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DNA Sequencing

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https://www.readbyqxmd.com/read/28241454/next-generation-sequencing-approach-in-methylation-analysis-of-hnf1b-and-gata4-genes-searching-for-biomarkers-in-ovarian-cancer
#1
Ivana Bubancova, Helena Kovarikova, Jan Laco, Ema Ruszova, Ondrej Dvorak, Vladimir Palicka, Marcela Chmelarova
DNA methylation is well-known to be associated with ovarian cancer (OC) and has great potential to serve as a biomarker in monitoring response to therapy and for disease screening. The purpose of this study was to investigate methylation of HNF1B and GATA4 and correlate detected methylation with clinicopathological characteristic of OC patients. The study group consisted of 64 patients with OC and 35 control patients. To determine the most important sites of HNF1B and GATA4, we used next-generation sequencing...
February 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28241310/editing-vegfr2-blocks-vegf-induced-activation-of-akt-and-tube-formation
#2
Xionggao Huang, Guohong Zhou, Wenyi Wu, Gaoen Ma, Patricia A D'Amore, Shizuo Mukai, Hetian Lei
Purpose: Vascular endothelial growth factor receptor 2 (VEGFR2) plays a key role in VEGF-induced angiogenesis. The goal of this project was to test the hypothesis that editing genomic VEGFR2 loci using the technology of clustered regularly interspaced palindromic repeats (CRISPR)-associated DNA endonuclease (Cas)9 in Streptococcus pyogenes (SpCas9) was able to block VEGF-induced activation of Akt and tube formation. Methods: Four 20 nucleotides for synthesizing single-guide RNAs based on human genomic VEGFR2 exon 3 loci were selected and cloned into a lentiCRISPR v2 vector, respectively...
February 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28241078/genetic-evidence-from-mitochondrial-dna-corroborates-the-origin-of-tibetan-chickens
#3
Long Zhang, Pu Zhang, Qingqing Li, Uma Gaur, Yiping Liu, Qing Zhu, Xiaoling Zhao, Yan Wang, Huadong Yin, Yaodong Hu, Aiping Liu, Diyan Li
Chicken is the most common poultry species and is important to human societies. Tibetan chicken (Gallus gallus domesticus) is a breed endemic to China that is distributed mainly on the Qinghai-Tibet Plateau. However, its origin has not been well characterized. In the present study, we sequenced partial mitochondrial DNA (mtDNA) control region of 239 and 283 samples from Tibetan and Sichuan indigenous chickens, respectively. Incorporating 1091 published sequences, we constructed the matrilineal genealogy of Tibetan chickens to further document their domestication history...
2017: PloS One
https://www.readbyqxmd.com/read/28241043/use-of-eschar-swabbing-for-the-molecular-diagnosis-and-genotyping-of-orientia-tsutsugamushi-causing-scrub-typhus-in-quang-nam-province-vietnam
#4
Nhiem Le Viet, Maureen Laroche, Hoa L Thi Pham, Nho L Viet, Oleg Mediannikov, Didier Raoult, Philippe Parola
BACKGROUND: Scrub typhus is a rickettsiosis which is caused by Orientia tsutsugamushi and occurs throughout the Asia-Pacific region. Molecular diagnosis of rickettsioses using eschar swabs has recently emerged, and may be very useful for the diagnosis of these diseases in tropical settings. METHODOLOGY/PRINCIPAL FINDINGS: Quantitative polymerase chain reaction (qPCR) was used to detect O. tsutsugamushi DNA in whole blood and eschar swab specimens of 67 patients who were clinically suspected of scrub typhus in Quang Nam province, Vietnam...
February 27, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28241016/rapid-and-simultaneous-detection-of-common-aneuploidies-by-quadruplex-real-time-polymerase-chain-reaction-combined-with-melting-curve-analysis
#5
Jiwu Lou, Manna Sun, Ying Zhao, Zhisong Ji, Fenghua Liu, Dongzhi Li, Wanfang Xu, Yangyang Lin, Yanhui Liu
BACKGROUND: During the prenatal period, the number variation of chromosomes 13, 18, 21, X and Y accounts for more than 80% of the clinically significant chromosomal abnormalities diagnosed. Rapid tests for prenatal diagnosis of these abnormalities can improve pregnancy management and alleviate parental anxiety. Here, we present a molecular alternative method for detecting common aneuploidies. METHODS: This method is based on co-amplification of segmental duplications located on two different chromosomes using a single pair of primers...
2017: PloS One
https://www.readbyqxmd.com/read/28240906/chimeric-autofluorescent-proteins-as-photophysical-model-system-for-multicolor-bimolecular-fluorescence-complementation-mcbifc
#6
Sébastien Peter, Sven Zur Oven-Krockhaus, Manikandan Veerabagu, Virtudes Mira-Rodado, Kenneth W Berendzen, Alfred J Meixner, Klaus Harter, Frank E Schleifenbaum
The yellow fluorescent protein YFP is frequently used in a protein complementation assay called Bimolecular Fluorescence Complementation (BiFC), employed to visualize protein-protein interactions. In this analysis, two different, nonfluorescent fragments of YFP are genetically attached to proteins of interest. Upon interaction of these proteins, the YFP fragments are brought into proximity close enough to reconstitute their original structure, enabling fluorescence. BiFC allows for a straightforward readout of protein-protein interactions and furthermore facilitates their functional investigation by in vivo imaging...
February 27, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28240846/identification-of-a-low-frequency-missense-variant-in-e2f-transcription-factor-7-associated-with-colorectal-cancer-risk-in-a-chinese-population
#7
Ai Ye Guo, Kan Zhai, Jin Ling Xu, Jin Long Hu, Lan Gao
Background: Transcription factors regulate gene expression and play important role in tumor genesis. Especially, the E2F transcription factor family controls the cell cycle and regulate many tumor suppressors. Missense variants in E2F family genes, which change the amino acid sequence, may alter the capacity for DNA binding or the protein structure, leading to a functional alteration. Material and Methods: We here searched for missense variants in E2F transcription family genes (E2F1~E2F8) and identified two (rs2075995 for E2F2 and rs3829295 for E2F7) with minor allele frequencies >0...
1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28240743/association-of-high-risk-human-papillomavirus-and-breast-cancer-a-uk-based-study
#8
Nadia Aziz Salman, Giles Davies, Farida Majidy, Fatima Shakir, Hilda Akinrinade, Dhayaneethie Perumal, G Hossein Ashrafi
Infection by human papillomaviruses (HPVs) has been implicated in the aetiology of a variety of cancers. Studies evaluating the presence of HPVs in breast cancer (BC) have generated considerable controversy. To date, most studies have focused on the presence of viral DNA in BC; however there are important gaps in evidencing the role of HPV persistence in the invasiveness of BC. While these studies have been conducted in several countries, none, on the presence and biological activity of high risk (HR) HPV in BC has been done in the UK...
February 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28240563/multiparametric-mr-imaging-of-diffusion-and-perfusion-in-contrast-enhancing-and-nonenhancing-components-in-patients-with-glioblastoma
#9
Natalie R Boonzaier, Timothy J Larkin, Tomasz Matys, Anouk van der Hoorn, Jiun-Lin Yan, Stephen J Price
Purpose To determine whether regions of low apparent diffusion coefficient (ADC) with high relative cerebral blood volume (rCBV) represented elevated choline (Cho)-to-N-acetylaspartate (NAA) ratio (hereafter, Cho/NAA ratio) and whether their volumes correlated with progression-free survival (PFS) and overall survival (OS) in patients with glioblastoma (GBM). Materials and Methods This retrospective analysis was approved by the local research ethics committee. Volumetric analysis of imaging data from 43 patients with histologically confirmed GBM was performed...
February 27, 2017: Radiology
https://www.readbyqxmd.com/read/28240528/novel-mutations-of-the-chrna3-gene-in-non-small-cell-lung-cancer-in-an-iranian-population
#10
Nahid Mehrabi, Seyed Mohammad Moshtaghioun, Hossein Neamatzadeh
Background: Lung cancer, the leading cause of cancer-related worldwide deaths, largely results from the combined effects of smoking exposure and genetic susceptibility. CHRNA3, a nicotinic acetylcholine receptor gene, is associated with lung cancer risk. This study sought to identify variations in exon 3 of CHRNA3 in an Iranian population with non-small cell lung cancer (NSCLC). Materials and methods: A case-control study including 147 individuals with lung cancer and 145 healthy individuals was conducted. As mobility shift caused by nucleotide substitutions might be due to a conformational change of single-stranded DNAs, we designated these as single-strand conformation polymorphisms (SSCPs)...
1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28240513/human-papillomavirus-genotypes-and-methylation-of-cadm1-pax1-mal-and-adcyap1-genes-in-epithelial-ovarian-cancer-patients
#11
Zeinab K Hassan, Mohamed M Hafez, Mahmoud M Kamel, Abdel Rahman N Zekri
Background: High-risk types of human papillomavirus (HR-HPV) may play a role in the development of epithelial ovarian cancer (EOC). The aim of this study was to determine any HPV genotypes and correlations to CADM1, PAX1, MAL and ADCYAP1 gene methylation in Egyptian EOC patients. Materials and methods: The prevalence of HR-HPV in 100 formalin fixed paraffin embedded EOC tissues was determined using nested polymerase chain reaction (PCR) with MY09/MY11 and GP5+/GP6 + primers to amplify a broad spectrum of HPV genotypes in a single reaction...
1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28240336/a-nanoplasmonic-label-free-surface-enhanced-raman-scattering-strategy-for-non-invasive-cancer-genetic-subtyping-in-patient-samples
#12
Jing Wang, Kevin M Koo, Eugene J H Wee, Yuling Wang, Matt Trau
Simple nucleic acid detection methods could facilitate the progress of disease diagnostics for clinical uses. An attractive strategy is label-free surface-enhanced Raman scattering (SERS) due to its capability of providing structural fingerprinting of analytes that are close to or on nanomaterial surfaces. However, current label-free SERS approaches for DNA/RNA biomarker detection are limited to short and synthetic nucleic acid targets and have not been fully realized in clinical samples due to two possible reasons: (i) low target copies in limited patient samples and (ii) poor capability in identifying specific biomarkers from complex samples...
February 27, 2017: Nanoscale
https://www.readbyqxmd.com/read/28240320/analysis-of-co-associated-transcription-factors-via-ordered-adjacency-differences-on-motif-distribution
#13
Gaofeng Pan, Jijun Tang, Fei Guo
Transcription factors (TFs) binding to specific DNA sequences or motifs, are elementary to the regulation of transcription. The gene is regulated by a combination of TFs in close proximity. Analysis of co-TFs is an important problem in understanding the mechanism of transcriptional regulation. Recently, ChIP-seq in mapping TF provides a large amount of experimental data to analyze co-TFs. Several studies show that if two TFs are co-associated, the relative distance between TFs exhibits a peak-like distribution...
February 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28240206/-dna-sequences-from-mobile-genetic-elements-a-hidden-half-of-the-human-genome
#14
Julie Medina, Hervé Perron
Current data estimate that mobile genetic elements represent more than one-half of the human genome. The literature is constantly updating data following the evolution of sequencing techniques and of algorithms for genome analyses. This review aims to provide an overview of the topic showing the complexity given by the various designations and classifications found in scientific papers. A particular focus is made on retrotransposons, including Endogenous RetroViruses (ERV), to introduce a second article focusing on their activation and their involvement in physiological functions and/or pathological mechanisms associated with diseases like multiple sclerosis (MS) or amyotrophic lateral sclerosis (ALS)...
February 2017: Médecine Sciences: M/S
https://www.readbyqxmd.com/read/28240205/-how-genomic-approaches-help-the-understanding-of-the-initiation-of-dna-replication
#15
Benoit Miotto
Eukaryotic DNA replication starts at multiple sites distributed throughout the genome called origins of replication. The identification of the position of these origins in the genome, as well as the description of their sequence features and chromatin structure, have been the center of many studies over the last years. A handful of sophisticated methods has been developed to capture replication initiation events, to detect replication factors binding sites onto the chromatin and to computationally analyze these data at the genome scale...
February 2017: Médecine Sciences: M/S
https://www.readbyqxmd.com/read/28240182/integration-of-novel-materials-and-advanced-omics-technologies-into-new-vaccine-design
#16
Wenzhen Liao, Tian-Tian Zhang, Liqian Gao, Su Seong Lee, Jie Xu, Han Zhang, Zhaogang Yang, Zhaoyu Liu, Wen Li
Designing new vaccines is one of the most challenging tasks for public health to prevent both infectious and chronic diseases. Even though many research scientists have spent great efforts in improving the specificity, sensitivity and safety of current available vaccines, there are still much space on how to effectively combine different biomaterials and technologies to design universal or personalized vaccines. Traditionally, vaccines were made based on empirical approaches designed to mimic immunity induced by natural infection...
February 24, 2017: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/28240049/deep-sequencing-of-the-tp53-gene-reveals-a-potential-risk-allele-for-non-small-cell-lung-cancer-and-supports-the-negative-prognostic-value-of-tp53-variants
#17
Christophe Deben, Jolien Van den Bossche, Nele Van Der Steen, Filip Lardon, An Wouters, Ken Op de Beeck, Christophe Hermans, Julie Jacobs, Marc Peeters, Guy Van Camp, Christian Rolfo, Vanessa Deschoolmeester, Patrick Pauwels
The TP53 gene remains the most frequently altered gene in human cancer, of which variants are associated with cancer risk, therapy resistance, and poor prognosis in several tumor types. To determine the true prognostic value of TP53 variants in non-small cell lung cancer, this study conducted further research, particularly focusing on subtype and tumor stage. Therefore, we determined the TP53 status of 97 non-small cell lung cancer adenocarcinoma patients using next generation deep sequencing technology and defined the prognostic value of frequently occurring single nucleotide polymorphisms and mutations in the TP53 gene...
February 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28239935/isolation-and-characterization-of-an-atypical-siberian-sturgeon-herpesvirus-strain-in-russia-novel-north-american-acipenserid-herpesvirus-2-strain-in-europe
#18
A Doszpoly, I M Kalabekov, R Breyta, I S Shchelkunov
Siberian sturgeon herpesvirus (SbSHV) was isolated in Russia for the first time in 2006. Nine SbSHV isolates were recovered from different fish hatcheries producing the same cytopathic effect in cell cultures, the same clinical signs and mortality kinetics in virus-infected fish and the same virus neutralization pattern and shared identical nucleotide sequences. In 2011, a new isolate was recovered from juvenile sturgeon, which caused completely different cytopathic effect. That isolate was not readily neutralized by Siberian sturgeon hyperimmune antisera, and its DNA was not recognized by the routine PCR developed for SbSHV detection...
February 27, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/28239713/enhancerpred2-0-predicting-enhancers-and-their-strength-based-on-position-specific-trinucleotide-propensity-and-electron-ion-interaction-potential-feature-selection
#19
Wenying He, Cangzhi Jia
Enhancers are cis-acting elements that play major roles in upregulating eukaryotic gene expression by providing binding sites for transcription factors and their complexes. Because enhancers are highly cell/tissue specific, lack common motifs, and are far from the target gene, the systematic and precise identification of enhancer regions in DNA sequences is a big challenge. In this study, we developed an enhancer prediction method called EnhancerPred2.0 by combining position-specific trinucleotide propensity (PSTNP) information with the electron-ion interaction potential (EIIP) values for trinucleotides, to predict enhancers and their subgroups...
February 27, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28239657/tissue-resident-macrophages-can-contain-replication-competent-virus-in-antiretroviral-naive-siv-infected-asian-macaques
#20
Sarah R DiNapoli, Alexandra M Ortiz, Fan Wu, Kenta Matsuda, Homer L Twigg, Vanessa M Hirsch, Kenneth Knox, Jason M Brenchley
SIV DNA can be detected in lymphoid tissue-resident macrophages of chronically SIV-infected Asian macaques. These macrophages also contain evidence of recently phagocytosed SIV-infected CD4(+) T cells. Here, we examine whether these macrophages contain replication-competent virus, whether viral DNA can be detected in tissue-resident macrophages from antiretroviral (ARV) therapy-treated animals and humans, and how the viral sequences amplified from macrophages and contemporaneous CD4(+) T cells compare. In ARV-naive animals, we find that lymphoid tissue-resident macrophages contain replication-competent virus if they also contain viral DNA in ARV-naive Asian macaques...
February 23, 2017: JCI Insight
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