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Pyrosequencing

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https://www.readbyqxmd.com/read/28101802/cold-pcr-technologies-in-the-area-of-personalized-medicine-methodology-and-applications
#1
REVIEW
Florence Mauger, Alexandre How-Kit, Jörg Tost
Somatic mutations bear great promise for use as biomarkers for personalized medicine, but are often present only in low abundance in biological material and are therefore difficult to detect. Many assays for mutation analysis in cancer-related genes (hotspots) have been developed to improve diagnosis, prognosis, prediction of drug resistance, and monitoring of the response to treatment. Two major approaches have been developed: mutation-specific amplification methods and methods that enrich and detect mutations without prior knowledge on the exact location and identity of the mutation...
January 18, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28100185/an-improved-genome-assembly-uncovers-prolific-tandem-repeats-in-atlantic-cod
#2
Ole K Tørresen, Bastiaan Star, Sissel Jentoft, William B Reinar, Harald Grove, Jason R Miller, Brian P Walenz, James Knight, Jenny M Ekholm, Paul Peluso, Rolf B Edvardsen, Ave Tooming-Klunderud, Morten Skage, Sigbjørn Lien, Kjetill S Jakobsen, Alexander J Nederbragt
BACKGROUND: The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies...
January 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28100022/mycorrhizal-specificity-does-not-limit-the-distribution-of-an-endangered-orchid-species
#3
Michael Waud, Rein Brys, Wouter Van Landuyt, Bart Lievens, Hans Jacquemyn
What factors determine the distribution of a species is a central question in ecology and conservation biology. In general, the distribution of plant species is assumed to be controlled by dispersal or environmentally controlled recruitment. For plant species which are critically dependent on mycorrhizal symbionts for germination and seedling establishment, specificity in mycorrhizal associations and availability of suitable mycorrhizal fungi can be expected to have a major impact on successful colonization and establishment, and thus ultimately on a species distribution...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28094047/methanogenic-biodegradation-of-paraffinic-solvent-hydrocarbons-in-two-different-oil-sands-tailings
#4
Mohd Faidz Mohamad Shahimin, Tariq Siddique
Microbial communities drive many biogeochemical processes in oil sands tailings and cause greenhouse gas emissions from tailings ponds. Paraffinic solvent (primarily C5-C6; n- and iso-alkanes) is used by some oil sands companies to aid bitumen extraction from oil sands ores. Residues of unrecovered solvent escape to tailings ponds during tailings deposition and sustain microbial metabolism. To investigate biodegradation of hydrocarbons in paraffinic solvent, mature fine tailings (MFT) collected from Albian and CNRL ponds were amended with paraffinic solvent at ~0...
January 13, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28087103/identifying-methanogen-community-structures-and-their-correlations-with-performance-parameters-in-four-full-scale-anaerobic-sludge-digesters
#5
Taewoan Koo, Seung Gu Shin, Joonyeob Lee, Gyuseong Han, Woong Kim, Kyungjin Cho, Seokhwan Hwang
Four full-scale mesophilic anaerobic digesters treating waste sludge were monitored to characterize methanogen communities and their relationship with process parameters. The performance of the four digesters were dissimilar with the average chemical oxygen demand removal efficiencies between 24 and 45% and differing pH. Real-time quantitative PCR showed that archaeal 16S rRNA gene concentration ([ARC]) and, more pronouncedly, its ratio to bacterial counterpart ([ARC]/[BAC]) correlated positively with the performance parameters, including the lipid removal efficiency...
January 4, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28077379/effects-of-supplementation-with-nondigestible-carbohydrates-on-fecal-calprotectin-and-on-epigenetic-regulation-of-sfrp1-expression-in-the-large-bowel-mucosa-of-healthy-individuals
#6
Fiona C Malcomson, Naomi D Willis, Iain McCallum, Long Xie, Idoia Ibero-Baraibar, Wing C Leung, Seamus Kelly, D Michael Bradburn, Nigel J Belshaw, Ian T Johnson, John C Mathers
BACKGROUND: Hyperactive Wnt signaling is frequently observed in colorectal cancer. Higher intakes of dietary fiber [nondigestible carbohydrates (NDCs)] and the fermentation product butyrate are protective against colorectal cancer and may exert their preventative effects via modulation of the Wnt pathway. OBJECTIVES: We investigated the effects of supplementing healthy individuals with 2 NDCs [resistant starch (RS) and polydextrose] on fecal calprotectin concentrations and Wnt pathway-related gene expression...
January 11, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28076841/clonal-evolution-in-therapy-related-neoplasms
#7
Emiliano Fabiani, Giulia Falconi, Luana Fianchi, Marianna Criscuolo, Tiziana Ottone, Laura Cicconi, Stefan Hohaus, Simona Sica, Massimiliano Postorino, Antonino Neri, Marta Lionetti, Giuseppe Leone, Francesco Lo-Coco, Maria Teresa Voso
Therapy-related myeloid neoplasms (t-MN) may occur as a late effect of cytotoxic therapy for a primary malignancy or autoimmune diseases in susceptible individuals. We studied the development of somatic mutations in t-MN, using a collection of follow-up samples from 14 patients with a primary hematologic malignancy, who developed a secondary leukemia (13 t-MN and 1 t-acute lymphoblastic leukemia), at a median latency of 73 months (range 18-108) from primary cancer diagnosis.Using Sanger and next generation sequencing (NGS) approaches we identified 8 mutations (IDH1 R132H, ASXL1 Y591*, ASXL1 S689*, ASXL1 R693*, SRSF2 P95H, SF3B1 K700E, SETBP1 G870R and TP53 Y220C) in seven of thirteen t-MN patients (54%), whereas the t-ALL patient had a t(4,11) translocation, resulting in the KMT2A/AFF1 fusion gene...
January 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28074437/aberrant-endometrial-dna-methylome-of-homeobox-a10-and-catechol-o-methyltransferase-in-endometriosis
#8
Fei Ji, Xinhua Yang, Yan He, Hui Wang, Aixingzi Aili, Yan Ding
PURPOSE: Differential methylation of both HOXA10 and catechol-O-methyltransferase (COMT) has been reported in different endometrium disorders, and the two genes are linked through the estrogen pathway. The current study investigates the DNA methylation of HOXA10 and COMT in ectopic and eutopic endometrial tissues and its correlation with and the occurrence of endometriosis in women from Xinjiang province in China. METHODS: In the current study, 120 patients with endometriosis were recruited from our hospital between January 2011 and June 2014...
January 10, 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/28073540/phylogenetic-structure-of-bacterial-assemblages-co-occurring-with-ostreopsis-cf-ovata-bloom
#9
Silvana Vanucci, Flavio Guidi, Rossella Pistocchi, Richard A Long
Extensive blooms of the toxic epiphytic/benthic dinoflagellate Ostreopsis cf. ovata are being reported with increasing frequency and spatial distribution in temperate coastal regions including the Mediterranean. These blooms are of human and environmental health concern due to the production of isobaric palytoxin and a wide range of ovatoxins by Ostreopsis cf. ovata. Bacterial-microalgal interactions are important regulators in algal bloom dynamics and potentially toxin dynamics. This study investigated the bacterial assemblages co-occurring with O...
May 2016: Harmful Algae
https://www.readbyqxmd.com/read/28073532/toxigenic-algae-and-associated-phycotoxins-in-two-coastal-embayments-in-the-ebro-delta-nw-mediterranean
#10
Julia A Busch, Karl B Andree, Jorge Diogène, Margarita Fernández-Tejedor, Kerstin Toebe, Uwe John, Bernd Krock, Urban Tillmann, Allan D Cembella
Harmful Algal Bloom (HAB) surveillance is complicated by high diversity of species and associated phycotoxins. Such species-level information on taxonomic affiliations and on cell abundance and toxin content is, however, crucial for effective monitoring, especially of aquaculture and fisheries areas. The aim addressed in this study was to determine putative HAB taxa and related phycotoxins in plankton from aquaculture sites in the Ebro Delta, NW Mediterranean. The comparative geographical distribution of potentially harmful plankton taxa was established by weekly field sampling throughout the water column during late spring-early summer over two years at key stations in Alfacs and Fangar embayments within the Ebro Delta...
May 2016: Harmful Algae
https://www.readbyqxmd.com/read/28072889/in-depth-analysis-of-compartmentalization-of-hiv-1-matrix-protein-p17-in-pbmc-and-plasma
#11
Marina Selleri, Riccardo Dolcetti, Francesca Caccuri, Emanuela Giombini, Gabriella Rozera, Isabella Abbate, Alessia Mammone, Stefania Zanussi, Debora Martorelli, Simona Fiorentini, Arnaldo Caruso, Maria Rosaria Capobianchi
HIV-1 p17 plays an important role in the virus life-cycle and disease pathogenesis. Recent studies indicated a high heterogeneity of p17. A high number of insertions in the p17 carboxy-terminal region have been more frequently detected in patients with non-Hodgkin lymphoma (NHL), suggesting a role of altered p17 in lymphomagenesis. Based on p17 heterogeneity, possible PBMC/plasma compartmentalization of p17 variants was explored by ultra-deep pyrosequencing in five NHL patients. The high variability of p17 with insertions at the carboxy-terminal region was confirmed in plasma and observed for the first time in proviral genomes...
January 9, 2017: New Microbiologica
https://www.readbyqxmd.com/read/28071986/evaluation-of-a-two-year-routine-application-of-molecular-testing-of-thyroid-fine-needle-aspirations-fna-using-a-7-gene-panel-in-a-primary-referral-setting-in-germany
#12
Markus Eszlinger, Katharina Böhme, Maha Ullmann, Fabian Görke, Udo Siebolts, Anna Neumann, Christiane Franzius, Sabine Adam, Thomas Molwitz, Christian Landvogt, Bassam Amro, Anja Hach, Berit Feldmann, Dieter Graf, Antje Wefer, Rainer Niemann, Catharina Bullmann, Günther Klaushenke, Reinhard Santen, Gregor Tönshoff, Velimir Ivancevic, Andreas Kögler, Eberhard Bell, Bernd Lorenz, Gerald Kluge, Christoph Hartenstein, Ilka Ruschenburg, Ralf Paschke
BACKGROUND: Major differences with respect to the diagnostic performance of a "ruling in" approach in the pre-surgical diagnosis of indeterminate thyroid fine needle aspirations (FNAs) have been reported. Therefore, the aim of this prospective multicenter study was to investigate the specific diagnostic impact of mutation testing using a 7-gene-panel in a routine primary referral setting analyzing FNAs from endocrinology and nuclear medicine practices in Germany. METHODS: RNA and DNA was extracted from 564 routine air-dried FNA smears obtained from 64 physicians and cytologically graded by one experienced cytopathologist...
January 10, 2017: Thyroid: Official Journal of the American Thyroid Association
https://www.readbyqxmd.com/read/28071697/diel-scale-temporal-dynamics-recorded-for-bacterial-groups-in-namib-desert-soil
#13
Eoin Gunnigle, Aline Frossard, Jean-Baptiste Ramond, Leandro Guerrero, Mary Seely, Don A Cowan
Microbes in hot desert soil partake in core ecosystem processes e.g., biogeochemical cycling of carbon. Nevertheless, there is still a fundamental lack of insights regarding short-term (i.e., over a 24-hour [diel] cycle) microbial responses to highly fluctuating microenvironmental parameters like temperature and humidity. To address this, we employed T-RFLP fingerprinting and 454 pyrosequencing of 16S rRNA-derived cDNA to characterize potentially active bacteria in Namib Desert soil over multiple diel cycles...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28070331/effects-of-bacillus-subtilis-csl2-on-the-composition-and-functional-diversity-of-the-faecal-microbiota-of-broiler-chickens-challenged-with-salmonella-gallinarum
#14
Ju Kyoung Oh, Edward Alain B Pajarillo, Jong Pyo Chae, In Ho Kim, Dong Soo Yang, Dae-Kyung Kang
BACKGROUND: The chicken gastrointestinal tract contains a diverse microbiota whose composition and structure play important roles in gut functionality. In this study, microbial shifts resulting from feed supplementation with Bacillus subtilis CSL2 were evaluated in broilers challenged and unchallenged with Salmonella Gallinarum. To analyse bacterial community composition and functionality, 454 GS-FLX pyrosequencing of 16S rRNA gene amplicons was performed. RESULTS: The Quantitative Insights into Microbial Ecology (QIIME) pipeline was used to analyse changes in the faecal microbiota over a 24-h period...
2017: Journal of Animal Science and Biotechnology
https://www.readbyqxmd.com/read/28069929/genomic-alterations-of-adamantinomatous-and-papillary-craniopharyngioma
#15
Tobias Goschzik, Marco Gessi, Verena Dreschmann, Ursel Gebhardt, Linghua Wang, Shigeru Yamaguchi, David A Wheeler, Libero Lauriola, Ching C Lau, Hermann L Müller, Torsten Pietsch
Craniopharyngiomas are rare histologically benign but clinically challenging neoplasms. To obtain further information on the molecular genetics and biology of craniopharyngiomas, we analyzed a cohort of 121 adamantinomatous and 16 papillary craniopharyngiomas (ACP, PCP). We extracted DNA from formalin-fixed paraffin-embedded tissue and determined mutational status of CTNNB1, BRAF, and DDX3X by Sanger sequencing, next generation panel sequencing, and pyrosequencing. Sixteen craniopharyngiomas were further analyzed by molecular inversion profiling (MIP); 76...
January 9, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/28069692/genes-involved-in-development-and-differentiation-are-commonly-methylated-in-cancers-derived-from-multiple-organs-a-single-institutional-methylome-analysis-using-1007-tissue-specimens
#16
Kentaro Ohara, Eri Arai, Yoriko Takahashi, Nanako Ito, Ayako Shibuya, Koji Tsuta, Ryoji Kushima, Hitoshi Tsuda, Hidenori Ojima, Hiroyuki Fujimoto, Shun-Ichi Watanabe, Hitoshi Katai, Takayuki Kinoshita, Tatsuhiro Shibata, Takashi Kohno, Yae Kanai
The aim of this study was to clarify the significance of DNA methylation alterations shared by cancers derived from multiple organs. We analyzed single-institutional methylome data by single-CpG-resolution Infinium assay for 1,007 samples of non-cancerous tissue (N) and corresponding cancerous tissue (T) obtained from lung, stomach, kidney, breast and liver. Principal component analysis revealed that N samples of each organ showed distinct DNA methylation profiles, DNA methylation profiles of N samples of each organ being inherited by the corresponding T samples and DNA methylation profiles of T samples being more similar to those of N samples in the same organ than those of T samples in other organs...
January 9, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28069683/targeted-deep-sequencing-reveals-full-methylation-profiles-of-multiple-hpv-types-and-potential-biomarkers-for-cervical-cancer-progression
#17
Pengyuan Liu, Marissa Iden, Samantha Fye, Yi-Wen Huang, Elizabeth Hopp, Chen Chu, Yan Lu, Janet S Rader
BACKGROUND: Invasive cervical cancer (ICC) and its premalignant phase (cervical intraepithelial neoplasia; CIN1-3) are distinguished by gynecological and pathological examination, yet no current methodologies can predict precancerous lesions that are destined to progress to ICC. Thus, development of reliable assays to assess patient prognosis is much needed. METHODS: HPV DNA methylation is significantly altered in cervical disease. Using an HPV-enrichment approach and next-generation DNA sequencing, methylation status was characterized in a case-case comparison of CIN (n = 2 CIN1; n = 2 CIN2; n = 20 CIN3) and ICC (n = 37) samples...
January 9, 2017: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/28066944/the-effect-of-lactobacillus-isolates-on-growth-performance-immune-response-intestinal-bacterial-community-composition-of-growing-rex-rabbits
#18
REVIEW
C Wang, Y Zhu, F Li, L Huang
The objective of this experiment was to investigate the effect of Lactobacillus isolates on intestinal bacterial community composition of growing Rex Rabbits. A total of 120 weaned Rex Rabbits (30 days old, 30 per group) were used for the experiment, which started after an adaptation period of 7 days. The control group was fed with basal diet only, while the treatment I, II and III groups were fed with basal diet adding antibiotics, Lactobacillus zeae (LB1) and Lactobacillus casei (L3) respectively. Growth performance, immune response and intestinal flora have been examined...
January 8, 2017: Journal of Animal Physiology and Animal Nutrition
https://www.readbyqxmd.com/read/28066812/the-denture-associated-oral-microbiome-in-health-and-stomatitis
#19
Baochen Shi, Tingxi Wu, Jeffrey McLean, Anna Edlund, Youngik Young, Xuesong He, Hongyang Lv, Xuedong Zhou, Wenyuan Shi, Huiying Li, Renate Lux
While investigation of the microbiome on natural oral surfaces has generated a wealth of information, few studies have examined the microbial communities colonizing dentures and their relationship to oral health. To address this knowledge gap, we characterized the bacterial community associated with dentures and remaining teeth in healthy individuals and patients with denture stomatitis. The microbiome compositions of matched denture and tooth plaque samples of 10 healthy individuals and 9 stomatitis patients were determined by 16S rRNA gene pyrosequencing...
November 2016: MSphere
https://www.readbyqxmd.com/read/28064216/prevalence-of-egfr-tyrosine-kinase-domain-mutations-in-head-and-neck-squamous-cell-carcinoma-cohort-study-and-systematic-review
#20
REVIEW
Christos Perisanidis
BACKGROUND: Mutations in the epidermal growth factor receptor (EGFR) tyrosine kinase domain (TKD) are associated with response and resistance to targeted therapy. The EGFR mutation status in patients with advanced oral and oropharyngeal squamous cell carcinoma (OOSCC) was evaluated. A systematic literature review was undertaken to summarize current evidence and estimate the overall prevalence of EGFR TKD mutations in patients with head and neck squamous cell carcinoma (HNSCC). MATERIALS AND METHODS: Genomic DNA was extracted from formalin-fixed, paraffin-embedded tumor samples of 113 patients with OOSCC...
2, 2017: In Vivo
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