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Novel dna extraction

Serife Yerlikaya, Gokhan Zengin, Adriano Mollica, Mehmet C Baloglu, Yasemin Celik Altunoglu, Abdurrahman Aktumsek
The genus Ononis has important value as traditional drugs and foods. In the present work, we aimed to assess the chemical profiles and biological effects of Ononis natrix subsp. hispanica extracts (ethyl acetate, methanol, and water). For chemical profile, total and individual phenolic components were detected. For biological effects, antioxidant (DPPH, ABTS, CUPRAC, FRAP, phosphomolybdenum, and metal chelating assays), enzyme inhibitory (against cholinesterase, tyrosinase, α-amylase and α-glucosidase), antimicrobial, DNA protection and cytotoxic abilities were tested...
2017: Frontiers in Pharmacology
Munir Aktas, Sezayi Özübek
During early lactation, dairy cows may present a transient immunosuppressive state and develop anaplasmosis caused by Anaplasma marginale. In this study, clinical anaplasmosis in dairy cattle in the Thrace region of Turkey was investigated with respect to within-herd prevalence, vertical transmission, and genetic diversity. In March and September 2015, thirty lactating cows showed primary clinical signs of anaplasmosis, including fever, anaemia, decreased milk yield, anorexia, and laboured breathing. Symptoms disappeared in most cows after administration of long-acting oxytetracycline, but nine of them (30%) died...
October 2017: Comparative Immunology, Microbiology and Infectious Diseases
Bin Wu, Wuyang Ji, Shengran Liang, Chao Ling, Yan You, Lai Xu, Min-Er Zhong, Yi Xiao, Hui-Zhong Qiu, Jun-Yang Lu, Santasree Banerjee
Lynch syndrome (LS) is one of the most common familial forms of colorectal cancer predisposing syndrome with an autosomal dominant mode of inheritance. LS is caused by the germline mutations in DNA mismatch repair (MMR) genes including MSH2, MLH1, MSH6 and PMS2. Clinically, LS is characterized by high incidence of early-onset colorectal cancer as well as endometrial, small intestinal and urinary tract cancers, usually occur in the third to fourth decade of the life. Here we describe a five generation Chinese family with LS clinically diagnosed according to the Amsterdam II criteria...
August 15, 2017: Oncotarget
Naoki Nanashima, Kayo Horie, Mitsuru Chiba, Manabu Nakano, Hayato Maeda, Toshiya Nakamura
Blackcurrants (Ribes nigrum L., Grossulariaceae) possess a high content of anthocyanin polyphenols, which have been demonstrated to exhibit beneficial effects on health due to their antioxidant and anticarcinogenic prope-rties. The present study investigated novel functions of anthocyanin‑rich blackcurrant extracts (BCEs) in a healthy mammary epithelial cell line, MCF10A. The percentages of viable cells were 85, 75, 53 and 31% following exposure to 50, 100, 200 and 400 µg/ml BCE, respectively. The half‑maximal response concentration of BCE was 237...
August 29, 2017: Molecular Medicine Reports
Satoshi Tamazawa, Daisuke Mayumi, Hanako Mochimaru, Susumu Sakata, Haruo Maeda, Tatsuki Wakayama, Masayuki Ikarashi, Yoichi Kamagata, Hideyuki Tamaki
A novel thermophilic, anaerobic, chemoheterotrophic, acetate-oxidizing and iron(III)-, manganese(IV)-, nitrate- and sulfate-reducing bacterium, designated strain ANAT, was isolated from a deep subsurface oil field in Japan (Yabase oil field, Akita Pref.). Cells of strain ANAT were Gram-stain-negative, non-motile, non-spore forming and slightly curved or twisted rods (1.5-5.0 µm long and 0.6-0.7 µm wide). The isolate grew at 25-60 °C (optimum 55 °C) and pH 6.0-8.0 (optimum pH 7.0). The isolate was capable of reducing iron(III), manganese(IV), nitrate and sulfate as an electron acceptor...
September 12, 2017: International Journal of Systematic and Evolutionary Microbiology
Verónica Soares-Santos, Isabel Pardo, Sergi Ferrer
A novel quantitative PCR assay called Cells-qPCR has been developed for the rapid detection and quantification of yeasts, lactic acid bacteria (LAB) and acetic acid bacteria (AAB) directly from grape must and wine that does not require DNA extraction. The assay was tested on Brettanomyces bruxellensis, Saccharomyces cerevisiae, Lactobacillus plantarum, Oenococcus oeni, Acetobacter aceti and Gluconobacter oxydans in culture media, and in white and red grape musts and wines. Standard curves were constructed from DNA and cells for the six target species in all the matrices...
September 4, 2017: International Journal of Food Microbiology
Ruth Alonso, Diana Pisa, Ana M Fernández-Fernández, Alberto Rábano, Luis Carrasco
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease and the main cause of motor neuron pathology. The etiology of the disease remains unknown, and no effective therapy exists to halt the disease or improve the quality of life. Here, we provide compelling evidence for the existence of fungal infection in ALS. Immunohistochemistry analysis using a battery of antifungal antibodies revealed fungal structures such as yeast and hyphae in the motor cortex, the medulla and the spinal cord, in eleven patients with ALS...
September 6, 2017: Neurobiology of Disease
Raj Kumar Salar, Sukhvinder Singh Purewal, Kawaljit Singh Sandhu
In the present study, pearl millet cultivar PUSA-415 was fermented by solid state fermentation (SSF) process using Aspergillus sojae (MTCC-8779) as starter culture. The fermentation was carried out for the period of ten days. The effect of SSF on phenolic content, condensed tannin content, antioxidant potential and DNA damage protection of pearl millet during different fermentation period was determined. Results showed that SSF and thermal processing significantly affect the bioactive profile and antioxidant potential of bio-transformed pearl millet...
October 2017: Food Research International
Aurélie Hautefort, Julie Chesné, Jens Preussner, Soni S Pullamsetti, Jorg Tost, Mario Looso, Fabrice Antigny, Barbara Girerd, Marianne Riou, Saadia Eddahibi, Jean-François Deleuze, Werner Seeger, Elie Fadel, Gerald Simonneau, David Montani, Marc Humbert, Frédéric Perros
Pulmonary arterial hypertension (PAH) is a severe and incurable pulmonary vascular disease. One of the primary origins of PAH is pulmonary endothelial dysfunction leading to vasoconstriction, aberrant angiogenesis and smooth muscle cell proliferation, endothelial-to-mesenchymal transition, thrombosis and inflammation. Our objective was to study the epigenetic variations in pulmonary endothelial cells (PEC) through a specific pattern of DNA methylation. DNA was extracted from cultured PEC from idiopathic PAH (n = 11), heritable PAH (n = 10) and controls (n = 18)...
August 8, 2017: Oncotarget
Akiko Kumagai, William G Dunphy
Treslin, which is essential for incorporation of Cdc45 into the replicative helicase, possesses a partner called MTBP. We have analyzed Xenopus and human MTBP to assess its role in DNA replication. Depletion of MTBP from Xenopus egg extracts, which also removes Treslin, abolishes DNA replication. These extracts be can rescued with recombinant Treslin-MTBP, but not Treslin or MTBP alone. Thus, Treslin-MTBP is collectively necessary for replication. We have identified a C-terminal region of MTBP (the CTM domain) that binds efficiently to both double-stranded DNA and G-quadruplex (G4) DNA...
September 6, 2017: Molecular Biology of the Cell
Martin Christner, Dirk Dressler, Mark Andrian, Claudia Reule, Orlando Petrini
The fast and reliable characterization of bacterial and fungal pathogens plays an important role in infectious disease control and tracking of outbreak agents. DNA based methods are the gold standard for epidemiological investigations, but they are still comparatively expensive and time-consuming. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a fast, reliable and cost-effective technique now routinely used to identify clinically relevant human pathogens. It has been used for subspecies differentiation and typing, but its use for epidemiological tasks, e...
2017: PloS One
Macarena Parra, Jimmy Jung, Travis D Boone, Luan Tran, Elizabeth A Blaber, Mark Brown, Matthew Chin, Tori Chinn, Jacob Cohen, Robert Doebler, Dzung Hoang, Elizabeth Hyde, Matthew Lera, Louie T Luzod, Mark Mallinson, Oana Marcu, Youssef Mohamedaly, Antonio J Ricco, Kathleen Rubins, Gregory D Sgarlato, Rafael O Talavera, Peter Tong, Eddie Uribe, Jeffrey Williams, Diana Wu, Rukhsana Yousuf, Charles S Richey, Julie Schonfeld, Eduardo A C Almeida
The International Space Station (ISS) National Laboratory is dedicated to studying the effects of space on life and physical systems, and to developing new science and technologies for space exploration. A key aspect of achieving these goals is to operate the ISS National Lab more like an Earth-based laboratory, conducting complex end-to-end experimentation, not limited to simple microgravity exposure. Towards that end NASA developed a novel suite of molecular biology laboratory tools, reagents, and methods, named WetLab-2, uniquely designed to operate in microgravity, and to process biological samples for real-time gene expression analysis on-orbit...
2017: PloS One
Yao Lin, Wei Yin, Zhuan Bian
BACKGROUND: The phenotypic characters of X -linked Hypohidrotic Ectodermal Dysplasia (XLHED) are the dysplasia of epithelial- and mesenchymal-derived organs. Ectodysplasin (EDA) is the causative gene of XLHED. METHODS: The current study reported a large Chinese XLHED pedigree. The genomic DNA of adult and fetus was extracted from peripheral blood and shed chorion cell respectively. The nucleotide variation in EDA gene was screened through direct sequencing the coding sequence...
2017: PeerJ
Yuya Hamano, Sho Manabe, Chie Morimoto, Shuntaro Fujimoto, Keiji Tamaki
There is high demand for forensic age prediction in actual crime investigations. In this study, a novel age prediction model for saliva samples using methylation-sensitive high resolution melting (MS-HRM) was developed. The methylation profiles of ELOVL2 and EDARADD showed high correlations with age and were used to predict age with support vector regression. ELOVL2 was first reported as an age predictive marker for saliva samples. The prediction model showed high accuracy with a mean absolute deviation (MAD) from chronological age of 5...
September 5, 2017: Scientific Reports
Gang Liu, Wenjing Huang, Juan Wang, Xiaohua Liu, Jun Yang, Yu Zhang, Yong Geng, Wenfu Tan, Ao Zhang
A systemic medicinal chemistry campaign was conducted based on a literature hit compound 5 bearing the 4,5-dihydro-2H-benzo[b][1,5]oxazocin-6(3H)-one core through cyclization of two side substituents of the bicyclic skeleton combined with N-atom walking or ring-walking and the central ring expansion or extraction approaches, leading to several series of structurally unique tricyclic compounds. Among these, compound 29a was identified as the most potent against the hedgehog (Hh) signaling pathway showing an IC50 value of 23 nM...
September 5, 2017: Journal of Medicinal Chemistry
Ofir Shukron, Michael Hauer, David Holcman
Stochastic single particle trajectories are used to explore the local chromatin organization. We present here a statistical analysis of the first contact time distributions between two tagged loci recorded experimentally. First, we extract the association and dissociation times from data for various genomic distances between loci, and we show that the looping time occurs in confined nanometer regions. Second, we characterize the looping time distribution for two loci in the presence of multiple DNA damages...
September 4, 2017: Scientific Reports
Abdoulaye Thioye, Zouhaier Ben Ali Gam, Malick Mbengue, Jean-Luc Cayol, Manon Joseph-Bartoli, Coumba Touré-Kane, Marc Labat
Several strains of sulfate-reducing bacteria were isolated from marine sediments recovered from Hann Bay (Senegal). All were related to members of the genus Desulfovibrio. A strictly anaerobic, mesophilic and moderately halophilic strain designated BLaC1T was further characterized. Cells of strain BLaC1T stained Gram-negative and were 0.5 µm wide and 2-4 µm long, motile, rod-shaped and non-spore-forming. The four major fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C17 : 0 and anteiso-C17 : 0...
September 4, 2017: International Journal of Systematic and Evolutionary Microbiology
Kaiser Jamil, Archana Jayaraman, Javeed Ahmad, Sindhu Joshi, Shiva Kumar Yerra
Several reports document the role of tumor necrosis factor alpha (TNF-α) and lipid metabolism in the context of acute inflammation as a causative factor in obesity-associated insulin resistance and as one of the causative parameter of type 2 diabetes mellitus (T2DM). Our aim was to investigate the association between -308G/A and -238G/A polymorphisms located in the promoter region of the TNF-α gene in T2DM in the Indian population with bioinformatics analysis of TNF-α protein networking with an aim to find new target sites for the treatment of T2DM...
September 2017: Saudi Journal of Biological Sciences
Jiyun Zhou, Qin Lu, Ruifeng Xu, Yulan He, Hongpeng Wang
BACKGROUND: Prediction of DNA-binding residue is important for understanding the protein-DNA recognition mechanism. Many computational methods have been proposed for the prediction, but most of them do not consider the relationships of evolutionary information between residues. RESULTS: In this paper, we first propose a novel residue encoding method, referred to as the Position Specific Score Matrix (PSSM) Relation Transformation (PSSM-RT), to encode residues by utilizing the relationships of evolutionary information between residues...
August 29, 2017: BMC Bioinformatics
Edna G O Morea, Maria Alejandra Viviescas, Carlos A H Fernandes, Fabio F Matioli, Cristina B B Lira, Maribel F Fernandez, Barbara S Moraes, Marcelo S da Silva, Camila B Storti, Marcos R M Fontes, Maria Isabel N Cano
BACKGROUND: Leishmania spp. telomeres are composed of 5'-TTAGGG-3' repeats associated with proteins. We have previously identified LaRbp38 and LaRPA-1 as proteins that bind the G-rich telomeric strand. At that time, we had also partially characterized a protein: DNA complex, named LaGT1, but we could not identify its protein component. METHODS AND RESULTS: Using protein-DNA interaction and competition assays, we confirmed that LaGT1 is highly specific to the G-rich telomeric single-stranded DNA...
August 24, 2017: Biochimica et Biophysica Acta
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