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https://www.readbyqxmd.com/read/28542338/a-technique-for-setting-analytical-thresholds-in-massively-parallel-sequencing-based-forensic-dna-analysis
#1
Brian Young, Jonathan L King, Bruce Budowle, Luigi Armogida
Amplicon (targeted) sequencing by massively parallel sequencing (PCR-MPS) is a potential method for use in forensic DNA analyses. In this application, PCR-MPS may supplement or replace other instrumental analysis methods such as capillary electrophoresis and Sanger sequencing for STR and mitochondrial DNA typing, respectively. PCR-MPS also may enable the expansion of forensic DNA analysis methods to include new marker systems such as single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) that currently are assayable using various instrumental analysis methods including microarray and quantitative PCR...
2017: PloS One
https://www.readbyqxmd.com/read/28523298/role-of-genetic-polymorphism-in-nutritional-supplementation-therapy-in-personalized-medicine
#2
Nicolae Ovidiu Peneş, Bernard Weber, Silviu Dumitru Păun
Genetic-guided nutritional supplementation therapy in personalized medicine is the type of treatment that prevents and acts against errors during the copying process of a cell's deoxyribonucleic acid (DNA), mistakes that lead to diversification in the DNA sequence at certain locations, called single nucleotide polymorphisms (SNPs). Positive results are quickly achieved using one of the four types of therapy. These types are: personalized, when individual human genetic variations drive individual treatment, preventive, with a tailored healthcare strategy and therapeutic preventive drugs and vaccines, participatory, when empowered patients make informed choices and take responsibility of their own health and predictive, using a proactive approach to health and medicine...
2017: Romanian Journal of Morphology and Embryology, Revue Roumaine de Morphologie et Embryologie
https://www.readbyqxmd.com/read/28522317/the-association-between-cytochrome-p450-3a-progesterone-receptor-polymorphisms-plasma-17-ohpc-concentrations-and-spontaneous-preterm-birth
#3
Martha L Bustos, Steve N Caritis, Kathleen A Jablonski, Uma M Reddy, Yoram Sorokin, John M Thorp, Michael W Varner, Ronald J Wapner, Jay D Iams, Marshall W Carpenter, Alan M Peaceman, Brian M Mercer, Anthony Sciscione, Dwight J Rouse, Susan M Ramin
BACKGROUND: Infants born before 37 weeks' gestation are of public health concern since complications associated with preterm birth are the leading cause of mortality in children under 5 years of age and a major cause of morbidity and lifelong disability. The administration of 17-hydroxyprogesterone caproate (17-OHPC) reduces preterm birth by 33% in women with history spontaneous preterm birth (SPTB). We demonstrated previously that plasma concentrations of 17-OHPC vary widely among pregnant women and that women with 17-OHPC plasma concentrations in the lowest quartile had SPTB rates of 40% vs rates of 25% in those women with higher concentrations...
May 15, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28521061/extracellular-camp-activates-molecular-signalling-pathways-associated-with-sperm-capacitation-in-bovines
#4
Carlos Agustín I Alonso, Claudia E Osycka-Salut, Luciana Castellano, Andreína Cesari, Nicolás Di Siervi, Adrián Mutto, Anders Johannisson, Jane M Morrell, Carlos Davio, Silvina Perez-Martinez
STUDY QUESTION: Is extracellular cAMP involved in the regulation of signalling pathways in bovine sperm capacitation? SUMMARY ANSWER: Extracellular cAMP-induced sperm capacitation through the activation of different signalling pathways that involve phospholipase C (PLC), PKC/ERK1-2 signalling and an increase in sperm Ca2+ levels, as well as soluble AC and cAMP/protein kinase A (PKA) signalling. WHAT IS KNOWN ALREADY: In order to fertilize the oocyte, ejaculated spermatozoa must undergo a series of changes in the female reproductive tract, known as capacitation...
May 18, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/28500271/causal-associations-of-adiposity-and-body-fat-distribution-with-coronary-heart-disease-stroke-subtypes-and-type-2-diabetes-a-mendelian-randomization-analysis
#5
Caroline Dale, Ghazaleh Fatemifar, Tom Palmer, Jonathan White, David Prieto-Merino, Delilah Zabaneh, Jorgen E L Engmann, Tina Shah, Andrew Wong, Helen R Warren, Stela McLachlan, Stella Trompet, Max Moldovan, Richard W Morris, Reecha Sofat, Meena Kumari, Elina Hyppönen, Barbara J Jefferis, Tom R Gaunt, Yoav Ben-Shlomo, Ang Zhou, Aleksandra Gentry-Maharaj, Andy Ryan, Renée de Mutsert, Raymond Noordam, Mark J Caulfield, J Wouter Jukema, Bradford B Worrall, Patricia B Munroe, Usha Menon, Chris Power, Diana Kuh, Debbie A Lawlor, Steve E Humphries, Dennis O Mook-Kanamori, George Davey Smith, Naveed Sattar, Mika Kivimaki, Jacqueline F Price, Frank Dudbridge, Aroon D Hingorani, Michael V Holmes, Juan-Pablo Casas
Background -Implications of different adiposity measures on cardiovascular disease aetiology remain unclear. In this paper we quantify and contrast causal associations of central adiposity (waist:hip ratio adjusted for BMI (WHRadjBMI)) and general adiposity (body mass index (BMI)) with cardiometabolic disease. Methods -97 independent single nucleotide polymorphisms (SNPs) for BMI and 49 SNPs for WHRadjBMI were used to conduct Mendelian randomization analyses in 14 prospective studies supplemented with CHD data from CARDIoGRAMplusC4D (combined total 66,842 cases), stroke from METASTROKE (12,389 ischaemic stroke cases), type 2 diabetes (T2D) from DIAGRAM (34,840 cases), and lipids from GLGC (213,500 participants) consortia...
May 12, 2017: Circulation
https://www.readbyqxmd.com/read/28498882/mutational-signatures-and-mutable-motifs-in-cancer-genomes
#6
Igor B Rogozin, Youri I Pavlov, Alexander Goncearenco, Subhajyoti De, Artem G Lada, Eugenia Poliakov, Anna R Panchenko, David N Cooper
Cancer is a genetic disorder, meaning that a plethora of different mutations, whether somatic or germ line, underlie the etiology of the 'Emperor of Maladies'. Point mutations, chromosomal rearrangements and copy number changes, whether they have occurred spontaneously in predisposed individuals or have been induced by intrinsic or extrinsic (environmental) mutagens, lead to the activation of oncogenes and inactivation of tumor suppressor genes, thereby promoting malignancy. This scenario has now been recognized and experimentally confirmed in a wide range of different contexts...
May 11, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28495197/randomized-allopurinol-controlled-trial-of-the-effects-of-dietary-nucleotides-and-active-hexose-correlated-compound-in-the-treatment-of-canine-leishmaniosis
#7
Sergi Segarra, Guadalupe Miró, Ana Montoya, Luis Pardo-Marín, Noemí Boqué, Lluis Ferrer, José Cerón
First-line treatment for canine leishmaniosis (CanL) is N-methylglucamine antimoniate (MGA) combined with allopurinol. However, in some dogs allopurinol may induce hyperxanthinuria leading to urolithiasis. Moreover, allopurinol resistance has recently been described in Leishmania infantum isolates from treated dogs with a relapse of the disease. Alternative treatments are thus needed. Since the type of host immune response strongly influences CanL progression and prognosis, dogs could benefit from treatments targeted at modulating such response, such as nucleotides and active hexose correlated compound (AHCC)...
May 30, 2017: Veterinary Parasitology
https://www.readbyqxmd.com/read/28483855/the-association-of-metal-homeostasis-and-p-ppgpp-regulation-in-the-pathophysiology-of-enterococcus-faecalis
#8
C Colomer-Winter, A O Gaca, J A Lemos
In Enterococcus faecalis, the regulatory nucleotides pppGpp and ppGpp, collectively (p)ppGpp, are required for growth in blood, survival within macrophages and virulence. However, a clear understanding of how (p)ppGpp promotes virulence in E. faecalis and other bacterial pathogens is still lacking. In the host, the essential transition metals iron (Fe) and manganese (Mn) are not readily available to invading pathogens because of a host-driven process called nutritional immunity. Considering its central role in adaptation to nutritional stresses, we hypothesized that (p)ppGpp mediates E...
May 8, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28481944/a-consistent-and-potentially-exploitable-response-during-chondrogenesis-of-mesenchymal-stem-cells-from-osteoarthritis-patients-to-the-protein-encoded-by-the-susceptibility-gene-gdf5
#9
Madhushika Ratnayake, Maria Tselepi, Robert Bloxham, Frank Plöger, Louise N Reynard, John Loughlin
Osteoarthritis (OA) is a common joint disease characterised by the focal loss of the protective cartilage layer at the ends of the bones. It is painful, disabling, multifactorial and polygenic. The growth differentiation factor 5 gene GDF5 was one of the first reported OA susceptibility signals that showed consistent association to OA, with the transcript single nucleotide polymorphism (SNP) rs143383 demonstrating association in Asians and Europeans. The functional effect of the signal is reduced expression of the gene...
2017: PloS One
https://www.readbyqxmd.com/read/28475111/riboflavin-responsive-mitochondrial-dysfunction-in-neurodegenerative-diseases
#10
REVIEW
Tamilarasan Udhayabanu, Andreea Manole, Mohan Rajeshwari, Perumal Varalakshmi, Henry Houlden, Balasubramaniem Ashokkumar
Mitochondria are the repository for various metabolites involved in diverse energy-generating processes, like the TCA cycle, oxidative phosphorylation, and metabolism of amino acids, fatty acids, and nucleotides, which rely significantly on flavoenzymes, such as oxidases, reductases, and dehydrogenases. Flavoenzymes are functionally dependent on biologically active flavin adenine dinucleotide (FAD) or flavin mononucleotide (FMN), which are derived from the dietary component riboflavin, a water soluble vitamin...
May 5, 2017: Journal of Clinical Medicine
https://www.readbyqxmd.com/read/28466400/the-relationship-of-19-functional-polymorphisms-in-iodothyronine-deiodinase-and-psychological-well-being-in-hypothyroid-patients
#11
Yoon Young Cho, Hye Jeong Kim, Hye Won Jang, Tae Hyuk Kim, Chang-Seok Ki, Sun Wook Kim, Jae Hoon Chung
PURPOSE: Levothyroxine supplementation is insufficient for the management of one tenth of patients with hypothyroidism. Iodothyronine deiodinases have been suggested to play a role in residual hypothyroid symptoms of these patients by controlling local thyroid hormone homeostasis. Previous research has suggested a relationship between commonly inherited variations in type 2 iodothyronine deiodinase and impaired well-being. We evaluated the prevalence of iodothyronine deiodinase genotypes and their association with psychological well-being in the Korean hypothyroid population...
May 2, 2017: Endocrine
https://www.readbyqxmd.com/read/28465212/cell-culture-media-supplemented-with-raffinose-reproducibly-enhances-high-mannose-glycan-formation
#12
David Brühlmann, Anais Muhr, Rebecca Parker, Thomas Vuillemin, Blanka Bucsella, Franka Kalman, Serena Torre, Fabio La Neve, Antonio Lembo, Tobias Haas, Markus Sauer, Jonathan Souquet, Hervé Broly, Jürgen Hemberger, Martin Jordan
Glycosylation plays a pivotal role in pharmacokinetics and protein physiochemical characteristics. In particular, effector functions including antibody-dependent cell-mediated cytotoxicity (ADCC) can be desired, and it has been described that high-mannose species exhibited enhanced ADCC. In this work we present the trisaccharide raffinose as a novel cell culture medium supplement to promote high mannose N-glycans in fed-batch cultures, which is sought after in the development of biosimilars to match the quality profile of the reference medicinal product (RMP) also...
April 29, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28464260/cellular-migration-ability-is-modulated-by-extracellular-purines-in-ovarian-carcinoma-skov-3-cells
#13
A S Martínez-Ramírez, M Díaz-Muñoz, A M Battastini, A Campos-Contreras, A Olvera, L Bergamin, T Glaser, C E Jacintho Moritz, H Ulrich, F G Vázquez-Cuevas
Extracellular nucleotides and nucleosides have emerged as important elements regulating tissue homeostasis. Acting through specific receptors, have the ability to control gene expression patterns to direct cellular fate. We observed that SKOV-3 cells express the ectonucleotidases: ectonucleotide pyrophosphatase 1 (ENPP1), ecto-5'-nucleotidase (NT5E), and liver alkaline phosphatase (ALPL). Strikingly, in pulse and chase experiments supplemented with ATP, SKOV-3 cells exhibited low catabolic efficiency in the conversion of ADP into AMP, but they were efficient in converting AMP into adenosine...
May 2, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28423480/the-effect-of-high-dose-vitamin-d-supplementation-on-muscular-function-and-quality-of-life-in-postmenopausal-women-a-randomized-controlled-trial
#14
G Grimnes, N Emaus, K D Cashman, R Jorde
OBJECTIVE: Observational studies have suggested positive associations between serum 25-hydroxyvitamin D (25(OH)D) levels and muscular strength, balance and quality of life. Our aim was to examine whether high-dose vitamin D supplementation would improve these measures as compared to standard-dose vitamin D, as well as the possible muscular effects of single nucleotide polymorphisms (SNPs) in genes encoding vitamin D-related enzymes. DESIGN: A 12-month randomized, double-blind, controlled trial where the participants received daily elemental calcium (1000 mg) plus vitamin D3 (800 IU)...
April 19, 2017: Clinical Endocrinology
https://www.readbyqxmd.com/read/28402597/gene-gene-interaction-of-single-nucleotide-polymorphisms-in-16p13-3-may-contribute-to-the-risk-of-non-syndromic-cleft-lip-with-or-without-cleft-palate-in-chinese-case-parent-trios
#15
Dongjing Liu, Hong Wang, Holger Schwender, Mary L Marazita, Zhuqing Wang, Yuan Yuan, Ping Wang, Kung Yee Liang, Yah Huei Wu-Chou, Mengying Wang, Bing Shi, Hongping Zhu, Tao Wu, Terri H Beaty
Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with a complex and heterogeneous etiology. A recent genome-wide association study (GWAS) among Chinese populations has identified a new region at 16p13.3 as being associated with NSCL/P, which requires further replication. Here, we attempted to replicate and further clarify the genetic association between this region and NSCL/P, as well as testing for potential gene-gene (G × G) and gene-environment (G × E) interactions...
June 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28388001/exploring-the-rna-bound-and-rna-free-human-argonaute-2-by-molecular-dynamics-simulation-method
#16
Ren Kong, Lei Xu, Lianhua Piao, Dawei Zhang, Ting-Jun Hou, Shan Chang
Argonaute 2 (Ago2) protein is the major vehicle of MicroRNAs (miRNAs) guided gene repression and silencing processes. Although the crystal structure of human Ago2 (hAgo2) has recently been disclosed but the information of dynamically structural character of protein-RNA recognition is still lacking. Molecular dynamics simulations were used to systematically explore hAgo2 in the presence and absence of RNA duplex. Stable direct and water-mediated hydrogen bonds were observed between guide RNA backbone atoms and hAgo2, especially for nucleotides 2-7...
April 7, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28356434/the-growth-promoting-effect-of-dietary-nucleotides-in-fish-is-associated-with-an-intestinal-microbiota-mediated-reduction-in-energy-expenditure
#17
Xiaoze Guo, Chao Ran, Zhen Zhang, Suxu He, Min Jin, Zhigang Zhou
Background: Nucleotides have been used as functional nutrients to improve the growth and health of animals, including fish. The mechanism involved in the growth-promotion effect of nucleotides is still unclear.Objective: We investigated the bioenergetic mechanism underlying the growth-promotion effect of nucleotides in zebrafish and the associated roles played by the intestinal microbiota.Methods: Larval zebrafish were fed a control or a 0.1% mixed nucleotides-supplemented diet for 2 wk. Standard metabolic rate, the minimal rate of energy expenditure by animals at rest, was evaluated by oxygen consumption with the use of a respirometer...
March 29, 2017: Journal of Nutrition
https://www.readbyqxmd.com/read/28330166/a-molecular-phylogenetic-framework-for-bacillus-subtilis-using-genome-sequences-and-its-application-to-bacillus-subtilis-subspecies-stecoris-strain-d7xpn1-an-isolate-from-a-commercial-food-waste-degrading-bioreactor
#18
Joseph Adelskov, Bharat K C Patel
A thermophilic, heterotrophic and facultatively anaerobic bacterium designated strain D7XPN1 was isolated from Baku BakuKing™, a commercial food-waste degrading bioreactor (composter). The strain grew optimally at 45 °C (growth range between 24 and 50 °C) and pH 7 (growth pH range between pH 5 and 9) in Luria Broth supplemented with 0.3 % glucose. Strain D7XPN1 tolerated up to 7 % NaCl and showed amylolytic and xylanolytic activities. 16S rRNA gene analysis placed strain D7XPN1 in the cluster represented by Bacillus subtilis and the genome analysis of the 4...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28327659/the-immunosuppressant-mycophenolic-acid-alters-nucleotide-and-lipid-metabolism-in-an-intestinal-cell-model
#19
Svenja Heischmann, Monika Dzieciatkowska, Kirk Hansen, Dieter Leibfritz, Uwe Christians
The study objective was to elucidate the molecular mechanisms underlying the negative effects of mycophenolic acid (MPA) on human intestinal cells. Effects of MPA exposure and guanosine supplementation on nucleotide concentrations in LS180 cells were assessed using liquid chromatography-mass spectrometry. Proteomics analysis was carried out using stable isotope labeling by amino acids in cell culture combined with gel-based liquid chromatography-mass spectrometry and lipidome analysis using (1)H nuclear magnetic resonance spectroscopy...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327206/lessons-learned-from-additional-research-analyses-of-unsolved-clinical-exome-cases
#20
Mohammad K Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R Lalani, Christian P Schaaf, Michael F Wangler, Carlos A Bacino, Richard Alan Lewis, Lorraine Potocki, Brett H Graham, John W Belmont, Fernando Scaglia, Jordan S Orange, Shalini N Jhangiani, Theodore Chiang, Harsha Doddapaneni, Jianhong Hu, Donna M Muzny, Fan Xia, Arthur L Beaudet, Eric Boerwinkle, Christine M Eng, Sharon E Plon, V Reid Sutton, Richard A Gibbs, Jennifer E Posey, Yaping Yang, James R Lupski
BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease...
March 21, 2017: Genome Medicine
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