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Rapid PCR

Surendra Kumar
BACKROUND: The outbreak of H1N1 virus had previously reported in India during 2009 flu pandemic. In 2015, the outbreak became widespread throughout India. The states of Gujarat and Rajasthan are severely elected. We studied an outbreak of H1N1 Virus in north-west zone of Rajasthan 2015. OBJECTIVE: To demonstrate the current epidemiological scenario of swine flu (H1N1) in north-west zone of Rajasthan with different demographic factors. METHODS: We screened total 6390 patients...
July 2016: Journal of the Association of Physicians of India
Hideharu Kimura, Shingo Nishikawa, Hayato Koba, Taro Yoneda, Takashi Sone, Kazuo Kasahara
Epidermal growth factor receptor (EGFR) T790M mutation is associated with resistance to EGFR tyrosine kinase inhibitors' (EGFR-TKIs) in non-small cell lung cancer (NSCLC). The aims of this study are to develop a blood-based, non-invasive approach to detecting the EGFR T790M mutation in advanced NSCLC patients, using PointMan™ EGFR DNA Enrichment Kit which is a novel method for selective amplification of genotype specific sequences.Pairs of blood samples and tumor tissues were collected from NSCLC patients with an EGFR activating mutation and who were resistant to EGFR-TKI treatment...
2016: Advances in Experimental Medicine and Biology
Yohei Kurosaki, Sayaka Okada, Sayuri Nakamae, Jiro Yasuda
Bovine papular stomatitis virus (BPSV) causes pustular cutaneous disease in cattle worldwide. This paper describes the development of a specific loop-mediated isothermal amplification (LAMP) assay to detect BPSV which did not cross-react with other parapoxviruses. To assess analytical sensitivity of this LAMP assay, DNA was extracted from serially diluted BPSV from which the infectious titer was determined by a novel assay based on calf kidney epithelial cells. The LAMP assay had equivalent analytical sensitivity to quantitative PCR, and could detect as few as 86 copies of viral DNA per reaction...
October 14, 2016: Journal of Virological Methods
Håvard Tetlie Garberg, Marianne U Huun, Lars O Baumbusch, Monica Åsegg-Atneosen, Rønnaug Solberg, Ola Didrik Saugstad
BACKGROUND: There is a lack of reliable biomarkers that can identify and grade acute hypoxic-ischemic encephalopathy in newborns. MicroRNAs (miRNA) are short, non-coding strands of RNA that are released into the circulation in response to tissue stress and injury. Some miRNAs are highly tissue specific and thus may potentially be non-invasive biomarkers of neonatal hypoxic-ischemic brain injury. OBJECTIVE: The aim of this study was to characterize the temporal expression of selected circulating miRNAs in a clinically relevant piglet model of neonatal hypoxia-ischemia (HI)...
October 18, 2016: Neonatology
Mukundh N Balasubramanian, Nejc Rački, José Gonçalves, Katarina Kovač, Magda T Žnidarič, Valentina Turk, Maja Ravnikar, Ion Gutiérrez-Aguirre
Currently, around 50% of the world's population lives in towns and cities within 100 km of the coast. Monitoring of viruses that are frequently present in contaminated coastal environments, such as rotavirus (RoV) and norovirus (NoV), which are also the major cause of human viral gastroenteritis, is essential to ensure the safe use of these water bodies. Since exposure to as few as 10-100 particles of RoV or NoV may induce gastrointestinal disease, there is a need to develop a rapid and sensitive diagnostic method for their detection in coastal water samples...
October 8, 2016: Water Research
Shradha Subedi, Fanrong Kong, Peter Jelfs, Timothy J Gray, Meng Xiao, Vitali Sintchenko, Sharon C-A Chen
Accurate identification of slowly growing nontuberculous mycobacteria (SG-NTM) of clinical significance remains problematic. This study evaluated a novel method of SG-NTM identification by amplification of the mycobacterial 16S-23S rRNA internal transcribed spacer (ITS) region followed by resolution of amplified fragments by sequencer-based capillary gel electrophoresis (SCGE). Fourteen American Type Culture Collection (ATCC) strains and 103 clinical/environmental isolates (total n = 24 species) of SG-NTM were included...
2016: PloS One
Liang Li, Jian-Wei Zhang, Gregory Jenkins, Fang Xie, Erin E Carlson, Brooke L Fridley, William R Bamlet, Gloria M Petersen, Robert R McWilliams, Liewei Wang
BACKGROUND: Pancreatic cancer is a rapidly fatal disease with gemcitabine remaining the first-line therapy. We performed a genotype-phenotype association study to identify biomarkers for predicting gemcitabine treatment outcome. MATERIALS AND METHODS: We selected the top 200 single nucleotide polymorphisms (SNPs) identified from our previous genome-wide association study to associate with overall survival using 400 patients treated with/or without gemcitabine, followed by imputation analysis for regions around the identified SNPs and a replication study using an additional 537 patients by the TaqMan genotyping assay...
October 4, 2016: Pharmacogenetics and Genomics
Sijia Yan, Sheng-An Chen, Wen Zhang, Fanping Yang, Ying Yang, Qinyuan Zhu, Huizhong Zhu, Xinfen Sun, Menglin Jiang, Yu Su, Lirong Zhang, Qinghe Xing, Xiaoqun Luo
OBJECTIVE: Tetanus antitoxin (TAT) is an effective antitetanus medicine, but may sometimes cause adverse drug reactions such as rapid-onset anaphylactic shock and late-onset cutaneous adverse drug reactions, including exanthematous drug eruptions (EDE). Human leukocyte antigen (HLA) class I alleles are strongly associated with different types of cutaneous adverse drug reactions. This study aimed to assess whether there is an association between TAT-induced EDE and HLA-A, HLA-B, and HLA-C alleles in the Chinese Han population...
October 5, 2016: Pharmacogenetics and Genomics
Ruiling Wen, Yingying Xiao, Yuhua Zhang, Min Yang, Yongping Lin, Jun Tang
Tubulin tyrosine ligase like 12 (TTLL12), a member of the tubulin tyrosine ligase (TTLL) family, has not been completely characterized to date. It is reported that histone methylation, tubulin modifications, mitotic duration and chromosome ploidy play crucial roles in a variety of cancers, and are related to tumorigenesis and cancer progression. A recent study showed that TTLL12 may be a pseudo-enzyme which has a SET-like domain and a TTL-like domain. In the present study, we first used 3'-rapid amplification of cDNA ends (3'-RACE) to amplify the transcripts of the TTLL12 gene from a human lung cancer cell line H1299, and unexpectedly discovered a new transcript isoform characterized with an additional 108-bp nucleotide sequence inserted at the location from 902 to 903 bases of the TTLL12 coding sequence (CDS), where it also locates between exons 5 and 6...
September 28, 2016: Oncology Reports
Nathan Crook, Joseph Abatemarco, Jie Sun, James M Wagner, Alexander Schmitz, Hal S Alper
Directed evolution remains a powerful, highly generalizable approach for improving the performance of biological systems. However, implementations in eukaryotes rely either on in vitro diversity generation or limited mutational capacities. Here we synthetically optimize the retrotransposon Ty1 to enable in vivo generation of mutant libraries up to 1.6 × 10(7) l(-1) per round, which is the highest of any in vivo mutational generation approach in yeast. We demonstrate this approach by using in vivo-generated libraries to evolve single enzymes, global transcriptional regulators and multi-gene pathways...
October 17, 2016: Nature Communications
Sylvie Y Doerflinger, Julia Tabatabai, Paul Schnitzler, Carlo Farah, Steffen Rameil, Peter Sander, Anna Koromyslova, Grant S Hansman
Human noroviruses are the dominant cause of outbreaks of acute gastroenteritis. These viruses are usually detected by molecular methods, including reverse transcriptase PCR (RT-PCR) and enzyme-linked immunosorbent assay (ELISA). Human noroviruses are genetically and antigenically diverse, with two main genogroups that are further subdivided into over 40 different genotypes. During the past decade, genogroup 2 genotype 4 (GII.4) has dominated in most countries, but recently, viruses belonging to GII.17 have increased in prevalence in a number of countries...
September 2016: MSphere
Jong-Hak Kim, Min-Kyeoung Kim, Hongtao Wang, Hee-Nyeong Lee, Chi-Gyu Jin, Woo-Saeng Kwon, Deok-Chun Yang
BACKGROUND: Korean ginseng (Panax ginseng) is one of the most important medicinal plants in the Orient. Among nine cultivars of P. ginseng, Chunpoong commands a much greater market value and has been planted widely in Korea. Chunpoong has superior quality "Chunsam" (1(st) grade ginseng) when made into red ginseng. METHODS: A rapid and reliable method for discriminating the Chunpoong cultivar was developed by exploiting a single nucleotide polymorphism (SNP) in the auxin repressed protein gene of nine Korean ginseng cultivars using specific primers...
October 2016: Journal of Ginseng Research
Laura Pérez-Lago, Santiago Izco, Marta Herranz, Griselda Tudó, María Carcelén, Iñaki Comas, Olalla Sierra, Juliá González, María Jesús Ruiz-Serrano, Juan Eyene, Emilio Bouza, Darío García-de-Viedma
OBJECTIVE: Molecular epidemiology techniques in tuberculosis (TB) can identify high-risk strains that are actively transmitted. We aimed to implement a novel strategy to optimize the identification and control of MDR-TB in a specific population. METHODS: We developed a strain-specific-PCR tailored from whole-genome-sequencing (WGS) data to track a specific multidrug-resistant prevalent strain in Equatorial Guinea (EG-MDR). RESULTS: The PCR was applied prospectively on remnants of GeneXpert reaction mixtures owing to the lack of culture facilities in EG...
October 13, 2016: Clinical Microbiology and Infection
Mansour Amin, Mozhgan Ghaderpanah, Tahereh Navidifar
Meningitis is a life-threatening infection associated with a high mortality and morbidity worldwide. Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae are the most prevalent infectious agents that cause bacterial meningitis (BM). The objective of this study was to determine the frequencies of these three bacteria using bacterial cultures and polymerase chain reaction (PCR). In our cross-sectional study, cerebrospinal fluid (CSF) specimens were obtained from 196 patients who were suspected of having BM and referred to the pediatric ward of Abuzar Hospital (Ahvaz, Iran)...
October 2016: Kaohsiung Journal of Medical Sciences
Tobias Opthof, Carol Ann Remme, Esther Jorge, Francisco Noriega, Rob F Wiegerinck, Arlin Tasiam, Leander Beekman, Jesus Alvarez-Garcia, Cristian Munoz-Guijosa, Ruben Coronel, Juan Cinca
BACKGROUND: The repolarization pattern of the human heart is unknown. OBJECTIVE: We performed a multisite analysis of the activation-repolarization patterns and mRNA expression patterns of ion channel subunits in isolated human hearts. METHODS: Hearts from three donors without reported cardiac disease were Langendorff perfused with the patient's own blood. A standard ECG was obtained prior to explantation. Up to 92 unipolar electrograms from 24 transmural needles were obtained during right atrial pacing...
October 10, 2016: Heart Rhythm: the Official Journal of the Heart Rhythm Society
Chrislean Jun Botanas, Seong Shoon Yoon, June Bryan de la Peña, Irene Joy Dela Peña, Mikyung Kim, Taeseon Woo, Joung-Wook Seo, Choon-Gon Jang, Kyung-Tae Park, Young Hun Lee, Yong Sup Lee, Hee Jin Kim, Jae Hoon Cheong
The recreational use of synthetic cathinones has grown rapidly which prompted concerns from legal authorities and health care providers. However, in response to legislative regulations, synthesis of novel synthetic cathinones by introducing substituents in cathinone molecule has dramatically increased the diversity of these substances. Based on current trends, the aromatic ring is one of the popular sites in cathinone molecule being explored by designer-type modifications. In this study, we designed and synthesized a novel synthetic cathinone, 2-(methylamino)-1-(naphthalen-2-yl) propan-1-one (BMAPN), which has a naphthalene substituent on the aromatic ring...
October 10, 2016: Behavioural Brain Research
Xiangfeng He, Fei Xue, Shufa Xu, Wenhe Wang
Lily symptomless virus (LSV) is one of the most prevalent viruses that infect lily plants worldwide. A rapid and sensitive reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detection of LSV, using two primer pairs that specifically amplified the conserved sequence of LSV coat protein. The optimum reaction conditions were as follows: 4mM MgCl2 and 0.8M betaine with incubation at 64°C for 30min. The limit of detection of LSV from infected lily leaves was 10-fold higher for RT-LAMP than for conventional RT-PCR...
October 10, 2016: Journal of Virological Methods
Chinn-Woan Lowe, Benjamin A Satterfield, Daniel B Nelson, Joseph D Thiriot, Michael J Heder, Jordon K March, David S Drake, Cynthia S Lew, Annette J Bunnell, Emily S Moore, Kim L O'Neill, Richard A Robison
The Burkholderia pseudomallei complex classically consisted of B. mallei, B. pseudomallei, and B. thailandensis, but has now expanded to include B. oklahomensis, B. humptydooensis, and three unassigned Burkholderia clades. Methods for detecting and differentiating the B. pseudomallei complex has been the topic of recent research due to phenotypic and genotypic similarities of these species. B. mallei and B. pseudomallei are recognized as CDC Tier 1 select agents, and are the causative agents of glanders and melioidosis, respectively...
2016: PloS One
Aksara Thongprachum, Pattara Khamrin, Ngan Thi Kim Pham, Sayaka Takanashi, Shoko Okitsu, Hiroyuki Shimizu, Niwat Maneekarn, Satoshi Hayakawa, Hiroshi Ushijima
Multiplex RT-PCR method using five sets of panel primers was developed for the detection of diarrheal viruses, including rotavirus A, B, and C, adenovirus, astrovirus, norovirus GI and GII, sapovirus, Aichi virus, parechovirus, enterovirus, cosavirus, bocavirus, and Saffold virus. The sensitivity of the method was evaluated and tested with 751 fecal specimens collected from Japanese children with acute diarrhea. Several kinds of viruses were detected in 528 out of 751 (70.3%) fecal specimens. Mixed-infection with different viruses in clinical specimens could also be effectively detected...
October 13, 2016: Journal of Medical Virology
Mike T Page, Alex C McCormac, Alison G Smith, Matthew J Terry
Retrograde signals from the plastid regulate photosynthesis-associated nuclear genes and are essential to successful chloroplast biogenesis. One model is that a positive haem-related signal promotes photosynthetic gene expression in a pathway that is abolished by the herbicide norflurazon. Far-red light (FR) pretreatment and transfer to white light also results in plastid damage and loss of photosynthetic gene expression. Here, we investigated whether norflurazon and FR pretreatment affect the same retrograde signal...
October 13, 2016: New Phytologist
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