogholt, Einar Ryeng, Sten Even Erlandsen, Frank Skorpen, Svanhild A Schønberg, Pål Sætrom
BACKGROUND: Gene expression profiling from blood is sensitive to technology choices. For example, the main blood RNA collection systems-the PAXgene and Tempus tubes-differently influence RNA expression signatures. The aim of this study was to establish a common RNA isolation protocol for these two systems and investigate if it could reduce the differences in gene expression between them. RESULTS: We collected identical blood samples on the PAXgene and Tempus systems and retrieved blood samples from two independent biobanks-NOWAC and HUNT3-which are based on PAXgene and Tempus, respectively...
March 23, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28335448/a-community-multi-omics-approach-towards-the-assessment-of-surface-water-quality-in-an-urban-river-system
#15
David J Beale, Avinash V Karpe, Warish Ahmed, Stephen Cook, Paul D Morrison, Christopher Staley, Michael J Sadowsky, Enzo A Palombo
A multi-omics approach was applied to an urban river system (the Brisbane River (BR), Queensland, Australia) in order to investigate surface water quality and characterize the bacterial population with respect to water contaminants. To do this, bacterial metagenomic amplicon-sequencing using Illumina next-generation sequencing (NGS) of the V5-V6 hypervariable regions of the 16S rRNA gene and untargeted community metabolomics using gas chromatography coupled with mass spectrometry (GC-MS) were utilized. The multi-omics data, in combination with fecal indicator bacteria (FIB) counts, trace metal concentrations (by inductively coupled plasma mass spectrometry (ICP-MS)) and in-situ water quality measurements collected from various locations along the BR were then used to assess the health of the river ecosystem...
March 14, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28335389/characteristics%C3%A2-and%C3%A2-lethality%C3%A2-of%C3%A2-a%C3%A2-novel%C3%A2-recombinant%C3%A2-dermonecrotic%C3%A2-venom%C3%A2-phospholipase%C3%A2-d%C3%A2-from%C3%A2-hemiscorpius%C3%A2-lepturus
#16
Elham Torabi, Mahdi Behdani, Mohammad Hosseininejad Chafi, Reza Moazzami, Jean-Marc Sabatier, Vahid Khalaj, Delavar Shahbazzadeh, Kamran Pooshang Bagheri
Hemoscorpius lepturus is the most medically important scorpion in Iran. The clinical signs of H. lepturus envenomation are remarkably similar to those reported for brown spiders, including dermonecrosis, hematuria, renal failure and even death. The lethality and toxicity of brown spiders' venom have been attributed to its phospholipase D activity. This study aims to identify a phospholipase D with possible lethality and dermonecrotic activity in H. lepturus venom. In this study, a cDNA library of the venom glands was generated by Illumina RNA sequencing...
March 13, 2017: Toxins
https://www.readbyqxmd.com/read/28334706/repetitive-dna-a-versatile-tool-for-karyotyping-in-festuca-pratensis-huds
#17
Anna Křivánková, David Kopecký, Štěpán Stočes, Jaroslav Doležel, Eva Hřibová
FISH is a useful method to identify individual chromosomes in a karyotype and to discover their structural changes accompanying genome evolution and speciation. DNA probes for FISH should be chromosome specific and/or exhibit specific patterns of distribution along each chromosome. Such probes are not available in many plants including meadow fescue (Festuca pratensis Huds.), an important forage grass species. In the present study, various DNA repeats identified in Illumina shotgun sequences specific to chromosome 4F of F...
March 24, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28334151/strategies-for-processing-and-quality-control-of-illumina-genotyping-arrays
#18
Shilin Zhao, Wang Jing, David C Samuels, Quanghu Sheng, Yu Shyr, Yan Guo
Illumina genotyping arrays have powered thousands of large-scale genome-wide association studies over the past decade. Yet, because of the tremendous volume and complicated genetic assumptions of Illumina genotyping data, processing and quality control (QC) of these data remain a challenge. Thorough QC ensures the accurate identification of single-nucleotide polymorphisms and is required for the correct interpretation of genetic association results. By processing genotyping data on > 100 000 subjects from >10 major Illumina genotyping arrays, we have accumulated extensive experience in handling some of the most peculiar scenarios related to the processing and QC of Illumina genotyping data...
February 20, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334129/transcriptional-responses-of-detoxification-genes-to-four-plant-allelochemicals-in-aphis-gossypii
#19
Fen Li, Kang-Sheng Ma, Ping-Zhuo Liang, Xue-Wei Chen, Ying Liu, Xi-Wu Gao
Aphis gossypii Glover (Hemiptera: Aphididae) can damage a variety of agricultural crops, so it is very important for cotton aphids to evolve adaptive mechanisms to various allelochemicals from host plants. Our results aim to provide a fundamental and rich resource for exploring aphid functional genes in A. gossypii. A transcriptome data set and five expression profile data sets of A. gossypii samples were analyzed by Illumina sequencing platform. In total, 53,763,866 reads were assembled into 1,963,516 contigs and 28,555 unigenes...
February 17, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28333283/rch51-a-multiply-antibiotic-resistant-acinetobacter-baumannii-st103ip-isolate-carries-resistance-genes-in-three-plasmids-including-a-novel-potentially-conjugative-plasmid-carrying-oxa235-in-transposon-tn6252
#20
Mohammad Hamidian, Steven J Nigro, Rebecca M Hartstein, Ruth M Hall
Objectives: To determine the identity and context of genes conferring antibiotic resistance in a sporadic multiply antibiotic-resistant Acinetobacter baumannii recovered at Royal Children's Hospital, Brisbane. Methods: The antibiotic resistance phenotype for 23 antibiotics was determined using disc diffusion or MIC determination. The whole-genome sequence of RCH51 was determined using the Illumina HiSeq platform. Antibiotic resistance determinants were identified using ResFinder...
March 13, 2017: Journal of Antimicrobial Chemotherapy
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