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Dna fragmentation

Pavlina Sasheva, Ueli Grossniklaus
Over the last years, it has become increasingly clear that environmental influences can affect the epigenomic landscape and that some epigenetic variants can have heritable, phenotypic effects. While there are a variety of methods to perform genome-wide analyses of DNA methylation in model organisms, this is still a challenging task for non-model organisms without a reference genome. Differentially methylated region-representational difference analysis (DMR-RDA) is a sensitive and powerful PCR-based technique that isolates DNA fragments that are differentially methylated between two otherwise identical genomes...
2017: Methods in Molecular Biology
María Ángeles Guevara, Nuria de María, Enrique Sáez-Laguna, María Dolores Vélez, María Teresa Cervera, José Antonio Cabezas
Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is the methylation-sensitive amplified polymorphism technique (MSAP) which is a modification of amplified fragment length polymorphism (AFLP). It has been used to study methylation of anonymous CCGG sequences in different fungi, plants, and animal species. The main variation of this technique resides on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent-cutter restriction enzyme...
2017: Methods in Molecular Biology
Diyendo Massilani, Silvia Guimaraes, Jean-Philip Brugal, E Andrew Bennett, Malgorzata Tokarska, Rose-Marie Arbogast, Gennady Baryshnikov, Gennady Boeskorov, Jean-Christophe Castel, Sergey Davydov, Stéphane Madelaine, Olivier Putelat, Natalia N Spasskaya, Hans-Peter Uerpmann, Thierry Grange, Eva-Maria Geigl
BACKGROUND: Climatic and environmental fluctuations as well as anthropogenic pressure have led to the extinction of much of Europe's megafauna. The European bison or wisent (Bison bonasus), one of the last wild European large mammals, narrowly escaped extinction at the onset of the 20th century owing to hunting and habitat fragmentation. Little is known, however, about its origin, evolutionary history and population dynamics during the Pleistocene. RESULTS: Through ancient DNA analysis we show that the emblematic European bison has experienced several waves of population expansion, contraction, and extinction during the last 50,000 years in Europe, culminating in a major reduction of genetic diversity during the Holocene...
October 21, 2016: BMC Biology
Liang Li, Jin-Yu Zhao, Hui-Xia Chen, Hui-Dong Ju, Meng An, Zhen Xu, Lu-Ping Zhang
The cinnamon flounder Pseudorhombus cinnamoneus is a frequently consumed marine fish in China. However, the occurrence of ascaridoid larvae in P. cinnamoneus remains unclear. In the present study, a total of 85 P. cinnamoneus caught from the Yellow Sea (off Shidao, 36°52'57″N, 122°26'42″E) in 2011, which is located between mainland China and the Korean Peninsula, was investigated for ascaridoid larval infection. Four ascaridoid larval types, including Anisakis type I of Berland (1961), Hysterothylacium type of Smith (1983), Hysterothylacium type HL of Guo et al...
October 14, 2016: International Journal of Food Microbiology
Szu-I Yeh, Wei-Feng Fang, Chao-Jyun Huang, Tzu-Ming Wang, Jing-Tang Yang
A simple and visual method to detect multi-nucleotide polymorphism (MNP) was performed on a pneumatic droplet manipulation platform on an open surface. This approach to colorimetric DNA detection was based on the hybridization-mediated growth of gold nanoparticle probes (AuNP probes). The growth size and configuration of the AuNP are dominated by the number of DNA samples hybridized with the probes. Based on the specific size- and shape-dependent optical properties of the nanoparticles, the number of mismatches in a sample DNA fragment to the probes is able to be discriminated...
September 27, 2016: Journal of Visualized Experiments: JoVE
Gosuke Hayashi, Kenta Koyama, Hidefumi Shiota, Asuka Kamio, Takayoshi Umeda, Genta Nagae, Hiroyuki Aburatani, Akimitsu Okamoto
5-hydroxymethylcytosine (hmC) is an essential intermediate in the active DNA demethylation pathway. Here we report a new base-resolution method for measuring hmC by combining peroxotungstate-mediated oxidation and sequencing analysis. We reveal that an oxidized product of hmC, trihydroxylated thymine (thT), tolerated the incorporation of dATP as a substrate in the process of DNA polymerase elongation. By comparing the results of Sanger sequencing before and after the oxidation, we observed that hmC sites on single-stranded DNAs could be discriminated from unmethylated cytosines...
October 21, 2016: Journal of the American Chemical Society
Brandon L Thompson, Christopher Birch, Daniel A Nelson, Jingyi Li, Jacquelyn A DuVall, Delphine Le Roux, An-Chi Tsuei, Daniel L Mills, Brian E Root, James P Landers
Current conventional methods utilized for forensic DNA analysis are time consuming and labor-intensive requiring large and expensive equipment and instrumentation. While more portable Rapid DNA systems have been developed, introducing them to a working laboratory still necessitates a high cost of initiation followed by the recurrent cost of the devices. This has highlighted the need for an inexpensive, rapid and portable DNA analysis tool for human identification in a forensic setting. In order for an integrated DNA analysis system such as this to be realized, device operations must always be concluded by a rapid separation of short-tandem repeat (STR) DNA fragments...
October 21, 2016: Lab on a Chip
Hassan Mansouri-Torshizi, Elham Rezaei, Farzaneh Kamranfar, Mostafa Heidari Majd
Purpose: High solubility, low renal toxicity and apoptosis-inducing ability of palladium complexes are the reasons for their synthesis. Methods: In vitro cytotoxic study of previously synthesized [Pd(en)(8HQ)]NO3 , was carried out on breast cancer MCF-7 cell lines and prostate cancer DU145 cell lines. DNA fragmentation indicative of apoptotic was also evaluated by TUNEL assay on DU145 cell line. Results: FT-IR spectra of final complex confirmed the existence of chelating ligands. The DU145 cells unlike the MCF-7 cells, demonstrated the significant influence of the Pd (II) complex...
September 2016: Advanced Pharmaceutical Bulletin
Guangxian Zhang, Xiancheng Zeng, Ren Zhang, Juan Liu, Weici Zhang, Yujun Zhao, Xiaoyuan Zhang, Zhixue Wu, Yuhui Tan, Yingya Wu, Biaoyan Du
BACKGROUND: Hepatocellular carcinoma (HCC) is the most commonly diagnosed malignancy of the liver, occurs frequently in the setting of chronic liver injury. Although multiple therapeutic approaches are available, the prognosis of patients with HCC remains poor. Dioscin is a natural steroid saponin that presents in various plants. The anti-cancer and anti-fibrotic effects have been extensively reported. However, the effect of dioscin on HCC remains unclear. We aimed to investigate the anti-HCC properties of dioscin in vitro and in vivo...
November 15, 2016: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
Birsen Yigit Arslan, Ferhat Arslan, Kerem Erkalp, Ayşin Alagöl, Mehmet Salih Sevdi, Güneş Yıldız, Suat Hayri Küçük, Serdar Altınay
INTRODUCTION AND AIM: To study the protective, preventive effect of luteolin from colistin-induced nephrotoxicity. MATERIAL AND METHOD: Four different treatment options were tested on rats: colistin, luteolin, and a combination of colistin and luteolin, intraperitoneally as two doses a day, for seven days. Another group of rats were used as the control and treated with sterile saline. Serum creatinine levels were measured before and after treatment. Histological changes and colistin-induced apoptosis (Insitu BrdU-red DNA Fragmentation Assay Kit) of the renal tissues were examined after the scarification procedure...
October 20, 2016: Renal Failure
Y Nouma, W Ben Amar, M Zribi, S Bardaa, Z Hammami, S Maatoug
We report a case of a Tunisian footballer who was found dead abroad under suspicious circumstances. The cause of death was, originally, attributed to a lightning strike. The corpse was buried without/autopsy. Over thirty years later, the family requested the exhumation to verify the identity and the cause of death. The exhumation was performed in 2011. DNA profiling from teeth and femur bone samples confirmed the identity of the deceased. The dry bone study revealed defects in the skull and the pelvis evoking firearm injuries...
October 11, 2016: Journal of Forensic and Legal Medicine
Maria Prokofjeva, Vladimir Tsvetkov, Dmitry Basmanov, Anna Varizhuk, Maria Lagarkova, Igor Smirnov, Kirill Prusakov, Dmitry Klinov, Vladimir Prassolov, Galina Pozmogova, Sergey N Mikhailov
New natural and chemically modified DNA aptamers that inhibit HIV-1 activity at submicromolar concentrations (presumably via preventing viral entry into target cells) are reported. The new DNA aptamers were developed based on known intramolecular G-quadruplexes (G4s) that were functionally unrelated to HIV inhibition [the thrombin-binding aptamer and the fragment of the human oncogene promoter (Bcl2)]. The majority of previously described DNA inhibitors of HIV infection adopt intermolecular structures, and thus their folding variability represents an obvious disadvantage...
October 20, 2016: Nucleic Acid Therapeutics
Magdalena M Bus, Ognjen Karas, Marie Allen
The capillary electrophoresis (CE) technology is commonly used for fragment length separation of markers in forensic DNA analysis. In this study, pyrosequencing technology was used as an alternative and rapid tool for the analysis of biallelic InDel (insertion/deletion) markers for individual identification. The DNA typing is based on a subset of the InDel markers that are included in the Investigator(®) DIPplex Kit, which are sequenced in a multiplex pyrosequencing analysis. To facilitate the analysis of degraded DNA, the polymerase chain reaction (PCR) fragments were kept short in the primer design...
October 20, 2016: Electrophoresis
E Yu Zemskova, Eksp Timoshenko, Eksp Leonov, P L Ivanov
The objective of the present work was to study the phenomenon of nucleotide sequence polymorphism in alleles of the STR-loci of human chromosomal DNA and to estimate its interpopulation differences with a view to the search for the molecular-genetic markers to be used as an efficient tool for the determination of belonging of the subjects of interest to a given population. We undertook the comprehensive analysis of amplified DNA fragment sequence polymorphism (AFSP) and amplified DNA fragment length polymorphism (AFLP) with the use of the PLEX-ID-TM analytical mass-spectrometry platform (Abbott Molecular, USA)...
2016: Sudebno-meditsinskaia Ekspertiza
Leonardo Romorini, Ximena Garate, Gabriel Neiman, Carlos Luzzani, Verónica Alejandra Furmento, Alejandra Sonia Guberman, Gustavo Emilio Sevlever, María Elida Scassa, Santiago Gabriel Miriuka
Human embryonic and induced pluripotent stem cells are self-renewing pluripotent stem cells (PSC) that can differentiate into a wide range of specialized cells. Basic fibroblast growth factor is essential for PSC survival, stemness and self-renewal. PI3K/AKT pathway regulates cell viability and apoptosis in many cell types. Although it has been demonstrated that PI3K/AKT activation by bFGF is relevant for PSC stemness maintenance its role on PSC survival remains elusive. In this study we explored the molecular mechanisms involved in the regulation of PSC survival by AKT...
October 20, 2016: Scientific Reports
Francielle Pelegrin Garcia, Jean Henrique da Silva Rodrigues, Zia Ud Din, Edson Rodrigues-Filho, Tânia Ueda-Nakamura, Rachel Auzély-Velty, Celso Vataru Nakamura
Leishmaniasis is a neglected tropical disease that affects millions of people worldwide. Current therapies mainly rely on antimonial drugs that are inadequate because of their high toxicity and increased drug resistance. An urgent need exists to discover new, more effective, more affordable, and more target-specific drugs. Pathways that are associated with apoptosis-like cell death have been identified in unicellular eukaryotes, including protozoan parasites. In the present study, we studied the mechanism of cell death that is induced by A3K2A3 against L...
October 19, 2016: Apoptosis: An International Journal on Programmed Cell Death
Riccardo Paolo Lia, Yasen Mutafchiev, Vincenzo Veneziano, Alessio Giannelli, Francesca Abramo, Mario Santoro, Maria Stefania Latrofa, Cinzia Cantacessi, Coralie Martin, Domenico Otranto, Andrea Bertuglia, Barbara Riccio
Equids can be infected by a range of skin-dwelling filarial nematodes, including four species of the genus Onchocerca. Current literature on equine onchocercosis is fragmentary and often limited to isolated case reports. The present study aimed to describe a clinical case of equine onchocercosis caused by Onchocerca boehmi (Supperer, 1953) (syn. Elaeophora boehmi) in an 8-year-old gelding Belgian show jumper from northern Italy. The horse was presented with a firm and painless mass on the proximal third of the right metacarpal region...
October 19, 2016: Parasitology Research
Seyed Hadi Mousavi, Azar Hosseini, Elham Bakhtiari, Hassan Rakhshandeh
OBJECTIVE: Doxorubicin (DOX) is an effective anticancer drug but its clinical application is limited because it induces apoptosis in cardiomyocytes and leads to permanent degenerative cardiomyopathy and heart failure possibly due to oxidative stress. Recent studies showed that Capparis spinosa (C. spinose) exhibits potent antioxidant activity. So, in this study, we explored the protective effect of hydro-alcoholic extract of C. spinosa against DOX-induced cytotoxicity in H9c2 cells. MATERIALS AND METHODS: Cell viability was quantified by MTT assay...
September 2016: Avicenna Journal of Phytomedicine
Séverine Fourdrilis, Patrick Mardulyn, Olivier J Hardy, Kurt Jordaens, António Manuel de Frias Martins, Thierry Backeljau
We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkle Melarhaphe neritoides (Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cytb gene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago. The mtDNA hyperdiversity in M...
2016: PeerJ
Daniel G Mulcahy, Kenneth S Macdonald, Seán G Brady, Christopher Meyer, Katharine B Barker, Jonathan Coddington
Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples-and their quantifiable metadata-preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher molecular weight, and overall "genome-quality" DNA (gDNA) will be desirable. Ideally, biorepositories should publish numerical scale measurements of DNA quality useful to the user community...
2016: PeerJ
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