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https://www.readbyqxmd.com/read/28441441/a-novel-multiplexed-probe-based-quantitative-pcr-assay-for-the-soybean-root-and-stem-rot-pathogen-phytophthora-sojae-utilizes-its-transposable-element
#1
James S Haudenshield, Jeong Y Song, Glen L Hartman
Phytophthora root rot of soybean [Glycine max (L.) Merr.] is caused by the oomycete Phytophthora sojae (Kaufm. & Gerd.). P. sojae has a narrow host range, consisting primarily of soybean, and it is a serious pathogen worldwide. It exists in root and stem tissues as mycelium, wherein it can form oospores which subsequently germinate to release motile, infectious zoospores. Molecular assays detecting DNA of P. sojae are useful in disease diagnostics, and for determining the presence of the organism in host tissues, soils, and runoff or ponded water from potentially infested fields...
2017: PloS One
https://www.readbyqxmd.com/read/28425010/a-novel-fibrinogen-variant-dysfibrinogenemia-associated-with-%C3%AE-asp185asn-substitution
#2
Na Zhou, Peipei Xu, Min Zhou, Yong Xu, Ping Li, Bin Chen, Jian Ouyang, Rongfu Zhou
To identify the pathogenesis of a Chinese woman diagnosed with dysfibrinogenemia. A patient from Nanjing presented with a low plasma concentration of fibrinogen and a normal level of antigen of fibrinogen. This abnormality was also detected in her son. To detect whether the genetic mutation was responsible for the dysfibrinogenemia, genomic DNA was extracted and amplified by polymerase chain reaction, and DNA sequencing was performed on the purified PCR products. Restriction fragment length polymorphism (RFLP), molecular modeling and homologous sequences alignment were performed...
April 19, 2017: Journal of Thrombosis and Thrombolysis
https://www.readbyqxmd.com/read/28423518/a-novel-pathogenic-splice-acceptor-site-germline-mutation-in-intron-14-of-the-apc-gene-in-a-chinese-family-with-familial-adenomatous-polyposis
#3
Dan Wang, Shengyun Liang, Zhao Zhang, Guoru Zhao, Yuan Hu, Shengran Liang, Xipeng Zhang, Santasree Banerjee
Familial adenomatous polyposis (FAP) is an autosomal dominant precancerous condition, clinically characterized by the presence of multiple colorectal adenomas or polyps. Patients with FAP has a high risk of developing colorectal cancer (CRC) from these colorectal adenomatous polyps by the mean age of diagnosis at 40 years. Germline mutations of the APC gene cause familial adenomatous polyposis (FAP). Colectomy has recommended for the FAP patients with significant polyposis. Here, we present a clinical molecular study of a four generation Chinese family with FAP...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28421464/a-novel-tp53-mutation-associated-with-twist1-and-sip1-expression-in-an-aggressive-adrenocortical-carcinoma
#4
Daniel Bulzico, Davi Coe Torres, Gerson Moura Ferreira, Bruno Ricardo Barreto Pires, Paulo Antônio Silvestre de Faria, Rocio Hassan, Eliana Abdelhay, Mario Vaisman, Leonardo Vieira Neto
Adrenocortical carcinomas (ACC) are very rare tumors related to TP53 mutations mostly in childhood onset cases. Epithelial-mesenchymal transition (EMT) transcription factors TWIST1 and Smad interacting protein 1 (SIP1) are related to poorer outcomes in other malignancies, but their role in ACC is unknown. We describe a case of an advanced metastatic ACC (Weiss-score of 9) in a patient at age 76. After primary tumor resection, mitotane therapy was started as palliation to low-volume liver metastasis. After a 2-year period of stable disease, the patient died due to brain metastasis...
April 18, 2017: Endocrine Pathology
https://www.readbyqxmd.com/read/28419064/the-application-of-next-generation-sequencing-for-mutation-detection-in-autosomal-dominant-hereditary-hearing-impairment
#5
Nicolas Gürtler, Benno Röthlisberger, Katja Ludin, Christoph Schlegel, Anil K Lalwani
OBJECTIVE: Identification of the causative mutation using next-generation sequencing in autosomal-dominant hereditary hearing impairment, as mutation analysis in hereditary hearing impairment by classic genetic methods, is hindered by the high heterogeneity of the disease. PATIENTS: Two Swiss families with autosomal-dominant hereditary hearing impairment. INTERVENTION: Amplified DNA libraries for next-generation sequencing were constructed from extracted genomic DNA, derived from peripheral blood, and enriched by a custom-made sequence capture library...
April 17, 2017: Otology & Neurotology
https://www.readbyqxmd.com/read/28414950/a-nanobiosensor-composed-of-exfoliated-graphene-oxide-and-gold-nano-urchins-for-detection-of-gmo-products
#6
Zahra Aghili, Navid Nasirizadeh, Adeleh Divsalar, Shahram Shoeibi, Parichehreh Yaghmaei
Genetically Modified Organisms, have been entered our food chain and detection of these organisms in market products are still the main challenge for scientists. Among several developed detection/quantification methods for detection of these organisms, the electrochemical nanobiosensors are the most attended which are combining the advantages of using nanomaterials, electrochemical methods and biosensors. In this research, a novel and sensitive electrochemical nanobiosensor for detection/quantification of these organisms have been developed using nanomaterials; Exfoliated Graphene Oxide and Gold Nano-Urchins for modification of the screen-printed carbon electrode, and also applying a specific DNA probe as well as hematoxylin for electrochemical indicator...
March 6, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28412374/a-novel-mitochondrial-atp6-frameshift-mutation-causing-isolated-complex-v-deficiency-ataxia-and-encephalomyopathy
#7
Christopher Benjamin Jackson, Dagmar Hahn, Barbara Schröter, Uwe Richter, Brendan Battersby, Thomas Schmitt-Mechelke, Paula Martinen, Jean-Marc Nuoffer, André Schaller
We describe a novel frameshift mutation in the mitochondrial ATP6 gene in a 4-year-old girl associated with ataxia, microcephaly, developmental delay and intellectual disability. A heteroplasmic frameshift mutation in the MT-ATP6 gene was confirmed in the patient's skeletal muscle and blood. The mutation was not detectable in the mother's DNA extracted from blood or buccal cells. Enzymatic and oxymetric analysis of the mitochondrial respiratory system in the patients' skeletal muscle and skin fibroblasts demonstrated an isolated complex V deficiency...
April 12, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28404952/high-throughput-detection-of-clinically-targetable-alterations-using-next-generation-sequencing
#8
Julie A Vendrell, David Grand, Isabelle Rouquette, Valérie Costes, Samira Icher, Janick Selves, Marion Larrieux, Aurore Barbe, Pierre Brousset, Jérôme Solassol
Next-generation sequencing (NGS) has revolutionized the therapeutic care of patients by allowing high-throughput and parallel sequencing of large numbers of genes in a single run. However, most of available commercialized cancer panels target a large number of mutations that do not have direct therapeutic implications and that are not fully adapted to low quality formalin-fixed, paraffin-embedded (FFPE) samples. Here, we designed an amplicon-based NGS panel assay of 16 currently actionable genes according to the most recent recommendations of the French National Cancer Institute (NCI)...
March 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28402975/frequent-pul27-variations-in-hiv-infected-patients
#9
Azam Mirarab, Alireza Mohebbi, Abdolvahab Moradi, Naeme Javid, Mohammad Ali Vakili, Alijan Tabarraei
OBJECTIVE: Drug-resistant isolates of human cytomegalovirus (HCMV) have led to the development of new anti-HCMV drugs. Maribavir (MBV) is a novel inhibitor of the HCMV viral kinase. Resistance to MBV is mapped to gene UL27, a viral nuclear protein. In this study, we investigated UL27 polymorphisms in MBV-naive HIV-positive and HCMV congenitally infected clinical samples. METHODS: DNA was extracted from 20 CMV-positive HIV (9/20) and congenitally infected (11/20) patients and used for UL27 polymerase chain reaction amplification...
April 13, 2017: Intervirology
https://www.readbyqxmd.com/read/28401470/streptomyces-artemisiae-mccb-248-isolated-from-arctic-fjord-sediments-has-unique-pks-and-nrps-biosynthetic-genes-and-produces-potential-new-anticancer-natural-products
#10
M Dhaneesha, C Benjamin Naman, K P Krishnan, Rupesh Kumar Sinha, P Jayesh, Valsamma Joseph, I S Bright Singh, William H Gerwick, T P Sajeevan
After screening marine actinomycetes isolated from sediment samples collected from the Arctic fjord Kongsfjorden for potential anticancer activity, an isolate identified as Streptomyces artemisiae MCCB 248 exhibited promising results against the NCI-H460 human lung cancer cell line. H460 cells treated with the ethyl acetate extract of strain MCCB 248 and stained with Hoechst 33342 showed clear signs of apoptosis, including shrinkage of the cell nucleus, DNA fragmentation and chromatin condensation. Further to this treated cells showed indications of early apoptotic cell death, including a significant proportion of Annexin V positive staining and evidence of DNA damage as observed in the TUNEL assay...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28397225/-clinical-features-and-genetic-analysis-of-a-case-with-carnitine-palmitoyltransferase-1a-deficiency
#11
Dong Cui, Yuhui Hu, Dan Shen, Gen Tang, Min Zhang, Jing Duan, Pengqiang Wen, Jianxiang Liao, Dongli Ma, Shuli Chen
OBJECTIVE: To analyze the clinical and molecular features of a child with carnitine palmitoyltransferase 1A (CPT1A) deficiency. METHODS: Clinical data of the child was collected. Blood acylcarnitine was determined with tandem mass spectrometry. DNA was extracted from the child and his parents. All exons and flanking regions of the CPT1A gene were analyzed by PCR and Sanger sequencing. RESULTS: Analysis showed that the patient carried compound heterozygous mutations c...
April 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28397217/-study-of-two-chinese-families-affected-with-resistant-ovarian-syndrome-resulted-from-novel-mutations-of-fshr-gene
#12
Wen Li, Wenbin He, Lihua Zhou, Xiao Hu, Shuangfei Li, Fei Gong, Yueqiu Tan
OBJECTIVE: To explore the genetic etiology for two Chinese families affected with hypergonadotropic amenorrhea and normal number of antral follicles. METHODS: Peripheral venous blood samples were collected from the families for the extraction of genomic DNA. Mutations of FSHR and LHCGR genes were screened using PCR and Sanger sequencing. Suspected pathogenic mutations were verified in other members of the families. Bioinformatics software and NCBI were used to analyze the pathogenicity of the mutations...
April 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28394451/ancient-dna-analysis-identifies-marine-mollusc-shells-as-new-metagenomic-archives-of-the-past
#13
Clio Der Sarkissian, Vianney Pichereau, Catherine Dupont, Peter C Ilsøe, Mickael Perrigault, Paul Butler, Laurent Chauvaud, Jón Eiríksson, James Scourse, Christine Paillard, Ludovic Orlando
Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity, and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories...
April 10, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28393022/two-mutations-in-the-transforming-growth-factor-beta-induced-gene-associated-with-familial-lattice-corneal-dystrophy
#14
Wen-Ping Cao, Hai-Gang Yuan, Ping Liu, Xue Li, Qi Hu
AIM: To report a phenotypic variant pedigree of lattice corneal dystrophy (LCD) associated with two mutations, R124C and A546D, in the transforming growth factor beta-induced gene (TGFBI). METHODS: A detailed ocular examination was taken for all participants of a LCD family. Peripheral blood leukocytes from each participant were extracted to obtain the DNA. Polymerase chain reaction (PCR) of all seventeen exons of TGFBI gene was performed. The products were sequenced and analyzed...
2017: International Journal of Ophthalmology
https://www.readbyqxmd.com/read/28389374/a-novel-brca1-associated-protein-1-isoform-affects-response-of-mesothelioma-cells-to-drugs-impairing-brca1-mediated-dna-repair
#15
Rossella Parrotta, Agata Okonska, Manuel Ronner, Walter Weder, Rolf Stahel, Lorenza Penengo, Emanuela Felley-Bosco
INTRODUCTION: BRCA1-associated protein-1, BAP1, is a tumor suppressor involved in multiple cellular processes such as transcriptional regulation, chromatin modification by deubiquitinating histone 2A and DNA repair. BAP1 mutations are frequent in malignant pleural mesothelioma (MPM). Our aim was to functionally characterize a newly identified isoform of BAP1 and investigate the effects of its expression on drug sensitivity in MPM. METHODS: Expression of BAP1 isoforms was detected by qPCR in MPM and normal mesothelium cell lines, tumor and non-tumor samples...
April 4, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28381603/comprehensive-whole-genome-sequencing-and-reporting-of-drug-resistance-profiles-on-clinical-cases-of-mycobacterium-tuberculosis-in-new-york-state
#16
Joseph Shea, Tanya A Halse, Pascal Lapierre, Matthew Shudt, Donna Kohlerschmidt, Patrick Van Roey, Ronald Limberger, Jill Taylor, Vincent Escuyer, Kimberlee A Musser
Whole-genome sequencing (WGS) is a newer alternative for tuberculosis (TB) diagnostics, capable of providing rapid drug resistance profiles while performing species identification and capturing the data necessary for genotyping. Our laboratory developed and validated a comprehensive and sensitive WGS assay to characterize Mycobacterium tuberculosis and other M. tuberculosis complex (MTBC) strains, comprised of a novel DNA extraction, optimized library preparation, paired-end WGS, and an in-house developed bioinformatics pipeline...
April 5, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28381299/emerging-concepts-in-liquid-biopsies
#17
REVIEW
Samantha Perakis, Michael R Speicher
Characterizing and monitoring tumor genomes with blood samples could achieve significant improvements in precision medicine. As tumors shed parts of themselves into the circulation, analyses of circulating tumor cells, circulating tumor DNA, and tumor-derived exosomes, often referred to as "liquid biopsies", may enable tumor genome characterization by minimally invasive means. Indeed, multiple studies have described how molecular information about parent tumors can be extracted from these components. Here, we briefly summarize current technologies and then elaborate on emerging novel concepts that may further propel the field...
April 6, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28378789/novel-micelle-pcr-based-method-for-accurate-sensitive-and-quantitative-microbiota-profiling
#18
Stefan A Boers, John P Hays, Ruud Jansen
In the last decade, many researchers have embraced 16S rRNA gene sequencing techniques, which has led to a wealth of publications and documented differences in the composition of microbial communities derived from many different ecosystems. However, comparison between different microbiota studies is currently very difficult due to the lack of a standardized 16S rRNA gene sequencing protocol. Here we report on a novel approach employing micelle PCR (micPCR) in combination with an internal calibrator that allows for standardization of microbiota profiles via their absolute abundances...
April 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28364702/multiplexed-nanoplasmonic-biosensor-for-one-step-simultaneous-detection-of-chlamydia-trachomatis-and-neisseria-gonorrhoeae-in-urine
#19
Maria Soler, Alexander Belushkin, Andrea Cavallini, Carole Kebbi-Beghdadi, Gilbert Greub, Hatice Altug
Development of rapid and multiplexed diagnostic tools is a top priority to address the current epidemic problem of sexually transmitted diseases. Here we introduce a novel nanoplasmonic biosensor for simultaneous detection of the two most common bacterial infections: Chlamydia trachomatis and Neisseria gonorrhoeae. Our plasmonic microarray is composed of gold nanohole sensor arrays that exhibit the extraordinary optical transmission (EOT), providing highly sensitive analysis in a label-free configuration. The integration in a microfluidic system and the precise immobilization of specific antibodies on the individual sensor arrays allow for selective detection and quantification of the bacteria in real-time...
March 21, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28360411/interplay-of-dna-methyltransferase-1-and-ezh2-through-inactivation-of-stat3-contributes-to-%C3%AE-elemene-inhibited-growth-of-nasopharyngeal-carcinoma-cells
#20
JingJing Wu, Qing Tang, LiJuan Yang, YuQing Chen, Fang Zheng, Swei Sunny Hann
β-elemene, a compound extracted from Curcuma wenyujin plant, exhibits anticancer activity in many cancer types. However, the detailed mechanism by which β-elemene inhibits growth of nasopharyngeal carcinoma (NPC) cells remains unknown. We showed that β-elemene reduced phosphorylation of signal transducer and activator of transcription 3 (Stat3), and protein expressions of DNA methyltransferase 1 (DNMT1) and enhancer of zeste homolog 2 (EZH2). Exogenously expressed Stat3 antagonized the effect of β-elemene on DNMT1 and EZH2 expressions...
March 30, 2017: Scientific Reports
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