keyword
MENU ▼
Read by QxMD icon Read
search

Pyrosequencing

keyword
https://www.readbyqxmd.com/read/29145627/bacterial-communities-associated-with-the-ectoparasitic-mites-varroa-destructor-and-tropilaelaps-mercedesae-of-honey-bees-apis-mellifera
#1
Chonthicha Pakwan, Martin Kaltenpoth, Benjamin Weiss, Panuwan Chantawannakul, Guo Jun, Terd Disayathanoowat
Varroa and Tropilaelaps mites have been reported as serious ectoparasites of honey bees (Apis mellifera). In this study, bacterial communities associated with Varroa destructor and Tropilaelaps mercedesae from Northern Thailand were determined, using both culture-dependent and culture-independent approaches. Adult female mites were collected from apiaries in Chiang Mai and Lampang provinces. Culturable bacteria were isolated from individual mites. On average, we observed approximately 1340 and 1140 CFU/mite in Varroa and Tropilaelaps, respectively...
November 14, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29145477/the-abundance-of-health-associated-bacteria-is-altered-in-pah-polluted-soils-implications-for-health-in-urban-areas
#2
Anirudra Parajuli, Mira Grönroos, Sari Kauppi, Tomasz Płociniczak, Marja I Roslund, Polina Galitskaya, Olli H Laitinen, Heikki Hyöty, Ari Jumpponen, Rauni Strömmer, Martin Romantschuk, Nan Hui, Aki Sinkkonen
Long-term exposure to polyaromatic hydrocarbons (PAHs) has been connected to chronic human health disorders. It is also well-known that i) PAH contamination alters soil bacterial communities, ii) human microbiome is associated with environmental microbiome, and iii) alteration in the abundance of members in several bacterial phyla is associated with adverse or beneficial human health effects. We hypothesized that soil pollution by PAHs altered soil bacterial communities that had known associations with human health...
2017: PloS One
https://www.readbyqxmd.com/read/29145102/remediation-of-a-soil-chronically-contaminated-with-hydrocarbons-through-persulfate-oxidation-and-bioremediation
#3
Rocío Medina, Pedro Maximiliano David Gara, Antonio José Fernández-González, Janina Alejandra Rosso, María Teresa Del Panno
The impact of remediation combining chemical oxidation followed by biological treatment on soil matrix and microbial community was studied, of a chronically hydrocarbon contaminated soil sourced from a landfarming treatment. Oxidation by ammonium persulfate produced a significant elimination of polycyclic aromatic hydrocarbons (PAHs) and an increase in PAH bioavailability. Organic-matter oxidation mobilized nutrients from the soil matrix. The bacterial populations were affected negatively, with a marked diminution in the diversity indices...
November 13, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29143604/fine-organization-of-genomic-regions-tagged-to-the-5s-rdna-locus-of-the-bread-wheat-5b-chromosome
#4
Ekaterina M Sergeeva, Andrey B Shcherban, Irina G Adonina, Michail A Nesterov, Alexey V Beletsky, Andrey L Rakitin, Andrey V Mardanov, Nikolai V Ravin, Elena A Salina
BACKGROUND: The multigene family encoding the 5S rRNA, one of the most important structurally-functional part of the large ribosomal subunit, is an obligate component of all eukaryotic genomes. 5S rDNA has long been a favored target for cytological and phylogenetic studies due to the inherent peculiarities of its structural organization, such as the tandem arrays of repetitive units and their high interspecific divergence. The complex polyploid nature of the genome of bread wheat, Triticum aestivum, and the technically difficult task of sequencing clusters of tandem repeats mean that the detailed organization of extended genomic regions containing 5S rRNA genes remains unclear...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29138492/the-antigenic-variability-of-hcv-in-viral-hla-ag-binding-is-related-to-the-activation-of-the-host-immune-response
#5
P Muñoz de Rueda, S M Jiménez-Ruiz, R Quiles, E J Pavón-Castillero, J A Muñoz-Gámez, J Casado, A Gila, A Ruiz-Extremera, J Salmerón
Our previous data show that hepatitis C virus (HCV) genotype 1 patients expressing the HLA-DQB1 * 0301 allele have a combined response probability of 69%, while the remaining 31% do not respond, probably because the HCV immunodominant epitope (IE) against the DQB1 * 0301 allele is mutated. HCV IE (region sequenced in NS3 is a region encoding aa 1253-1272) from 37 patients (21 Sustained Virological Response, SVR; 16 non-SVR) HLA-DQB1 * 0301+, were analysed by pyrosequencing. In vitro cultures were also determined by CD4+ proliferation, using non-mutated IE (wild-type synthetic peptide) and synthetic mutated peptide...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29137437/dna-hypermethyation-and-silencing-of-pitx1-correlated-with-advanced-stage-and-poor-postoperative-prognosis-of-esophageal-squamous-cell-carcinoma
#6
Takeshi Otsubo, Kazuhiko Yamada, Teruki Hagiwara, Kenshiro Oshima, Kei Iida, Koro Nishikata, Tetsuro Toyoda, Toru Igari, Kyoko Nohara, Satoshi Yamashita, Masahira Hattori, Taeko Dohi, Yuki I Kawamura
Esophageal squamous cell carcinoma (ESCC) is associated with the accumulation of genetic and epigenetic changes in the background mucosa. Dysregulated DNA methylation is known to lead to the inactivation of tumor suppressor genes and the activation of oncogenes. To identify the genes whose expression is perturbed by abnormal DNA methylation in ESCC, integrative transcriptomics by serial analysis of gene expression (SAGE) and methylome sequencing by methyl-DNA immunoprecipitation (MeDIP) analysis were performed...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29136648/imprinting-alterations-in-sperm-may-not-significantly-influence-art-outcomes-and-imprinting-patterns-in-the-cord-blood-of-offspring
#7
Li Tang, Zichao Liu, Ruopeng Zhang, Cunmei Su, Wenjuan Yang, Youlin Yao, Shuhua Zhao
An increase in imprinting disorders in children conceived though assisted reproductive technologies (ARTs) has been the subject of several reports. The transmission of imprinting errors from the sperm of infertile fathers is believed to be a possible reason for the increased occurrence of these disorders. However, whether the imprinting alterations in sperm affect ART outcomes and the imprinting of offspring is unclear. In the current study, we analyzed the methylation of H19, SNRPN and KCNQ1OT1 by pyrosequencing sperm samples from 97 infertile patients and 31 proven fertile males as well as cord blood samples from 13 infantswho were conceived by infertile parents through intracytoplasmic sperm injection (ICSI) and 30 healthy newborns who were conceived naturally...
2017: PloS One
https://www.readbyqxmd.com/read/29136413/first-metagenomic-survey-of-the-microbial-diversity-in-bioaerosols-emitted-in-waste-sorting-plants
#8
Jodelle Degois, Frederic Clerc, Xavier Simon, Cyril Bontemps, Pierre Leblond, Philippe Duquenne
Waste sorting activities are source of occupational bioaerosol exposures that are associated with several health disorders. New analytical tools, based on next-generation sequencing (NGS) technologies, provide powerful methods to assess the microbial composition of bioaerosols. The objectives of the study were (i) to assess the feasibility and the repeatability of NGS-based biodiversity measurements and (ii) to study the microbial biodiversity using NGS in bioaerosols emitted in a waste sorting plant (WSP)...
November 10, 2017: Annals of Work Exposures and Health
https://www.readbyqxmd.com/read/29133290/cd137-4-1bb-costimulation-modifies-dna-methylation-in-cd8-t-cell-relevant-genes
#9
M Angela Aznar, Sara Labiano, Angel Diaz-Lagares, Carmen Molina, Saray Garasa, Arantza Azpilicueta, Inaki Etxeberria, Alfonso R Sanchez-Paulete, Alan J Korman, Manel Esteller, Juan Sandoval, Ignacio Melero
CD137 (4-1BB) costimulation imprints long-term changes that instruct the ultimate behavior of T cells that have previously experienced CD137 ligation. Epigenetic changes could provide a suitable mechanism for these long-term consequences. Genome-wide DNA-methylation arrays were carried out on human peripheral blood CD8+ T lymphocytes stimulated with agonist monoclonal antibody to CD137, including urelumab, which is in phase I/II clinical trials for cancer immunotherapy. Several genes showed consistent methylation patterns in response to CD137 costimulation, which were confirmed by pyrosequencing in a series of healthy donors...
November 13, 2017: Cancer Immunology Research
https://www.readbyqxmd.com/read/29129825/npm1-mutation-analysis-in-acute-myeloid-leukemia-comparison-of-three-techniques-sanger-sequencing-pyrosequencing-and-real-time-pcr
#10
Dushyant Kumar, Anurag Mehta, Manoj Kumar Panigrahi, Sukanta Nath, Kandarpa Kumar Saikia
OBJECTIVE: Nucleophosmin-1 (NPM1) mutations have prognostic importance in acute myeloid leukemia (AML) patients with intermediate-risk karyotype at diagnosis. Approximately 30% of newly diagnosed cytogenetically normal AML (CN-AML) patients harbor NPM1 mutation in India. In this study we compared the efficiency of three molecular techniques in detecting NPM1 mutation in perepherial blood and bone marrow samples. MATERIALS AND METHODS: In a single centre cohort we analyzed 165 CN-AML bone marrow/peripheral blood for NPM1 mutation analysis...
November 13, 2017: Turkish Journal of Haematology: Official Journal of Turkish Society of Haematology
https://www.readbyqxmd.com/read/29129434/mutational-landscape-of-ddr2-gene-in-lung-squamous-cell-carcinoma-using-next-generation-sequencing
#11
Charles Ricordel, Alexandra Lespagnol, Francisco Llamas-Gutierrez, Marie de Tayrac, Mallorie Kerjouan, Alice Fievet, Houda Hamdi-Rozé, Amyrat Aliouat, Benoit Desrues, Jean Mosser, Hervé Léna
BACKGROUND: Lung cancer represents the leading cause of cancer-related death worldwide. Despite great advances in lung cancer management with the recent emergence of molecular targeted therapies for non-squamous non-small-cell lung cancer, no dramatic improvements have been achieved in lung squamous cell carcinoma (SCC). Mutations in discoidin domain receptor 2 (DDR2) gene were recently identified as promising molecular targets in this histology. The aim of this study is to describe the DDR2 mutational landscape of lung SCC and investigate the associated clinical factors...
October 19, 2017: Clinical Lung Cancer
https://www.readbyqxmd.com/read/29129016/exploring-genes-involved-in-benzoic-acid-biosynthesis-in-the-populus-davidiana-transcriptome-and-their-transcriptional-activity-upon-methyl-jasmonate-treatment
#12
Seong-Bum Park, Jong Youn Kim, Jung Yeon Han, Chang-Ho Ahn, Eung-Jun Park, Yong Eui Choi
Benzoic acids (BAs) are important structural elements in a wide variety of essential compounds and natural products, and play crucial roles in plant fitness. BA is a precursor of diverse benzenoid compounds, including the hormone salicylic acid (SA) and the aglycone moiety of salicin, which is particularly important in the Salicaceae family. The biosynthetic pathways leading to BA formation in plants are largely unknown. Recently, the CoA-dependent β-oxidative BA biosynthesis pathway, which occurs in peroxisomes, has been characterized in petunia...
November 11, 2017: Journal of Chemical Ecology
https://www.readbyqxmd.com/read/29124413/assessment-of-bacterial-diversity-in-hyalomma-aegyptium-h-marginatum-and-h-excavatum-ticks-through-tag-encoded-pyrosequencing
#13
Adem Keskin, Ahmet Bursali, David E Snow, Scot E Dowd, Saban Tekin
Ticks are among the most significant human-biting ectoparasites and they play a major role in transmission of many pathogenic agents to humans. In the present study, three species of Hyalomma ticks, Hyalomma aegyptium, H. marginatum and H. excavatum, were examined for the presence of zoonotic bacteria, both male and female ticks alike. Examination of microbial diversity with tag-encoded pyrosequencing indicates that H. marginatum and H. excavatum were more diversity rich than H. aegyptium. Although numerous pathogenic and non-pathogenic bacterial genera were detected, including Acidovorax, Bacillus, Bacteroides, Bdellovibrio, Clostridium, Curvibacter, Escherichia, Flavobacterium, Limnohabitans, Paenibacillus, Ralstonia, Sarcina, Sediminibacterium, Segetibacter Stenotrophomonas and Variovorax, the predominant zoonotic bacteria represented in these ticks were genera Borrelia, Francisella, and Rickettsia...
November 9, 2017: Experimental & Applied Acarology
https://www.readbyqxmd.com/read/29122290/bacterial-community-dynamic-associated-with-autochthonous-bioaugmentation-for-enhanced-cu-phytoremediation-of-salt-marsh-sediments
#14
C Marisa R Almeida, Tânia Oliveira, Izabela Reis, Carlos R Gomes, Ana P Mucha
Autochthonous bioaugmentation for metal phytoremediation is still little explored, particularly its application to estuarine salt marshes, but results obtained so far are promising. Nevertheless, understanding the behaviour of the microbial communities in the process of bioaugmentation and their role in improving metal phytoremediation is very important to fully validate the application of this biological technology. This study aimed to characterize the bacterial community dynamic associated with the application of autochthonous bioaugmentation in an experimentation which showed that Phragmites australis rhizosphere microorganisms could increase this salt marsh plant potential to phytoremediate Cu contaminated sediments...
October 16, 2017: Marine Environmental Research
https://www.readbyqxmd.com/read/29121255/adipocyte-expression-of-slc19a1-links-dna-hypermethylation-to-adipose-tissue-inflammation-and-insulin-resistance
#15
Paul Petrus, Lucia Bialesova, Antonio Checa, Alastair Kerr, Shama Naz, Jesper Bäckdahl, Ana Gracia, Sofia Toft, Karin Dahlman-Wright, Per Hedén, Ingrid Dahlman, Craig E Wheelock, Peter Arner, Niklas Mejhert, Hui Gao, Mikael Rydén
Context: Insulin resistance (IR) is promoted by a chronic low-grade inflammation in white adipose tissue (WAT). The latter may be regulated through epigenetic mechanisms such as DNA-methylation. The one carbon cycle (1CC) is a central metabolic process governing DNA-methylation. Objective: To identify adipocyte-expressed 1CC genes linked to WAT inflammation, IR and their causal role. Design: Cohort study. Setting: Outpatient academic clinic...
November 7, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29118064/leukocyte-counts-based-on-dna-methylation-at-individual-cytosines
#16
Joana Frobel, Tanja Božić, Michael Lenz, Peter Uciechowski, Yang Han, Reinhild Herwartz, Klaus Strathmann, Susanne Isfort, Jens Panse, André Esser, Carina Birkhofer, Uwe Gerstenmaier, Thomas Kraus, Lothar Rink, Steffen Koschmieder, Wolfgang Wagner
BACKGROUND: White blood cell counts are routinely measured with automated hematology analyzers, by flow cytometry, or by manual counting. Here, we introduce an alternative approach based on DNA methylation (DNAm) at individual CG dinucleotides (CpGs). METHODS: We identified candidate CpGs that were nonmethylated in specific leukocyte subsets. DNAm levels (ranging from 0% to 100%) were analyzed by pyrosequencing and implemented into deconvolution algorithms to determine the relative composition of leukocytes...
November 8, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/29116183/time-resolved-analysis-of-a-denitrifying-bacterial-community-revealed-a-core-microbiome-responsible-for-the-anaerobic-degradation-of-quinoline
#17
Yun Wang, Hao Tian, Fei Huang, Wenmin Long, Qianpeng Zhang, Jing Wang, Ying Zhu, Xiaogang Wu, Guanzhou Chen, Liping Zhao, Lars R Bakken, Åsa Frostegård, Xiaojun Zhang
Quinoline is biodegradable under anaerobic conditions, but information about the degradation kinetics and the involved microorganisms is scarce. Here, the dynamics of a quinoline-degrading bacterial consortium were studied in anoxic batch cultures containing nitrate. The cultures removed 83.5% of the quinoline during the first 80 hours, which were dominated by denitrification, and then switched to methanogenesis when the nitrogen oxyanions were depleted. Time-resolved community analysis using pyrosequencing revealed that denitrifiying bacteria belonging to the genus Thauera were enriched during the denitrification stage from 12...
November 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29109713/basin-scale-variation-on-the-composition-and-diversity-of-archaea-in-the-pacific-ocean
#18
Xiaomin Xia, Wang Guo, Hongbin Liu
The Archaea are a widely distributed group of prokaryotes that inhabit and thrive in many different environments. In the sea, they play key roles in various global biogeochemical processes. Here, in order to investigate the vertical profiles of archaeal community across a large geographic distance, the compositions of archaeal communities in seven seawater columns in the Pacific Ocean were investigated using high throughput 454 pyrosequencing of the 16S rRNA gene. The surface archaeal communities showed lower diversity and greater variability than those in the deeper layers...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29109406/new-microbial-resource-microbial-diversity-function-and-dynamics-in-chinese-liquor-starter
#19
Yuhong Huang, Zhuolin Yi, Yanling Jin, Yonggui Zhao, Kaize He, Dayu Liu, Dong Zhao, Hui He, Huibo Luo, Wenxue Zhang, Yang Fang, Hai Zhao
Traditional Chinese liquor (Baijiu) solid state fermentation technology has lasted for several thousand years. The microbial communities that enrich in liquor starter are important for fermentation. However, the microbial communities are still under-characterized. In this study, 454 pyrosequencing technology was applied to comprehensively analyze the microbial diversity, function and dynamics of two most-consumed liquor starters (Jiang- and Nong-flavor) during production. In total, 315 and 83 bacterial genera and 72 and 47 fungal genera were identified in Jiang- and Nong-flavor liquor starter, respectively...
November 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29107416/evaluation-of-pyromark-q24-pyrosequencing-as-a-method-for-the-identification-of-mycobacteria
#20
Kinuyo Chikamatsu, Akio Aono, Hiroyuki Hata, Yuriko Igarashi, Akiko Takaki, Hiroyuki Yamada, Kentaro Sakashita, Satoshi Mitarai
We evaluated PyroMark Q24 (QIAGEN) pyrosequencing as a method for the identification of mycobacteria, with potential application in clinical practice. Sequence data from the hypervariable region A of the 16S rRNA gene (43 and 35bp sequences) were obtained using PyroMark Q24, and a similarity search was performed automatically with PyroMark IdentiFire software. Of the 148 mycobacterial type strains tested, 138 (93.2%) were accurately identified to single or clade species level, including complex level. From the remaining 10 strains, 3 (Mycobacterium gilvum, Mycobacterium goodi, and Mycobacterium thermoresistible) showed poor sequencing quality of homopolymers...
September 15, 2017: Diagnostic Microbiology and Infectious Disease
keyword
keyword
29284
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"