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Sathish Kumar T, Navaneeth Krishnan A, Joseph Sahaya Rajan J, Makesh M, Jithendran K P, Alavandi S V, Vijayan K K
The emerging microsporidian parasite Enterocytozoon hepatopenaei (EHP), the causative agent of hepatopancreatic microsporidiosis, has been widely reported in shrimp-farming countries. EHP infection can be detected by light microscopy observation of spores (1.7 × 1 μm) in stained hepatopancreas (HP) tissue smears, HP tissue sections, and fecal samples. EHP can also be detected by polymerase chain reaction (PCR) targeting the small subunit (SSU) ribosomal RNA (rRNA) gene or the spore wall protein gene (SWP)...
March 17, 2018: Parasitology Research
Karteek Kadimisetty, Jinzhao Song, Aoife M Doto, Young Hwang, Jing Peng, Michael G Mauk, Frederic D Bushman, Robert Gross, Joseph N Jarvis, Changchun Liu
Molecular diagnostics that involve nucleic acid amplification tests (NAATs) are crucial for prevention and treatment of infectious diseases. In this study, we developed a simple, inexpensive, disposable, fully 3D printed microfluidic reactor array that is capable of carrying out extraction, concentration and isothermal amplification of nucleic acids in variety of body fluids. The method allows rapid molecular diagnostic tests for infectious diseases at point of care. A simple leak-proof polymerization strategy was developed to integrate flow-through nucleic acid isolation membranes into microfluidic devices, yielding a multifunctional diagnostic platform...
March 10, 2018: Biosensors & Bioelectronics
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
Jinzhao Song, Vikram Pandian, Michael G Mauk, Haim H Bau, Sara Cherry, Laurence C Tisi, Changchun Liu
Rapid and quantitative molecular diagnostics in the field, at home, and at remote clinics is essential for evidence-based disease management, control, and prevention. Conventional molecular diagnostics requires extensive sample preparation, complex instruments, and skilled personnel, restricting its use to centralized laboratories. To overcome these limitations, we designed a simple, inexpensive, hand-held, smartphone-based mobile detection platform, dubbed "smart-connected cup" (SCC), for rapid, connected and quantitative molecular diagnostics...
March 15, 2018: Analytical Chemistry
Sonja Günther, Sandra Felten, Gerhard Wess, Katrin Hartmann, Karin Weber
Feline infectious peritonitis (FIP) is a fatal disease in cats worldwide. The aim of this study was to test two commercially available reaction mixtures in a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to detect feline Coronavirus (FCoV) in body cavity effusions of cats with and without FIP, in order to minimize the time from sampling to obtaining results. RNA was extracted from body cavity effusion samples of 71 cats, including 34 samples from cats with a definitive diagnosis of FIP, and 37 samples of control cats with similar clinical signs but other confirmed diseases...
March 11, 2018: Journal of Virological Methods
Yan Yan, Yue Ding, Fenfei Leng, David Dunlap, Laura Finzi
Supercoiling can alter the form and base pairing of the double helix and directly impact protein binding. More indirectly, changes in protein binding and the stress of supercoiling also influence the thermodynamic stability of regulatory, protein-mediated loops and shift the equilibria of fundamental DNA/chromatin transactions. For example, supercoiling affects the hierarchical organization and function of chromatin in topologically associating domains (TADs) in both eukaryotes and bacteria. On the other hand, a protein-mediated loop in DNA can constrain supercoiling within a plectonemic structure...
March 10, 2018: Nucleic Acids Research
Q Zhong, K Li, D Chen, H Wang, Q Lin, W Liu
Objective Condyloma acuminatum (CA) is a common, viral, sexually transmitted disease worldwide. Human papillomavirus (HPV) genotyping has important clinical implications for the treatment of CA. We developed a loop-mediated isothermal amplification (LAMP) method for the detection of HPV. Methods We collected 294 cervical scrape samples, including 30 HPV-6-positive, 30 HPV-11-positive, 22 HPV-16-positive, 20 HPV-42-positve, 30 HPV-43-positive, 20 HPV-44-positive and 142 HPV-negative samples. Tissues from 40 patients with a pathological diagnosis of CA were paraffin-embedded and analyzed by LAMP and Luminex...
March 14, 2018: British Journal of Biomedical Science
Cielo M León, Marina Muñoz, Juan H Tabares, Carolina Hernandez, Carolina Florez, Martha S Ayala, Juan David Ramírez
Loop-mediated isothermal amplification (LAMP) is ideal for the detection of Leishmania DNA as it is a quick and easy-to-perform test that does not require complex or sophisticated equipment or infrastructure. However, the application of this technique in the detection of Leishmania DNA has not been comprehensively analyzed to date (analytical validation). Our objective was to evaluate the sensitivity and analytical specificity (anticipated reportable range [ARR], the limit of detection [LoD], and accuracy) of LAMP targeting the 18S rRNA gene in the diagnosis of six New World Leishmania species...
March 12, 2018: American Journal of Tropical Medicine and Hygiene
Maria Cryskely Agra Batinga, Julia Teresa Ribeiro de Lima, Fabio Gregori, Jaqueline Assumpção Diniz, Kerstin Muner, Trícia M F S Oliveira, Helena Lage Ferreira, Rodrigo Martins Soares, Lara Borges Keid
Canine brucellosis is caused by Brucella canis, a gram negative and facultative intracellular bacterium that is commonly associated with reproductive failures in dogs. The accurate diagnosis of the infection relies on the use of serological tests associated with blood culturing to guarantee sensitivity. The polymerase chain reaction (PCR) can replace the culturing procedure for the direct diagnosis of the infection because of its speed, high specificity and sensitivity values; however, it depends on some laboratory infrastructure to be conducted...
March 7, 2018: Molecular and Cellular Probes
Mazen Alssahen, Osama Sammra, Jörn-Peter Wickhorst, Abdulwahed Ahmed Hassan, Christoph Lämmler, Mirja Raunio Saarnisto, Ellen Prenger-Berninghoff, Markus Timke, Andrè Becker, Amir Abdulmawjood
In the present study 12 Arcanobacterium phocae strains isolated from fur animals in Finland, including foxes, minks and Finnraccoons, could successfully be identified phenotypically, by matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS) and genotypically by sequencing 16S rDNA and phocaelysin (PHL) encoding gene phl. The PHL of all 12 A. phocae strains in the present study and reference strains A. phocae DSM 10002T and A. phocae DSM 10003 displayed, as typical members of the cholesterol dependent cytolysin-group of toxins, the variant undecapeptide sequence EATGLAWDPWW which appeared to be most closely related to arcanolysin of Arcanobacterium haemolyticum and pyolysin of Trueperella pyogenes...
March 2018: Veterinary Microbiology
Waqas Ali, Mudasser Habib, Rai Shafqat Ali Khan, Muhammad Ashir Zia, Muhammad Farooq, Sanaullah Sajid, Muhammad Salah Ud Din Shah
This study reports the molecular characterization of foot-and-mouth disease virus (FMDV) in the provinces of Punjab and Sindh, Pakistan during 2014-17. FMDV genome was detected in 42 and 41 out of 46 samples (epithelial tissue and saliva) by reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and reverse transcriptase polymerase chain reaction (RT-PCR), respectively. Sequences of the complete VP1 coding region of the samples (n = 33) was achieved showing that 10, 4 and 19 samples belonged to serotype O, A and Asia1 respectively...
March 7, 2018: Archives of Virology
Matthias Karrasch, Sven Eisenach, Ulrich Vogel, Jan Zinke, Otto W Witte, Albrecht Günther, Bernd Romeike, Jürgen Rödel
There is a need for easy-to-use molecular assays for diagnosis of invasive meningococcal disease. Here, we report the rapid identification of Neisseria meningitidis in a cerebrospinal fluid sample from a patient with purulent meningitis using a commercially available loop-mediated isothermal amplification assay, resulting in a prompt de-escalation of the initial empiric antibiotic therapy.
March 7, 2018: Acta Microbiologica et Immunologica Hungarica
Lisa Becherer, Mohammed Bakheit, Sieghard Frischmann, Silvina Stinco, Nadine Borst, Roland Zengerle, Felix von Stetten
A variety of real-time detection techniques for LAMP based on the change in fluorescence intensity during DNA amplification enable simultaneous detection of multiple targets. However these techniques depend on fluorogenic probes containing target-specific sequences. That complicates the adaption to different targets leading to time-consuming assay optimization. Here, we present the first universal real-time detection technique for multiplex LAMP. The novel approach allows simple assay design and is easy to implement for various targets...
March 6, 2018: Analytical Chemistry
S Zheng, X Wu, J Shi, Z Peng, M Gao, C Xin, Y Liu, S Wang, S Xu, H Han, J Yu, W Sun, X Cong, J Li, J Wang
In this study, a rapid and specific assay for the detection of porcine circovirus type 3 (PCV3) was established using loop-mediated isothermal amplification (LAMP). Four primers were specifically designed to amplify PCV3. The LAMP assay was effectively optimized to amplify PCV3 by water bath at 60°C for 60 min. The detection limit was approximately 1 × 101 copy in this LAMP assay. Compared to porcine circovirus type 2 (PCV2), both gE and gD genes of pseudorabies virus (PRV) and porcine parvovirus (PPV), the LAMP assay showed a high specific detection of PCV3...
March 4, 2018: Transboundary and Emerging Diseases
Junguk Ko, Jae-Chern Yoo
The design and fabrication of temperature measurement systems that facilitate successful realization of DNA amplification using a lab-on-a-disc (LOD) device are a highly challenging task. The major challenge lies in the fact that such a system must be directly attached to a heating chamber in a way that enables the accurate measurement of temperature of the chamber while allowing the LOD to rotate. This paper presents a temperature control system for implementing isothermal amplification of DNA samples using an LOD device...
March 5, 2018: Applied Biochemistry and Biotechnology
Tyler D R Vance, Laurie A Graham, Peter L Davies
Out of the dozen different ice-binding protein (IBP) structures known, the DUF3494 domain is the most widespread, having been passed many times between prokaryotic and eukaryotic microorganisms by horizontal gene transfer. This ~25-kDa β-solenoid domain with an adjacent parallel α-helix is most commonly associated with an N-terminal secretory signal peptide. However, examples of the DUF3494 domain preceded by tandem Bacterial Immunoglobulin-like (BIg) domains are sometimes found, though uncharacterized. Here we present one such protein (SfIBP_1) from the Antarctic bacterium Shewanella frigidimarina...
March 2, 2018: FEBS Journal
Laura E Lamb, Sarah N Bartolone, Maya O Tree, Michael J Conway, Julien Rossignol, Christopher P Smith, Michael B Chancellor
Infection with Zika virus (ZIKV) is of growing concern since infection is associated with the development of congenital neurological disease. Quantitative reverse transcription PCR (qRT-PCR) has been the standard for ZIKV detection; however, Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) may allow for faster and cheaper testing. Studies have suggested that ZIKV detection in urine is more sensitive and has a longer window of detection compared to serum and saliva. The objective of this study was to develop a urine diagnostic test that could be completed in under 30 minutes...
February 28, 2018: Scientific Reports
Reona Takabatake, Yukari Kagiya, Yasutaka Minegishi, Sabina Yeasmin, Satoshi Futo, Akio Noguchi, Kazunari Kondo, Junichi Mano, Kazumi Kitta
We developed new loop-mediated isothermal amplification (LAMP)-based detection methods for the screening of genetically modified (GM) maize and soybean events. The LAMP methods developed targeted seven sequences: cauliflower mosaic virus 35S promoter; 5-enolpyruvylshikimate-3-phosphate synthase gene from Agrobacterium tumefaciens strain CP4 (cp4epsps); phosphinothricin acetyltransferase (pat) gene; mannose-6-phosphate isomerase gene; Pisum sativum ribulose 1, 5-bisphosphate carboxylase terminator; a common sequence between Cry1Ab and Cry1Ac genes; and a GA21 construct-specific sequence...
June 30, 2018: Food Chemistry
Emmanuelle Varlet-Marie, Yvon Sterkers, Marina Perrotte, Patrick Bastien
Toxoplasmosis is generally a benign infection caused by the protozoan parasite Toxoplasma gondii but can have severe consequences in fetuses of mothers infected during pregnancy (congenital toxoplasmosis) and immunocompromised individuals. PCR-based diagnostic tests have become crucial for its diagnosis. However, this molecular diagnosis essentially relies upon laboratory-developed methods and suffers from a lack of standardization, leading to great variation in methods and performance among laboratories. With the need for accreditation of clinical microbiological laboratories, the use of commercial PCR kits has become an attractive alternative; but thorough evaluation of newly commercialized kits by proficient groups is necessary before any recommendation can be made to parasitology laboratories by health authorities or learned societies...
February 22, 2018: International Journal for Parasitology
HyeSoon Song, YouChan Bae, SeokChan Park, HyukMan Kwon, HeeSoo Lee, SeongJoon Joh
Loop-mediated isothermal amplification (LAMP) methods to detect chicken infectious anemia virus (CIAV), reticuloendotheliosis virus (REV), and Marek's disease virus (MDV), and a reverse transcription (RT)-LAMP assay to detect infectious bursal disease virus (IBDV), were developed. The CIAV-LAMP, REV-LAMP, MDV-LAMP, and IBDV-RT-LAMP methods were performed using four sets of six primers targeting the VP1 gene of CIAV, the gp90 gene of REV, the Meq gene of MDV, and the VP2 gene of IBDV. The results (a change in color) were observed visually...
February 21, 2018: Journal of Virological Methods
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