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https://www.readbyqxmd.com/read/27902415/inversion-of-correia-repeat-enclosed-elements-in-neisseria-gonorrhoeae
#1
Firat Elbeyioglu, Sabrina B Roberts, Russell Spencer-Smith, Madhuri Pulijala, Marta A Zelewska, Jean-Christophe Nebel, Lori As Snyder
Neisseria gonorrhoeae is capable of causing gonorrhoea and more complex diseases in the human host. Within the gonococcal genome are over 100 copies of the IS-like Correia Repeat Enclosed Element, which has been predicted to be mobile within the neisserial genomes. Although there is evidence of ancestral movement of these elements, no previous study has provided evidence for current mobilisation. The Correia Repeat Enclosed Element has the ability to alter gene expression and regulation in many ways: by insertional mutagenesis; by introducing promoter elements; by generating mRNA processing sites, and by association with ncRNAs...
November 16, 2016: Microbiology
https://www.readbyqxmd.com/read/27898681/common-lung-microbiome-identified-among-mechanically-ventilated-surgical-patients
#2
Ashley D Smith, Yan Zhang, Robert C Barber, Christian T Minshall, Ryan M Huebinger, Michael S Allen
The examination of the pulmonary microbiome in patients with non-chronic disease states has not been extensively examined. Traditional culture based screening methods are often unable to identify bacteria from bronchoalveolar lavage samples. The advancement of next-generation sequencing technologies allows for a culture-independent molecular based analysis to determine the microbial composition in the lung of this patient population. For this study, the Ion Torrent PGM system was used to assess the microbial complexity of culture negative bronchoalveolar lavage samples...
2016: PloS One
https://www.readbyqxmd.com/read/27894793/a-quick-reference-on-anion-gap-and-strong-ion-gap
#3
REVIEW
Carlos Torrente Artero
Metabolic acid-base disorders are common in emergency and critically ill patients. Clinicians may have difficulty recognizing their presence when multiple acid-base derangements are present in a single patient simultaneously. The anion gap and the strong ion gap concepts are useful calculations to identify the components of complex metabolic acid-base associated to the presence of unmeasured anions. This article presents their definition, normal values, indications, limitations, and guidelines for interpretation of changes in the clinical setting...
November 25, 2016: Veterinary Clinics of North America. Small Animal Practice
https://www.readbyqxmd.com/read/27884156/targeted-myocardial-gene-expression-in-failing-hearts-by-rna-sequencing
#4
Kajari Dhar, Alexandra M Moulton, Eric Rome, Fang Qiu, Jeff Kittrell, Eugenia Raichlin, Ronald Zolty, John Y Um, Michael J Moulton, Hesham Basma, Daniel R Anderson, James D Eudy, Brian D Lowes
BACKGROUND: Myocardial recovery with left ventricular assist device (LVAD) therapy is highly variable and difficult to predict. Next generation ribonucleic acid (RNA) sequencing is an innovative, rapid, and quantitative approach to gene expression profiling in small amounts of tissue. Our primary goal was to identify baseline transcriptional profiles in non-ischemic cardiomyopathies that predict myocardial recovery in response to LVAD therapy. We also sought to verify transcriptional differences between failing and non-failing human hearts...
November 25, 2016: Journal of Translational Medicine
https://www.readbyqxmd.com/read/27875997/identification-of-the-transcripts-associated-with-spontaneous-hcv-clearance-in-individuals-co-infected-with-hiv-and-hcv
#5
Yue Chen, Chengli Shen, Debjani Guha, Ming Ding, Scott Kulich, Aiymkul Ashimkhanova, Charles Rinaldo, Eric Seaberg, Joseph B Margolick, Valentina Stosor, Otoniel Martínez-Maza, Phalguni Gupta
BACKGROUND: Infection with human immunodeficiency virus (HIV) influences the outcome and natural disease progression of hepatitis C virus (HCV) infection. While the majority of HCV mono-infected and HCV/HIV co-infected subjects develop chronic HCV infection, 20-46% of mono- and co-infected subjects spontaneously clear HCV infection. The mechanism underlying viral clearance is not clearly understood. Analysis of differential cellular gene expression (mRNA) between HIV-infected patients with persistent HCV infection or spontaneous clearance could provide a unique opportunity to decipher the mechanism of HCV clearance...
November 22, 2016: BMC Infectious Diseases
https://www.readbyqxmd.com/read/27861539/vertical-structure-of-phyllosphere-fungal-communities-in-a-tropical-forest-in-thailand-uncovered-by-high-throughput-sequencing
#6
Ayako Izuno, Mamoru Kanzaki, Taksin Artchawakom, Chongrak Wachrinrat, Yuji Isagi
Phyllosphere fungi harbor a tremendous species diversity and play important ecological roles. However, little is known about their distribution patterns within forest ecosystems. We examined how species diversity and community composition of phyllosphere fungi change along a vertical structure in a tropical forest in Thailand. Fungal communities in 144 leaf samples from 19 vertical layers (1.28-34.4 m above ground) of 73 plant individuals (27 species) were investigated by metabarcoding analysis using Ion Torrent sequencing...
2016: PloS One
https://www.readbyqxmd.com/read/27848044/detection-of-false-positive-mutations-in-brca-gene-by-next-generation-sequencing
#7
Moushumi Suryavanshi, Dushyant Kumar, Manoj Kumar Panigrahi, Meenakshi Chowdhary, Anurag Mehta
BRCA1 and BRCA2 genes are implicated in 20-25% of hereditary breast and ovarian cancers. New age sequencing platforms have revolutionized massively parallel sequencing in clinical practice by providing cost effective, rapid, and sensitive sequencing. This study critically evaluates the false positives in multiplex panels and suggests the need for careful analysis. We employed multiplex PCR based BRCA1 and BRCA2 community Panel with ion torrent PGM machine for evaluation of these mutations. Out of all 41samples analyzed for BRCA1 and BRCA2 five were found with 950_951 insA(Asn319fs) at Chr13:32906565 position and one sample with 1032_1033 insA(Asn346fs) at Chr13:32906647, both being frame-shift mutations in BRCA2 gene...
November 15, 2016: Familial Cancer
https://www.readbyqxmd.com/read/27843768/functional-alterations-due-to-amino-acid-changes-and-evolutionary-comparative-analysis-of-arpkd-and-adpkd-genes
#8
Burhan M Edrees, Mohammad Athar, Zainularifeen Abduljaleel, Faisal A Al-Allaf, Mohiuddin M Taher, Wajahatullah Khan, Abdellatif Bouazzaoui, Naffaa Al-Harbi, Ramzia Safar, Howaida Al-Edressi, Khawala Alansary, Abulkareem Anazi, Naji Altayeb, Muawia A Ahmed
A targeted customized sequencing of genes implicated in autosomal recessive polycystic kidney disease (ARPKD) phenotype was performed to identify candidate variants using the Ion torrent PGM next-generation sequencing. The results identified four potential pathogenic variants in PKHD1 gene [c.4870C > T, p.(Arg1624Trp), c.5725C > T, p.(Arg1909Trp), c.1736C > T, p.(Thr579Met) and c.10628T > G, p.(Leu3543Trp)] among 12 out of 18 samples. However, one variant c.4870C > T, p.(Arg1624Trp) was common among eight patients...
December 2016: Genomics Data
https://www.readbyqxmd.com/read/27824160/bacterial-community-structure-and-function-shift-along-a-successional-series-of-tidal-flats-in-the-yellow-river-delta
#9
Xiaofei Lv, Bin Ma, Junbao Yu, Scott X Chang, Jianming Xu, Yunzhao Li, Guangmei Wang, Guangxuan Han, Guan Bo, Xiaojing Chu
Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations...
November 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27822964/massive-parallel-sequencing-of-human-whole-mitochondrial-genomes-with-ion-torrent-technology-an-optimized-workflow-for-anthropological-and-population-genetics-studies
#10
Sara De Fanti, Dario Vianello, Cristina Giuliani, Andrea Quagliariello, Anna Cherubini, Federica Sevini, Nicoletta Iaquilano, Claudio Franceschi, Marco Sazzini, Donata Luiselli
Investigation of human mitochondrial DNA variation patterns and phylogeny has been extensively used in Anthropological and Population Genetics studies and sequencing the whole mitochondrial genome is progressively becoming the gold standard. Among the currently available massive parallel sequencing technologies, Ion Torrent™ semiconductor sequencing represents a promising approach for such studies. Nevertheless, an experimental protocol conceived to enable the achievement of both as high as possible yield and of the most homogeneous sequence coverage through the whole mitochondrial genome is still not available...
November 8, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/27801421/-cdc73-mutations-in-young-patients-with-primary-hyperparathyroidism-a-description-of-two-clinical-cases
#11
E O Mamedova, N G Mokrysheva, E A Pigarova, E G Przhiyalkovskaya, I A Voronkova, E V Vasil'ev, V M Petrov, V A Gorbunova, L Ya Rozhinskaya, Zh E Belaya, A N Tyul'pakov
The article describes two clinical cases of severe primary hyperparathyroidism (PHPT) caused by parathyroid carcinoma in young female patients who underwent molecular genetic testing to rule out the hereditary forms of PHPT. In both patients, heterozygous germline nonsense mutations of tumor suppressor gene CDC73 encoding parafibromin (p.R91X and p.Q166X) were identified using next-generation sequencing with Ion Torrent Personal Genome Machine (Thermo Fisher Scientific - Life Technologies, USA). It is the first description of CDC73 mutations in Russia, one of the mutations is described for the first time in the world...
2016: Terapevticheskiĭ Arkhiv
https://www.readbyqxmd.com/read/27797077/measuring-sister-chromatid-cohesion-protein-genome-occupancy-in-drosophila-melanogaster-by-chip-seq
#12
Dale Dorsett, Ziva Misulovin
This chapter presents methods to conduct and analyze genome-wide chromatin immunoprecipitation of the cohesin complex and the Nipped-B cohesin loading factor in Drosophila cells using high-throughput DNA sequencing (ChIP-seq). Procedures for isolation of chromatin, immunoprecipitation, and construction of sequencing libraries for the Ion Torrent Proton high throughput sequencer are detailed, and computational methods to calculate occupancy as input-normalized fold-enrichment are described. The results obtained by ChIP-seq are compared to those obtained by ChIP-chip (genomic ChIP using tiling microarrays), and the effects of sequencing depth on the accuracy are analyzed...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27789964/rare-frequency-of-gene-variation-and-survival-analysis-in-thymic-epithelial-tumors
#13
Zhengbo Song, Xinmin Yu, Yiping Zhang
OBJECTIVE: Thymic epithelial tumor (TET) is a rare mediastinal neoplasm and little is known about its genetic variability and prognostic factors. This study investigated the genetic variability and prognostic factors of TET. PATIENTS AND METHODS: We sequenced 22 cancer-related hotspot genes in TET tissues and matched normal tissues using Ampliseq Ion Torrent next-generation technology. Overall survival was evaluated using Kaplan-Meier methods and compared with log-rank tests...
2016: OncoTargets and Therapy
https://www.readbyqxmd.com/read/27784934/high-throughput-sequencing-an-overview-of-sequencing-chemistry
#14
REVIEW
Sheetal Ambardar, Rikita Gupta, Deepika Trakroo, Rup Lal, Jyoti Vakhlu
In the present century sequencing is to the DNA science, what gel electrophoresis was to it in the last century. From 1977 to 2016 three generation of the sequencing technologies of various types have been developed. Second and third generation sequencing technologies referred commonly to as next generation sequencing technology, has evolved significantly with increase in sequencing speed, decrease in sequencing cost, since its inception in 2004. GS FLX by 454 Life Sciences/Roche diagnostics, Genome Analyzer, HiSeq, MiSeq and NextSeq by Illumina, Inc...
December 2016: Indian Journal of Microbiology
https://www.readbyqxmd.com/read/27771467/investigating-kinship-of-neolithic-post-lbk-human-remains-from-krusza-zamkowa-poland-using-ancient-dna
#15
Anna Juras, Maciej Chyleński, Marta Krenz-Niedbała, Helena Malmström, Edvard Ehler, Łukasz Pospieszny, Sylwia Łukasik, Józef Bednarczyk, Janusz Piontek, Mattias Jakobsson, Miroslawa Dabert
We applied an interdisciplinary approach to investigate kinship patterns and funerary practices during the middle Neolithic. Genetic studies, radiocarbon dating, and taphonomic analyses were used to examine two grave clusters from Krusza Zamkowa, Poland. To reconstruct kinship and determine biological sex, we extracted DNA from bones and teeth, analyzed mitochondrial genomes and nuclear SNPs using the HID-Ion AmpliSeq™ Identity panel generated on Illumina and Ion Torrent platforms, respectively. We further dated the material (AMS (14)C) and to exclude aquatic radiocarbon reservoir effects, measures of carbon and nitrogen stable isotopes for diet reconstruction were used...
October 14, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27763790/improving-adequacy-of-small-biopsy-and-fine-needle-aspiration-specimens-for-molecular-testing-by-next-generation-sequencing-in-patients-with-lung-cancer-a-quality-improvement-study-at-dartmouth-hitchcock-medical-center
#16
Vijayalakshmi Padmanabhan, Heather B Steinmetz, Elizabeth J Rizzo, Amber J Erskine, Tamara L Fairbank, Francine B de Abreu, Gregory J Tsongalis, Laura J Tafe
CONTEXT: -At our medical center, cytopathologists perform rapid on-site evaluation for specimen adequacy of fine-needle aspiration and touch imprint of needle core biopsy lung cancer samples. Two years ago the molecular diagnostics laboratory at our institution changed to next-generation sequencing using the Ion Torrent PGM and the 50-gene AmpliSeq Cancer Hotspot Panel v2 for analyzing mutations in a 50-gene cancer hot spot panel. This was associated with in a dramatic fall in adequacy rate (68%)...
October 20, 2016: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/27755594/correction-molecular-heterogeneity-of-ewing-sarcoma-as-detected-by-ion-torrent-sequencing
#17
Nana Zhang, Guanjun Yue, Yan Zhang, Jiangfeng You, Hua Wang
[This corrects the article DOI: 10.1371/journal.pone.0153546.].
2016: PloS One
https://www.readbyqxmd.com/read/27725223/next-generation-sequencing-of-human-opioid-receptor-genes-based-on-a-custom-ampliseq%C3%A2-library-and-ion-torrent-personal-genome-machine
#18
Dario Kringel, Jörn Lötsch
BACKGROUND: The opioid system is involved in the control of pain, reward, addictive behaviors and vegetative effects. Opioids exert their pharmacological actions through the agonistic binding at opioid receptors and variation in the coding genes has been found to modulate opioid receptor expression or signaling. However, a limited selection of functional opioid receptor variants is perceived as insufficient in providing a genetic diagnosis of clinical phenotypes and therefore, unrestricted access to opioid receptor genetics is required...
October 8, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/27717530/effect-of-silver-nano-particles-on-soil-microbial-growth-activity-and-community-diversity-in-a-sandy-loam-soil
#19
A D Samarajeewa, J R Velicogna, J I Princz, R M Subasinghe, R P Scroggins, L A Beaudette
Silver nano-particles (AgNPs) are widely used in a range of consumer products as a result of their antimicrobial properties. Given the broad spectrum of uses, AgNPs have the potential for being released to the environment. As a result, environmental risks associated with AgNPs need to be assessed to aid in the development of regulatory guidelines. Research was performed to assess the effects of AgNPs on soil microbial activity and diversity in a sandy loam soil with an emphasis on using a battery of microbial tests involving multiple endpoints...
January 2017: Environmental Pollution
https://www.readbyqxmd.com/read/27716627/precise-erbb2-copy-number-assessment-in-breast-cancer-by-means-of-molecular-inversion-probe-array-analysis
#20
Matthias Christgen, Jana L van Luttikhuizen, Mieke Raap, Peter Braubach, Lars Schmidt, Danny Jonigk, Friedrich Feuerhake, Ulrich Lehmann, Brigitte Schlegelberger, Hans H Kreipe, Doris Steinemann
HER2/ERBB2 amplification/overexpression determines the eligibility of breast cancer patients to HER2-targeted therapy. This study evaluates the agreement between ERBB2 copy number assessment by fluorescence in situ hybridization, a standard method recommended by the American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP), and newly available DNA extraction-based methods. A series of n=29 formalin-fixed paraffin-embedded breast cancers were subjected to ERBB2 copy number assessment by fluorescence in situ hybridization (FISH, Vysis, Abbott)...
October 3, 2016: Oncotarget
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