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DNA Sequencing

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https://www.readbyqxmd.com/read/27933702/multiparameter-particle-display-mppd-a-quantitative-screening-method-for-the-discovery-of-highly-specific-aptamers
#1
Jinpeng Wang, Jingwen Yu, Qin Yang, John McDermott, Alexander Scott, Matthew Vukovich, Remy Lagrois, Qiang Gong, William Greenleaf, Michael Eisenstein, B Scott Ferguson, H Tom Soh
Aptamers are a promising class of affinity reagents because they are chemically synthesized, thus making them highly reproducible and distributable as sequence information rather than a physical entity. Although many high-quality aptamers have been previously reported, it is difficult to routinely generate aptamers that possess both high affinity and specificity. One of the reasons is that conventional aptamer selection can only be performed either for affinity (positive selection) or for specificity (negative selection), but not both simultaneously...
December 9, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27933665/detection-of-dna-sequences-from-a-novel-papillomavirus-in-a-feline-basal-cell-carcinoma
#2
John S Munday, Adrienne French, Neroli Thomson
BACKGROUND: Basal cell carcinomas (BCCs) are uncommon feline skin neoplasms of uncertain cause. CASE: A 14-year-old Abyssinian cat developed a soft dermal nodule on the dorsal thorax. This mass grew slowly over a six month period before being surgically excised. METHODS AND RESULTS: Histology revealed a BCC. Additionally, changes suggestive of an early Bowenoid in situ carcinoma (BISC) were present in the overlying epidermis. Both the BCC and the BISC contained papillomavirus-induced cell changes and prominent basophilic intracytoplasmic bodies...
December 8, 2016: Veterinary Dermatology
https://www.readbyqxmd.com/read/27933557/atypical-presentation-and-treatment-response-in-a-child-with-familial-hypercholesterolemia-having-a-novel-ldlr-mutation
#3
S Varma, A D McIntyre, R A Hegele
Familial hypercholesterolemia (FH) is an autosomal codominantly inherited disease. The severity of clinical presentation depends on the zygosity of the mutations in the LDLR, APOB, or PCSK9 genes. The homozygous form (HoFH) is associated with high mortality rate by third decade of life, while individuals with HeFH begin to suffer from premature cardiovascular disease in fourth or fifth decade of life. Statin drugs have helped to improve the biochemical profile and life expectancy in HeFH, while they are only minimally effective in HoFH...
December 9, 2016: JIMD Reports
https://www.readbyqxmd.com/read/27933533/systems-genetics-as-a-tool-to-identify-master-genetic-regulators-in-complex-disease
#4
Aida Moreno-Moral, Francesco Pesce, Jacques Behmoaras, Enrico Petretto
Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933525/expression-qtls-mapping-and-analysis-a-bayesian-perspective
#5
Martha Imprialou, Enrico Petretto, Leonardo Bottolo
The aim of expression Quantitative Trait Locus (eQTL) mapping is the identification of DNA sequence variants that explain variation in gene expression. Given the recent yield of trait-associated genetic variants identified by large-scale genome-wide association analyses (GWAS), eQTL mapping has become a useful tool to understand the functional context where these variants operate and eventually narrow down functional gene targets for disease. Despite its extensive application to complex (polygenic) traits and disease, the majority of eQTL studies still rely on univariate data modeling strategies, i...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933517/a-novel-mutation-in-the-fibrinogen-a%C3%AE-chain-gly13arg-fibrinogen-nanning-causes-congenital-dysfibrinogenemia-associated-with-defective-peptide-a-release
#6
Jie Yan, Meiling Luo, Peng Cheng, Lin Liao, Xuelian Deng, Donghong Deng, Faquan Lin
Dysfibrinogenemia is characterized by blood coagulation dysfunction induced by an abnormal molecular structure of fibrinogen. Here, we describe a new case. A 32-year-old female was suspected of having dysfibrinogenemia during routine laboratory screening, based on her decreased functional fibrinogen level, normal fibrinogen antigen level, and prolonged thrombin time. We extracted DNA and performed polymerase chain reaction and DNA sequencing to identify genetic mutation. Fibrin polymerization, the kinetics of the fibrinopeptide release, scanning electron microscopy, mass spectrometric analysis, fibrin cross-linking, sodium dodecyl sulfate polyacrylamide gel electrophoresis and western blot were conducted...
December 8, 2016: International Journal of Hematology
https://www.readbyqxmd.com/read/27933433/full-length-infectious-clone-of-an-iranian-isolate-of-chicken-anemia-virus
#7
Amir Kaffashi, Fatemeh Eshratabadi, Abdelhamed Shoushtari
An Iranian field strain of chicken anemia virus (CAV), designated IR CAV, was isolated in the Marek's disease virus-transformed lymphoblastoid cell line MDCC-MSB1 (MSB1) culture for the first time. The full-length CAV DNA of this strain was cloned in the bacterial plasmid pTZ57R/T to create the molecular clone pTZ-CAV. The nucleotide and deduced amino acid sequences of viral proteins of IR CAV were compared with those of representative CAV sequences including reference and commercial vaccine strains. IR CAV was not related to vaccine strains and also found to have glutamine at positions 139 and 144 confirming previous studies in which such mutations were associated with a slow rate of virus spread in cell culture...
December 8, 2016: Virus Genes
https://www.readbyqxmd.com/read/27933305/robust-generation-of-transgenic-mice-by-simple-hypotonic-solution-mediated-delivery-of-transgene-in-testicular-germ-cells
#8
Abul Usmani, Nirmalya Ganguli, Subodh K Jain, Nilanjana Ganguli, Rajesh Kumar Sarkar, Mayank Choubey, Mansi Shukla, Hironmoy Sarkar, Subeer S Majumdar
Our ability to decipher gene sequences has increased enormously with the advent of modern sequencing tools, but the ability to divulge functions of new genes have not increased correspondingly. This has caused a remarkable delay in functional interpretation of several newly found genes in tissue and age specific manner, limiting the pace of biological research. This is mainly due to lack of advancements in methodological tools for transgenesis. Predominantly practiced method of transgenesis by pronuclear DNA-microinjection is time consuming, tedious, and requires highly skilled persons for embryo-manipulation...
2016: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/27933115/effects-of-trimethylamine-n-oxide-and-urea-on-dna-duplex-and-g-quadruplex
#9
Yu-Mi Ueda, Yu-Ki Zouzumi, Atsushi Maruyama, Shu-Ichi Nakano, Naoki Sugimoto, Daisuke Miyoshi
We systematically investigated effects of molecular crowding with trimethylamine N-oxide (TMAO) as a zwitterionic and protective osmolyte and urea as a nonionic denaturing osmolyte on conformation and thermodynamics of the canonical DNA duplex and the non-canonical DNA G-quadruplex. It was found that TMAO and urea stabilized and destabilized, respectively, the G-quadruplex. On the other hand, these osmolytes generally destabilize the duplex; however, it was observed that osmolytes having the trimethylamine group stabilized the duplex at the lower concentrations because of a direct binding to a groove of the duplex...
2016: Science and Technology of Advanced Materials
https://www.readbyqxmd.com/read/27933111/aberrant-dna-hypermethylation-silenced-sox21-as1-gene-expression-and-its-clinical-importance-in-oral-cancer
#10
Cheng-Mei Yang, Tsung-Han Wang, Hung-Chih Chen, Sung-Chou Li, Ming-Chien Lee, Huei-Han Liou, Pei-Feng Liu, Yu-Kai Tseng, Yow-Ling Shiue, Luo-Ping Ger, Kuo-Wang Tsai
BACKGROUND: Long noncoding RNAs (lncRNAs) are more than 200 nucleotides in length and lack transcriptional ability. The biological function of lncRNAs in oral squamous cell carcinoma (OSCC) remains unclear. The aim of this study was to identify the dysfunction of lncRNA in OSCC. RESULTS: We analyzed the transcriptome profiles of human OSCC tissues and paired adjacent normal tissues from two patients through a next-generation sequencing approach. A total of 14 lncRNAs were upregulated (fold change ≥3) and 13 were downregulated (fold change ≤-3) in OSCC tissues compared with the adjacent normal tissues...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27933110/profiling-lung-adenocarcinoma-by-liquid-biopsy-can-one-size-fit-all
#11
Harry W Clifford, Amy P Cassidy, Courtney Vaughn, Evaline S Tsai, Bianka Seres, Nirmesh Patel, Hannah L O'Neill, Emil Hewage, John W Cassidy
BACKGROUND: Cancer is first and foremost a disease of the genome. Specific genetic signatures within a tumour are prognostic of disease outcome, reflect subclonal architecture and intratumour heterogeneity, inform treatment choices and predict the emergence of resistance to targeted therapies. Minimally invasive liquid biopsies can give temporal resolution to a tumour's genetic profile and allow the monitoring of treatment response through levels of circulating tumour DNA (ctDNA). However, the detection of ctDNA in repeated liquid biopsies is currently limited by economic and time constraints associated with targeted sequencing...
2016: Cancer Nanotechnology
https://www.readbyqxmd.com/read/27933109/functional-characterization-of-rare-foxp2-variants-in-neurodevelopmental-disorder
#12
Sara B Estruch, Sarah A Graham, Swathi M Chinnappa, Pelagia Deriziotis, Simon E Fisher
BACKGROUND: Heterozygous disruption of FOXP2 causes a rare form of speech and language impairment. Screens of the FOXP2 sequence in individuals with speech/language-related disorders have identified several rare protein-altering variants, but their phenotypic relevance is often unclear. FOXP2 encodes a transcription factor with a forkhead box DNA-binding domain, but little is known about the functions of protein regions outside this domain. METHODS: We performed detailed functional analyses of seven rare FOXP2 variants found in affected cases, including three which have not been previously characterized, testing intracellular localization, transcriptional regulation, dimerization, and interaction with other proteins...
2016: Journal of Neurodevelopmental Disorders
https://www.readbyqxmd.com/read/27933100/genome-and-methylome-of-the-oleaginous-diatom-cyclotella-cryptica-reveal-genetic-flexibility-toward-a-high-lipid-phenotype
#13
Jesse C Traller, Shawn J Cokus, David A Lopez, Olga Gaidarenko, Sarah R Smith, John P McCrow, Sean D Gallaher, Sheila Podell, Michael Thompson, Orna Cook, Marco Morselli, Artur Jaroszewicz, Eric E Allen, Andrew E Allen, Sabeeha S Merchant, Matteo Pellegrini, Mark Hildebrand
BACKGROUND: Improvement in the performance of eukaryotic microalgae for biofuel and bioproduct production is largely dependent on characterization of metabolic mechanisms within the cell. The marine diatom Cyclotella cryptica, which was originally identified in the Aquatic Species Program, is a promising strain of microalgae for large-scale production of biofuel and bioproducts, such as omega-3 fatty acids. RESULTS: We sequenced the nuclear genome and methylome of this oleaginous diatom to identify the genetic traits that enable substantial accumulation of triacylglycerol...
2016: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/27933097/molecular-mechanisms-of-hpv-mediated-neoplastic-progression
#14
REVIEW
Rashmirani Senapati, Nihar Nalini Senapati, Bhagirathi Dwibedi
Human Papillomavirus is the major etiological agent in the development of cervical cancer but not a sufficient cause. Despite significant research, the underlying mechanisms of progression from a low-grade squamous intraepithelial lesion to high grade squamous intraepithelial lesion are yet to be understood. Deregulation of viral gene expression and host genomic instability play a central role in virus-mediated carcinogenesis. Key events such as viral integration and epigenetic modifications may lead to the deregulation of viral and host gene expression...
2016: Infectious Agents and Cancer
https://www.readbyqxmd.com/read/27933036/functional-analysis-of-the-nitrogen-metabolite-repression-regulator-gene-nmra-in-aspergillus-flavus
#15
Xiaoyun Han, Mengguang Qiu, Bin Wang, Wen-Bing Yin, Xinyi Nie, Qiuping Qin, Silin Ren, Kunlong Yang, Feng Zhang, Zhenhong Zhuang, Shihua Wang
In Aspergillus nidulans, the nitrogen metabolite repression (NMR) regulator NmrA plays a major role in regulating the activity of the GATA transcription factor AreA during nitrogen metabolism. However, the function of nmrA in A. flavus has not been previously studied. Here, we report the identification and functional analysis of nmrA in A. flavus. Our work showed that the amino acid sequences of NmrA are highly conserved among Aspergillus species and that A. flavus NmrA protein contains a canonical Rossmann fold motif...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27933035/life-without-dutpase
#16
Csaba Kerepesi, Judit E Szabó, Veronika Papp-Kádár, Orsolya Dobay, Dóra Szabó, Vince Grolmusz, Beáta G Vértessy
Fine-tuned regulation of the cellular nucleotide pools is indispensable for faithful replication of Deoxyribonucleic Acid (DNA). The genetic information is also safeguarded by DNA damage recognition and repair processes. Uracil is one of the most frequently occurring erroneous bases in DNA; it can arise from cytosine deamination or thymine-replacing incorporation. Two enzyme activities are primarily involved in keeping DNA uracil-free: dUTPase (dUTP pyrophosphatase) activity that prevent thymine-replacing incorporation and uracil-DNA glycosylase activity that excise uracil from DNA and initiate uracil-excision repair...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27932868/analysis-of-parallel-algorithms-on-smp-node-and-cluster-of-workstations-using-parallel-programming-models-with-new-tile-based-method-for-large-biological-datasets
#17
D D Shrimankar, S R Sathe
Sequence alignment is an important tool for describing the relationships between DNA sequences. Many sequence alignment algorithms exist, differing in efficiency, in their models of the sequences, and in the relationship between sequences. The focus of this study is to obtain an optimal alignment between two sequences of biological data, particularly DNA sequences. The algorithm is discussed with particular emphasis on time, speedup, and efficiency optimizations. Parallel programming presents a number of critical challenges to application developers...
2016: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/27932860/rebound-macular-edema-following-oral-acetazolamide-therapy-for-juvenile-x-linked-retinoschisis-in-an-italian-family
#18
Maria Silvana Galantuomo, Maurizio Fossarello, Alberto Cuccu, Roberta Farci, Markus N Preising, Birgit Lorenz, Pietro Emanuele Napoli
BACKGROUND: Juvenile X-linked retinoschisis (RS1, OMIM: 312700) is a hereditary vitreoretinal dystrophy characterized by bilateral foveal schisis and, in half of the patients, splitting through the nerve fiber layer in the peripheral retina. In the first decade of life, patients usually develop a decrease in visual acuity. Long-term visual outcomes can be poor due to the limited number of known successful treatments. PURPOSE: The purposes of this study were to present, for the first time, a p...
2016: Clinical Ophthalmology
https://www.readbyqxmd.com/read/27932801/dna-encoded-chemistry-enabling-the-deeper-sampling-of-chemical-space
#19
Robert A Goodnow, Christoph E Dumelin, Anthony D Keefe
DNA-encoded chemical library technologies are increasingly being adopted in drug discovery for hit and lead generation. DNA-encoded chemistry enables the exploration of chemical spaces four to five orders of magnitude more deeply than is achievable by traditional high-throughput screening methods. Operation of this technology requires developing a range of capabilities including aqueous synthetic chemistry, building block acquisition, oligonucleotide conjugation, large-scale molecular biological transformations, selection methodologies, PCR, sequencing, sequence data analysis and the analysis of large chemistry spaces...
December 9, 2016: Nature Reviews. Drug Discovery
https://www.readbyqxmd.com/read/27932754/-overexpression-of-lentivirus-rfx1-and-its-inhibitory-effect-on-proliferation-of-glioblastoma-cells
#20
Kai Cheng, Haojie Sun, Mingzhi Zhang, Li Shen
To construct overexpression lentivirus vector for human regulatory factor X1 (RFX1) gene, and to explore its effect on proliferation of F98 cell line.
 Methods: Huamn RFX1 gene was amplified by polymerase reaction. Gene amplification products were inserted into lentivirus vector pITA, and the lentivirus vector pITA-RFX1 was constructed. The constructed vector was verified by agarose gel electrophoresis and DNA sequencing. Lentivirus vector pITA-RFX1 and virus packaging plasmids were cotransfected into 293T cells, and then transfected into F98 cells...
November 28, 2016: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
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