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https://www.readbyqxmd.com/read/28821188/panmixia-and-limited-interspecific-introgression-in-coyotes-canis-latrans-from-west-virginia-and-virginia-usa
#1
Justin H Bohling, Lauren L Mastro, Jennifer R Adams, Eric M Gese, Sheldon F Owen, Lisette P Waits
The expansion of coyotes (Canis latrans) into the eastern United States has had major consequences for ecological communities and wildlife managers. Despite this, there has been little investigation of the genetics of coyotes across much of this region, especially outside of the northeast. Understanding patterns of genetic structure and interspecific introgression would provide insights into the colonization history of the species, its response to the modern environment, and interactions with other canids. We examined the genetic characteristics of 121 coyotes from the mid-Atlantic states of West Virginia and Virginia by genotyping 17 polymorphic nuclear DNA microsatellite loci...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28821185/phylogeography-and-ecological-niche-modeling-of-the-desert-iguana-dipsosaurus-dorsalis-baird-girard-1852-in-the-baja-california-peninsula
#2
Tania Valdivia-Carrillo, Francisco J García-De León, Ma Carmen Blázquez, Carina Gutiérrez-Flores, Patricia González Zamorano
Understanding the factors that explain the patterns of genetic structure or phylogeographic breaks at an intraspecific level is key to inferring the mechanisms of population differentiation in its early stages. These topics have been well studied in the Baja California region, with vicariance and the dispersal ability of individuals being the prevailing hypothesis for phylogeographic breaks. In this study, we evaluated the phylogeographic patterns in the desert iguana (Dipsosaurus dorsalis), a species with a recent history in the region and spatial variation in life history traits...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28821184/repetitive-dna-in-the-catfish-genome-rdna-microsatellites-and-tc1-mariner-transposon-sequences-in-imparfinis-species-siluriformes-heptapteridae
#3
Juceli Gonzalez Gouveia, Ivan Rodrigo Wolf, Laurival Antonio Vilas-Boas, John Seymour Heslop-Harrison, Trude Schwarzacher, Ana Lúcia Dias
Physical mapping of repetitive DNA families in the karyotypes of fish is important to understand the organization and evolution of different orders, families, genera, or species. Fish in the genus Imparfinis show diverse karyotypes with various diploid numbers and ribosomal DNA (rDNA) locations. Here we isolated and characterized Tc1-mariner nucleotide sequences from Imparfinis schubarti, and mapped their locations together with 18S rDNA, 5S rDNA, and microsatellite probes in Imparfinis borodini and I. schubarti chromosomes...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28821183/improvement-of-the-threespine-stickleback-genome-using-a-hi-c-based-proximity-guided-assembly
#4
Catherine L Peichel, Shawn T Sullivan, Ivan Liachko, Michael A White
Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28821160/leuconostoc-mesenteroides-derived-anticancer-pharmaceuticals-hinder-inflammation-and-cell-survival-in-colon-cancer-cells-by-modulating-nf-%C3%AE%C2%BAb-akt-pten-mapk-pathways
#5
Sepideh Zununi Vahed, Abolfazl Barzegari, Yalda Rahbar Saadat, Ali Goreyshi, Yadollah Omidi
Promising results from different studies on the effect of probiotics in cancer prevention and therapy have so far been reported. However, the molecular mechanism of the interaction of probiotics with cancer cells is yet to be fully understood. In the present study, Leuconostoc mesenteroides was isolated from traditional dairy products, and its probiotic characteristics were determined. HT-29 cells were treated with conditioned-medium of designated bacteria and the cell apoptosis was studied at cellular and molecular level using DAPI staining, flow cytometry, DNA ladder assays, and real-time quantitative-PCR (q-PCR)...
August 14, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28821159/inhibition-of-dna-pk-enhances-chemosensitivity-of-b-cell-precursor-acute-lymphoblastic-leukemia-cells-to-doxorubicin
#6
Fatemeh Alikarami, Majid Safa, Mohammad Faranoush, Parisa Hayat, Ahmad Kazemi
DNA damage repair pathways greatly affect the response to genotoxic drugs in cancer cells, so inhibition of such pathways could be a potentially useful strategy to enhance chemosensitivity. DNA-dependent protein kinase (DNA-PK) plays a crucial role in the repair of DNA double-strand breaks (DSBs) that are probably one of the most detrimental types of DNA damage. It has been shown that DNA-PK is highly expressed in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) cells. Less well appreciated was the effect of DNA-PK inhibition on sensitivity of BCP-ALL cells to DNA-damaging agents...
August 14, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28821014/efficient-and-accurate-causal-inference-with-hidden-confounders-from-genome-transcriptome-variation-data
#7
Lingfei Wang, Tom Michoel
Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for higly accurate causal inference between gene expression traits using cis-regulatory DNA variations as causal anchors, which improves current methods by taking into consideration hidden confounders and weak regulations. Findr outperformed existing methods on the DREAM5 Systems Genetics challenge and on the prediction of microRNA and transcription factor targets in human lymphoblastoid cells, while being nearly a million times faster...
August 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28821011/the-photodynamic-action-of-pheophorbide-a-induces-cell-death-through-oxidative-stress-in-leishmania-amazonensis
#8
Nathielle Miranda, Hélito Volpato, Jean Henrique da Silva Rodrigues, Wilker Caetano, Tânia Ueda-Nakamura, Sueli de Oliveira Silva, Celso Vataru Nakamura
Leishmaniasis is a disease caused by hemoflagellate protozoa, affecting millions of people worldwide. The difficulties of treating patients with this parasitosis include the limited efficacy and many side effects of the currently available drugs. Therefore, the search for new compounds with leishmanicidal action is necessary. Photodynamic therapy has been studied in the medical field because of its selectivity, utilizing a combination of visible light, a photosensitizer compound, and singlet oxygen to reach the area of treatment...
August 11, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28820971/ultrasensitive-detection-of-ag-i-based-on-the-conformational-switching-of-a-multifunctional-aptamer-probe-induced-by-silver-i
#9
Yu-Feng Zhu, Yong-Sheng Wang, Bin Zhou, Yan-Qin Huang, Xue-Jiao Li, Si-Han Chen, Xiao-Feng Wang, Xian Tang
We for the first time confirmed that the low concentrations of Ag(I) could induce a silver specific aptamer probe (SAP) from a random coil sequence form to G-quadruplex structure. Thereby, a novel highly sensitive fluorescence strategy for silver(I) assay was established. The designed multifunctional SAP could act as a recognition element for Ag(I) and a signal reporter. The use of such a SAP can ultrasensitively and selectively detect Ag(I), giving a detection limit down to 0.64nM. This is much lower than those reported by related literatures...
August 10, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28820963/ketone-body-acetoacetate-buffers-methylglyoxal-via-a-non-enzymatic-conversion-during-diabetic-and-dietary-ketosis
#10
Trine Salomón, Christian Sibbersen, Jakob Hansen, Dieter Britz, Mads Vandsted Svart, Thomas Schmidt Voss, Niels Møller, Niels Gregersen, Karl Anker Jørgensen, Johan Palmfeldt, Thomas Bjørnskov Poulsen, Mogens Johannsen
The α-oxoaldehyde methylglyoxal is a ubiquitous and highly reactive metabolite known to be involved in aging- and diabetes-related diseases. If not detoxified by the endogenous glyoxalase system, it exerts its detrimental effects primarily by reacting with biopolymers such as DNA and proteins. We now demonstrate that during ketosis, another metabolic route is operative via direct non-enzymatic aldol reaction between methylglyoxal and the ketone body acetoacetate, leading to 3-hydroxyhexane-2,5-dione. This novel metabolite is present at a concentration of 10%-20% of the methylglyoxal level in the blood of insulin-starved patients...
August 17, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28820950/combined-aerobic-and-resistance-exercise-training-for-improving-reproductive-function-in-infertile-men-a-randomized-controlled-trial
#11
Behzad Hajizadeh Maleki, Bakhtyar Tartibian
This randomized controlled trial was conducted to examine the effects of 24 weeks of combined aerobic and resistance exercise training on seminal markers of inflammation and oxidative stress as well as markers of male reproductive function and reproductive performance in infertile patients. Of a total of 1296 infertile patients (aged 25-40 years) who were screened, 556 were randomly assigned to exercise (EX, n = 278) and non-exercise (NON-EX, n = 278) groups. Semen samples were taken before, 12 and 24 weeks as well as 7 and 30 days post intervention...
August 18, 2017: Applied Physiology, Nutrition, and Metabolism, Physiologie Appliquée, Nutrition et Métabolisme
https://www.readbyqxmd.com/read/28820917/whole-exome-sequencing-of-lacrimal-gland-adenoid-cystic-carcinoma
#12
David W Sant, Wensi Tao, Matthew G Field, Daniel Pelaez, Ke Jin, Anthony Capobianco, Sander R Dubovy, David T Tse, Gaofeng Wang
Purpose: To identify genomic mutations in lacrimal gland adenoid cystic carcinoma (LGACC) samples from patients. Methods: Genomic DNA was extracted from LGACC specimens. Whole exome sequencing (exome-seq) was conducted to screen for mutations. Capillary sequencing was performed to verify mutations in genes shared by multiple samples. Luciferase assays were used to evaluate functional consequences of NOTCH1 mutations. Results: The mutation profile of LGACC was complicated...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28820895/identification-of-leishmania-donovani-antigen-in-circulating-immune-complexes-of-visceral-leishmaniasis-subjects-for-diagnosis
#13
Fauzia Jamal, Pushkar Shivam, Sarita Kumari, Manish Kumar Singh, Abul Hasan Sardar, Pushpanjali, Selvasankar Murugesan, Shyam Narayan, Anil Kumar Gupta, Krishna Pandey, V N R Das, Vahab Ali, Sanjiva Bimal, Pradeep Das, Shubhankar K Singh
The unreliability of most of the existing antibody-based diagnostic kits to discriminate between active and treated VL cases, relapse situation and reinfection are a major hurdle in controlling the cases of Kala-azar in an endemic area. An antigen targeted diagnostic approaches can be an attractive strategy to overcome these problems. Hence, this study was focused on identifying the Leishmania antigens, lies in circulating immune complex (CICs), can be used for diagnostic as well as prognostic purposes. The present study was conducted on peripheral blood samples of 115 human subjects, based on isolation of CICs...
2017: PloS One
https://www.readbyqxmd.com/read/28820751/importance-of-pcr-based-tumor-testing-in-the-evaluation-of-lynch-syndrome-associated-endometrial-cancer
#14
Amanda S Bruegl, Annessa Kernberg, Russell R Broaddus
Lynch syndrome (LS) is a hereditary cancer syndrome caused by a germline mutation in a DNA mismatch repair gene, usually MLH1, MSH2, MSH6, or PMS2. The most common cancers associated with LS are colorectal adenocarcinoma and endometrial carcinoma. Identification of women with LS-associated endometrial cancer is important, as these women and their affected siblings and children are at-risk of developing these same cancers. Germline testing of all endometrial cancer patients is not cost effective, and screening using young age of cancer diagnosis and/or presence of family history of syndrome-associated is underutilized and ineffective...
August 17, 2017: Advances in Anatomic Pathology
https://www.readbyqxmd.com/read/28820741/electromagnetic-and-optical-characteristics-of-nb5-doped-double-crossover-and-salmon-dna-thin-films
#15
Mitta Sekhar Babu, Sreekantha Reddy Dugasani, Soon-Gil Jung, Srivithya Vellampatti, Tuson Park, Sung Ha Park
We report the fabrication and physical characteristics of niobium ion (Nb5+)-doped double-crossover DNA (DX-DNA) and salmon DNA (SDNA) thin films. Different concentrations of Nb5+ ([Nb5+]) are coordinated into the DNA molecules, and the thin films are fabricated via substrate-assisted growth (DX-DNA) and drop-casting (SDNA) on oxygen plasma treated substrates. We conducted atomic force microscopy to estimate the optimum concentration of Nb5+ ([Nb5+]O = 0.08 mM) in Nb5+-doped DX-DNA thin films, up to which the DX-DNA lattices maintain their structures without deformation...
August 18, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28820723/a-lncrna-fine-tunes-the-dynamics-of-a-cell-state-transition-involving-lin28-let-7-and-de-novo-dna-methylation
#16
Meng Amy Li, Paulo P Amaral, Priscilla Cheung, Jan H Bergmann, Masaki Kinoshita, Tüzer Kalkan, Meryem Ralser, Sam Robson, Ferdinand von Meyenn, Maike Paramor, Fengtang Yang, Caifu Chen, Jennifer Nichols, David L Spector, Tony Kouzarides, Lin He, Austin Smith
Execution of pluripotency requires progression from the naïve status represented by mouse embryonic stem cells (ESCs) to a state capacitated for lineage specification. This transition is coordinated at multiple levels. Non-coding RNAs may contribute to this regulatory orchestra. We identified a rodent-specific long non-coding RNA (lncRNA) linc1281, hereafter Ephemeron (Eprn), that modulates the dynamics of exit from naïve pluripotency. Eprn deletion delays the extinction of ESC identity, an effect associated with perduring Nanog expression...
August 18, 2017: ELife
https://www.readbyqxmd.com/read/28820700/rapid-detection-of-plasmodium-knowlesi-by-isothermal-recombinase-polymerase-amplification-assay
#17
Meng-Yee Lai, Choo-Huck Ooi, Yee-Ling Lau
In this study, we developed a recombinase polymerase amplification (RPA) assay for specific diagnosis of Plasmodium knowlesi. Genomic DNA was extracted from whole blood samples using a commercial kit. With incubation at 37°C, the samples were successfully amplified within 20 minutes. The end product of RPA was further examined by loading onto agarose gel and a specific band was observed with a size of 128 bp. The RPA assay exhibited high sensitivity with limits of detection down to one copy of the plasmid...
August 14, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28820654/locus-specific-dna-methylation-in-the-placenta-is-associated-with-levels-of-pro-inflammatory-proteins-in-cord-blood-and-they-are-both-independently-affected-by-maternal-smoking-during-pregnancy
#18
Sanne D van Otterdijk, Alexandra M Binder, Karin B Michels
We investigated the impact of maternal smoking during pregnancy on placental DNA methylation and how this may mediate the association between maternal smoking and pro-inflammatory proteins in cord blood. The study population consisted of 27 individuals exposed to maternal smoking throughout pregnancy, 32 individuals exposed during a proportion of the pregnancy, and 61 unexposed individuals. Methylation of 11 regions within 6 genes in placenta tissue was assessed by pyrosequencing. Levels of 7 pro-inflammatory proteins in cord blood were assessed by electrochemiluminescence...
August 18, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28820597/deterministic-symmetry-breaking-of-plasmonic-nanostructures-enabled-by-dna-programmable-assembly
#19
Matthew R Jones, Kevin L Kohlstedt, Matthew N O'Brien, Jinsong Wu, George C Schatz, Chad A Mirkin
The physical properties of matter rely fundamentally on the symmetry of constituent building blocks. This is particularly true for structures that interact with light via the collective motion of their conduction electrons (i.e., plasmonic materials), where the observation of exotic optical effects, such as negative refraction and electromagnetically induced transparency, require the coupling of modes that are only present in systems with nontrivial broken symmetries. Lithography has been the predominant fabrication technique for constructing plasmonic metamaterials, as it can be used to form patterns of arbitrary complexity, including those with broken symmetry...
August 18, 2017: Nano Letters
https://www.readbyqxmd.com/read/28820590/conformational-heterogeneity-in-a-fully-complementary-dna-three-way-junction-with-a-gc-rich-branchpoint
#20
Anita Toulmin, Laura E Baltierra-Jasso, Michael J Morten, Tara Sabir, Peter McGlynn, Gunnar F Schröder, Brian O Smith, Steven W Magennis
DNA three-way junctions (3WJs) are branched structures that serve as important biological intermediates and as components in DNA nanostructures. We recently derived the global structure of a fully-complementary 3WJ and found that it contained unpaired bases at the branchpoint, in support of previous observations of branch flexibility and branchpoint reactivity. By combining high-resolution single-molecule FRET, molecular modeling, time-resolved ensemble fluorescence spectroscopy and the first 19F NMR observations of fully complementary 3WJs, we now show that the 3WJ structure can adopt multiple distinct conformations depending upon the sequence at the branchpoint...
August 18, 2017: Biochemistry
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