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Molecular test

Yurika Fujita, Hiroshi Honda, Masayuki Yamane, Takeshi Morita, Tomonari Matsuda, Osamu Morita
Genotoxicity evaluation has been widely used to estimate the carcinogenicity of test substances during safety evaluation. However, the latest strategies using genotoxicity tests give more weight to sensitivity; therefore, their accuracy has been very low. For precise carcinogenicity evaluation, we attempted to establish an integrated testing strategy for the tailor-made carcinogenicity evaluation of test materials, considering the relationships among genotoxicity test results (Ames, in vitro mammalian genotoxicity and in vivo micronucleus), carcinogenicity test results and chemical properties (molecular weight, logKow and 179 organic functional groups)...
December 14, 2018: Mutagenesis
Anne-Sophie Voisin, Dietmar Kültz, Frédéric Silvestre
Early-life represents a critically sensitive window to endocrine disrupting chemicals, potentially leading to long-term repercussions on the phenotype later in life. The mechanisms underlying this phenomenon, referred to as the Developmental Origins of Health and Disease (DOHaD), are still poorly understood. To gain molecular understanding of these effects, we exposed mangrove rivulus (Kryptolebias marmoratus) for 28 days post hatching (dph) to 4 and 120 ng/L 17-α-ethinylestradiol, a model xenoestrogen...
December 11, 2018: Journal of Proteomics
Jason C Chang, Lei Zhang, Alexander E Drilon, Ping Chi, Rita Alaggio, Laetitia Borsu, Ryma Benayed, William D Travis, Marc Ladanyi, Cristina R Antonescu
BACKGROUND: Half of inflammatory myofibroblastic tumors (IMTs) regardless of anatomic location harbor ALK gene rearrangements and overexpress ALK protein. The wide application of next generation sequencing (NGS) and the clinical benefit to tyrosine kinase inhibitors have opened new opportunities for investigation of ALK-negative IMT. DESIGN: In this study we investigate a series of pediatric and adult thoracic IMT for abnormalities in a wide spectrum of actionable kinases, by applying a variety of molecular and NGS techniques, including FISH, targeted RNA sequencing and NanoString...
December 11, 2018: Journal of Thoracic Oncology
Han Shi, Simin Liu, Junqi Chen, Xuan Li, Qin Ma, Bin Yu
The identification of drug-target interactions has great significance for pharmaceutical scientific research. Since traditional experimental methods identifying drug-target interactions is costly and time-consuming, the use of machine learning methods to predict potential drug-target interactions has attracted widespread attention. This paper presents a novel drug-target interactions prediction method called LRF-DTIs. Firstly, the pseudo-position specific scoring matrix (PsePSSM) and FP2 molecular fingerprinting were used to extract the features of drug-target...
December 11, 2018: Genomics
Amaiur Esnaola, Aitor Arrizabalaga-Escudero, Jorge González-Esteban, Arturo Elosegi, Joxerra Aihartza
Molecular techniques allow non-invasive dietary studies from faeces, providing an invaluable tool to unveil ecological requirements of endangered or elusive species. They contribute to progress on important issues such as genomics, population genetics, dietary studies or reproductive analyses, essential knowledge for conservation biology. Nevertheless, these techniques require general methods to be tailored to the specific research objectives, as well as to substrate- and species-specific constraints. In this pilot study we test a range of available primers to optimise diet analysis from metabarcoding of faeces of a generalist aquatic insectivore, the endangered Pyrenean desman (Galemys pyrenaicus, É...
2018: PloS One
M R Nagaraja, Satya Prakash Gubbala, C R Wilma Delphine Silvia, Ramars Amanchy
We aimed to survey the monogenic causes of disorders of sex development (DSD) and thereby its prevalence in India. This study revealed mutations resulting in androgen insensitivity syndrome, 5α-reductase type 2 deficiency, and gonadal dysgenesis were commonly reported. Intriguingly, AR deficits were the most prevalent (32 mutations) and of 11/26 missense mutations were in exons 4-8 (encoding ligand binding domain). The unique features of SRD5A2 defects were p.R246Q (most prevalent) and p.G196S could be mutational hotspots, dual gene defects (p...
December 14, 2018: Systems Biology in Reproductive Medicine
Hao Wang, Weitao Yang
Accurate force fields are crucial for molecular dynamics investigation of complex biological systems. Building accurate protein force fields from quantum mechanical (QM) calculations is challenging due to the complexity of proteins and high computational costs of QM methods. In order to overcome these two difficulties, here we developed the residue-based systematic molecular fragmentation method to partition general proteins into only twenty types of amino acid dipeptides and one type of peptide bond at Level 1...
December 14, 2018: Journal of Chemical Theory and Computation
Monika Janeczko
Candidiasis is the most common opportunistic yeast infection, with Candida albicans as a paramount causative species. (1,3)- β -D-glucan is one of the three main targets of clinically available antifungal agents used to treat Candida infections. It is one of the most abundant fungal cell wall components. Echinocandins represent the newest class of antifungals affecting cell wall biosynthesis through non-competitive inhibition of (1,3)- β -D-glucan synthase. Therefore, treatment with echinocandins causes defects in fungal cell integrity...
2018: Polish Journal of Microbiology
Maryam Labibzadeh, Gholam Abbas Kaydani, Mohammad Savari, Alireza Ekrami
Enterococcus faecalis and Enterococcus faecium are among the main agents associated with nosocomial infections with high mortality in immunocompromised patients. Antibiotic resistance, especially against gentamicin and vancomycin among Enterococci , is a risk factor that could increase the morbidity and mortality rate. 179 Enterococci isolates from burn patients were included in this study. Antibiotic susceptibility testing was done using the disk diffusion test and minimum inhibitory concentration (MIC) was evaluated by agar microdilution...
2018: Polish Journal of Microbiology
Savas Aslan, Mustafa Altindis, Recep Kara, Tayfur Demiray, Mehmet Koroglu
<i>Background:</i> Screening of transmission routes and routine control of the food for foodborne-pathogens are vital in terms of public health. In this study, we aimed to investigate and evaluate the presence of E. coli O157:H7 strains and toxins in the cattle meat samples collected from different markets and butchers. <i>Methods:</i> We collected 116 raw minced cattle beef samples from the supermarkets and the butcher stores. We used bacterial culture-based conventional isolation methods as recommended by the CDC and FDA determination of STEC in the minced cattle beef samples...
October 31, 2018: Clinical Laboratory
Leonie Glinski, Dushyant Shetty, Stephen Iles, Benjamin Diggins, James Garvican
No standardised, comprehensive approach to Rapid On-Site Evaluation (ROSE) of cytology samples currently exists. Recent meta-analysis indicates variation in the effectiveness of ROSE [1], however, reviews commonly omit the details of how ROSE is conducted. This review demonstrates the clinical effectiveness of Single Slide Assessment (SSA) for ROSE of cytology samples, providing a highly effective, standardised methodology, maximising cell yield and the diagnostic potential of samples obtained via Endobronchial or Endoscopic ultrasound (EBUS/EUS)...
December 14, 2018: Cytopathology: Official Journal of the British Society for Clinical Cytology
Robert A Weiss, Jan Bernardy
OBJECTIVES: While controlled thermal changes in subcutaneous tissue have been used to trigger apoptosis of fat cells and have been proven clinically efficacious, another mechanism of electromagnetic stress suggests that fat apoptosis could be achieved by a non-thermal manner as well. This animal model study investigates the use of a non-invasive high-intensity magnetic field device to induce apoptosis in fat cells. METHODS: Yorkshire pigs (N = 2) received one treatment (30 minutes) in the abdominal area using a High-Intensity Focused Electromagnetic (HIFEM) device...
December 14, 2018: Lasers in Surgery and Medicine
Sarah M Neuner, Shengyuan Ding, Catherine C Kaczorowski
Identifying genetic factors that modify an individual's susceptibility to cognitive decline in aging is critical to understanding biological processes involved and mitigating risk associated with a number of age-related disorders. Recently, heterochromatin protein 1 binding protein 3 (Hp1bp3) was identified as a mediator of cognitive aging. Here, we provide a mechanistic explanation for these findings and show that targeted knockdown of Hp1bp3 in the hippocampus by 50%-75% is sufficient to induce cognitive deficits and transcriptional changes reminiscent of those observed in aging and Alzheimer's disease brains...
December 13, 2018: Aging Cell
Adam C Seegmiller, Eric D Hsi, Fiona E Craig
Flow cytometry (FC) has a well-established role in the diagnostic evaluation of mature B-cell neoplasms. Effective assessment for lineage associated antigens, aberrant antigen expression, and immunoglobulin light chain restriction requires a well-designed, optimized, and controlled FC assay. However, it is important for hematopathologists to know when flow cytometry has a more limited role, and other modalities, such as immunohistochemistry, cytogenetic and molecular testing, are more important. This review will discuss the features of an optimal FC assay for the evaluation of mature B-cell neoplasms, and the current role of FC in the diagnosis and sub-classification, prognostic assessment, identification of therapeutic targets, and assessment for disease response to therapy...
December 13, 2018: Cytometry. Part B, Clinical Cytometry
Norbert Reich, Yuedong Wang
We investigate the effectiveness of an active learning curriculum designed for an upper division Biochemistry series at a large, public research university. The goal was to determine how effective this format was when compared to a parallel conventional course, and to see if the active learning series can be run with limited resources (one instructor, one teaching assistant). The study involved 160 students in the first quarter and 92 students in the second quarter. The active learning curriculum consists of learning goals for each chapter, online quizzes, in-class questions targeting the problematic areas, small group (3-4 students) discussions during class in which students presented their assumptions and arguments in support of their responses to online and in-class questions, and two-stage exams involving the ability to "re-answer" as a group following a discussion)...
December 13, 2018: Biochemistry and Molecular Biology Education
Wan Qiu Xia, Hui Cai Zhang, Geng Nan Wang, Jing Liu, Jian Ping Wang
The residues of phenothiazines and benzodiazepines in foods of animal origin are dangerous to consumers. For inspection of their abuses, this study for the first time reported on the use of a chemiluminescence array sensor for the simultaneous determination of four phenothiazines and five benzodiazepines in pig urine. Two molecularly imprinted polymers were coated in different wells of a conventional 96-well microtiter plate as the recognition reagents. After sample loading, the absorbed analytes were initiated directly by using an imidazole enhanced bis(2,4,6-trichlorophenyl)oxalate-hydrogen peroxide system to emit light...
December 12, 2018: Luminescence: the Journal of Biological and Chemical Luminescence
Constantin Hays, Thibault Delerue, Dominique Lamarque, Christophe Burucoa, Ghislaine Collobert, Annick Billöet, Nicolas Kalach, Josette Raymond
BACKGROUND: Adapted treatments for Helicobacter pylori infection, guided by determining antimicrobial resistance, are associated with high eradication rates. We evaluated the performance of the Amplidiag® H. pylori + ClariR PCR assay (Amplidiag® ) for detecting H. pylori and its clarithromycin resistance from gastric biopsies taken during endoscopy in comparison to culture and our "in-house" PCR. MATERIALS AND METHODS: A total of 127 gastric biopsies were analyzed (98 adults; 29 children)...
December 12, 2018: Helicobacter
Alexander Gheldof, Sara Seneca, Katrien Stouffs, Willy Lissens, Anna Jansen, Hilde Laeremans, Patrick Verloo, An-Sofie Schoonjans, Marije Meuwissen, Diana Barca, Geert Martens, Linda De Meirleir
BACKGROUND: The diagnostic workup in patients with a clinical suspicion of lysosomal storage diseases (LSD) is often difficult due to the variability in the clinical phenotype. The gold standard for diagnosis of LSDs consists of enzymatic testing. However, due to the sequential nature of this methodology and inconsistent genotype-phenotype correlations of certain LSDs, finding a diagnosis can be challenging. METHOD: We developed and clinically implemented a gene panel covering 50 genes known to cause LSDs when mutated...
December 11, 2018: Molecular Genetics & Genomic Medicine
Yaser Mansoori, Zahra Zendehbad, Alireza Askari, Amin Kouhpayeh, Javad Tavakkoly-Bazzaz, Ziba Nariman-Saleh-Fam, Milad Bastami, Zahra Saadatian, Behnam Mansoori, Amin Yousefvand, Hosein Mansoori, Abdolreza Daraei
Recently, it has been revealed that estrogen-related reproductive factors are linked with some early gene expression lesions associated with malignancy in clinically healthy breasts. Accordingly, the aim of the current study was to evaluate the association of expression levels of estrogen-related long noncoding RNAs (lncRNAs) upstream Eleanor (u-Eleanor) and HOX antisense intergenic RNA (HOTAIR) with the different patterns of reproductive factors in breast tissue of healthy women. The subjects of this study were 98 cancer-free women who had undergone cosmetic mammoplasty...
December 11, 2018: Journal of Cellular Biochemistry
Shangjun Chen, Yuhong Chen, Yadong Gao, Yi Zuo, Xiaowei Zhou
BACKGROUND: Stroke is a leading cause of long-term disability and further one of the main causes of motor impairment. The current study aimed to investigate whether miR-124 polymorphism (rs531564) influences the motor function of patients after stroke. METHODS: In total, 56 patients with stroke-induced motor dysfunction were enrolled. Box and block test (BBT) and Fugl-Meyer assessment (FMA) were performed to evaluate the motor functions in all participants. Computation analysis, luciferase activity, PCR assays, and Western blot analysis were performed to reveal the molecular mechanism underlying the effect of miR-124 polymorphism on motor functions...
December 11, 2018: Journal of Cellular Biochemistry
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