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https://www.readbyqxmd.com/read/28088415/qualitative-and-quantitative-adulteration-identification-of-milk-powder-using-the-dna-with-novel-extraction-method
#1
J Liao, Y F Liu, T Ku, M H Liu, Y Huang
The extraction of high-quality DNA from processed dairy products can often represent the crucial step in an authentication process by PCR-based methods. In this study, we optimized a novel DNA extraction method for milk powder and used the extracted DNA for identification of milk powder based on PCR analysis. The DNA quality was assessed by amplifying target sequences from mitochondrial genes, as well as by monitoring the yield, purity, and integrity of the extracted DNA. In addition, a laboratory adulteration model of milk powder was detected by PCR-based methods (PCR and real-time PCR) using primers targeting the mitochondrial 12S rRNA gene...
January 11, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28088334/subtype-identification-of-human-blastocystis-spp-isolated-from-lao-people-s-democratic-republic
#2
Oranuch Sanpool, Sakhone Laymanivong, Tongjit Thanchomnang, Rutchanee Rodpai, Lakkhana Sadaow, Issarapong Phosuk, Wanchai Maleewong, Pewpan M Intapan
Blastocystis sp. is the most common protist found in the intestinal tract of humans and animals. Blastocystis subtypes (STs) are classified based on the molecular phylogeny of the small subunit rRNA gene (SSU rDNA). At least 17 Blastocystis STs have been reported and, of these, STs 1-9 have been found in humans. This study revealed the presence of human Blastocystis STs in Lao People's Democratic Republic (Lao PDR). Fecal samples were collected from apparently healthy people from the central province of Khammouane and the southern province of Champasak...
January 11, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28087944/laboratory-diagnosis-and-susceptibility-testing-for-mycobacterium-tuberculosis
#3
Gary W Procop
The laboratory, which utilizes some of the most sophisticated and rapidly changing technologies, plays a critical role in the diagnosis of tuberculosis. Some of these tools are being employed in resource-challenged countries for the rapid detection and characterization of Mycobacterium tuberculosis. Foremost, the laboratory defines appropriate specimen criteria for optimal test performance. The direct detection of mycobacteria in the clinical specimen, predominantly done by acid-fast staining, may eventually be replaced by rapid-cycle PCR...
December 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/28087533/polysaccharide-degradation-capability-of-actinomycetales-soil-isolates-from-a-semi-arid-grassland-of-the-colorado-plateau
#4
Chris M Yeager, La Verne Gallegos-Graves, John Dunbar, Cedar N Hesse, Hajnalka Daligault, Cheryl R Kuske
: Among the bacteria, members of the Actinomycetales are considered quintessential degraders of complex polysaccharides in soils. However, studies examining complex polysaccharide degradation by Actinomycetales (other than Streptomyces spp.) in soils are limited. Here, we examine the lignocellulolytic and chitinolytic potential of 112 Actinomycetales strains, encompassing 13 families, isolated from a semi-arid grassland of the Colorado Plateau, Utah, USA. Members of the Streptomycetaceae, Pseudonocardiaceae, Micromonosporaceae and Promicromonosporaceae exhibited robust activity against carboxymethylcellulose, xylan, chitin and pectin substrates (except for low/no pectinase activity by the Micromonosporaceae)...
January 13, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28086860/nicotiana-attenuata-data-hub-nadh-an-integrative-platform-for-exploring-genomic-transcriptomic-and-metabolomic-data-in-wild-tobacco
#5
Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T Baldwin, Shuqing Xu
BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28086783/de-novo-transcriptome-analysis-of-rose-scented-geranium-provides-insights-into-the-metabolic-specificity-of-terpene-and-tartaric-acid-biosynthesis
#6
Lokesh K Narnoliya, Girija Kaushal, Sudhir P Singh, Rajender S Sangwan
BACKGROUND: Rose-scented geranium (Pelargonium sp.) is a perennial herb that produces a high value essential oil of fragrant significance due to the characteristic compositional blend of rose-oxide and acyclic monoterpenoids in foliage. Recently, the plant has also been shown to produce tartaric acid in leaf tissues. Rose-scented geranium represents top-tier cash crop in terms of economic returns and significance of the plant and plant products. However, there has hardly been any study on its metabolism and functional genomics, nor any genomic expression dataset resource is available in public domain...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28081278/population-structure-of-annona-crassiflora-an-endemic-plant-species-of-the-brazilian-cerrado
#7
R Gwinner, T A Setotaw, F A Rodrigues, D V C França, F A da Silveira, L A S Pio, M Pasqual
Habitat fragmentation has numerous consequences, particularly to endemic species, and has a negative impact on the genetic diversity of neglected species, leading to genetic drift. Annona crassiflora Mart. is a species that is endemic to Brazil, and its incidence in the Cerrado biome has decreased. The identification and characterization of its remaining diversity is necessary for its conservation. Our aim was to study the population structure of A. crassiflora populations from different Cerrado regions in Minas Gerais State, Brazil (Corinto, Curvelo, Carmo da Mata, Boa Esperança, and Paraguaçu) using inter-simple sequence repeat (ISSR) markers and DNA content...
December 23, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28078711/systematics-of-cladophora-spp-chlorophyta-from-north-carolina-usa-based-upon-morphology-and-dna-sequence-data-with-a-description-of-cladophora-subtilissima-sp-nov
#8
Robin L Taylor, Craig J Bailey, D Wilson Freshwater
Identification of Cladophora species is challenging due to conservation of gross morphology, few discrete autapomorphies, and environmental influences on morphology. Twelve species of marine Cladophora were reported from North Carolina waters. Cladophora specimens were collected from inshore and offshore marine waters for DNA sequence and morphological analyses. The nuclear-encoded rRNA internal transcribed spacer regions (ITS) were sequenced for 105 specimens and used in Molecular Assisted Identification (MAI)...
January 12, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28077639/identification-of-a-continuous-neutralizing-epitope-within-ul128-of-human-cytomegalovirus
#9
Flavia Chiuppesi, Teodora Kaltcheva, Meng Zhuo, Peter A Barry, Don J Diamond, Felix Wussow
: As human cytomegalovirus (HCMV) is the most common infectious cause of fetal anomalies during pregnancy, developing a vaccine that prevents HCMV infection is considered a global health priority. Although HCMV immune correlates of protection are only poorly defined, neutralizing antibodies (NAb) targeting the envelope pentamer complex (PC) composed of subunits gH, gL, UL128, UL130, and UL131A are thought to contribute in preventing HCMV infection. Here, we describe a continuous target sequence within UL128 that is recognized by a previously isolated potent PC-specific NAb, termed 13B5...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28077570/ktcnlncdb-a-first-platform-to-investigate-lncrnas-expressed-in-human-keratoconus-and-non-keratoconus-corneas
#10
Michał W Szcześniak, Michal Kabza, Justyna A Karolak, Malgorzata Rydzanicz, Dorota M Nowak, Barbara Ginter-Matuszewska, Piotr Polakowski, Rafal Ploski, Jacek P Szaflik, Marzena Gajecka
Keratoconus (KTCN, OMIM 148300) is a degenerative eye disorder characterized by progressive stromal thinning that leads to a conical shape of the cornea, resulting in optical aberrations and even loss of visual function. The biochemical background of the disease is poorly understood, which motivated us to perform RNA-Seq experiment, aimed at better characterizing the KTCN transcriptome and identification of long non-coding RNAs (lncRNAs) that might be involved in KTCN etiology. The in silico functional studies based on predicted lncRNA:RNA base-pairings led us to recognition of a number of lncRNAs possibly regulating genes with known or plausible links to KTCN...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28076437/mutations-in-splicing-factor-genes-are-a-major-cause-of-autosomal-dominant-retinitis-pigmentosa-in-belgian-families
#11
Caroline Van Cauwenbergh, Frauke Coppieters, Dimitri Roels, Sarah De Jaegere, Helena Flipts, Julie De Zaeytijd, Sophie Walraedt, Charlotte Claes, Erik Fransen, Guy Van Camp, Fanny Depasse, Ingele Casteels, Thomy de Ravel, Bart P Leroy, Elfride De Baere
PURPOSE: Autosomal dominant retinitis pigmentosa (adRP) is characterized by an extensive genetic heterogeneity, implicating 27 genes, which account for 50 to 70% of cases. Here 86 Belgian probands with possible adRP underwent genetic testing to unravel the molecular basis and to assess the contribution of the genes underlying their condition. METHODS: Mutation detection methods evolved over the past ten years, including mutation specific methods (APEX chip analysis), linkage analysis, gene panel analysis (Sanger sequencing, targeted next-generation sequencing or whole exome sequencing), high-resolution copy number screening (customized microarray-based comparative genomic hybridization)...
2017: PloS One
https://www.readbyqxmd.com/read/28076398/identification-of-a-novel-mutation-in-brd4-that-causes-autosomal-dominant-syndromic-congenital-cataracts-associated-with-other-neuro-skeletal-anomalies
#12
Hyun-Seok Jin, Jeonhyun Kim, Woori Kwak, Hyeonsoo Jeong, Gyu-Bin Lim, Cha Gon Lee
Congenital cataracts can occur as a non-syndromic isolated ocular disease or as a part of genetic syndromes accompanied by a multi-systemic disease. Approximately 50% of all congenital cataract cases have a heterogeneous genetic basis. Here, we describe three generations of a family with an autosomal dominant inheritance pattern and common complex phenotypes, including bilateral congenital cataracts, short stature, macrocephaly, and minor skeletal anomalies. We did not find any chromosomal aberrations or gene copy number abnormalities using conventional genetic tests; accordingly, we conducted whole-exome sequencing (WES) to identify disease-causing genetic alterations in this family...
2017: PloS One
https://www.readbyqxmd.com/read/28076350/emergence-of-rare-species-of-nontuberculous-mycobacteria-as-potential-pathogens-in-saudi-arabian-clinical-setting
#13
Bright Varghese, Mushira Enani, Mohammed Shoukri, Sahar AlThawadi, Sameera AlJohani, Sahal Al-Hajoj
BACKGROUND: Clinical relevance of nontuberculous mycobacteria (NTM) is increasing worldwide including in Saudi Arabia. A high species diversity of NTM's has been noticed in a recent study. However, the identification in diagnostic laboratories is mostly limited to common species. The impact of NTM species diversity on clinical outcome is so far neglected in most of the clinical settings. METHODOLOGY/PRINCIPAL FINDINGS: During April 2014 to September 2015, a nationwide collection of suspected NTM clinical isolates with clinical and demographical data were carried out...
January 11, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28076288/transfer-rnas-with-novel-cloverleaf-structures
#14
Takahito Mukai, Oscar Vargas-Rodriguez, Markus Englert, H James Tripp, Natalia N Ivanova, Edward M Rubin, Nikos C Kyrpides, Dieter Söll
We report the identification of novel tRNA species with 12-base pair amino-acid acceptor branches composed of longer acceptor stem and shorter T-stem. While canonical tRNAs have a 7/5 configuration of the branch, the novel tRNAs have either 8/4 or 9/3 structure. They were found during the search for selenocysteine tRNAs in terabytes of genome, metagenome and metatranscriptome sequences. Certain bacteria and their phages employ the 8/4 structure for serine and histidine tRNAs, while minor cysteine and selenocysteine tRNA species may have a modified 8/4 structure with one bulge nucleotide...
October 5, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/28074630/quantification-of-phenotype-information-aids-the-identification-of-novel-disease-genes
#15
Anneke T Vulto-van Silfhout, Christian Gilissen, Jelle J Goeman, Sandra Jansen, Claudia J M van Amen-Hellebrekers, Bregje W M van Bon, David A Koolen, Erik A Sistermans, Han G Brunner, Arjan P M de Brouwer, Bert B A de Vries
Next generation sequencing led to the identification of many potential novel disease genes. The presence of mutations in the same gene in multiple unrelated patients is, however, a priori insufficient to establish that these genes are truly involved in the respective disease. Here, we show how phenotype information can be incorporated within statistical approaches to provide additional evidence for the causality of mutations. We developed a broadly applicable statistical model that integrates gene-specific mutation rates, cohort size, mutation type and phenotype frequency information to assess the chance of identifying de novo mutations affecting the same gene in multiple patients with shared phenotype features...
January 10, 2017: Human Mutation
https://www.readbyqxmd.com/read/28073847/identification-of-ccr2-and-cd180-as-robust-pharmacodynamic-tumor-and-blood-biomarkers-for-clinical-use-with-brd4-bet-inhibitors
#16
Tammie C Yeh, Greg O'Connor, Philip Petteruti, Austin Dulak, Maureen Hattersley, J Carl Barrett, Huawei Chen
PURPOSE: AZD5153 is a novel BRD4/BET inhibitor with a distinctive bivalent bromodomain binding mode. To support its clinical development, we identified pharmacodynamic (PD) biomarkers for use in clinical trials to establish target engagement. EXPERIMENTAL DESIGN: CCR2 and CD180 mRNAs, initially identified from whole transcriptome profiling, were further evaluated by quantitative PCR in hematologic cell lines, xenografts, and whole blood from rat, healthy volunteers, and patients with cancer...
January 10, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28071972/genetic-identification-for-prey-birds-of-the-endangered-peregrine-falcon-falco-peregrinus
#17
Sang-Hyun Han, Hong-Shik Oh
To reveal the dietary ecology of the peregrine falcon (Falco peregrinus), we conducted a molecular analysis for mitochondrial genes (COI and CYTB) to identify the prey species collected from a feeding place found on Sasu Island, South Korea. The results from noninvasive genetic analysis showed that the sequences obtained came from nine species of birds (Cuculus canorus, Eurystomus orientalis, Limosa limosa, Microscelis amaurotis, Oriolus chinensis, Phasianus colchicus, Sterna hirundo, Streptopelia orientalis, and Turdus pallidus)...
January 10, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28069590/identification-of-ssr-markers-closely-linked-to-the-yellow-seed-coat-color-gene-in-heading-chinese-cabbage-brassica-rapa-l-ssp-pekinensis
#18
Yanjing Ren, Junqing Wu, Jing Zhao, Lingyu Hao, Lugang Zhang
Research on the yellow-seeded variety of heading Chinese cabbage will aid in broadening its germplasm resources and lay a foundation for AA genome research in Brassica crops. Here, an F2 segregating population of 1,575 individuals was constructed from two inbred lines (brown-seeded '92S105' and yellow-seeded '91-125'). This population was used to identify the linkage molecular markers of the yellow seed coat trait using simple sequence repeat (SSR) techniques combined with a bulk segregant analysis (BSA). Of the 144 SSR primer pairs on the A01- A10 chromosomes from the Brassica database (http://brassicadb...
January 9, 2017: Biology Open
https://www.readbyqxmd.com/read/28069063/the-ribosomal-transcription-units-of-haplorchis-pumilio-and-h-taichui-and-the-use-of-28s-rdna-sequences-for-phylogenetic-identification-of-common-heterophyids-in-vietnam
#19
Thanh Hoa Le, Khue Thi Nguyen, Nga Thi Bich Nguyen, Huong Thi Thanh Doan, Do Trung Dung, David Blair
BACKGROUND: Heterophyidiasis is now a major public health threat in many tropical countries. Species in the trematode family Heterophyidae infecting humans include Centrocestus formosanus, Haplorchis pumilio, H. taichui, H. yokogawai, Procerovum varium and Stellantchasmus falcatus. For molecular phylogenetic and systematic studies on trematodes, we need more prospective markers for taxonomic identification and classification. This study provides near-complete ribosomal transcription units (rTU) from Haplorchis pumilio and H...
January 9, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28068403/normalisation-against-circadian-and-age-related-disturbances-enables-robust-detection-of-gene-expression-changes-in-liver-of-aged-mice
#20
Sara S Fonseca Costa, Daniel Wegmann, Jürgen A Ripperger
The expression of some genes is affected by age. To detect such age-related changes, their expression levels are related to constant marker genes. However, transcriptional noise increasing with advancing age renders difficult the identification of real age-related changes because it may affect the marker genes as well. Here, we report a selection procedure for genes appropriate to normalise the mouse liver transcriptome under various conditions including age. These genes were chosen from an initial set of 16 candidate genes defined based on a RNA-sequencing experiment and published literature...
2017: PloS One
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