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https://www.readbyqxmd.com/read/28092918/complete-sequence-and-organization-of-pfr260-the-bacillus-thuringiensis-inta-fr7-4-plasmid-harboring-insecticidal-genes
#1
Laura E Navas, Ariel F Amadio, Elio M Ortiz, Diego H Sauka, Graciela B Benintende, Marcelo F Berretta, Rubén O Zandomeni
We report the complete sequence and analysis of pFR260, a novel megaplasmid of 260,595 bp from the Bacillus thuringiensis strain INTA Fr7-4 isolated in Argentina. It carries 7 insecticidal genes: 3 cry8 copies previously reported, 2 vip1, and 2 vip2. Also, it carries a gene encoding a putative atypical Cry protein. These genes are arranged in a region of approximately 105 kbp in size with characteristics of a pathogenicity island with a potential coleopteran-specific insecticide profile. DNA strand composition asymmetry, as determined by GC skew analysis, and the presence of a Rep protein involved in the initiation of replication suggest a bidirectional theta mechanism of replication...
January 17, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28092860/design-synthesis-and-biological-evaluation-of-quinazoline-phosphoramidate-mustard-conjugates-as-anticancer-drugs
#2
Songwen Lin, Yingbo Li, Yufen Zheng, Laichun Luo, Qi Sun, Zemei Ge, Tieming Cheng, Runtao Li
A series of novel compounds with phosphoramide mustard functionality incorporated into the quinazoline scaffold of EGFR/HER2 inhibitors were designed and synthesized as multi-target-directed ligands against tumor cells. In vitro assays showed that tumor cell lines with high HER2 level were more sensitive to the compounds than tumor cells with low HER2 level. Compound 10d (EMB-3) was one of the most potent inhibitors with IC50 of 7.4 nM and 82 nM against EGFR and HER2, respectively. The mechanism studies were also supported by the effect of 10d-induced DNA damage in MDA-MB-468 cells...
January 3, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28092851/plasmid-dna-affinity-partitioning-using-polyethylene-glycol-sodium-sulfate-aqueous-two-phase-systems
#3
Behzad Nazer, Mohammad Reza Dehghani, Bahram Goliaei
Extraction of plasmid DNA (pDNA) from an alkaline bacterial cell lysate has been investigated using partitioning and affinity partitioning in aqueous two-phase systems (ATPSs) containing 12% (w/w) polyethylene glycol and 12% (w/w) sodium sulfate. In this work, a modified 20bp pyrimidine oligonucleotide acting as a triplex-forming oligonucleotide (TFO) was employed as an affinity ligand to improve the partition behavior. The pUC118 plasmid was chosen to be extracted because of its specific oligonucleotide recognition sequence...
January 3, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28092843/therapeutic-effects-of-bach1-sirna-on-human-breast-adenocarcinoma-cell-line
#4
Mansoor Aletaha, Behzad Mansoori, Ali Mohammadi, Mehdi Fazeli, Behzad Baradaran
BACKGROUND: Despite the great improvements in clinical and therapeutic techniques in recent years, many advanced breast cancer patients still died of the postoperative recurrence and metastasis of disease. Bach1 plays a role in the development of the invasive phenotypes of cancer, cell division and apoptosis in tumor cells. The aim of this study was to investigate the effect of specific bach1 siRNAs, on the proliferation, migration, invasive, induction of apoptosis, cell cycle arrest and alter EMT related miRNA of MDA-MB-468 cells (breast cancer)...
January 13, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28092810/expectation-and-futurity-the-remarkable-success-of-genetic-determinism
#5
Maurizio Esposito
Genetic determinism is nowadays largely questioned and widely criticized. However, if we look at the history of biology in the last one hundred years, we realize that genetic determinism has always been controversial. Why, then, did it acquire such relevance in the past despite facing longstanding criticism? Through the analysis of some of the ambitious expectations of future scientific applications, this article explores the possibility that part of the historical success of genetic determinism lies in the powerful rhetorical strategies that have connected the germinal matter with alluring bio-technological visions...
January 13, 2017: Studies in History and Philosophy of Biological and Biomedical Sciences
https://www.readbyqxmd.com/read/28092795/moderate-aerobic-exercise-training-for-improving-reproductive-function-in-infertile-patients-a-randomized-controlled-trial
#6
Behzad Hajizadeh Maleki, Bakhtyar Tartibian
This study investigated for the first time the changes in seminal markers of inflammation, oxidative stress status, semen parameters, sperm DNA integrity as well as pregnancy rate following 24weeks of moderate aerobic exercise in infertile patients. A total of 1026 sedentary men (aged 25-40years) attending the infertility clinic with history of more than one year of infertility, were screened and 419 were randomized to either exercise (EX, n=210) or non-exercise (NON-EX, n=209) groups. Exercise training favorably attenuated seminal markers of both inflammation (IL-1β, IL-6, IL-8, and TNF-α) and oxidative stress (ROS, MDA, 8-Isoprostane) as well as enhanced antioxidant defense system (SOD, catalase and TAC) (P<0...
January 13, 2017: Cytokine
https://www.readbyqxmd.com/read/28092772/the-expression-of-endothelin-1-in-chronic-lymphocytic-leukemia-is-controlled-by-epigenetic-mechanisms-and-extracellular-stimuli
#7
Silvia Martinelli, Rossana Maffei, Stefania Fiorcari, Chiara Quadrelli, Patrizia Zucchini, Stefania Benatti, Leonardo Potenza, Mario Luppi, Roberto Marasca
Endothelin-1 (ET-1) is a hormone peptide widely expressed and is involved in several biological processes, important not only for normal cell function but also for tumor development, including cell proliferation, invasion, metastasis, angiogenesis and osteogenesis. In accordance, ET-1 was already shown to contribute to the growth and progression of many different solid cancers. We recently demonstrated that ET-1 has a role in the pathogenesis of chronic lymphocytic leukemia (CLL) where it is abnormally expressed...
December 30, 2016: Leukemia Research
https://www.readbyqxmd.com/read/28092742/short-term-in-vivo-exposure-to-graphene-oxide-can-cause-damage-to-the-gut-and-testis
#8
Marta Dziewięcka, Julia Karpeta-Kaczmarek, Maria Augustyniak, Magdalena Rost-Roszkowska
Graphene oxide (GO) has unique physicochemical properties and also has a potentially widespread use in every field of daily life (industry, science, medicine). Demand for nanotechnology is growing every year, and therefore many aspects of its toxicity and biocompatibility still require further clarification. This research assesses the in vivo toxicity of pure and manganese ion-contaminated GO that were administrated to Acheta domesticus with food (at 200mgkg(-1) of food) throughout their ten-day adult life...
January 9, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/28092692/smile-seq-identifies-binding-motifs-of-single-and-dimeric-transcription-factors
#9
Alina Isakova, Romain Groux, Michael Imbeault, Pernille Rainer, Daniel Alpern, Riccardo Dainese, Giovanna Ambrosini, Didier Trono, Philipp Bucher, Bart Deplancke
Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq). SMiLE-seq is neither limited by DNA bait length nor biased toward strong affinity binders; it probes the DNA-binding properties of TFs over a wide affinity range in a fast and cost-effective fashion. We validated SMiLE-seq by analyzing 58 full-length human, mouse, and Drosophila TFs from distinct structural classes...
January 16, 2017: Nature Methods
https://www.readbyqxmd.com/read/28092679/genome-wide-analysis-of-p53-regulated-transcription-in-myc-driven-lymphomas
#10
C Tonelli, M J Morelli, A Sabò, A Verrecchia, L Rotta, T Capra, S Bianchi, S Campaner, B Amati
The tumour suppressor p53 is a transcription factor that controls cellular stress responses. Here, we dissected the transcriptional programmes triggered upon restoration of p53 in Myc-driven lymphomas, based on the integrated analysis of p53 genomic occupancy and gene regulation. p53 binding sites were identified at promoters and enhancers, both characterized by the pre-existence of active chromatin marks. Only a small fraction of these sites showed the 20 base-pair p53 consensus motif, suggesting that p53 recruitment to genomic DNA was primarily mediated through protein-protein interactions in a chromatin context...
January 16, 2017: Oncogene
https://www.readbyqxmd.com/read/28092669/interplay-between-epigenetics-and-metabolism-in-oncogenesis-mechanisms-and-therapeutic-approaches
#11
REVIEW
C C Wong, Y Qian, J Yu
Epigenetic and metabolic alterations in cancer cells are highly intertwined. Oncogene-driven metabolic rewiring modifies the epigenetic landscape via modulating the activities of DNA and histone modification enzymes at the metabolite level. Conversely, epigenetic mechanisms regulate the expression of metabolic genes, thereby altering the metabolome. Epigenetic-metabolomic interplay has a critical role in tumourigenesis by coordinately sustaining cell proliferation, metastasis and pluripotency. Understanding the link between epigenetics and metabolism could unravel novel molecular targets, whose intervention may lead to improvements in cancer treatment...
January 16, 2017: Oncogene
https://www.readbyqxmd.com/read/28092654/promoter-polymorphism-of-toll-like-receptor-4-is-associated-with-a-decreased-risk-of-coronary-artery-disease-a-case-control-study-in-the-chinese-han-population
#12
Dandan Sun, Liping Sun, Qian Xu, Honghu Wang, Jun Yang, Yuan Yuan
BACKGROUND Coronary artery disease (CAD) is considered a chronic inflammatory disease of the blood vessels. Toll-like receptor 4 (TLR4) is a transmembrane receptor involved in inflammatory reactions. The aim of this study was to determine the association between polymorphisms in the promoter region and 3'-untranslated region (3'-UTR) of TLR4, and the associated CAD risk. MATERIAL AND METHODS This study enrolled 424 participants with CAD and 424 controls without CAD. The polymorphisms in the promoter region and 3'-UTR of TLR4 were identified from the HapMap database, including rs10116253, rs10983755, and rs11536889...
January 16, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28092632/the-tilt-dependent-potential-of-mean-force-of-a-pair-of-dna-oligomers-from-all-atom-molecular-dynamics-simulations
#13
Ruggero Cortini, Xiaolin Cheng, Jeremy C Smith
Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups...
January 16, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28092611/prevalence-of-bovine-herpesvirus-type-4-in-aborting-dairy-cows
#14
Đ Cvetojević, B Savić, V Milićević, B Kureljušić, N Jezdimirović, D Jakić-Dimić, M Pavlović, Lj Spalević
Bovine herpesvirus type 4 (BHV-4) is related to many different conditions: infertility, postpartal metritis, vulvovaginitis, mastitis, encephalitis, calf pneumonia, keratoconjunctivitis, cutaneous lesions, digital dermatitis and abortion. In this study a retrospective PCR examination of 100 extracted DNA samples from aborting cows was performed in order to determine: prevalence of BHV-4 in abortive cattle, whether coinfections BHV-4 with other abortifacient pathogens are present in the same sample and to determine the month of gestation when BHV-4 associated abortions were detected...
December 1, 2016: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/28092604/replication-kinetics-of-neuropathogenic-and-non-neuropathogenic-equine-herpesvirus-type-1-ehv-1-strains-in-primary-murine-neurons-and-ed-cell-line
#15
J Cymerys, A Słońska, J Brzezicka, A Tucholska, A Chmielewska, J Rola, P Malik, M W Bańbura
Equine herpesvirus type 1 (EHV-1) causes respiratory infections, abortion and neurological disorders in horses. Molecular epidemiology studies have demonstrated that a single-point mutation in DNA polymerase gene, resulting in an amino acid variation (N752/D752), is significantly associated with the neuropathogenic potential of EHV-1 strains. The aim of the study was to elucidate if there are any differences between neuropathogenic (EHV-1 26) and non-neuropathogenic (Jan-E and Rac-H) EHV-1 strains in their ability to infect neuronal cells...
December 1, 2016: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/28092571/machine-learned-replacement-of-n-labels-for-basecalled-sequences-in-dna-barcoding
#16
Eddie Ma, Sujeevan Ratnasingham, Stefan Kremer
This study presents a machine learning method that increases the number of identified bases in Sanger Sequencing. The system post-processes a KB basecalled chromatogram. It selects a recoverable subset of N-labels in the KB-called chromatogram to replace with basecalls (A,C,G,T). An N-label correction is defined given an additional read of the same sequence, and a human finished sequence. Corrections are added to the dataset when an alignment determines the additional read and human agree on the identity of the N-label...
August 11, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28092481/the-effect-of-main-urine-inhibitors-on-the-activity-of-different-dna-polymerases-in-loop-mediated-isothermal-amplification
#17
Jekaterina Jevtuševskaja, Katrin Krõlov, Indrek Tulp, Ülo Langel
BACKGROUND: The use of rapid amplification methods to detect pathogens in biological samples is mainly limited by the amount of pathogens present in the sample and the presence of inhibiting substances. Inhibitors can affect the amplification efficiency by either binding to the polymerase, interacting with the DNA, or interacting with the polymerase during primer extension. Amplification is performed using DNA polymerase enzymes and even small changes in their activity can influence the sensitivity and robustness of molecular assays Methods: The main purpose of this research was to examine which compounds present in urine inhibit polymerases with strand displacement activity...
January 16, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28092466/clinical-performance-of-the-solana%C3%A2-point-of-care-trichomonas-assay-from-clinician-collected-vaginal-swabs-and-urine-specimens-from-symptomatic-and-asymptomatic-women
#18
C A Gaydos, J Schwebke, J Dombrowski, J Marrazzo, J Coleman, B Silver, M Barnes, L Crane, P Fine
BACKGROUND: Solana® (Quidel) is a new rapid (<40 min.) point-of-care (POC) test for qualitative detection of Trichomonas vaginalis (TV) DNA. The assay has two steps: 1) specimen preparation, and 2) amplification and detection using isothermal Helicase-Dependent Amplification (HDA). The objective was to demonstrate the performance of Solana for vaginal swabs and female urines based on comparison to wet mount and TV culture. Performance was also compared to the Aptima-TV assay. METHODS: Urine and four clinician-collected vaginal swabs were collected...
January 16, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28092459/toward-high-throughput-and-multiplexed-imaging-of-genome-organization
#19
Eric F Joyce
Dr. Eric Joyce from the Department of Genetics at the University of Pennsylvania was awarded The President's Innovation award at the annual Society of Biomolecular Imaging and Informatics meeting held in Boston, September 2016. Chromosome interactions are a fundamental aspect of nuclear organization that can activate and silence genes or even direct chromosome rearrangements. However, the molecular mechanisms underlying how chromosomal segments find each other and form stable interactions within cells remain unknown...
January 2017: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/28092440/molecular-interactions-between-graphene-and-biological-molecules
#20
Xingquan Zou, Shuai Wei, Joshua Jasensky, Minyu Xiao, Qiuming Wang, Charles L Brooks, Zhan Chen
Applications of graphene have extended into areas of nanobio-technology such as nanobio-medicine, nanobio-sensing, as well as nanoelectronics with biomolecules. These applications involve interactions between proteins, peptides, DNA, RNA etc. and graphene, therefore understanding such molecular interactions is essential. For example, many applications based on using graphene and peptides require peptides to interact with (e.g., noncovalently bind to) graphene at one end, while simultaneously exposing the other end to the surrounding medium (e...
January 16, 2017: Journal of the American Chemical Society
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