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Genetic testing

Zoran Marinović, Jelena Lujić, Eszter Kása, Zsolt Csenki, Béla Urbányi, Ákos Horváth
Current trends in science and biotechnology lead to creation of thousands of new lines in model organisms thereby leading to the necessity for new methods for safe storage of genetic resources beyond the common practices of keeping breeding colonies. The main purpose of this study was to adapt the needle immersed vitrification (NIV) procedure to cryopreserve whole zebrafish testes. Cryopreservation of early-stage germ cells by whole testes NIV offers possibilities for the storage of zebrafish genetic resources, especially since after transplantation they can mature into both male and female gametes...
March 4, 2018: Journal of Visualized Experiments: JoVE
Vid Leko, Smitha Sripathy, Robin L Adrianse, Taylor Loe, Angela Park, Uyen Lao, Eric J Foss, Marisa S Bartolomei, Antonio Bedalov
Forward genetic screens using reporter genes inserted into the heterochromatin have been extensively used to investigate mechanisms of epigenetic control in model organisms. Technologies including short hairpin RNAs (shRNAs) and clustered regularly interspaced short palindromic repeats (CRISPR) have enabled such screens in diploid mammalian cells. Here we describe a large-scale shRNA screen for regulators of X-chromosome inactivation (XCI), using a murine cell line with firefly luciferase and hygromycin resistance genes knocked in at the C-terminus of the methyl CpG binding protein 2 (MeCP2) gene on the inactive X-chromosome (Xi)...
March 2, 2018: Journal of Visualized Experiments: JoVE
Alhassane Diallo, Heike Jacobi, Arron Cook, Robyn Labrum, Alexandra Durr, Alexis Brice, Perrine Charles, Cecilia Marelli, Caterina Mariotti, Lorenzo Nanetti, Marta Panzeri, Maria Rakowicz, Anna Sobanska, Anna Sulek, Tanja Schmitz-Hübsch, Ludger Schöls, Holger Hengel, Bela Melegh, Alessandro Filla, Antonella Antenora, Jon Infante, José Berciano, Bart P van de Warrenburg, Dagmar Timmann, Sylvia Boesch, Massimo Pandolfo, Jörg B Schulz, Peter Bauer, Paola Giunti, Jun-Suk Kang, Thomas Klockgether, Sophie Tezenas du Montcel
BACKGROUND: Spinocerebellar ataxias are dominantly inherited progressive ataxia disorders that can lead to premature death. We aimed to study the overall survival of patients with the most common spinocerebellar ataxias (SCA1, SCA2, SCA3, and SCA6) and to identify the strongest contributing predictors that affect survival. METHODS: In this longitudinal cohort study (EUROSCA), we enrolled men and women, aged 18 years or older, from 17 ataxia referral centres in ten European countries; participants had positive genetic test results for SCA1, SCA2, SCA3, or SCA6 and progressive, otherwise unexplained, ataxias...
April 2018: Lancet Neurology
Akiko Yamazaki, Mioko Honda, Naoki Kobayashi, Naoto Ishizaki, Hiroshi Asakura, Yoshiko Sugita-Konishi
The expansion of the wild deer population is a major problem for the Japanese farm and forestry industries because their damage to farm products and vegetation results in huge economic loss. To promote game meat consumption, hygiene inspections should be performed to detect main bacterial pathogens before products are shipped. In this study, we aimed to evaluate the ability of commercial test kits to genetically detect EHEC, Salmonella and Listeria monocytogenes in venison. Our results demonstrated that the kits for three pathogens could be useful for venison as well as other domestic meat products...
March 19, 2018: Journal of Veterinary Medical Science
Xiao Yi
Biological functions - studied by molecular, systems and behavioral biology - are referred to as proximate mechanisms. Why and how they have emerged from the course of evolution are referred to as ultimate mechanisms. Despite the conceptual and technical schism between the disciplines that focus on each, studies from one side can benefit the other. Experimental evolution is an emerging field at the crossroads of functional and evolutionary biology. Herein microorganisms and mammalian cell lines evolve in well-controlled laboratory environments over multiple generations...
December 2017: Synthetic and Systems Biotechnology
John A Calarco, Adam D Norris
Genetic interaction screens are a powerful methodology to establish novel roles for genes and elucidate functional connections between genes. Such studies have been performed to great effect in single-cell organisms such as yeast and E. coli (Schuldiner et al ., 2005; Butland et al ., 2008; Costanzo et al ., 2010), but similar large-scale interaction studies using targeted reverse-genetic deletions in multi-cellular organisms have not been feasible. We developed a CRISPR/Cas9-based method for deleting genes in C...
March 5, 2018: Bio-protocol
Rose Mary Xavier, Jennifer R Dungan, Richard S E Keefe, Allison Vorderstrasse
Genetic etiology of psychopathology symptoms and cognitive performance in schizophrenia is supported by candidate gene and polygenic risk score (PRS) association studies. Such associations are reported to be dependent on several factors - sample characteristics, illness phase, illness severity etc. We aimed to examine if schizophrenia PRS predicted psychopathology symptoms and cognitive performance in patients with chronic schizophrenia. We also examined if schizophrenia associated autosomal loci were associated with specific symptoms or cognitive domains...
June 2018: Schizophrenia Research. Cognition
Camila S Souza, Guilherme J Costa-Silva, Fábio F Roxo, Fausto Foresti, Claudio Oliveira
Schizolecis is a monotypic genus of Siluriformes widely distributed throughout isolated coastal drainages of southeastern Brazil. Previous studies have shown that fish groups found in isolated river basins tend to differentiate over time in the absence of gene flow, resulting in allopatric speciation. In this study, we used partial sequences of the mitochondrial gene COI with the analysis of the General Mixed Yule Coalescent model (GMYC) and the Automatic Barcode Gap Discovery (ABGD) for single locus species delimitation, and a Principal Component Analysis (PCA) of external morphology to test the hypothesis that Schizolecis guntheri is a complex of species...
2018: Frontiers in Genetics
Andrew S Fister, Lena Landherr, Siela N Maximova, Mark J Guiltinan
Theobroma cacao , the source of cocoa, suffers significant losses to a variety of pathogens resulting in reduced incomes for millions of farmers in developing countries. Development of disease resistant cacao varieties is an essential strategy to combat this threat, but is limited by sources of genetic resistance and the slow generation time of this tropical tree crop. In this study, we present the first application of genome editing technology in cacao, using Agrobacterium-mediated transient transformation to introduce CRISPR/Cas9 components into cacao leaves and cotyledon cells...
2018: Frontiers in Plant Science
Rafał Muda, Mariusz Kicia, Małgorzata Michalak-Wojnowska, Michał Ginszt, Agata Filip, Piotr Gawda, Piotr Majcher
The Dopamine receptor D4 gene (DRD4) has been previously linked to financial risk-taking propensity. Past works demonstrated that individuals with a specific variant of the DRD4 gene (7R+) are more risk-seeking than people without it (7R-). The most prominent explanation for this effect is the fact that 7R+ individuals are less sensitive to dopamine and thus seek more stimulation to generate "normal" dopaminergic activity and feel pleasure. However, results about this relationship have not been conclusive, and some revealed a lack of the relationship...
2018: Frontiers in Behavioral Neuroscience
Qiang Zuo, Jing Liu, Liping Huang, Yifei Qin, Teresa Hawley, Claire Seo, Glenn Merlino, Yanlin Yu
Multiple genetic mutations within melanoma not only cause lesion-specific responses to targeted therapy but also alter the molecular route of resistance to that therapy. Inactivation of PTEN occurs in up to 30% of melanomas, frequently with a concurrent activating BRAF mutation. PTEN loss regulates both acquired and intrinsic drug resistance. Here we show that AXL/AKT axis mediated-resistance to BRAF inhibitor (BRAFi) depends upon PTEN status in melanoma. Hyperactivation of both ERK and AKT pathways was associated with BRAFi resistance in melanoma with wildtype PTEN...
March 19, 2018: Oncogene
Jing Dong, David M Levine, Matthew F Buas, Rui Zhang, Lynn Onstad, Rebecca C Fitzgerald, Douglas A Corley, Nicholas J Shaheen, Jesper Lagergren, Laura J Hardie, Brian J Reid, Prasad G Iyer, Harvey A Risch, Carlos Caldas, Isabel Caldas, Paul D Pharoah, Geoffrey Liu, Marilie D Gammon, Wong-Ho Chow, Leslie Bernstein, Nigel C Bird, Weimin Ye, Anna H Wu, Lesley A Anderson, Stuart MacGregor, David C Whiteman, Thomas L Vaughan, Aaron P Thrift
BACKGROUND & AIMS: Genome-wide association studies (GWAS) have identified more than 20 susceptibility loci for esophageal adenocarcinoma (EA) and Barrett's esophagus (BE). However, variants in these loci account for a small fraction of cases of EA and BE. Genetic factors might interact with environmental factors to affect risk of EA and BE. We aimed to identify single nucleotide polymorphisms (SNPs) that may modify the associations of body mass index (BMI), smoking, and gastroesophageal reflux disease (GERD), with risks of EA and BE...
March 15, 2018: Clinical Gastroenterology and Hepatology
Daniel B Hawcutt, Ben Francis, Daniel F Carr, Andrea L Jorgensen, Peng Yin, Naomi Wallin, Natalie O'Hara, Eunice J Zhang, Katarzyna M Bloch, Amitava Ganguli, Ben Thompson, Laurence McEvoy, Matthew Peak, Andrew A Crawford, Brian R Walker, Joanne C Blair, Jonathan Couriel, Rosalind L Smyth, Munir Pirmohamed
BACKGROUND: A serious adverse effect of corticosteroid therapy is adrenal suppression. Our aim was to identify genetic variants affecting susceptibility to corticosteroid-induced adrenal suppression. METHODS: We enrolled children with asthma who used inhaled corticosteroids as part of their treatment from 25 sites across the UK (discovery cohort), as part of the Pharmacogenetics of Adrenal Suppression with Inhaled Steroids (PASS) study. We included two validation cohorts, one comprising children with asthma (PASS study) and the other consisting of adults with chronic obstructive pulmonary disorder (COPD) who were recruited from two UK centres for the Pharmacogenomics of Adrenal Suppression in COPD (PASIC) study...
March 15, 2018: Lancet Respiratory Medicine
Alexandra Shadrina, Yakov Tsepilov, Ekaterina Sokolova, Mariya Smetanina, Elena Voronina, Eugene Pakhomov, Kseniya Sevost'ianova, Andrey Shevela, Evgeny Ilyukhin, Evgeny Seliverstov, Igor Zolotukhin, Maxim Filipenko
Heredity is a well-known risk factor for varicose veins, but genetic basis of this condition remains poorly studied. Our aim was to conduct a large-scale genetic association study for primary varicose veins (PVVs) in the population of ethnic Russians. An initial scan using Illumina HumanExome-12 v1.0 BeadChip was performed for 273 patients with PVVs and 250 controls without a history of chronic venous disease and other venous disorders. After quality control and removal of monomorphic markers, 25,424 common and 48,232 rare variants were included in the analysis...
March 15, 2018: Gene
Hanting Liu, Haixia Zhu, Yadi Lin, Gaoxiang Ma, Guoquan Tao, Weida Gong, Qinghong Zhao, Mulong Du, Meilin Wang, Haiyan Chu, Zhengdong Zhang
OBJECTIVE: We explored the association between single nucleotide polymorphisms (SNPs) rs207454 and rs494852 located in xanthine dehydrogenase (XDH) and gastric cancer (GC) survival. METHODS: A total of 940 patients with gastric cancer were enrolled and genotyped using TaqMan allelic discrimination method. The Kaplan-Meier test and log-rank examine were used to assess the effect of genetic variation. RESULTS: Patients carrying rs207454 CC genotype had a longer survival time than those with the AA genotype (P = 0...
March 15, 2018: Gene
Lilian O Guimarães, Francisco Fernandes, Eliana F Monteiro, Izilda Curado, Marcia M Holcman, Gerhard Wunderlich, Sidney E Santos, Júlia M Soler, Karin Kirchgatter
In low-endemic areas for malaria transmission, asymptomatic individuals play an important role as reservoirs for malarial infection. Understanding the dynamics of asymptomatic malaria is crucial for its efficient control in these regions. Genetic host factors such as Toll-like receptor (TLR) polymorphisms may play a role in the maintenance or elimination of infection. In this study, the effect of TLR polymorphisms on the susceptibility to malaria was investigated among individuals living in the Atlantic Forest of São Paulo, Southern Brazil...
March 15, 2018: Acta Tropica
Hiroyuki Awano, Chieko Itoh, Yasuhiro Takeshima, Tomoko Lee, Masaaki Matsumoto, Akihiro Kida, Toshihiko Kaise, Takeo Suzuki, Masafumi Matsuo
INTRODUCTION: Few long-term cohort studies have addressed changes in the ambulatory capacity of patients with Duchenne muscular dystrophy (DMD), and no reports have evaluated the factors associated with ambulatory capacity in Japanese. METHODS: The longitudinal changes in 10-meter run/walk ability and associated factors were retrospectively investigated using general practice data. The factors associated with loss of this ability before the age of 10 years were explored by logistic regression analysis using parameters of genetic mutations, corticosteroid use, the manual muscle test (MMT), and the joint range of motion (ROM)...
March 15, 2018: Brain & Development
Alfred Mitema, Sheila Okoth, Mohamed S Rafudeen
Toxigenic Aspergillus species produce mycotoxins that are carcinogenic, hepatotoxic and teratogenic immunosuppressing agents in both human and animals. Kenya frequently experiences outbreaks of aflatoxicosis with the worst occurring in 2010, which resulted in 215 deaths. We examined the possible reasons for these frequent aflatoxicosis outbreaks in Kenya by studying Aspergillus flavus diversity, phenotypes and mycotoxin profiles across various agricultural regions. Using diagonal transect random sampling, maize kernels were collected from Makueni, Homa Bay, Nandi, and Kisumu counties...
April 2018: Fungal Biology
M McGowan, M K Holland, G Boe-Hansen
This review focuses on current understanding of prenatal, prepubertal and post-pubertal development of the male reproductive system of cattle. The critical developmental events occur during the first 3 to 4 months of gestation and the first ~6 to 9 months after birth. The Wilms Tumor-1 and SRY proteins play critical roles in early development and differentiation of the fetal testis, which in turn drives gestational development of the entire male reproductive system. The hypothalamic-pituitary-gonadal axis matures earlier in the bovine fetus than other domestic species with descent of the testes into the scrotum occurring around the 4th month of gestation...
March 19, 2018: Animal: An International Journal of Animal Bioscience
Jun-Cheng Guo, Yi-Jun Yang, Min Guo, Xiao-Dan Wang, Yang Juan, Yun-Suo Gao, Lin-Qiu Fu, Xiang-Ling Jiang, Lin-Mei Fu, Tao Huang
Objective: To investigate the correlations of four genetic single nucleotide polymorphisms (SNPs) of brain-derived neurotrophic factor (BDNF) with posttraumatic stress disorder (PTSD). Methods: A total of 300 patients with sporadic PTSD and 150 healthy subjects (the control group) were selected according to the diagnostic criteria of PTSD (DSM-IV), and the genotypes of the BDNF SNPs G-712A, C270T, rs6265, and rs7103411 were detected by polymerase chain reaction and direct DNA sequencing to determine intergroup differences in the genotypes and allele frequencies; the p values were corrected with the permutation test...
March 19, 2018: Psychiatry Investigation
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