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Novel dna extraction

Ju-Mi Hong, Sung-Suk Suh, Tai Kyoung Kim, Jung Eun Kim, Se Jong Han, Ui Joung Youn, Joung Han Yim, Il-Chan Kim
Lobaric acid and lobarstin, secondary metabolites derived from the antarctic lichen Stereocaulon alpnum , exert various biological activities, including antitumor, anti-proliferation, anti-inflammation, and antioxidant activities. However, the underlying mechanisms of these effects have not yet been elucidated in human cervix adenocarcinoma and human colon carcinoma. In the present study, we evaluated the anticancer effects of lobaric acid and lobarstin on human cervix adenocarcinoma HeLa cells and colon carcinoma HCT116 cells...
March 14, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Wei Hu, Xian Shi, Hongwen Li, Luzhu Chen, Tingmei Wang, Yingying Dong, Yanhong Zhang, Man Hu, Xiaoli Liu, Caie Zhang, Dongxian Liu, Yunhua Deng
BACKGROUND: Novel mutations in adenosine deaminase acting on RNA 1 gene (ADAR1) are responsible for dyschromatosis symmetrica hereditaria (DSH). DSH patients display a mixture of hyperpigmented and hypopigmented macules on the dorsal aspects of the extremities, and freckle-like macules on the face. AIMS: To provide new evidence for further study of the etiopathogenisis of DSH. METHODS: Genomic DNA was extracted and used as a template for the polymerase chain reaction (PCR) amplification of all 15 coding exons as well as intron-exon boundaries of ADAR1...
March 12, 2018: Indian Journal of Dermatology, Venereology and Leprology
Maurizio Giordano, Kumar Parijat Tripathi, Mario Rosario Guarracino
BACKGROUND: System toxicology aims at understanding the mechanisms used by biological systems to respond to toxicants. Such understanding can be leveraged to assess the risk of chemicals, drugs, and consumer products in living organisms. In system toxicology, machine learning techniques and methodologies are applied to develop prediction models for classification of toxicant exposure of biological systems. Gene expression data (RNA/DNA microarray) are often used to develop such prediction models...
March 8, 2018: BMC Bioinformatics
Shifu Chen, Ming Liu, Yanqing Zhou
As a major biomarker of liquid biopsy, cell-free tumor DNA (ctDNA), which can be extracted from blood, urine, or other circulating liquids, is able to provide comprehensive genetic information of tumor and better overcome the tumor heterogeneity problem comparing to tissue biopsy. Developed in recent years, next-generation sequencing (NGS) is a widely used technology for analyzing ctDNA. Although the technologies of processing ctDNA samples are mature, the task to detect low mutated allele frequency (MAF) variations from noisy sequencing data remains challenging...
2018: Methods in Molecular Biology
Atulabh Vajpeyee, Teddy Wijatmiko, Manisha Vajpeyee, Onjal Taywade
Purpose: Several blood markers have been evaluated in stroke patients, but their role remains limited in clinical practice. This study was designed to evaluate the utility of cell free DNA (cf DNA) in stroke patients undergoing therapeutic intervention in the form of mechanical thrombectomy in acute ischemic stroke patients. Materials and Methods: Twenty-six patients with ischemic stroke who were managed with interventions like intravenous thrombolysis (IVT) and mechanical thrombectomy were recruited consecutively in this study...
March 2018: Neurointervention
Elena Castellanos-Rizaldos, Dominik G Grimm, Vasisht Tadigotla, James Hurley, John Healy, Patricia L Neal, Mia Sher, Raajdeep Venkatesan, Chris Karlovich, Mitch Raponi, Anne K Krug, Mikkel Noerholm, Jihane Tannous, Bakhos A Tannous, Luis E Raez, Johan Skog
PURPOSE: About 60% of non-small cell lung cancer (NSCLC) patients develop resistance to targeted epidermal growth factor receptor (EGFR) inhibitor therapy through the EGFR T790M mutation. Patients with this mutation respond well to third generation tyrosine kinase inhibitors, but obtaining a tissue biopsy to confirm the mutation poses risks and is often not feasible. Liquid biopsies using circulating free tumor DNA (cfDNA) have emerged as a non-invasive option to detect the mutation, however sensitivity is low as many patients have too few detectable copies in circulation...
March 13, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Jingjing Zhang, Zhijun Zhang, Benshui Shu, Gaofeng Cui, Guohua Zhong
Harmine, one of the natural β-carboline alkaloids extracted from Peganum harmala L., exhibits broad spectrum but limited insecticidal ability against many pests. So there is an urgent need to synthesize novel derivatives with high efficiency. In the present study, a new synthetic compound, [1-(2-naphthyl)-3-(2-thioxo-1,3,4-oxadiazol-5-yl) β-carboline] (ZC-14), showed a strong proliferation inhibition effect against the Spodoptera frugiperda Sf9 cell line in a dose-dependent manner. Simultaneously, apoptosis induced by 7...
March 11, 2018: International Journal of Molecular Sciences
Hannah Serna, Ann Pocknell, Anthony W Sainsbury, Gabriela Peniche, Damer P Blake, Katie M Beckmann
Eimeria crecis and Eimeria nenei have been detected in association with enteric disease ('coccidiosis') in the corncrake (Crex crex: Family Rallidae, Order Gruiformes). Both parasite species are common in apparently healthy free-living corncrakes, but captive-bred juvenile birds reared for reintroduction appeared particularly susceptible to clinical coccidiosis. We investigated the occurrence and relative pathogenicity of these Eimeria species in this juvenile corncrake population and developed a diagnostic species-specific polymerase chain reaction (PCR) for their identification...
March 13, 2018: Avian Pathology: Journal of the W.V.P.A
Saud Alsahli, Muhammad Talal Alrifai, Saeed Al Tala, Fuad Al Mutairi, Majid Alfadhel
Background: Cerebellar ataxia, mental retardation, and disequilibrium syndrome (CAMRQ) is a heterogeneous group of genetic disorders that have been grouped by shared clinical features; all of these features are transmitted via an autosomal recessive mechanism. Four variants of this syndrome have been identified so far, and each one differs in terms of both clinical and genotypical features. CAMRQ4 is a rare genetic disorder characterized by mental retardation, ataxia or an inability to walk, dysarthria and, in some patients, quadrupedal gait...
2018: Journal of Central Nervous System Disease
Mehir Un Nisa Iqbal, Syed Amir Maqbool, Taseer Ahmed Khan
Objective The aim of this study was to determine whether a novel polymorphism ( Tru9I) in the low penetrance vitamin D receptor (VDR) gene is associated with risk of premenopausal breast cancer (BC). Methods This case-control study included 228 patients with BC and 503 healthy women living in Pakistan who were analyzed for the VDR Tru9I (rs757343) single nucleotide polymorphism. BC cases were histopathologically confirmed, and all healthy controls were age-matched with patients (age range, 20-45 years). DNA was extracted, and the polymerase chain reaction and restriction fragment length polymorphism assays were performed...
January 1, 2018: Journal of International Medical Research
MingXia Yu, Tao Cao, Dan Yu, Fusheng Huang
Genetic susceptibility to high mercury body burden has been suggested as an autism risk factor in children. Metallothionein III (MT3) is the brain-specific form of the metallothionein family, which plays a key role in metal metabolism. We therefore looked for genetic variations in the MT3 gene that might increase the predisposition to autism. DNA was extracted from 132 autistic children and 132 age and gender-matched unrelated controls. All the samples were analyzed for nine single nucleotide polymorphisms (SNPs) with minor allele frequency > 10% in the MT3 gene...
March 9, 2018: Neurotoxicity Research
T Guan, H J Wu, L J Zhang, D J Xu, L B Zheng, Y F Yao
Objective: To investigate the possibility of the visual system homeobox 1 (VSX1) gene as a candidate susceptibility gene for Chinese patients with sporadic keratoconus, and to identify sequence variants of the VSX1 gene in such patients. Methods: Cross-sectional study. Genomic DNA was extracted from the leukocytes in the peripheral venous blood of 50 patients with sporadic keratoconus and 50 control subjects without this ocular disorder. Five exons and the intron-exon splicing of the VSX1 gene were amplified by polymerase chain reaction (PCR)...
March 11, 2018: [Zhonghua Yan Ke za Zhi] Chinese Journal of Ophthalmology
Marianne Smedegaard Hede, Søren Fjelstrup, Felix Lötsch, Rella Manego Zoleko, Anna Klicpera, Mirjam Groger, Johannes Mischlinger, Lilian Endame, Luzia Veletzky, Ronja Neher, Anne Katrine Wrist Simonsen, Eskild Petersen, Ghyslain Mombo-Ngoma, Magnus Stougaard, Yi-Ping Ho, Rodrigo Labouriau, Michael Ramharter, Birgitta Ruth Knudsen
Malaria is among the major threats to global health with the main burden of disease being in rural areas of developing countries where accurate diagnosis based on non-invasive samples is in high demand. We here present a novel molecular assay for detection of malaria parasites based on technology that may be adapted for low-resource settings. Moreover, we demonstrate the exploitation of this assay for detection of malaria in saliva. The setup relies on pump-free microfluidics enabled extraction combined with a DNA sensor substrate that is converted to a single-stranded DNA circle specifically by topoisomerase I expressed by the malaria causing Plasmodium parasite...
March 7, 2018: Scientific Reports
Nontuthuko E Maningi, Luke T Daum, John D Rodriguez, Halima M Said, Remco P H Peters, John Osei Sekyere, Gerald W Fischer, James P Chambers, P Bernard Fourie
Modern advances in genomics provide an opportunity to re-interpret historical bacterial culture collections. In this study, genotypic antibiotic resistance profiles of Mycobacterium tuberculosis isolates from an historical 20-year-old multidrug-resistant tuberculosis (MDR-TB) culture collection in South Africa are described. DNA samples extracted from the phenotypically MDR-TB isolates (n=240) were assayed by Hain line probe assay (LPA) for the confirmation of MDR-TB and by Illumina Miseq whole genome sequencing (WGS) for the characterization of mutations in eight genes ( rpo B, kat G, inh A, rps L, pnc A, emb B, gyr A and rrs ) that are known to code for resistance to commonly used anti-TB agents...
March 7, 2018: Journal of Clinical Microbiology
Xue-Hong Chen, Yan-Tao Han, Jun-Li Ye, Zhi-Shang Chang, Chun-Bo Wang, Shou-Guo Chen
Haishengsu (HSS) is an active natural extract isolated from Tegillarca granosa, which has previously been demonstrated to inhibit the proliferation of several types of cancer cells in vitro. Our previous study indicated that HSS may induce apoptosis to suppress growth of human hepatocellular carcinoma BEL‑7402 cells by activating Fas pathway. The present study demonstrated that HSS treatment induces the in vitro apoptosis of BEL‑7402 cells via the mitochondrial‑mediated apoptotic pathway detected by DNA fragmentation assay, caspase activity assay and transmission electron microscopy assay, and inhibits tumor xenograft growth in vivo...
March 1, 2018: Molecular Medicine Reports
Kawther Taleb, Eva Lauridsen, Jette Daugaard-Jensen, Pekka Nieminen, Sven Kreiborg
BACKGROUND: Dentinogenesis imperfecta (DI) is a rare debilitating hereditary disorder affecting dentin formation and causing loss of the overlying enamel. Clinically, DI sufferers have a discolored and weakened dentition with an increased risk of fracture. The aims of this study were to assess genotype-phenotype findings in three families with DI-II with special reference to mutations in the DSPP gene and clinical, histological, and imaging manifestations. METHODS: Nine patients participated in the study (two from family A, four from family B, and three from family C)...
March 6, 2018: Molecular Genetics & Genomic Medicine
Debora Sugiaman-Trapman, Morana Vitezic, Eeva-Mari Jouhilahti, Anthony Mathelier, Gilbert Lauter, Sougat Misra, Carsten O Daub, Juha Kere, Peter Swoboda
BACKGROUND: Evolutionarily conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. Here, we provide a comprehensive analysis of all the eight human RFX genes (RFX1-8), their spatial and temporal expression profiles, potential upstream regulators and target genes. RESULTS: We extracted all known human RFX1-8 gene expression profiles from the FANTOM5 database derived from transcription start site (TSS) activity as captured by Cap Analysis of Gene Expression (CAGE) technology...
March 6, 2018: BMC Genomics
Mahbobeh Koohiyan, Morteza Hashemzadeh-Chaleshtori, Mansoor Salehi, Hamidreza Abtahi, Somayeh Reiisi, Mohammad Reza Pourreza, Mohammad Reza Noori-Daloii, Mohammad Amin Tabatabaiefar
OBJECTIVE: Hereditary hearing loss (HL) is a noticeable concern in medicine all over the world. On average, 1 in 166 babies born are diagnosed with HL in Iran, which makes it a major public health issue. Autosomal recessive non-syndromic HL (ARNSHL) is the most prevalent form of HL. Although over 60 genes have been identified for ARNSHL, GJB2 mutations are the most prevalent causes of ARNSHL in many populations. Previous studies have estimated the average frequency of GJB2 mutations to be between 16 and 18% in Iran, but would vary among different ethnic groups...
April 2018: International Journal of Pediatric Otorhinolaryngology
Kai-Chih Chang, Chin-Yi Chung, Chen-Hsing Yeh, Kuo-Hsiu Hsu, Ya-Ching Chin, Sin-Siang Huang, Bo-Rong Liu, Hsi-An Chen, Anren Hu, Po-Chi Soo, Wen-Ping Peng
The appearance and spread of carbapenem-resistant Acinetobacter baumannii (CRAB) pose a challenge for optimization of antibiotic therapies and outbreak preventions. The carbapenemase production can be detected through culture-based methods (e.g. Modified Hodge Test-MHT) and DNA based methods (e.g. Polymerase Chain Reaction-PCR). The culture-based methods are time-consuming, whereas those of PCR assays need only a few hours but due to its specificity, can only detect known genetic targets encoding carbapenem-resistance genes...
February 27, 2018: Journal of Microbiological Methods
Sándor Hornok, Krisztina Szőke, Péter Estók, Aleksandra Krawczyk, Anne-Jifke Haarsma, Dávid Kováts, Sándor A Boldogh, Pál Morandini, Sándor Szekeres, Nóra Takács, Jenő Kontschán, Marina L Meli, Isabel G Fernández de Mera, José de la Fuente, Miklós Gyuranecz, Kinga M Sulyok, Beatrice Weibel, Enikő Gönczi, Arnout de Bruin, Hein Sprong, Regina Hofmann-Lehmann
In Europe, several species of bats, owls and kestrels exemplify highly urbanised, flying vertebrates, which may get close to humans or domestic animals. Bat droppings and bird pellets may have epidemiological, as well as diagnostic significance from the point of view of pathogens. In this work 221 bat faecal and 118 bird pellet samples were screened for a broad range of vector-borne bacteria using PCR-based methods. Rickettsia DNA was detected in 13 bat faecal DNA extracts, including the sequence of a rickettsial insect endosymbiont, a novel Rickettsia genotype and Rickettsia helvetica...
February 28, 2018: Antonie Van Leeuwenhoek
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