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Molecular testing

Farajzadah Sheikh Ahmad, Mohammad Jaafar Yadyad, Hamed Goodarzi, Seyed Jalal Hashemi, Sajad Aslani, Mohammad-Ali Assarzadegan, Reza Ranjbar
BACKGROUND: Allelic variation of the virulence genes, vacA and cagA, as the most important virulence associated genes play an important role in the pathogenesis of severe gastrointestinal disease. OBJECTIVE: The aim of the present study was to identify the diversity of the virulence genes in patients with Gastric Cancer (GC), who were referred to the gastro-endoscopy unit of Imam Khomeini Hospital, Ahvaz Jundishapur University of medical science, Ahvaz, Iran. METHODS: Gastric biopsy specimens from 301 patients suspected to gastrointestinal disorders, were analyzed for H...
June 13, 2018: Microbial Pathogenesis
Selma Mahiout, Sara Giani Tagliabue, Atefeh Nasri, Iyekhoetin Matthew Omoruyi, Lars Pettersson, Laura Bonati, Raimo Pohjanvirta
The mediator of dioxin toxicity, aryl hydrocarbon receptor (AHR), has also important physiological functions. Selective AHR modulators (SAHRMs) share some effects of dioxins, except for their marked toxicity. We recently characterised toxicologically two novel SAHRMs, prodrugs IMA-08401 and IMA-07101 in rats, demonstrating that they are far less deleterious than the most toxic AHR-agonist, TCDD. Here, we analysed the in vitro toxicity and in silico AHR binding of the respective active, deacetylated metabolites, IMA-06201 (N-ethyl-N-phenyl-5-chloro-1,2-dihydro-4-hydroxy-1-methyl-2-oxo-quinoline-3-carboxamide) and IMA-06504 (N-(4-trifluoromethylphenyl)-1,2-dihydro-4-hydroxy-5-methoxy-1-methyl-2-oxo-quinoline-3-carboxamide)...
June 13, 2018: Toxicology in Vitro: An International Journal Published in Association with BIBRA
Maryam Noorbakhshnia, Arsham Rashidkaboli, Mahnaz Pakatchian, Siamak Beheshti
Methamphetamine (METH) abuse is one the most worldwide problems with wide-ranging effects on the central nervous system (CNS). Chronic METH abuse can associate with cognitive abnormalities and neurodegenerative changes in the brain. Agmatine, a cationic polyamine, has been proposed as a neuromodulator that modulates many effects of abused drugs. The aim of this study was to determine if agmatine can decrease the impairment effect of METH on memory and hippocampal CaMKII-α gene expression, a gene that plays a major role in memory...
June 13, 2018: Physiology & Behavior
Ila Mishra, Neha Agarwal, Sangeeta Rani, Vinod Kumar
Circannual rhythm regulates annual timing of reproduction in spotted munia, with sex-differences in its relationship with the external photoperiod environment. Interestingly, munia show an atypical photosensitivity and exhibit gonadal maturation when acutely exposed to an unnatural short photoperiod (e.g. 3 h light per day; i.e. a long scotoperiod). The proximate mechanisms regulating scotoperiod-induced hypothalamus-pituitary-gonadal (HPG) activation are unclear. Since thyroid hormone signalling plays a central role in photoperiodic induction, we hypothesized the involvement of similar mechanism, i...
June 16, 2018: Journal of Neuroendocrinology
Edenir Inêz Palmero, Dirce Maria Carraro, Barbara Alemar, Miguel Angelo Martins Moreira, Ândrea Ribeiro-Dos-Santos, Kiyoko Abe-Sandes, Henrique Campos Reis Galvão, Rui Manuel Reis, Cristiano de Pádua Souza, Natalia Campacci, Maria Isabel Achatz, Rafael Canfield Brianese, Maria Nirvana da Cruz Formiga, Fabiana Baroni Makdissi, Fernando Regla Vargas, Anna Cláudia Evangelista Dos Santos, Hector N Seuanez, Kelly Rose Lobo de Souza, Cristina B O Netto, Patrícia Santos-Silva, Gustavo Stumpf da Silva, Rommel M R Burbano, Sidney Santos, Paulo Pimentel Assumpção, Izabel Maria Monteiro Bernardes, Taisa Manuela Bonfim Machado-Lopes, Thais Ferreira Bomfim, Maria Betânia Pereira Toralles, Ivana Nascimento, Bernardo Garicochea, Sergio D Simon, Simone Noronha, Fernanda Teresa de Lima, Anisse Marques Chami, Camila Matzenbacher Bittar, Jose Bines, Osvaldo Artigalas, Maria Del Pilar Esteves-Diz, Tirzah Braz Petta Lajus, Ana Carolina Leite Vieira Costa Gifoni, Rodrigo S C Guindalini, Terezinha Sarquis Cintra, Ida V D Schwartz, Pricila Bernardi, Diego Miguel, Sonia Tereza Dos Santos Nogueira, Josef Herzog, Jeffrey N Weitzel, Patricia Ashton-Prolla
The detection of germline mutations in BRCA1 and BRCA2 is essential to the formulation of clinical management strategies, and in Brazil, there is limited access to these services, mainly due to the costs/availability of genetic testing. Aiming at the identification of recurrent mutations that could be included in a low-cost mutation panel, used as a first screening approach, we compiled the testing reports of 649 probands with pathogenic/likely pathogenic variants referred to 28 public and private health care centers distributed across 11 Brazilian States...
June 15, 2018: Scientific Reports
Kenji Imai, Tomomi Kotani, Hiroyuki Tsuda, Tomoko Nakano, Takafumi Ushida, Akira Iwase, Taku Nagai, Shinya Toyokuni, Akio Suzumura, Fumitaka Kikkawa
The aim of the present study was to investigate long-term outcomes of the offspring in a lipopolysaccharide (LPS)-induced maternal immune activation (MIA) model and the effect of maternal molecular hydrogen (H2 ) administration. We have previously demonstrated in the MIA mouse model that maternal administration of H2 attenuates oxidative damage and neuroinflammation, including induced pro-inflammatory cytokines and microglial activation, in the fetal brain. Short-term memory, sociability and social novelty, and sensorimotor gating were evaluated using the Y-maze, three-chamber, and prepulse inhibition (PPI) tests, respectively, at postnatal 3 or 4 weeks...
June 15, 2018: Scientific Reports
Sarah Sheppard, Sawona Biswas, Mindy H Li, Vijayakumar Jayaraman, Ian Slack, Edward J Romasko, Ariella Sasson, Joshua Brunton, Ramakrishnan Rajagopalan, Mahdi Sarmady, Jenica L Abrudan, Sowmya Jairam, Elizabeth T DeChene, Xiahoan Ying, Jiwon Choi, Alisha Wilkens, Sarah E Raible, Maria I Scarano, Avni Santani, Jeffrey W Pennington, Minjie Luo, Laura K Conlin, Batsal Devkota, Matthew C Dulik, Nancy B Spinner, Ian D Krantz
PURPOSE: Hearing loss (HL) is the most common sensory disorder in children. Prompt molecular diagnosis may guide screening and management, especially in syndromic cases when HL is the single presenting feature. Exome sequencing (ES) is an appealing diagnostic tool for HL as the genetic causes are highly heterogeneous. METHODS: ES was performed on a prospective cohort of 43 probands with HL. Sequence data were analyzed for primary and secondary findings. Capture and coverage analysis was performed for genes and variants associated with HL...
June 15, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Vandana Shashi, Kelly Schoch, Rebecca Spillmann, Heidi Cope, Queenie K-G Tan, Nicole Walley, Loren Pena, Allyn McConkie-Rosell, Yong-Hui Jiang, Nicholas Stong, Anna C Need, David B Goldstein
PURPOSE: Sixty to seventy-five percent of individuals with rare and undiagnosed phenotypes remain undiagnosed after exome sequencing (ES). With standard ES reanalysis resolving 10-15% of the ES negatives, further approaches are necessary to maximize diagnoses in these individuals. METHODS: In 38 ES negative patients an individualized genomic-phenotypic approach was employed utilizing (1) phenotyping; (2) reanalyses of FASTQ files, with innovative bioinformatics; (3) targeted molecular testing; (4) genome sequencing (GS); and (5) conferring of clinical diagnoses when pathognomonic clinical findings occurred...
June 15, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Shaofei Rao, Zhaoyang Zhou, Pei Miao, Guozhi Bi, Man Hu, Ying Wu, Feng Feng, Xiaojuan Zhang, Jian-Min Zhou
Pattern-recognition receptors (PRRs), which consist of receptor kinases (RKs) and receptor-like proteins (RLPs), sense microbial- and host-derived molecular patterns associated with pathogen infection to trigger immune responses in plants. Several kinases of the 46-member Arabidopsis thaliana receptor-like cytoplasmic kinase (RLCK) subfamily VII play important roles in pattern-triggered immunity, but it is unclear whether different RLCK VII members act specifically or redundantly in immune signaling. Here, we constructed nine higher order mutants of this subfamily (named rlck vii-1 to rlck vii-9) and systematically characterized their immune phenotypes...
June 15, 2018: Plant Physiology
Xiaofei Song, Christine R Beck, Renqian Du, Ian M Campbell, Zeynep Coban-Akdemir, Shen Gu, Amy M Breman, Pawel Stankiewicz, Grzegorz Ira, Chad A Shaw, James R Lupski
Alu elements, the short interspersed element numbering >1 million copies per human genome, can mediate the formation of copy number variants (CNVs) between substrate pairs. These Alu/Alu-mediated rearrangements (AAMR) can result in pathogenic variants that cause diseases. To investigate the impact of AAMR on gene variation and human health, we first characterized Alus that are involved in mediating CNVs (CNV-Alus) and observed that these Alus tend to be evolutionarily younger. We then computationally generated, with the assistance of a supercomputer, a test dataset consisting of 78 million Alu pairs and predicted ~18% of them are potentially susceptible to AAMR...
June 15, 2018: Genome Research
Ran He, Haojie Zhang, Nengxing Shen, Cheng Guo, Yongjun Ren, Yue Xie, Xiaobin Gu, Weimin Lai, Xuerong Peng, Guangyou Yang
Scabies is an allergic skin disease that affects millions of mammals worldwide, including humans. It is a neglected tropical disease that represents a significant public health threat, particularly in economically disadvantaged populations. An effective vaccine is not currently available, and the exact mode of pathogenesis remains unclear. Herein, we identified, cloned and recombinantly expressed triosephosphate isomerase from Sarcoptes scabiei (S. scabiei). Immunohistochemical analyses showed that S. scabiei triosephosphate isomerase (Ss-TIM) is localized in the legs and chewing mouthparts of mites, and in infected rabbit skin (keratinized skin and embedded mites)...
June 15, 2018: Veterinary Parasitology
Hao Liu, Xiang Guo, Jingcheng Han, Ray Luo, Hai-Feng Chen
Transcription factor cyclic Adenosine monophosphate response-element binding protein plays a critical role in the cyclic AMP response pathway via its intrinsically disordered kinase inducible transactivation domain (KID). KID is one of the most studied intrinsically disordered proteins (IDPs), although most previous studies focus on characterizing its disordered state structures. An interesting question that remains to be answered is how the order-disorder transition occurs at experimental conditions. Thanks to the newly developed IDP-specific force field ff14IDPSFF, the quality of conformer sampling for IDPs has been dramatically improved...
June 14, 2018: Journal of Chemical Physics
Timothy T Duignan, Marcel D Baer, Christopher J Mundy
The tetra-phenyl arsonium and tetra-phenyl borate (TATB) assumption is a commonly used extra-thermodynamic assumption that allows single ion free energies to be split into cationic and anionic contributions. The assumption is that the values for the TATB salt can be divided equally. This is justified by arguing that these large hydrophobic ions will cause a symmetric response in water. Experimental and classical simulation work has raised potential flaws with this assumption, indicating that hydrogen bonding with the phenyl ring may favor the solvation of the TB- anion...
June 14, 2018: Journal of Chemical Physics
Susan Swindells
People with HIV infection with latent tuberculosis (TB) infection (LTBI) are at a 10-fold greater risk of developing active disease. Interferon gamma release assays and tuberculin skin testing have approximately 65% to 70% specificity for diagnosing LTBI in HIV-infected patients. LTBI can be successfully treated with isoniazid preventive therapy and early antiretroviral therapy (ART). Rapid molecular diagnostics have approximately 88% sensitivity and 98% specificity for identifying active TB. ART should be started early in patients with TB...
June 2018: Topics in Antiviral Medicine
Cristian Román-Palacios, Jose Tavera, María Del Rosario Castañeda
Whereas most of the studies that discuss the evolutionary divergence of Anolis lizards have dated the clade's crown group in between 31-64 Ma, a single study has recovered a significantly older age for the same node (87 Ma). These differences also entail notable consequences on the preferred biogeographical hypothesis for the whole clade. Here we analyze a total of seven dating strategies by combining three calibration sources in independent BEAST runs to infer the most probable divergence timing for anole lizards (a mitochondrial rate for ND2 gene, the Anolis dominicanus fossil, and a group of fossils assigned to the Priscagamines, Iguanines, and Idontosaurus clades)...
June 12, 2018: Molecular Phylogenetics and Evolution
Yanan Sun, Eunice Wong, Shane T Ahyong, Jane E Williamson, Pat A Hutchings, Elena K Kupriyanova
Hydroides is a large and diverse group of calcareous tubeworms (Serpulidae, Annelida) recognised by a distinctive but variable two-tiered operculum. Despite considerable research using several species of Hydroides as models in ecological and biofouling studies, phylogenetic and biogeographic relationships within the genus are still poorly understood. Using combined mitochondrial (COI, cytochrome b) and nuclear (18S, 28S and ITS) gene markers for 284 individuals of 45 morphospecies of Hydroides, we investigated the global phylogenetic and biogeographic relationships within the genus...
June 12, 2018: Molecular Phylogenetics and Evolution
Kelvin Kw To, Cyril Cy Yip, Cherie Yw Lai, Carlos Kh Wong, Deborah Ty Ho, Polly Kp Pang, Anthony Ck Ng, Kit-Hang Leung, Rosana Ws Poon, Kwok-Hung Chan, Vincent Cc Cheng, Ivan Fn Hung, Kwok-Yung Yuen
OBJECTIVES: Automated point-of-care molecular assays have greatly shortened the turnaround time of respiratory virus testing. One of the major bottlenecks now lies at the step of the specimen collection especially in a busy clinical setting. Saliva is a convenient specimen type which can be provided easily from adult patients. This study assessed the diagnostic validity, specimen collection time, and cost associated with the use of saliva. METHODS: This was a prospective diagnostic validity study comparing the detection rate of respiratory viruses between saliva and nasopharyngeal aspirate (NPA) among adult hospitalized patients using Xpert® Xpress Flu/RSV...
June 12, 2018: Clinical Microbiology and Infection
Maria Antonia Mariezcurrena-Berasain, Gisela Velázquez-Garduño, Perla Mabel Marín-Mendoza, Alberto Barbabosa Pliego, Luis Fernando Vega Castillo, Benjamín Valladares Carranza, Ameer Khusro, Eziuche Amadika Ugbogu, Abdelfattah Z M Salem
The current context was investigated to evaluate the antibacterial potency of aqueous extract of coriander (Coriandrum sativum L.) leaves against bacterial pathogens isolated from the digestive system associated organs of rabbit. Another part of this study was also aimed to estimate the influence of varied doses of aqueous extract of C. sativum (AECS) leaves on in vitro gas production (GP), methane (CH4 ) production, and some other pivotal fermentation parameters from caecal samples of rabbits. The pathogenic bacteria were isolated from mouth, caecum, and anus of rabbits, and further identified through morphological, biochemical, and molecular tools...
June 12, 2018: Microbial Pathogenesis
Feridun Akkafa, İsmail Koyuncu, Ebru Temiz, Hasan Dagli, Fuat Dïlmec, Halit Akbas
Lung has critic function in gas exchange, supplying oxygen to all cells. Rapid metastasis and the high rate of mortality characterises lung cancer. There are two types of this disease, small cell and non-small cell, which differs from each other according to histopathologic features. To date, many therapeutic approaches have been developed to destroy this deadly type of cancer, which one of them is mRNA targeted therapies through miRNA. miRNAs are 19-25 base paired molecules be able to suppress and destruct mRNA and found to be involved in development and progression of lung cancer...
June 12, 2018: Biochemical and Biophysical Research Communications
Henry Reyer, Michael Oster, Elizabeth Magowan, Eduard Murani, Helga Sauerwein, Dirk Dannenberger, Björn Kuhla, Siriluck Ponsuksili, Klaus Wimmers
Feed efficiency (FE) is a measure of the rate between feed intake and body weight gain and is subject to constant progress in pigs, based on extensive performance tests and analyses of physiological parameters. However, endocrine regulatory circuits which comprise the sensation and perception of intrinsic requirements and appropriate systemic responses have not yet been fully elucidated. It is hypothesized that the gut-brain-axis, which is a network of hierarchical anterior regulatory tissues, contributes largely to variations in FE...
June 15, 2018: Physiological Genomics
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