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https://www.readbyqxmd.com/read/28806597/a-nested-multivariate-chemometrics-based-calibration-strategy-for-direct-trace-biometal-analysis-in-soft-tissue-utilizing-energy-dispersive-x-ray-fluorescence-edxrf-and-scattering-spectrometry
#1
REVIEW
J J Okonda, K H Angeyo, J M Mangala, S M Kisia
Compton scatter-modulated fluorescence and multivariate chemometric (artificial neural network (ANN) and principal component regression (PCR)) calibration strategy was explored for direct rapid trace biometals (Mn, Fe, Cu, Zn, Se) analysis in "complex" matrices (model soft tissues). This involved spectral feature selection (multiple fluorescence signatures) normalized to or in conjunction with Compton scatter. ANN model resulted in more accurate trace biometal determination (R(2)>0.9) compared to PCR. Hybrid nested (ANN and PCR) approach led to optimized accurate biometals' concentrations in Oyster tissue (≤ ± 10%)...
August 8, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/28806064/conditional-displacement-hybridization-assay-for-multiple-snp-phasing
#2
Tsz Wing Fan, Henson L Lee Yu, I-Ming Hsing
The two chromosomal copies of the human genome are highly polymorphic, and the allelic content on each strand can dictate a person's biological outcomes. While many of the current diagnostic tools are able to detect the presence of multiple mutations at the same time, most cannot determine the phase of these mutations unless long-range PCR or sequencing techniques are used or if templates are compartmentalized into single copies prior to amplification. Here, an enzyme-coupled hybridization assay, named Conditional Displacement Hybridization Assay (CDHA), is described for the concurrent and rapid determination of the presence and phase of SNP variants...
August 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28804970/arrhythmogenic-gene-remodelling-in-elderly-patients-with-type-2-diabetes-with-aortic-stenosis-and-normal-left-ventricular-ejection-fraction
#3
R Ashrafi, P Modi, A Y Oo, D M Pullan, K Jian, H Zhang, J Yanni Gerges, G Hart, M R Boyett, G K Davis, J P H Wilding
Type 2 diabetes is associated with higher rate of ventricular arrhythmias and this is hypothesised to be independent of coronary artery disease or hypertension. To investigate further we compared changes in left ventricular myocardial gene expression in Type 2 diabetes to patients in a control group with left ventricular hypertrophy. 9 control patients and 7 patients with type 2 diabetes with aortic stenosis undergoing aortic valve replacement had standard ECGs, signal averaged ECGs and echocardiograms prior to surgery...
August 14, 2017: Experimental Physiology
https://www.readbyqxmd.com/read/28803792/rapid-and-visual-detection-of-leptospira-in-urine-by-ligb-lamp-assay-with-pre-addition-of-dye
#4
Syed Atif Ali, Gurpreet Kaur, Nongthombam Boby, T Sabarinath, Khushal Solanki, Dheeraj Pal, Pallab Chaudhuri
Leptospirosis is considered to be the most widespread zoonotic disease caused by pathogenic species of Leptospira. The present study reports a novel set of primers targeting LigB gene for visual detection of pathogenic Leptospira in urine samples through Loop-mediated isothermal amplification (LAMP). The results were recorded by using Hydroxyl napthol blue (HNB), SYBR GREEN I and calcein. Analytical sensitivity of LAMP was as few as 10 leptospiral organisms in spiked urine samples from cattle and dog. LigB gene based LAMP, termed as LigB-LAMP, was found 10 times more sensitive than conventional PCR...
August 10, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28803013/short-communication-detection-of-stx2-and-elt-genes-in-bovine-milk-by-using-a-multiplex-pcr-system
#5
R D S Nandi, A C Campos, J J Puño-Sarmiento, R P Maluta, S P D Rocha, R K T Kobayashi, G Nakazato
The aim of this study was to detect 2 important toxin genes from diarrheagenic Escherichia coli (DEC) in bovine milk using a new multiplex PCR. To standardize the multiplex PCR, the stx2 and elt genes were investigated for the detection of Shiga toxin-producing Escherichia coli (STEC) and enterotoxigenic E. coli (ETEC), respectively. The DNA template was prepared with a thermal procedure (boiling) and a commercial kit. Samples consisted of UHT and pasteurized milk, both skimmed, and STEC and ETEC were tested in concentrations between 10(1) and 10(9) cfu/mL...
August 9, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28803008/two-step-large-volume-magnetic-separation-combined-with-pcr-assay-for-sensitive-detection-of-listeria-monocytogenes-in-pasteurized-milk
#6
Dan Luo, Xiaolin Huang, Yan Mao, Chaochao Chen, Fulai Li, Hengyi Xu, Yonghua Xiong
Immunomagnetic separation (IMS) is an effective tool for the preconcentration and purification of food-borne pathogens from complex food samples because of its high capture efficiency (CE). In conventional IMS, antibodies are usually conjugated on the surface of magnetic beads (MB); the random orientation and conformation changes of antibodies on the MB surface can decrease their bioactivity. Moreover, the Brownian motion of immobilized antibodies is weakened, thereby rendering their binding efficiency with bacteria lower than that of free antibodies...
August 9, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28802758/impact-of-rapid-identification-of-staphylococcus-aureus-bloodstream-infection-without-antimicrobial-stewardship-intervention-on-antibiotic-optimization-and-clinical-outcomes
#7
R Brigg Turner, Karineh Lalikian, Madeline Fry, Jacqueline Schwartz, Dominic Chan, Regina Won
Few studies have evaluated the clinical impact of polymerase chain reaction (PCR) for Staphylococcus aureus bloodstream infections in resource-limited settings that lack direct antimicrobial stewardship intervention. This retrospective cohort study compared patients with standard microbiological identification (n=343) to those with additional identification by (PCR) (n=130). Time to initiation of optimal therapy was similar between groups but substantially shorter in the PCR group for those infected with methicillin susceptible S...
July 8, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28802644/rapid-characterization-of-the-cho-platform-cell-line-and-identification-of-pseudo-attp-sites-for-phic31-integrase
#8
Narges Damavandi, Mozhgan Raigani, Atefeh Joudaki, Fatemeh Davami, Sirous Zeinali
The Chinese Hamster Ovary (CHO) cell lines, applicable to post-translational modifications, are preferred systems for biopharmaceutical protein production. In this study, by using the Jump-In™ TI™ technology which employs PhiC31 and R4 bacteriophage recombinases, a platform CHO-K1 cell line containing a R4-attP site was generated. Here, a combination of Quantitative Fluorescent-Polymerase Chain Reaction (QF-PCR) and semi-random, two-step PCR (ST-PCR), was performed to feature the platform cell clones. Our results show that QF-PCR and ST-PCR, can be utilized for efficient and accelerated cell line characterization...
August 9, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28802406/real-time-pcr-followed-by-high-resolution-melting-curve-analysis-a-rapid-and-pragmatic-approach-for-screening-of-multidrug-resistant-extrapulmonary-tuberculosis
#9
Kusum Sharma, Megha Sharma, Shreya Singh, Manish Modi, Aman Sharma, Pallab Ray, Subhash Varma
INTRODUCTION: Multidrug resistance (MDR) in extrapulmonary tuberculosis (EPTB) is a diagnostic challenge in an endemic country like India. Timely detection of MDR-TB can contribute to a better patient outcome. OBJECTIVE: To perform real-time PCR (qPCR) using rpoB, mpb64 and IS6110 gene on a variety of EPTB samples and to compare the performance of different gene targets. All qPCR positive samples were subjected to high resolution melt-curve analysis (HRM analysis) for rpoB and katG gene to evaluate its potential for MDR screening among different sample types...
September 2017: Tuberculosis
https://www.readbyqxmd.com/read/28802405/detection-of-mycobacterium-tuberculosis-from-paraffin-embedded-tissues-by-genexpert-mtb-rif
#10
Laura Rindi, Greta Alì, Barbara Fabiani, Gabriella Fontanini, Carlo Garzelli
GeneXpert MTB/RIF (Xpert) assay, a rapid and automated system based on real-time PCR and molecular beacon technology, proved to be a sensitive and specific tool capable of detecting Mycobacterium tuberculosis and rifampin resistance in clinical specimens. In this study we provide a Xpert-dedicated successful protocol for processing paraffin-embedded tissue and assess the feasibility of the Xpert assay-based tuberculosis (TB) diagnosis on these specimens, thus proving the Xpert assay as a valuable TB diagnostic tool in supporting conventional histopathological methods...
September 2017: Tuberculosis
https://www.readbyqxmd.com/read/28802157/droplet-digital-pcr-for-rapid-enumeration-of-viral-genomes-and-particles-from-cells-and-animals-infected-with-orthopoxviruses
#11
Jeffrey L Americo, Patricia L Earl, Bernard Moss
Droplet digital polymerase chain reaction (ddPCR) was adapted for quantifying the number of orthopoxviral genomes in purified virus samples, infected cell lysates and tissues of infected animals. In contrast to the more commonly used qPCR, the newer ddPCR provides absolute numbers of DNA copies in samples without need for standard curves and has the ability to detect rare mutants in a population. The genome/infectious unit ratio for several sucrose gradient-purified orthopoxviruses varied from 5 to 10, which correlated well with values obtained using the Virocyt, a dedicated fluorescence flow cytometer...
August 9, 2017: Virology
https://www.readbyqxmd.com/read/28801087/cause-of-acute-encephalitis-encephalopathy-in-japanese-children-diagnosed-by-a-rapid-and-comprehensive-virological-detection-system-and-differences-in-their-clinical-presentations
#12
Kei Takasawa, Ryuichi Nakagawa, Shigeru Takishima, Kengo Moriyama, Ken Watanabe, Koji Kiyohara, Takeshi Hasegawa, Masahiro Shimohira, Kenichi Kashimada, Norio Shimizu, Tomohiro Morio
BACKGROUND: Acute encephalitis/encephalopathy (AE/E) is a rare and severe complication of common childhood infections; however, a treatment strategy based on clinical and pathological evidence has not been established. METHODS: The clinical data and aetiological results using a rapid and comprehensive virological detection system of 62 Japanese children diagnosed with AE/E from 2010 to 2014 were collected. We assessed clinical differences between causes and effectiveness of our multiplex PCR system to establish a pathogen-based treatment strategy for AE/E...
August 8, 2017: Brain & Development
https://www.readbyqxmd.com/read/28800594/species-identification-and-molecular-typing-of-human-brucella-isolates-from-kuwait
#13
Abu S Mustafa, Nazima Habibi, Amr Osman, Faraz Shaheed, Mohd W Khan
Brucellosis is a zoonotic disease of major concern in Kuwait and the Middle East. Human brucellosis can be caused by several Brucella species with varying degree of pathogenesis, and relapses are common after apparently successful therapy. The classical biochemical methods for identification of Brucella are time-consuming, cumbersome, and provide information limited to the species level only. In contrast, molecular methods are rapid and provide differentiation at intra-species level. In this study, four molecular methods [16S rRNA gene sequencing, real-time PCR, enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus variable-number tandem-repeat analysis (MLVA)-8, MLVA-11 and MLVA-16 were evaluated for the identification and typing of 75 strains of Brucella isolated in Kuwait...
2017: PloS One
https://www.readbyqxmd.com/read/28798758/an-efficient-plant-regeneration-and-transformation-system-of-ma-bamboo-dendrocalamus-latiflorus-munro-started-from-young-shoot-as-explant
#14
Shanwen Ye, Changyang Cai, Huibo Ren, Wenjia Wang, Mengqi Xiang, Xiaoshan Tang, Caiping Zhu, Tengfei Yin, Li Zhang, Qiang Zhu
Genetic engineering technology has been successfully used in many plant species, but is limited in woody plants, especially in bamboos. Ma bamboo (Dendrocalamus latiflorus Munro) is one of the most important bamboo species in Asia, and its genetic improvement was largely restricted by the lack of an efficient regeneration and transformation method. Here we reported a plantlet regeneration and Agrobacterium-mediated transformation protocol by using Ma bamboo young shoots as explants. Under our optimized conditions, embryogenic calluses were successfully induced from the excised young shoots on callus induction medium and rapidly grew on callus multiplication medium...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28798494/identification-and-functional-characterization-of-the-sex-determining-gene-doublesex-in-the-sawfly-athalia-rosae%C3%A2-hymenoptera-tenthredinidae
#15
Shotaro Mine, Megumi Sumitani, Fugaku Aoki, Masatsugu Hatakeyama, Masataka G Suzuki
Sexual fate of the sawfly, Athalia rosae (Hymenoptera: Tenthredinidae) is determined by the complementary sex determination (CSD) mechanism as is the case in honeybees. However, to date, genes involved in sex determination have not been identified in this species. In this study, we attempted to identify orthologs of complementary sex-determiner (csd), feminizer (fem), and doublesex (dsx) from the A. rosae genome, all of which are crucial components of the sex determination cascade in the honeybee. As a result, we identified a sawfly ortholog of dsx (designated as Ardsx)...
2017: Applied Entomology and Zoology
https://www.readbyqxmd.com/read/28797637/temporal-changes-in-innate-immunity-parameters-epinecidin-gene-expression-and-mortality-in-orange-spotted-grouper-epinephelus-coioides-experimentally-infected-with-a-fish-pathogen-vibrio-harveyi-jml1
#16
Edgar C Amar, Joseph P Faisan, Mary Jane S Apines-Amar, Rolando V Pakingking
Changes in innate immunity parameters and epinecidin mRNA transcript levels were examined to characterize the non-specific immune response of E. coioides to pathogenic V. harveyi JML1 isolated from affected cage-cultured fish. After fish had been injected with bacteria at a dose causing 30% mortality, blood and tissue samples were collected at 0, 6, 12, 24, 48, 72, 96, 120, and 240 h post-infection (hpi) for assessment of indices such as the oxidative burst (OB) and phagocytic index (PI) of head kidney cells, and lysozyme activity (LYS) and total immunoglobulin (Total Ig) levels of the plasma...
August 7, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28797261/evaluation-of-carestart%C3%A2-malaria-hrp2-pldh-pf-pan-combo-test-in-a-malaria-low-transmission-region-of-senegal
#17
Mamadou Alpha Diallo, Khadim Diongue, Mouhamadou Ndiaye, Amy Gaye, Awa Deme, Aida S Badiane, Daouda Ndiaye
BACKGROUND: This study was initiated from the observation that prevalence of malaria obtained with rapid diagnostic test (RDT) (CareStart™Malaria HRP2/pLDH Combo Test) was higher than in microscopy in a malaria low transmission area of Senegal. PCR was then performed to evaluate the performance of the RDT compared to microscopy in clinical settings. METHODS: The study included 215 patients suspected of malaria in two peri-urban area of Dakar. Finger-pick blood samples were tested using RDT (CareStart™Malaria HRP2/pLDH Combo Test)...
August 10, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28796791/evaluating-turnaround-times-for-early-infant-diagnosis-samples-in-kenya-from-2011-2014-a-retrospective-analysis-of-hitsystem-program-data
#18
Catherine Wexler, An-Lin Cheng, Brad Gautney, Sarah Finocchario-Kessler, Kathy Goggin, Samoel Khamadi
Long turnaround times (TAT) for the processing and posting of results of infant HIV DNA PCR samples can hinder the success of early infant diagnosis (EID) programs. The HITSystem is an eHealth intervention that alerts staff when services are overdue or results are delayed. We conducted a retrospective analysis of 3669 HIV-exposed infants enrolled in 15 Kenya hospital EID programs and three laboratories using the HITSystem from 2011-2014. We assessed mean and median TAT from when a sample was: 1) obtained to when it was shipped to the laboratory, 2) shipped to when it was received at the laboratory, 3) received to when a result was posted, and 4) the total time from obtaining the sample (step 1) to posting the result (step 3)...
2017: PloS One
https://www.readbyqxmd.com/read/28795847/successful-containment-of-the-first-kpc-producing-klebsiella-pneumoniae-outbreak-in-croatia
#19
Dijana Varda Brkic, Irina Pristas, Ivan Cipris, Marko Jelic, Iva Butic, Arjana Tambic Andrasevic
AIM: We report the first outbreak caused by Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae sequence type 258 (ST 258) clone that occurred in Croatia from May to December 2012. MATERIALS & METHODS: 23 carbapenem-resistant K. pneumoniae isolates were recovered from clinical and screening specimens of 12 patients hospitalized in a regional hospital. The first isolates from the 12 patients were typed using pulsed-field gel electrophoresis and multilocus sequence typing...
August 10, 2017: Future Microbiology
https://www.readbyqxmd.com/read/28795230/improved-multiplex-pcr-primers-for-rapid-identification-of-coagulase-negative-staphylococci
#20
Jonguk Kim, Jisoo Hong, Jeong-A Lim, Sunggi Heu, Eunjung Roh
Coagulase-negative staphylococci (CNS) are opportunistic pathogens that are currently emerging as causative agents of human disease. Though CNS are widespread in the clinic and food, their precise identification at species level is important. Here, using 16S rRNA sequencing, 55 staphylococcal isolates were identified as S. capitis, S. caprae, S. epidermidis, S. haemolyticus, S. pasteuri, S. saprophyticus, S. warneri, and S. xylosus. Although 16S rRNA sequencing is universally accepted as a standard for bacterial identification, the method did not effectively discriminate closely related species, and additional DNA sequencing was required...
August 9, 2017: Archives of Microbiology
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