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Multiplex PCR

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https://www.readbyqxmd.com/read/29790294/jak-stat-blockade-alters-synovial-bioenergetics-mitochondrial-function-and-pro-inflammatory-mediators-in-rheumatoid-arthritis
#1
Trudy McGarry, Carl Orr, Sarah Wade, Monika Biniecka, Siobhan Wade, Lorna Gallagher, Candice Low, Douglas J Veale, Ursula Fearon
OBJECTIVE: To examine the effect of tofacitinib on metabolic activity, mitochondrial function and pro-inflammatory mechanisms in Rheumatoid Arthritis. METHODS: Ex-vivo RA synovial explants and primary RA synovial fibroblasts (RAFLS) were cultured with tofacitinib (1μM). RAFLS bioenergetics was assessed using the XF24-Flux-analyser, and key metabolic genes by real-time PCR. Mitochondrial function was assessed using specific cell fluorescent probes and by mitochondrial gene arrays...
May 23, 2018: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/29790273/serological-cultural-and-molecular-evidence-of-brucella-melitensis-infection-in-goats-in-al-jabal-al-akhdar-sultanate-of-oman
#2
Yasmin ElTahir, Al Ghalya Al Toobi, Waleed Al-Marzooqi, Osman Mahgoub, Maryne Jay, Yannick Corde, Hadi Al Lawati, Shekar Bose, Abeer Al Hamrashdi, Kaadhia Al Kharousi, Nasseb Al-Saqri, Rudaina Al Busaidi, Eugene H Johnson
Brucellosis, one of the most common zoonotic diseases and has significant public health and economic importance worldwide. Few studies and reports have been performed to estimate the true prevalence of animal brucellosis in the Sultanate of Oman; however, no incidence of the disease was previously reported in Al Jabal Al Akhdar. The purpose of this study was to investigate the prevalence of brucellosis in goats in eight villages in Al Jebal Al Akhdar, Sultanate of Oman, namely: Al Aqaieb, Al Helailat, Al Ghilayil, Hail Al Hedap, Da'an Al Hamra, Shnoot, Al Qasha'e and Al Sarah, Al Jabal Al Akhdar in the Sultanate of Oman...
May 23, 2018: Veterinary Medicine and Science
https://www.readbyqxmd.com/read/29788964/rna-sequencing-analysis-reveals-quiescent-microglia-isolation-methods-from-postnatal-mouse-brains-and-limitations-of-bv2-cells
#3
Yingbo He, Xiang Yao, Natalie Taylor, Yuchen Bai, Timothy Lovenberg, Anindya Bhattacharya
BACKGROUND: Microglia play key roles in neuron-glia interaction, neuroinflammation, neural repair, and neurotoxicity. Currently, various microglial in vitro models including primary microglia derived from distinct isolation methods and immortalized microglial cell lines are extensively used. However, the diversity of these existing models raises difficulty in parallel comparison across studies since microglia are sensitive to environmental changes, and thus, different models are likely to show widely varied responses to the same stimuli...
May 22, 2018: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/29782292/evaluation-of-symptomatic-patients-with-resistant-discharge
#4
Cemile Sonmez, Selma Usluca, Ismail Hakki Usluca, Irem Kalipci, Figen Sezen, Cemal Resat Atalay, Selcuk Kilic
The aim of this study was to detect the presence of Chlamydia trachomatis, Neisseria (N.) gonorrhoeae, Mycoplasma (M.) hominis, M. genitalium, Ureaplasma (U.) urealyticum, and Trichomonas (T.) vaginalis in patients with resistant discharge. The study also evaluated the concordance of the diagnostic tests. Samples from 156 patients were tested by direct microscopy and culture for T. vaginalis and Mycoplasma IES for M. hominis and U. urealyticum. Multiplex Polymerase Chain Reaction (PCR) was used to determine the presence of six agents...
April 2018: Acta Dermatovenerologica Croatica: ADC
https://www.readbyqxmd.com/read/29782216/carbapenemase-producing-carbapenem-resistant-enterobacteriaceae-from-bangkok-thailand-and-their-detection-by-the-carba-np-and-modified-carbapenem-inactivation-method-tests
#5
Warawut Laolerd, Yukihiro Akeda, Likit Preeyanon, Panan Ratthawongjirakul, Pitak Santanirand
AIM: The purpose of the study was to determine the epidemiology of carbapenemase genes among carbapenem-resistant Enterobacteriaceae and evaluate the Carba NP and modified carbapenem inactivation method (mCIM) tests in their detection. MATERIALS AND METHODS: A total of 287 nonduplicated Enterobacteriaceae isolates, which were at least resistant to one of the carbapenems, were identified and detected for carbapenemase genes by multiplex PCR covering blaKPC , blaNDM , blaVIM , blaIMP , and blaOXA-48-like ...
May 21, 2018: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/29781987/retrospective-microrna-sequencing-complementary-dna-library-preparation-protocol-using-formalin-fixed-paraffin-embedded-rna-specimens
#6
Olivier Loudig, Christina Liu, Thomas Rohan, Iddo Z Ben-Dov
-Archived, clinically classified formalin-fixed paraffin-embedded (FFPE) tissues can provide nucleic acids for retrospective molecular studies of cancer development. By using non-invasive or pre-malignant lesions from patients who later develop invasive disease, gene expression analyses may help identify early molecular alterations that predispose to cancer risk. It has been well described that nucleic acids recovered from FFPE tissues have undergone severe physical damage and chemical modifications, which make their analysis difficult and generally requires adapted assays...
May 5, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29778819/detection-of-tem-and-ctx-m-genes-from-ciprofloxacin-resistant-proteus-mirabilis-and-escherichia-coli-isolated-on-urinary-tract-infections-utis
#7
Govindan Rajivgandhi, Muthuchamy Maruthupandy, Natesan Manoharan
The multidrug resistant Gram negative bacteria (MDRGNB) is an emerging burden and now represents a daily challenge for the management of antimicrobial therapy in healthcare settings. The present study was aimed to detect the prevalence of TEM and CTX-M type genes from GNB on urinary tract infection (UTIs). The ciprofloxacin resistant uropathogens were detected by HEXA UTI 5 disc diffusion method. The phenotypic detection of uropathogens producing extended spectrum beta lactamases (ESBLs) was confirmed by double disc combination (DDCT) and phenotype confirmation methods (PCT)...
May 17, 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29778790/applicability-of-integrated-cell-culture-reverse-transcriptase-quantitative-pcr-icc-rtqpcr-for-the-simultaneous-detection-of-the-four-human-enteric-enterovirus-species-in-disinfection-studies
#8
Hodon Ryu, Karen A Schrantz, Nichole E Brinkman, Laura A Boczek
A newly developed integrated cell culture reverse transcriptase quantitative PCR (ICC-RTqPCR) method and its applicability in UV disinfection studies is described. This method utilizes a cell culture system coupled with four RTqPCR assays to detect four species of human enterovirus (e.g., Enterovirus A, Enterovirus B, Enterovirus C and Enterovirus D). Evaluation of the RTqPCR assays was conducted with coxsackievirus A10, echovirus 30, poliovirus 1 and enterovirus 70 and resulted in 100% specificity for the tested assays...
May 17, 2018: Journal of Virological Methods
https://www.readbyqxmd.com/read/29776709/rapid-real-time-pcr-for-the-detection-of-imp-ndm-vim-kpc-and-oxa-48-carbapenemase-genes-in-isolates-and-spiked-stool-samples
#9
Marianne Lund, Marianne Bøgild Petersen, Anders Lægaard Jørgensen, Dorte Paulmann, Mikala Wang
An in-house real-time PCR was developed to detect the carbapenemase genes IMP, NDM, VIM, KPC and OXA-48 from both bacterial colonies and directly from fecal material. The assay is a multiplex PCR performed in two tubes with NDM, VIM and IMP genes detected in one tube and OXA-48 and KPC genes in the other. Despite the large amount of primers and probes necessary to cover all variants of especially the VIM and IMP genes, the efficiency of the PCR reactions was from 95 to 100%. When tested on 170 clinical strains and compared to culture results from a reference laboratory, 100% correspondence was found...
April 13, 2018: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/29773138/multiplex-hydrolysis-probe-assay-for-the-simultaneous-detection-of-theileria-equi-and-babesia-caballi-infections-in-equids
#10
Raksha V Bhoora, Ronel Pienaar, Frances Cornelius, Antoinette Josemans, Olivier Matthee, Ratselane Marumo, Christo Troskie, Ben J Mans
Quantitative real-time PCR assays previously developed for the detection of Theileria equi and Babesia caballi, were combined in a single multiplex TaqMan qPCR platform for the simultaneous detection of both heamoprotozoan parasites in equids. The multiplex equine piroplasmosis (M-EP) qPCR assay was shown to be efficient and specific. The detection limit was determined to be 1.4 × 10-4 % parasitized erythrocytes (PE) for T. equi and 2.8 × 10-4 % PE for B. caballi. The effect of differential DNA concentrations on the outcome of the M-EP qPCR for each target species was also investigated...
May 15, 2018: Veterinary Parasitology
https://www.readbyqxmd.com/read/29772597/development-of-a-massively-parallel-sequencing-assay-for-investigating-sequence-polymorphisms-of-15-strs-in-a-chinese-northern-han-population
#11
Qing-Xia Zhang, Meng Yang, Ya-Jiao Pan, Jing Zhao, Bao-Wang Qu, Feng Cheng, Ya-Ran Yang, Zhang-Ping Jiao, Li Liu, Jiang-Wei Yan
Massively parallel sequencing (MPS) has been used in forensic genetics in recent years owing to several advantages, such as MPS can provide precise descriptions of the repeat allele structure and variation in the repeat-flanking regions, increasing the discriminating power among loci and individuals. However, it cannot be fully utilized unless sufficient population data is available for all loci. Thus, there is a pressing need to perform population studies providing a basis for the introduction of MPS into forensic practice...
May 17, 2018: Electrophoresis
https://www.readbyqxmd.com/read/29771780/biomarkers-of-aging-in-hiv-infected-children-on-suppressive-antiretroviral-therapy
#12
Stephanie Shiau, Renate Strehlau, Jing Shen, Avy Violari, Faeezah Patel, Afaaf Liberty, Marc Foca, Shuang Wang, Mary Beth Terry, Michael T Yin, Ashraf Coovadia, Elaine J Abrams, Stephen M Arpadi, Louise Kuhn
BACKGROUND: Data on accelerated aging in HIV-infected children are limited. In this study we assess two biomarkers of aging - telomere length and DNA methylation (DNAm) age - in a cohort of early-treated HIV-infected children and compare these aging biomarkers to HIV-exposed uninfected (HEU) and HIV-unexposed uninfected (HUU) children. SETTING: Cross-sectional study of 120 HIV-infected, 33 HEU, and 25 HUU children enrolled in a cohort study in Johannesburg, South Africa...
April 27, 2018: Journal of Acquired Immune Deficiency Syndromes: JAIDS
https://www.readbyqxmd.com/read/29767362/microrna-expression-analysis-next-generation-sequencing
#13
Poching Liu
MicroRNAs are a class of small noncoding RNAs that function as regulators involving in many biological processes. The evaluation of miRNAs and their targets has been aided by miRNA expression profiling studies including multiplex PCR, microarrays, and recent next-generation sequencing tools. Next-generation sequencing has enabled us to profile thousands of genes in a single experiment and overcome the background signal and cross-hybridization issues of microarrays. Next-generation sequencing also allows for the simultaneous confirmation of known miRNAs and discovery of new miRNAs, and significantly reduces costs while providing billions of nucleotide information within a single experiment...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29767361/making-and-sequencing-heavily-multiplexed-high-throughput-16s-ribosomal-rna-gene-amplicon-libraries-using-a-flexible-two-stage-pcr-protocol
#14
Ankur Naqib, Silvana Poggi, Weihua Wang, Marieta Hyde, Kevin Kunstman, Stefan J Green
Deep sequencing of polymerase chain reaction (PCR)-amplified small subunit (16S or 18S) ribosomal RNA (rRNA) genes fragments is commonly employed to characterize the composition and structure of microbial communities. Preparing genomic DNA for sequencing of such gene fragments on Illumina sequencers can be performed in a straightforward, two-stage PCR method, described herein. The protocol described allows for up to 384 samples to be sequenced simultaneously, and provides great flexibility in choice of primers...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29766270/parasitological-and-molecular-diagnostic-of-a-clinical-babesia-caballi-outbreak-in-southern-romania
#15
Mariana Ionita, Isabela Madalina Nicorescu, Kurt Pfister, Ioan Liviu Mitrea
Equine piroplasmosis (EP) is a tick-borne disease of equids caused by Babesia caballi and/or Theileria equi, which is endemic in many tropical and temperate areas of the world. However, clinical outbreaks of EP in Romania during the last decades have not been reported Therefore, the aim of this paper is (i) to describe a clinical B. caballi outbreak in horses on several farms in Southern Romania using a diagnostic and therapeutic approach and (ii) the molecular diagnostic of EP in an endemic area of Romania...
May 15, 2018: Parasitology Research
https://www.readbyqxmd.com/read/29764277/human-papillomavirus-hpv-is-absent-in-branchial-cleft-cysts-of-the-neck-distinguishing-them-from-hpv-positive-cystic-metastasis
#16
Lars Sivars, David Landin, Marzia Rizzo, Linnea Haeggblom, Cinzia Bersani, Eva Munck-Wikland, Anders Näsman, Tina Dalianis, Linda Marklund
BACKGROUND: Distinguishing branchial cleft cysts (BCCs) from cystic metastases of a human papillomavirus (HPV) positive oropharyngeal squamous cell carcinoma (OPSCC) is challenging. Fine needle aspirates (FNAs) from cystic metastasis may be non-representative, while reactive squamous cells from BCC can be atypic. Based on cytology and with the support of HPV DNA positivity many centers treat cystic metastasis oncological and thus patients are spared neck dissection. To do so safely, one must investigate whether HPV DNA and p16INK4a overexpression is found exclusively in cystic metastases and not in BCC...
May 15, 2018: Acta Oto-laryngologica
https://www.readbyqxmd.com/read/29762774/occurrence-and-antimicrobial-susceptibility-of-campylobacter-spp-on-fresh-and-refrigerated-chicken-meat-products-in-central-italy
#17
P Casagrande Proietti, S Pergola, S Bellucci, L Menchetti, D Miraglia, M P Franciosini
This study investigated the presence and the level of Campylobacter spp. contamination in 41 thigh samples (with skin) and 37 skinless breast samples collected at the end of slaughter (T1) and after 10 day period at refrigeration temperature (4°C) (T2), corresponding to their commercial shelf life. The isolates were phenotypically classified as Campylobacter spp. and successively identified by conventional multiplex PCR. The antimicrobial susceptibility of the isolates from fresh thigh and breast samples was also determined via the microdilution method (MIC) in Eucamp microtitre plates with known scalar concentrations of: gentamicin (GEN), streptomycin (ST), ciprofloxacin (CIP), tetracycline (TET), erythromycin (ERY), and nalidixic acid (NA)...
May 11, 2018: Poultry Science
https://www.readbyqxmd.com/read/29762748/molecular-type-specific-multiplex-pcr-produces-a-distinct-vnii-pcr-pattern-among-cryptococcus-neoformans-species-complex
#18
Massimo Cogliati, Mala Rakoto Andrianarivelo, Mohamed Ellabib, Emmanuel N Nnadi, Muriel Cornet
Prevalence of molecular type VNII among Cryptococcus neoformans species complex is probably underestimated since it can be distinguished from VNI only using molecular typing methods such as URA5-RFLP, AFLP, MLST, or whole genome sequencing. Previously, we described a multiplex polymerase chain reaction (PCR) method able to identify VNI, VNIV, and VNIII hybrids, but, at that time, VNII molecular type was not described yet. In this study, 16 VNII global isolates were analyzed by our multiplex PCR method, and results showed that it was able to produce a specific pattern for all the studied VNII isolates, which was different from those of VNI, VNIV, and VNIII...
May 14, 2018: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/29762721/clinical-evaluation-of-the-dermagenius%C3%A2-nail-real-time-pcr-assay-for-the-detection-of-dermatophytes-and-candida-albicans-in-nails
#19
Marie-Pierre Hayette, Laurence Seidel, Caroline Adjetey, Rajae Darfouf, Marie Wéry, Raphaël Boreux, Rosalie Sacheli, Pierrette Melin, Jorge Arrese
Onychomycosis represents one of the most frequent mycoses in the world. Causative agents are mainly dermatophytes, but yeasts and nondermatophyte moulds can also be involved. Conventional diagnostic methods include direct microscopy (or histology) and culturing. However, molecular methods are becoming increasingly popular in this field. The DermaGenius® (DG) Nail multiplex assay (PathoNostics, The Netherlands) is a new commercial real-time polymerase chain reaction (PCR) kit, which can detect Trichophyton rubrum, Trichophyton interdigitale and Candida albicans directly in nails...
May 11, 2018: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/29762365/multiplex-real-time-pcr-detection-of-intestinal-protozoa-in-hiv-infected-children-in-malawi-enterocytozoon-bieneusi-is-common-and-associated-with-gastrointestinal-complaints-and-may-delay-bmi-nutritional-status-recovery
#20
Minke H W Huibers, Peter Moons, Nelson Maseko, Monfort B Gushu, Oluwadamilola H Iwajomo, Robert S Heyderman, Michael Boele van Hensbroek, Eric A Brienen, Lisette van Lieshout, Job C J Calis
BACKGROUND: Intestinal protozoa are common opportunistic infections in HIV patients. Longitudinal studies on either the clinical relevance, or the effect of immune reconstitution by anti-retroviral therapy on intestinal protozoan infections are children is lacking however. This study investigates prevalence and clinical relevance of intestinal protozoa in HIV-infected Malawian children prior to and during their first year of ART. METHODS: Stool samples collected at enrolment and during follow-up were tested for non-opportunistic (Giardia lamblia, Dientamoeba fragilis, Entamoeba histolytica) and opportunistic protozoa (Entroctytoon bieneusi, Encephalitozoon spp...
May 14, 2018: Pediatric Infectious Disease Journal
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