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Rapid PCR

Davina Gale, Andrew R J Lawson, Karen Howarth, Mikidache Madi, Bradley Durham, Sarah Smalley, John Calaway, Shannon Blais, Greg Jones, James Clark, Peter Dimitrov, Michelle Pugh, Samuel Woodhouse, Michael Epstein, Ana Fernandez-Gonzalez, Alexandra S Whale, Jim F Huggett, Carole A Foy, Gerwyn M Jones, Hadas Raveh-Amit, Karin Schmitt, Alison Devonshire, Emma Green, Tim Forshew, Vincent Plagnol, Nitzan Rosenfeld
INTRODUCTION: Detection and monitoring of circulating tumor DNA (ctDNA) is rapidly becoming a diagnostic, prognostic and predictive tool in cancer patient care. A growing number of gene targets have been identified as diagnostic or actionable, requiring the development of reliable technology that provides analysis of multiple genes in parallel. We have developed the InVision™ liquid biopsy platform which utilizes enhanced TAm-Seq™ (eTAm-Seq™) technology, an amplicon-based next generation sequencing method for the identification of clinically-relevant somatic alterations at low frequency in ctDNA across a panel of 35 cancer-related genes...
2018: PloS One
Else M Balke, Eric V Balti, Bart Van der Auwera, Ilse Weets, Olivier Costa, Simke Demeester, Pascale Abrams, Kristina Casteels, Marina Coeckelberghs, Sylvie Tenoutasse, Bart Keymeulen, Daniel G Pipeleers, Frans K Gorus
OBJECTIVE: We investigated the effect of HLA class I risk alleles on disease progression in various phases of subclinical islet autoimmunity in first-degree relatives of patients with type 1 diabetes. RESEARCH DESIGN AND METHODS: A registry-based group of siblings/offspring (aged 0-39 years) was monitored from single- to multiple-autoantibody positivity ( n = 267) and from multiple-autoantibody positivity to clinical onset ( n = 252) according to HLA-DQ , -A*24 , -B*18 and -B*39 status...
March 15, 2018: Diabetes Care
E A R Engku Nur Syafirah, A B Nurul Najian, Phiaw Chong Foo, Mohammad Ridhuan Mohd Ali, Maizan Mohamed, Chan Yean Yean
Cholera, caused by Vibrio cholerae is a foodborne disease that frequently reported in food and water related outbreak. Rapid diagnosis of cholera infection is important to avoid potential spread of disease. Among available diagnostic platforms, loop-mediated isothermal amplification (LAMP) is regarded as a potential diagnostic tool due to its rapidity, high sensitivity and specificity and independent of sophisticated thermalcycler. However, the current LAMP often requires multiple pipetting steps, hence is susceptible to cross contamination...
March 12, 2018: Acta Tropica
Meryem Mniouil, Hajiba Fellah, Fatima Amarir, Abderrahim Sadak, Abdeslam Et-Touys, Youssef Bakri, Aziza Moustachi, Fatima Zahraa Tassou, Mostapha Hida, Mohamed Lyagoubi, El Bachir Adlaoui, Mohamed Rhajaoui, Faiza Sebti
A rapid, sensitive and specific tool for detection of Leishmania infantum infection in Humans would be highly desirable, because it would allow control interventions in endemic areas of visceral leishmaniasis. This study was carried out at the Reference National Laboratory of Leishmaniasis (RNLL) in National Institute of Hygiene (NIH) Morocco, in order to evaluate the diagnostic potential of immunochromatographic dipstick test (ICT) rk39 in Moroccan suspected VL patients. A total of 49 admitted patients with strong clinical suspicion of VL and 40 healthy controls were investigated for the performance of the ICT rk39...
March 12, 2018: Acta Tropica
Muhammad Shoaib Siddique, Alvia Saad, Sana Shoaib
OBJECTIVE: To determine the change in rapid virological response for chronic hepatitis C by qualitative PCR testing after treatment with sofosbuvir. STUDY DESIGN: A descriptive study. PLACE AND DURATION OF STUDY: Memon Medical Institute Hospital, Karachi, from January to September 2016. METHODOLOGY: The study population consisted of patients above 18 years, till 80 years of age, of both genders, having chronic infection with HCV...
March 2018: Journal of the College of Physicians and Surgeons—Pakistan: JCPSP
Christopher J Lambert, Briana C Freshner, Arlen Chung, Tamara J Stevenson, D Miranda Bowles, Raheel Samuel, Bruce K Gale, Joshua L Bonkowsky
Zebrafish are a valuable model organism in biomedical research. Their rapid development, ability to model human diseases, utility for testing genetic variants identified from next-generation sequencing, amenity to CRISPR mutagenesis, and potential for therapeutic compound screening, has led to their wide-spread adoption in diverse fields of study. However, their power for large-scale screens is limited by the absence of automated genotyping tools for live animals. This constrains potential drug screen options, limits analysis of embryonic and larval phenotypes, and requires raising additional animals to adulthood to ensure obtaining an animal of the desired genotype...
2018: PloS One
Kurt A Zimmerman, Cheng Jack Song, Nancy Gonzalez-Mize, Zhang Li, Bradley K Yoder
Hepatorenal fibrocystic disease (HRFCD) is characterized by cysts in the kidney and liver with associated fibrosis and is the result of defects in proteins required for cilia function or assembly. Previous reports indicate that macrophages, mainly M2-like macrophages, contribute to HRFCD, although the origin (yolk-sac derived resident macrophages vs bone-marrow derived infiltrating macrophages) and contribution of these cells to the observed phenotypes is unknown. Herein, we utilize a congenital model of cilia dysfunction (IFT88Orpk ) to study the importance of macrophages in HRFCD...
March 15, 2018: American Journal of Physiology. Gastrointestinal and Liver Physiology
Giulia Ravasi, Sara Pelucchi, Gaia Buoli Comani, Federico Greni, Raffaella Mariani, Irene Pelloni, Silvia Bombelli, Roberto Perego, Donatella Barisani, Alberto Piperno
OBJECTIVE: During hypoxia hepcidin expression is inhibited to allow iron mobilization to sustain erythropoietic expansion. We analysed molecular mechanisms underlying hypoxia-induced hepcidin inhibition in an in vivo model of acute hypoxia. METHODS: Mice were kept under normal or hypoxic conditions for 6h and 15h and treated with α-PDGF-BB antibody or PDGF-BB receptor inhibitor. Blood, liver, spleen, and bone marrow were collected to extract RNA and protein or to quantify EPO and PDGF-BB...
March 15, 2018: European Journal of Haematology
Md Abu Sayeed, Kamrul Islam, Motaher Hossain, Noor Jahan Akter, Md Nur Alam, Nishat Sultana, Farhana Khanam, Meagan Kelly, Richelle C Charles, Pavol Kováč, Peng Xu, Jason R Andrews, Stephen B Calderwood, Jakia Amin, Edward T Ryan, Firdausi Qadri
Recognizing cholera cases early, especially in the initial phase of an outbreak and in areas where cholera has not previously circulated, is a high public health priority. Laboratory capacity in such settings is often limited. To address this, we have developed a rapid diagnostic test (RDT) termed Cholkit that is based on an immunochromatographic lateral flow assay for the diagnosis of cholera cases using stool. Cholkit contains a monoclonal antibody (ICL-33) to the O-specific polysaccharide (OSP) component of V...
March 14, 2018: PLoS Neglected Tropical Diseases
Robert R Gruhl, Andrew Wu, Micah Niermann, Andrew Olson
BACKGROUND: Eczema coxsackium (EC) can manifest in patients with underlying atopic dermatitis (AD) as a diffuse vesicular rash in a febrile child. The presentation overlaps clinically with the feared diagnosis of eczema herpeticum (EH), which makes differentiating between the conditions very important. CASE PRESENTATION: A 6-month-old girl with known AD presented with fever and rapidly spreading vesicular rash. The patient had multiple exposures including a new antibiotic prescription, introduction of new foods, 6-month vaccinations and a sick contact...
November 27, 2017: Diagnosis
Yi-Yi Wang, Bing-di Xie
Central nervous system (CNS) disease caused by Mycobacterium tuberculosis (MTB) is highly devastating. Tuberculous meningitis (TBM) is the most common form of CNS tuberculosis (TB). Rapid, sensitive, and affordable diagnostic tests are not available. Ziehl-Neelsen (ZN) stain has a very low sensitivity in cases of TBM, the sensitivity rates is of about 10-20%.The detection rate can be improved by taking large volume CSF samples (>6 ml) and prolonged slide examination (30 min). Culture of MTB from the CSF is slow and insufficiently sensitive...
2018: Methods in Molecular Biology
Mohamad Assi, Nicolas Dauguet, Patrick Jacquemin
The isolation of ribonucleic acid (RNA) suitable for gene expression studies is challenging in the pancreas, due to its high ribonuclease activity. This is even more complicated during pancreatitis, a condition associated with inflammation and fibrosis. Our aim was to implement a time-effective and reproducible protocol to isolate high quality RNA from specific pancreatic cell subtypes, in normal and inflammatory conditions. We used two genetically engineered mouse models (GEMM), Ela-CreER/YFP and Sox9-CreER/YFP, to isolate acinar and ductal cells, respectively...
2018: Frontiers in Physiology
Fulai Li, Fan Li, Dan Luo, Weihua Lai, Yonghua Xiong, Hengyi Xu
Infectious diseases caused by Listeria monocytogenes pose a great threat to public health worldwide. Therefore, a rapid and efficient method for L. monocytogenes detection is needed. In this study, a biotin-exposure-based immunomagnetic separation (IMS) method was developed. That is, biotinylated antibody was first targeted to L. monocytogenes. Then, streptavidin-functionalized magnetic nanoparticles were added and anchored onto L. monocytogenes cells indirectly through the strong noncovalent interaction between streptavidin and biotin...
August 9, 2018: Analytica Chimica Acta
D Zidekova, I Waczulikova, L Dolesova, L Vavrova, O Hamidova, R Lohajova Behulova, M Konecny
The average risk of breast cancer in general Slovak population of women is 4-5% and the risk of ovarian cancer is 2%. Probability of breast/ovarian cancer development is higher in individuals carrying a causative germline DNA variant in BRCA1 or BRCA2 gene responsible for hereditary breast/ovarian cancer (HBOC). Although a major proportion of inherited breast/ovarian cancers are due to the mentioned causal mutations, a number of new genes have emerged. Here we describe a rapid, multiplex and comprehensive approach for the detection of pathogenic variants in BRCA1 and BRCA2 genes which most frequently occur in Slovak HBOC population...
2018: Neoplasma
Wanying Li, Dan Yu, Jingjuan Yu, Dengyun Zhu, Qian Zhao
ZmbZIP25 ( Zea mays bZIP (basic leucine zipper) transcription factor 25) is a function-unknown protein that belongs to the D group of the bZIP transcription factor family. RNA-seq data showed that the expression of ZmbZIP25 was tissue-specific in maize silks, and this specificity was confirmed by RT-PCR (reverse transcription-polymerase chain reaction). In situ RNA hybridization showed that ZmbZIP25 was expressed exclusively in the xylem of maize silks. A 5' RACE (rapid amplification of cDNA ends) assay identified an adenine residue as the transcription start site of the ZmbZIP25 gene...
March 12, 2018: International Journal of Molecular Sciences
J R Bowers, K L Parise, E J Kelley, D Lemmer, J M Schupp, E M Driebe, D M Engelthaler, P Keim, B M Barker
Coccidioides immitis and Coccidioides posadasii are soil fungi endemic to desert regions of the southwestern United States, and the causative agents of valley fever, or coccidioidomycosis. Studies have shown that the distribution of Coccidioides in soils is sporadic and cannot be explained by soil characteristics alone, suggesting that biotic and other abiotic factors should be examined. However, tools to reliably and robustly screen the large number of soils needed to investigate these potential associations have not been available...
March 8, 2018: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
Concetta Federico, Debora Lombardo, Noemi La Porta, Anna Maria Pappalardo, Venera Ferrito, Francesco Lombardo, Salvatore Saccone
The arrival of arthropods at a corpse exhibits specific temporal patterns, and Diptera play a key role in the initial stages of the decomposition process. Thus, the correct species assignment of the insect larvae found on a decomposing body is an important step in forensic investigations. Here, we describe a molecular procedure to define the species at larval age found on a corpse more quickly and easily than current systems. Our method involves a unique PCR amplification of a DNA segment within the evolutionarily conserved wingless gene, involved in embryo development...
March 6, 2018: Journal of Forensic and Legal Medicine
Nicole M Bzdyl, Nadezda Urosevic, Ben Payne, Ray Brockenshire, Michael McIntyre, Michael J Leung, Graham Weaire-Buchanan, Elizabeth Geelhoed, Timothy J J Inglis
PURPOSE: In this field trial of rapid blood culture identification (BCID), we aimed to determine whether the improved speed and accuracy of specific BCID predicted in our earlier pilot study could be obtained in regional hospitals by deploying a multiplex PCR FilmArray (Biomerieux, France) capability in their laboratories. METHODS: We trained local hospital laboratory staff to operate the FilmArray equipment and act on the results. To do this, we integrated the multiplex PCR into the standard laboratory blood culture workflow and reporting procedure...
March 13, 2018: Journal of Medical Microbiology
Allan B James, Cristiane P G Calixto, Nikoleta A Tzioutziou, Wenbin Guo, Runxuan Zhang, Craig G Simpson, Wenying Jiang, Gillian A Nimmo, John W S Brown, Hugh G Nimmo
One of the ways in which plants can respond to temperature is via alternative splicing (AS). Previous work showed that temperature changes affected the splicing of several circadian clock gene transcripts. Here we investigated the role of RNA-binding splicing factors (SFs) in temperature-sensitive alternative splicing (AS) of the clock gene LATE ELONGATED HYPOCOTYL (LHY). We characterised, in wild type plants, temperature-associated isoform switching and expression patterns for SF transcripts from a high-resolution temperature and time series RNA-seq experiment...
March 13, 2018: Plant, Cell & Environment
Omnia A Shaker, Howayda E Gomaa, Shereen A ElMasry, Rania M Abdel Halim, Amany H Abdelrahman, Jackline S Kamal
AIM: To evaluate the diagnostic performance of MDI and temocillin disk (30 μg) for detection of carbapenem-resistant Enterobacteriaceae in comparison to real-time PCR. MATERIAL AND METHODS: Fifty specimens submitted to the Microbiology Laboratory of Ain Shams University Hospitals and showed resistance to carbapenem drugs through routine culture and susceptibility testing, were assessed by both temocillin disk (30 μg) and MDI set to detect carbapenem-resistant Enterobacteriaceae ...
February 15, 2018: Open Access Macedonian Journal of Medical Sciences
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