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https://www.readbyqxmd.com/read/28735486/detection-and-quantification-of-acute-myeloid-leukemia-associated-fusion-transcripts
#1
Jonathan Schumacher, Philippe Szankasi, Todd W Kelley
Real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR)-based detection of abnormal fusion transcripts is an important strategy for the diagnosis and monitoring of patients with acute myeloid leukemia (AML) with t(8;21)(q22;q22); RUNX1-RUNX1T1, inv(16)(p13.1;q22); CBFB-MYH11 or t(15;17)(q22;q12); PML-RARA. In RT-qPCR assays, patient-derived cDNA is subjected to amplification using PCR primers directed against the fusion transcript of interest as well as a reference gene for normalization...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735327/genotyping-and-clinicoepidemiological-characterization-of-rotavirus-acute-gastroenteritis-in-egyptian-children
#2
Niveen Saudy, Walaa Othman Elshabrawy, Ahmed Megahed, Mona F Foad, Aly F Mohamed
Group A rotavirus (RVA) acute gastroenteritis (AGE) is a common cause of severe childhood diarrhea. The dominant circulating RVA genotypes in a given region may vary between and within the geographic regions and from year to year. Our cross-sectional study was designed to determine the burden of RVA genotypes among children with AGE admitted to referral Children Hospital at Egypt prior to implementation of the vaccine. Stool samples with clinico-epidemiological data were collected from 92 children ≤ 3 years-old with AGE...
January 2, 2017: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/28735310/an-improve-protocol-for-pcr-using-lm1-and-lm2-primers-for-listeria-monocytogenes-detection-in-food-matrices
#3
Angélica Godínez-Oviedo, Gerardo M Nava, Sofía M Arvizu-Medrano, Montserrat Hernández-Iturriaga
Several studies have observed that a conventional PCR protocol using primers LM1 and LM2 for the identification of gene hlyA Listeria monocytogenes generates non-specific PCR amplifications and false positives. For this reason in this study, we provide a modified PCR protocol that improves the specificity of the LM1 and LM2 primers.
July 6, 2017: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/28735305/molecular-study-of-indigenous-bacterial-community-composition-on-exposure-to-soil-arsenic-concentration-gradient
#4
Semanti Basu, Tanima Paul, Priya Yadav, Abhijit Debnath, Keka Sarkar
Community structure of bacteria present in arsenic contaminated agricultural soil was studied with qPCR (quantitative PCR) and DGGE (Denaturing Gradient Gel Electrophoresis) as an indicator of extreme stresses. Copy number of six common bacterial taxa (Acidobacteria, Actinobacteria, α-, β- and γ-Proteobacteria, Firmicutes) was calculated using group specific primers of 16S rDNA. It revealed that soil contaminated with low concentration of arsenic was dominated by both Actinobacteria and Proteobacteria but a shift towards Proteobacteria was observed with increasing arsenic concentration, and number of Actinobacteria eventually decreases...
July 6, 2017: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/28733817/enriching-an-intraspecific-genetic-map-and-identifying-qtl-for-fiber-quality-and-yield-component-traits-across-multiple-environments-in-upland-cotton-gossypium-hirsutum-l
#5
Xueying Liu, Zhonghua Teng, Jinxia Wang, Tiantian Wu, Zhiqin Zhang, Xianping Deng, Xiaomei Fang, Zhaoyun Tan, Iftikhar Ali, Dexin Liu, Jian Zhang, Dajun Liu, Fang Liu, Zhengsheng Zhang
Cotton is a significant commercial crop that plays an indispensable role in many domains. Constructing high-density genetic maps and identifying stable quantitative trait locus (QTL) controlling agronomic traits are necessary prerequisites for marker-assisted selection (MAS). A total of 14,899 SSR primer pairs designed from the genome sequence of G. raimondii were screened for polymorphic markers between mapping parents CCRI 35 and Yumian 1, and 712 SSR markers showing polymorphism were used to genotype 180 lines from a (CCRI 35 × Yumian 1) recombinant inbred line (RIL) population...
July 21, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28733282/differentiating-botulinum-neurotoxin-producing-clostridia-with-a-simple-multiplex-pcr-assay
#6
Charles H D Williamson, Adam J Vazquez, Karen Hill, Theresa J Smith, Roxanne Nottingham, Nathan E Stone, Colin J Sobek, Jill H Cocking, Rafael A Fernández, Patricia A Caballero, Owen P Leiser, Paul Keim, Jason W Sahl
Diverse members of the genus clostridium produce botulinum neurotoxins (BoNTs), which cause a flaccid paralysis known as botulism. While multiple species of clostridia produce BoNTs, the majority of human botulism cases have been attributed to Clostridium botulinum Groups I and II. Recent comparative genomic studies have demonstrated the genomic diversity within these BoNT-producing species. This study introduces a multiplex polymerase chain reaction (PCR) assay for differentiating members of C. botulinum Group I, C...
July 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28732438/investigation-of-killer-immunoglobulin-like-receptor-kir-and-hla-genotypes-to-predict-the-occurrence-of-acute-allograft-rejection-after-kidney-transplantation
#7
Davood Jafari, Mohsen Nafar, Mir Saeed Yekaninejad, Razieh Abdolvahabi, Mahboob Lesan Pezeshki, Efat Razaghi, Ali Akbar Amirzargar
After kidney transplantation, natural killer (NK) cells play a pivotal role in triggering the immune response to the allogeneic grafts primarily by their killer-cell immunoglobulin-like receptors (KIR). This process may be one mechanism that contributes to graft rejection. In this study, we have evaluated whether acute rejection after kidney transplantation was associated with predicted NK cell alloreactivity based on KIR gene and ligand along with KIR/HLA compound genotype analysis. After kidney transplantation, natural killer (NK) cells play a pivotal role in triggering the immune response to the allogeneic grafts primarily by their killer-cell immunoglobulin-like receptors (KIR)...
June 2017: Iranian Journal of Allergy, Asthma, and Immunology
https://www.readbyqxmd.com/read/28732216/development-of-hla-b-57-01-genotyping-real-time-pcr-with-optimized-hydrolysis-probe-design
#8
Hou-Sung Jung, Gregory J Tsongalis, Joel A Lefferts
HLA-B*57:01 genotyping before abacavir (ABC) administration is a standard of care to avoid ABC-driven hypersensitivity reactions. Several HLA-B*57:01 tests have been developed, each with advantages and disadvantages. Some have limited accuracy, require special instrumentation, and/or are labor intensive and expensive. We developed a novel hydrolysis probe-based real-time PCR method of HLA-B*57:01 genotyping. Primer and probes were designed based on published sequence variations in exon 3 of HLA-B that distinguish HLA-B*57:01 from ABC-insensitive alleles such as HLA-B*57:03 and HLA-B*58:01...
July 18, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28731643/transcriptome-based-identification-of-the-optimal-reference-cho-genes-for-normalisation-of-qpcr-data
#9
Adam J Brown, Suzanne Gibson, Diane Hatton, David C James
Real-time quantitative PCR (qPCR) is the standard method for determination of relative changes in mRNA transcript abundance. Analytical accuracy, precision, and reliability are critically dependent on the selection of internal control reference genes. In this study we have identified optimal reference genes that can be utilized universally for qPCR analysis of CHO cell mRNAs. Initially, transcriptomic datasets were analysed to identify eight endogenous genes that exhibited high expression stability across four distinct CHO cell lines sampled in different culture phases...
July 21, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28730458/generation-and-screening-of-t-dna-insertion-mutants-mediated-by-agrobacterium-tumefaciens-in-the-garden-asparagus-stem-blight-pathogen-phomopsis-asparagi
#10
Yueping Zhang, Huaxiang Qu, Ping Zhao, Yongping Tang, Jingsong Zhou, Shaochun Luo, Yuling Yin, Guangyu Chen
The garden asparagus stem blight caused by filamentous fungus Phomopsis asparagi exposes a serious threat on asparagus production globally. However, to present, we understand poorly about the molecular mechanisms of fungal pathogenicity. To facilitate functional genomics research of P. asparagi, here we developed a highly efficient and stable Agrobacterium tumefaciens-mediated transformation approach which yielded 150-200 transformants per 1 × 10(6) conidia. Our results indicated that 25 °C, acetosyringone concentration of 150 μmol/L, and 72 h were recommended as optimal co-cultivation conditions for the transformation...
July 20, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28730333/identification-of-a-novel-leukemic-specific-splice-variant-of-dnmt3b-and-its-stability
#11
Prachi Singh, Sarvagalla Sailu, Elango Palchamy, Mohane Selvaraj Coumar, Sudhakar Baluchamy
DNA methyltransferases make use of alternative splicing mechanism to generate various splice variants, but their role(s) in modulating DNA methylation patterns in the cells is unclear. Notably, DNMT3B alone contains nearly 40 different splice variants. In this study, we have identified a novel splice variant of DNMT3B, which lacks exon 7 and 10 from leukemic cell lines which we termed as DNMT3B9. The exon 7 codes for the major part of PWWP domain, and exon 10 inclusion serves as a pluripotent marker. By quantitative RT-PCR using exon-exon junction-specific primers, we showed higher level of DNMT3B9 transcripts in several leukemic cell lines...
August 2017: Medical Oncology
https://www.readbyqxmd.com/read/28729817/ssr-marker-variations-in-brassica-species-provide-insight-into-the-origin-and-evolution-of-brassica-amphidiploids
#12
Ajay Kumar Thakur, Kunwar Harendra Singh, Lal Singh, Joghee Nanjundan, Yasin Jeshima Khan, Dhiraj Singh
BACKGROUND: Oilseed Brassica represents an important group of oilseed crops with a long history of evolution and cultivation. To understand the origin and evolution of Brassica amphidiploids, simple sequence repeat (SSR) markers were used to unravel genetic variations in three diploids and three amphidiploid Brassica species of U's triangle along with Eruca sativa as an outlier. RESULTS: Of 124 Brassica-derived SSR loci assayed, 100% cross-transferability was obtained for B...
2018: Hereditas
https://www.readbyqxmd.com/read/28728910/rapid-differentiation-of-bacterial-communities-using-high-resolution-melting-analysis
#13
Steven Everman, Shiao Y Wang
Analysis of microbial communities is of broad interest in biology and high throughput sequencing is now the preferred method. However, some studies may not need the level of detail high throughput sequencing provides and its cost may limit the number of samples that can be sequenced. High resolution melting analysis (HRM) of 16S rRNA gene variable regions has been proposed as an efficient and low cost method to prioritize samples for sequencing but more specific primers are needed and its efficacy needs to be confirmed...
July 17, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28728835/a-multiplex-pcr-for-detection-of-six-viruses-in-ducks
#14
Yongjuan Wang, Shanyuan Zhu, Weiming Hong, Anping Wang, Weiyong Zuo
In this study, six pairs of specific primers that can amplify DNA fragments of different sizes were designed and synthesized according to viral protein gene sequences published in GenBank. Then, a multiplex PCR method was established for rapid detection of duck hepatitis virus 1, duck plague virus, duck Tembusu virus, muscovy duck parvovirus, muscovy duck reovirus, and duck H9N2 avian influenza virus, and achieve simple and rapid detection of viral diseases in ducks. Single PCR was used to confirm primer specificity, and PCR conditions were optimized to construct a multiplex PCR system...
July 17, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28728591/antimicrobial-susceptibility-pattern-of-clinical-isolates-of-burkholderia-pseudomallei-in-bangladesh
#15
Subarna Dutta, Sabah Haq, Mohammad Rokibul Hasan, Jalaluddin Ashraful Haq
BACKGROUND: Melioidosis an infectious disease, caused by a Gram negative bacterium called Burkholderia pseudomallei, is endemic in Bangladesh. This organism is sensitive to limited number of antimicrobial agents and need prolonged treatment. There is no comprehensive data on the antimicrobial susceptibility profile of B. pseudomallei isolated in Bangladesh over last several years. The present study aimed to determine the antimicrobial susceptibility pattern of B. pseudomallei isolated in a tertiary care hospital of Dhaka city from 2009 to 2015...
July 20, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28727474/a-primer-on-exocrine-pancreatic-insufficiency-fat-malabsorption-and-fatty-acid-abnormalities
#16
Samer Alkaade, Ashley A Vareedayah
Exocrine pancreatic insufficiency (EPI) is characterized by a deficiency of exocrine pancreatic enzymes, resulting in deficits in digestion of all macronutrients, with deficiencies in digestion of fats being the most clinically relevant. The leading cause of EPI is chronic pancreatitis. However, many other causes and conditions may be implicated, including cystic fibrosis, pancreatic duct obstruction, gastric and pancreatic surgery, diabetes mellitus and other conditions. Physical and biochemical causes of EPI include decreased production and secretion of lipase, increased lipase destruction, pancreatic duct obstruction, decreased lipase stimulation and degradation, as well as gastrointestinal motility disorders...
July 2017: American Journal of Managed Care
https://www.readbyqxmd.com/read/28727319/novel-evaluation-and-treatment-techniques-for-white-spot-lesions-an-in-vitro-study
#17
T A Bakhsh, A S Bakry, M M Mandurah, M A Abbassy
OBJECTIVE: White spot lesions (WSLs) are commonly seen during and after orthodontic treatment. Therefore, the objective of this in vitro study was to assess the effect of 45S5-bioglass in remineralizing WSLs using cross-polarization optical coherence tomography (CP-OCT) and confirm the findings by micro-hardness test. METHODS: Ceramic orthodontic brackets were bonded to the buccal surface of 45 human premolars with Transbond XT primer followed by Transbond PLUS according to the manufacturer's instructions...
August 2017: Orthodontics & Craniofacial Research
https://www.readbyqxmd.com/read/28725990/molecular-characterization-of-the-indigenous-stingless-bees-tetragonula-spp-complex-using-issr-marker-from-southern-peninsular-india
#18
P P Nayak, J Prakash
India is a country bestowed enormously with stingless bees, but genetic information about them is extremely minimal. This study focused to tap the geographic allocation, genetic variability, and differentiation among Tetragonula species complexes from natural and semi-urban habitats. Genetic analyses were assessed among 36 contrasting genotypes utilizing 20 ISSR primers. The dual combination exquisitely and productively amplified 245 DNA fragments at the loci, of which 240 bands were polymorphic (97.95%). Low to moderate level of genetic differentiation was detected from different estimators (Ht 0...
July 19, 2017: Neotropical Entomology
https://www.readbyqxmd.com/read/28725674/study-of-infectious-diseases-in-archaeological-bone-material-a-dataset
#19
Elisa Pucu, Paula Cascardo, Marcia Chame, Gisele Felice, Niéde Guidon, Maria Cleonice Vergne, Guadalupe Campos, José Roberto Machado-Silva, Daniela Leles
Bones of human and ground sloth remains were analyzed for presence of Trypanosoma cruzi by conventional PCR using primers TC, TC1 and TC2. Sequence results amplified a fragment with the same product size as the primers (300 and 350pb). Amplified PCR product was sequenced and analyzed on GenBank, using Blast. Although these sequences did not match with these parasites they showed high amplification with species of bacteria. This article presents the methodology used and the alignment of the sequences. The display of this dataset will allow further analysis of our results and discussion presented in the manuscript "Finding the unexpected: a critical view on molecular diagnosis of infectious diseases in archaeological samples" (Pucu et al...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28724886/modulation-of-rna-primer-formation-by-mn-ii-substituted-t7-dna-primase
#20
Stefan Ilic, Sabine R Akabayov, Roy Froimovici, Ron Meiry, Dan Vilenchik, Alfredo Hernandez, Haribabu Arthanari, Barak Akabayov
Lagging strand DNA synthesis by DNA polymerase requires RNA primers produced by DNA primase. The N-terminal primase domain of the gene 4 protein of phage T7 comprises a zinc-binding domain that recognizes a specific DNA sequence and an RNA polymerase domain that catalyzes RNA polymerization. Based on its crystal structure, the RNA polymerase domain contains two Mg(II) ions. Mn(II) substitution leads to elevated RNA primer synthesis by T7 DNA primase. NMR analysis revealed that upon binding Mn(II), T7 DNA primase undergoes conformational changes near the metal cofactor binding site that are not observed when the enzyme binds Mg(II)...
July 19, 2017: Scientific Reports
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