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Molecular diagnostic methods

Cornelia Wiegand, Peter Mugisha, Grace K Mulyowa, Peter Elsner, Uta-Christina Hipler, Yvonne Gräser, Silke Uhrlaß, Pietro Nenoff
Tinea capitis is a dermatophyte infection common among prepubertal children in sub-Saharan Africa and mainly caused by Trichophyton and Microsporum species. Accurate identification is challenging as conventional methods like culture and microscopy are slow and mostly based on morphological characteristics, which make them less sensitive and specific. Modern molecular methods, like polymerase chain reaction (PCR) assays, are gaining acceptance and are quick as well as accurate. The aim of this study was to investigate the clinical patterns of tinea capitis and to accurately identify the most common causative dermatophytes affecting the scalps of children aged 1 to 16 years attending the Skin Clinic at Mbarara University of Science and Technology (MUST), Mbarara, Uganda, East Africa, using both conventional mycological methods and PCR-ELISA for detection of dermatophyte DNA...
October 19, 2016: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
Yong Suk Jo, Ju-Hee Park, Jung Kyu Lee, Eun Young Heo, Hee Soon Chung, Deog Kyeom Kim
The prevalence and clinical implications of discordance between Xpert MTB/RIF assays and the AdvanSure TB/NTM real-time polymerase chain reaction (PCR) for bronchial washing specimens have not been studied in pulmonary TB (PTB) patients. The discordant proportion and its clinical impact were evaluated in 320 patients from the bronchoscopy registry whose bronchial washing specimens were tested simultaneously with Xpert MTB/RIF and the TB/NTM PCR assay for three years, and the accuracy of the assays, including the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), were studied...
2016: PloS One
Ryan Stables, Graeme Clemens, Holly J Butler, Katherine M Ashton, Andrew Brodbelt, Timothy P Dawson, Leanne M Fullwood, Michael D Jenkinson, Matthew J Baker
Spectroscopic diagnostics have been shown to be an effective tool for the analysis and discrimination of disease states from human tissue. Furthermore, Raman spectroscopic probes are of particular interest as they allow for in vivo spectroscopic diagnostics, for tasks such as the identification of tumour margins during surgery. In this study, we investigate a feature-driven approach to the classification of metastatic brain cancer, glioblastoma (GB) and non-cancer from tissue samples, and we provide a real-time feedback method for endoscopic diagnostics using sound...
October 19, 2016: Analyst
Liang Li, Wan-Jun Zhou, Ping Fang, Ze-Yan Zhong, Jian-Sheng Xie, Ti-Zhen Yan, Jian Zeng, Xu-Hui Tan, Xiang-Min Xu
BACKGROUND: Spinal muscular atrophy (SMA) is mainly caused by deletions in SMA-related genes. The objective of this study was to develop gene-dosage assays for diagnosing SMA. METHODS: A multiplex, quantitative PCR assay and a CNVplex assay were developed for determining the copy number of SMN1, SMN2, and NAIP. Reproducibility and specificity of the two assays were compared to a multiple ligation-dependent probe amplification (MLPA) assay. To evaluate reproducibility, 30 samples were analyzed three times using the three assays...
October 18, 2016: Clinical Chemistry and Laboratory Medicine: CCLM
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
Anita Chopra, Sushant Soni, Haraprasad Pati, Dev Kumar, Rahul Diwedi, Deepak Verma, Garima Vishwakama, Sameer Bakhshi, Suman Kumar, Ajay Gogia, Rajive Kumar
BACKGROUND & OBJECTIVES: Mutation of nucleophosmin (NPM1) gene in the absence of FLT3-ITD (FMS related tyrosine kinase 3 - internal tandem duplications) mutation carries a good prognosis in cytogenetically normal acute myeloid leukaemia (AML). NPM1, a multifunctional nucleolar phosphoprotein that shuttles between nucleus and cytoplasm, gets trapped in the cytoplasm when mutated. Immunohistochemical (IHC) demonstration of its aberrant cytoplasmic location (NPMc+) has been suggested as a simple substitute for the standard screening molecular method...
June 2016: Indian Journal of Medical Research
Kim E M van Kessel, Willemien Beukers, Irene Lurkin, Angelique Ziel-van der Made, Kirstin A van der Keur, Joost L Boormans, Lars Dyrskjøt, Mirari Márquez, Torben F Ørntoft, Francisco X Real, Ulrika Segersten, Núria Malats, Per-Uno Malmström, Wim Van Criekinge, Ellen C Zwarthoff
PURPOSE: Only 3-28% of patients referred to the urology clinic for hematuria are diagnosed with bladder cancer (BC). Cystoscopies lead to high diagnostic costs and patient burden. Therefore, to improve selection of patients for cystoscopy, reduce costs and over-testing we aimed to validate a recently developed diagnostic urine assay MATERIALS AND METHODS: We included 200 patients from three European countries undergoing cystoscopy for hematuria (n=97 BC, n=103 non-malignant). Voided urine samples were collected prior to cystoscopy...
October 13, 2016: Journal of Urology
Zehra Ordulu, Tammy Kammin, Harrison Brand, Vamsee Pillalamarri, Claire E Redin, Ryan L Collins, Ian Blumenthal, Carrie Hanscom, Shahrin Pereira, India Bradley, Barbara F Crandall, Pamela Gerrol, Mark A Hayden, Naveed Hussain, Bibi Kanengisser-Pines, Sibel Kantarci, Brynn Levy, Michael J Macera, Fabiola Quintero-Rivera, Erica Spiegel, Blair Stevens, Janet E Ulm, Dorothy Warburton, Louise E Wilkins-Haug, Naomi Yachelevich, James F Gusella, Michael E Talkowski, Cynthia C Morton
In this exciting era of "next-gen cytogenetics," integrating genomic sequencing into the prenatal diagnostic setting is possible within an actionable time frame and can provide precise delineation of balanced chromosomal rearrangements at the nucleotide level. Given the increased risk of congenital abnormalities in newborns with de novo balanced chromosomal rearrangements, comprehensive interpretation of breakpoints could substantially improve prediction of phenotypic outcomes and support perinatal medical care...
October 5, 2016: American Journal of Human Genetics
Christiane Gebhardt
This article evaluates the main contributions of tomato, tobacco, petunia, potato, pepper and eggplant to classical and molecular plant genetics and genomics since the beginning of the twentieth century. Species from the Solanaceae family form integral parts of human civilizations as food sources and drugs since thousands of years, and, more recently, as ornamentals. Some Solanaceous species were subjects of classical and molecular genetic research over the last 100 years. The tomato was one of the principal models in twentieth century classical genetics and a pacemaker of genome analysis in plants including molecular linkage maps, positional cloning of disease resistance genes and quantitative trait loci (QTL)...
October 15, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
John V Thomas, Rupan Sanyal, Janis P O'Malley, Satinder P Singh, Desiree E Morgan, Cheri L Canon
The academic educator's portfolio is a collection of materials that document academic performance and achievements, supplementing the curriculum vitae, in order to showcase a faculty member's most significant accomplishments. A decade ago, a survey of medical schools revealed frustration in the nonuniform methods of measuring faculty's medical education productivity. A proposed solution was the use of an academic educator's portfolio. In the academic medical community, compiling an academic portfolio is always a challenge because teaching has never been confined to the traditional classroom setting and often involves active participation of the medical student, resident, or fellow in the ongoing care of the patient...
October 11, 2016: Academic Radiology
Natalija Topić Popović, Snježana P Kazazić, Ivančica Strunjak-Perović, Rozelindra Čož-Rakovac
Identification of bacteria in aquatic and environmental applications, for monitoring purposes and research, for health assessments and therapy considerations of farmed and free-living aquatic organisms, still relies on conventional phenotypic and biochemical protocols. Although molecular techniques based on DNA amplification and sequencing are finding ways into diagnostic laboratories, they are time-consuming, costly and difficult in the case of multiplex assays. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is a rapid and accurate proteomic method reliable for identification of unknown bacteria to the genus and species level...
October 11, 2016: Environmental Research
Manik Lal Saha, Xuzhou Yan, Peter J Stang
Over the past couple of decades, coordination-driven self-assembly has evolved as a broad multidisciplinary domain that not only covers the syntheses of aesthetically pleasing supramolecular architectures but also emerges as a method to form new optical materials, chemical sensors, theranostic agents, and compounds with light-harvesting and emissive properties. The majority of these applications depend upon investigations that reveal the photophysical nature and electronic structure of supramolecular coordination complexes (SCCs), including two-dimensional (2D) metallacycles and three-dimensional (3D) metallacages...
October 13, 2016: Accounts of Chemical Research
Olivier Fernandez, Maria Urrutia, Stéphane Bernillon, Catherine Giauffret, François Tardieu, Jacques Le Gouis, Nicolas Langlade, Alain Charcosset, Annick Moing, Yves Gibon
BACKGROUND: In the last decade, metabolomics has emerged as a powerful diagnostic and predictive tool in many branches of science. Researchers in microbes, animal, food, medical and plant science have generated a large number of targeted or non-targeted metabolic profiles by using a vast array of analytical methods (GC-MS, LC-MS, (1)H-NMR….). Comprehensive analysis of such profiles using adapted statistical methods and modeling has opened up the possibility of using single or combinations of metabolites as markers...
2016: Metabolomics: Official Journal of the Metabolomic Society
Stéphane Grison, Gaëlle Favé, Matthieu Maillot, Line Manens, Olivia Delissen, Éric Blanchardon, Isabelle Dublineau, Jocelyne Aigueperse, Sandra Bohand, Jean-Charles Martin, Maâmar Souidi
INTRODUCTION: Data are sparse about the potential health risks of chronic low-dose contamination of humans by uranium (natural or anthropogenic) in drinking water. Previous studies report some molecular imbalances but no clinical signs due to uranium intake. OBJECTIVES: In a proof-of-principle study, we reported that metabolomics is an appropriate method for addressing this chronic low-dose exposure in a rat model (uranium dose: 40 mg L(-1); duration: 9 months, n = 10)...
2016: Metabolomics: Official Journal of the Metabolomic Society
Patricia J Simner, Gail L Woods, Nancy L Wengenack
The immunocompromised host is at increased risk of Mycobacterium tuberculosis complex and nontuberculous mycobacteria infection. Although Mycobacterium tuberculosis complex is a significant mycobacterial pathogen, nontuberculous mycobacteria causes substantial disease in those with suppressed immune responses. Mycobacterial infections can cause significant morbidity and mortality in this patient population, and rapid identification and susceptibility testing of the mycobacterial species is paramount to patient management and outcomes...
August 2016: Microbiology Spectrum
Raquel M Martinez, Donna M Wolk
Bacteremia and sepsis are conditions associated with high mortality and are of great impact to health care operations. Among the top causes of mortality in the United States, these conditions cause over 600 fatalities each day. Empiric, broad-spectrum treatment is a common but often a costly approach that may fail to effectively target the correct microbe, may inadvertently harm patients via antimicrobial toxicity or downstream antimicrobial resistance. To meet the diagnostic challenges of bacteremia and sepsis, laboratories must understand the complexity of diagnosing and treating septic patients, in order to focus on creating algorithms that can help direct a more targeted approach to antimicrobial therapy and synergize with existing clinical practices defined in new Surviving Sepsis Guidelines...
August 2016: Microbiology Spectrum
Leila Sabour, Maryam Sabour, Saeid Ghorbian
With the advancement and improvement of new sequencing technology, next-generation sequencing (NGS) has been applied increasingly in cancer genomics research fields. More recently, NGS has been adopted in clinical oncology to advance personalized treatment of cancer. NGS is utilized to novel diagnostic and rare cancer mutations, detection of translocations, inversions, insertions and deletions, detection of copy number variants, detect familial cancer mutation carriers, provide the molecular rationale for appropriate targeted, therapeutic and prognostic...
October 8, 2016: Pathology Oncology Research: POR
N Grimaldi, F Andrade, N Segovia, L Ferrer-Tasies, S Sala, J Veciana, N Ventosa
Molecular self-assembly has enabled the fabrication of biologically inspired, advanced nanostructures as lipid-based nanovesicles (L-NVs). The oldest L-NVs, liposomes, have been widely proposed as potential candidates for drug delivery, diagnostic and/or theranostic applications and some liposome-based drug products have already stepped from the lab-bench to the market. This success is attributed to their ability to encapsulate both hydrophobic and/or hydrophilic molecules, efficiently carry and protect them within the body and finally deliver them at the target site...
September 13, 2016: Chemical Society Reviews
Kyung-Taek Rim, Soo-Jin Kim
In vivo studies regarding biochemical, molecular biological, and histopathological changes in cancer tissues have been widely performed by the administration of carcinogens in rodents. In these established methods, dissection of the animal following sacrifice must be carried out. Exosomes are cell-derived vesicles that are present in all body fluids and these vesicles have specific roles within cells. Thus, much attention is given to the clinical application of exosomes that can possibly be used for prediction and therapy and as biomarkers related to cancer...
September 2016: Journal of Cancer Prevention
Yanbing Zu, Min-Han Tan, Chee Ren Ee, Jackie Y Ying
A number of human leukocyte antigen (HLA) gene alleles have been found to be genetic risk markers for immunologically mediated drug hypersensitivity. Clinical adoption of HLA pharmacogenomics requires facile and accurate allele screening assays. As HLA genes are highly polymorphic, currently available methods are usually labor-intensive and liable to generate false positives. Herein we report a general strategy for screening HLA alleles with nanoparticle probes. Specific HLA alleles can be identified by gauging three to five sequence variants...
October 5, 2016: Nanomedicine: Nanotechnology, Biology, and Medicine
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