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DNA molecular dynamics

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https://www.readbyqxmd.com/read/28433420/dna-methylation-program-in-normal-and-alcohol-induced-thinning-cortex
#1
Nail Can Öztürk, Marisol Resendiz, Hakan Öztürk, Feng C Zhou
While cerebral underdevelopment is a hallmark of fetal alcohol spectrum disorders (FASD), the mechanism(s) guiding the broad cortical neurodevelopmental deficits are not clear. DNA methylation is known to regulate early development and tissue specification through gene regulation. Here, we examined DNA methylation in the onset of alcohol-induced cortical thinning in a mouse model of FASD. C57BL/6 (B6) mice were administered a 4% alcohol (v/v) liquid diet from embryonic (E) days 7-16, and their embryos were harvested at E17, along with isocaloric liquid diet and lab chow controls...
February 20, 2017: Alcohol
https://www.readbyqxmd.com/read/28431395/correlation-of-genomic-alterations-assessed-by-next-generation-sequencing-ngs-of-tumor-tissue-dna-and-circulating-tumor-dna-ctdna-in-metastatic-renal-cell-carcinoma-mrcc-potential-clinical-implications
#2
Andrew W Hahn, David M Gill, Benjamin Maughan, Archana Agarwal, Lubina Arjyal, Sumati Gupta, Jessica Streeter, Erin Bailey, Sumanta K Pal, Neeraj Agarwal
INTRODUCTION: Tumor tissue and circulating tumor DNA (ctDNA) next-generation sequencing (NGS) testing are frequently performed to detect genomic alterations (GAs) to help guide treatment in metastatic renal cell carcinoma (mRCC), especially after progression on standard systemic therapy. Our objective was to assess if GAs detected by ctDNA NGS are different from those detected by tumor tissue NGS, specifically in patients with mRCC, and if these platforms are interchangeable or complimentary...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28428851/screening-mitochondrial-dna-sequence-variation-as-an-alternative-method-for-tracking-established-and-outbreak-populations-of-queensland-fruit-fly-at-the-species-southern-range-limit
#3
Mark J Blacket, Mali B Malipatil, Linda Semeraro, Peter S Gillespie, Bernie C Dominiak
Understanding the relationship between incursions of insect pests and established populations is critical to implementing effective control. Studies of genetic variation can provide powerful tools to examine potential invasion pathways and longevity of individual pest outbreaks. The major fruit fly pest in eastern Australia, Queensland fruit fly Bactrocera tryoni (Froggatt), has been subject to significant long-term quarantine and population reduction control measures in the major horticulture production areas of southeastern Australia, at the species southern range limit...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28425525/exploiting-hydrogen-bonding-interactions-to-probe-smaller-linear-and-cyclic-diamines-binding-to-g-quadruplexes-a-dft-and-molecular-dynamics-study
#4
Mrinal Kanti Si, Anik Sen, Bishwajit Ganguly
G-quadruplexes are formed by the association of four guanine bases through Hoogsteen hydrogen bonding in guanine-rich sequences of DNA and exist in the telomere as well as in promoter regions of certain oncogenes. The sequences of G-quadruplex-DNA are targets for the design of molecules that can bind and can be developed as anti-cancer drugs. The linear and cyclic protonated diamines have been explored to bind to G-quadruplex-DNA through hydrogen bonding interactions. The quadruplex-DNA binders exploit π-stacking and hydrogen bonding interactions with the phosphate backbone of loops and grooves...
April 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28424513/super-multiplex-vibrational-imaging
#5
Lu Wei, Zhixing Chen, Lixue Shi, Rong Long, Andrew V Anzalone, Luyuan Zhang, Fanghao Hu, Rafael Yuste, Virginia W Cornish, Wei Min
The ability to visualize directly a large number of distinct molecular species inside cells is increasingly essential for understanding complex systems and processes. Even though existing methods have successfully been used to explore structure-function relationships in nervous systems, to profile RNA in situ, to reveal the heterogeneity of tumour microenvironments and to study dynamic macromolecular assembly, it remains challenging to image many species with high selectivity and sensitivity under biological conditions...
April 19, 2017: Nature
https://www.readbyqxmd.com/read/28423907/effects-of-active-site-mutations-on-specificity-of-nucleobase-binding-in-human-dna-polymerase-%C3%AE
#6
Melek N Ucisik, Sharon Hammes-Schiffer
Human DNA polymerase η (Pol η) plays a vital role in protection against skin cancer caused by damage from ultraviolet light. This enzyme rescues stalled replication forks at cyclobutane thymine-thymine dimers (TTDs) by inserting nucleotides opposite these DNA lesions. Residue R61 is conserved in the Pol η enzymes across species, but the corresponding residue, as well as its neighbor S62, is different in other Y-family polymerases, Pol ι and Pol κ. Herein, R61 and S62 are mutated to their Pol ι and Pol κ counterparts...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28423671/genome-wide-dna-methylation-analysis-reveals-molecular-subtypes-of-pancreatic-cancer
#7
Nitish Kumar Mishra, Chittibabu Guda
Pancreatic cancer (PC) is the fourth leading cause of cancer deaths in the United States with a five-year patient survival rate of only 6%. Early detection and treatment of this disease is hampered due to lack of reliable diagnostic and prognostic markers. Recent studies have shown that dynamic changes in the global DNA methylation and gene expression patterns play key roles in the PC development; hence, provide valuable insights for better understanding the initiation and progression of PC. In the current study, we used DNA methylation, gene expression, copy number, mutational and clinical data from pancreatic patients...
March 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423273/conformational-dynamics-of-mechanically-compliant-dna-nanostructures-from-coarse-grained-molecular-dynamics-simulations
#8
Ze Shi, Carlos E Castro, Gaurav Arya
Structural DNA nanotechnology, the assembly of rigid 3D structures of complex yet precise geometries, has recently been used to design dynamic, mechanically-compliant nanostructures with tunable equilibrium conformations and conformational distributions. Here we use coarse-grained molecular dynamics simulations to provide in- sights into the conformational dynamics of a set of mechanically compliant DNA nanostructures-DNA hinges that use single-stranded DNA "springs" to tune the equilibrium conformation of a layered double-stranded DNA "joint" connecting two stiff "arms" constructed from DNA helix bundles...
April 19, 2017: ACS Nano
https://www.readbyqxmd.com/read/28419534/endocrine-imbalance-associated-with-proteome-changes-in-diabetes
#9
Amr A Sayed, Ahmed M Alhawary, Aboalela Farag, Dina R Johar, Larry H Bernstein
The dynamics of cellular metabolism involves rapid interactions between proteins and nucleotides, proteins and proteins, proteins and mRNA, the action of miRNA, and signaling. These also involve the interactions with respect to the sulfur bond, oxygen radicals that initiate a change in conformation and a chain of events. We review a development in molecular medicine that is a very promising work in progress. We also review the current and future research methods involving mitochondria. Long-term effects of diabetes include glycation of proteins, e...
April 17, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28418649/nature-s-selection-of-geranyl-group-as-a-trna-modification-the-effects-of-chain-length-on-base-pairing-specificity
#10
Phensinee Haruehanroengra, Sweta Vangaveti, Srivathsan V Ranganathan, Rui Wang, Alan Chen, Jia Sheng
The recently discovered geranyl modification on the 2-thio position of wobble U34 residues in tRNA(Glu), tRNA(Lys), and tRNA(Gln) in several bacteria has been found to enhance the U:G pairing specificity and reduce the frameshifting error during translation. It is a fundamentally interesting question why nature chose a C10 terpene group in tRNA systems. In this study, we explore the significance of the terpene length on base-paring stability and specificity using a series of 2-thiouridine analogues containing different lengths of carbon chains, namely, methyl- (C1), dimethylallyl- (C5), and farnesyl-modified (C15) 2-thiothymidines in a DNA duplex...
April 18, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28417973/excitability-in-the-p53-network-mediates-robust-signaling-with-tunable-activation-thresholds-in-single-cells
#11
Gregor Mönke, Elena Cristiano, Ana Finzel, Dhana Friedrich, Hanspeter Herzel, Martin Falcke, Alexander Loewer
Cellular signaling systems precisely transmit information in the presence of molecular noise while retaining flexibility to accommodate the needs of individual cells. To understand design principles underlying such versatile signaling, we analyzed the response of the tumor suppressor p53 to varying levels of DNA damage in hundreds of individual cells and observed a switch between distinct signaling modes characterized by isolated pulses and sustained oscillations of p53 accumulation. Guided by dynamic systems theory we show that this requires an excitable network structure comprising positive feedback and provide experimental evidence for its molecular identity...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28415607/thymoquinone-exerts-potent-growth-suppressive-activity-on-leukemia-through-dna-hypermethylation-reversal-in-leukemia-cells
#12
Jiuxia Pang, Na Shen, Fei Yan, Na Zhao, Liping Dou, Lai-Chu Wu, Christopher L Seiler, Li Yu, Ke Yang, Veronika Bachanova, Eric Weaver, Natalia Y Tretyakova, Shujun Liu
Thymoquinone (TQ), a bioactive constituent of the volatile oil of Monarda fistulosa and Nigella sativa, possesses cancer-specific growth inhibitory effects, but the underlying molecular mechanisms remain largely elusive. We propose that TQ curbs cancer cell growth through dysfunction of DNA methyltransferase 1 (DNMT1). Molecular docking analysis revealed that TQ might interact with the catalytic pocket of DNMT1 and compete with co-factor SAM/SAH for DNMT1 inhibition. In vitro inhibitory assays showed that TQ decreases DNMT1 methylation activity in a dose-dependent manner with an apparent IC50 of 30 nM...
March 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/28415207/model-of-polar-auxin-transport-coupled-to-mechanical-forces-retrieves-robust-morphogenesis-along-the-arabidopsis-root
#13
J Roberto Romero-Arias, Valeria Hernández-Hernández, Mariana Benítez, Elena R Alvarez-Buylla, Rafael A Barrio
Stem cells are identical in many scales, they share the same molecular composition, DNA, genes, and genetic networks, yet they should acquire different properties to form a functional tissue. Therefore, they must interact and get some external information from their environment, either spatial (dynamical fields) or temporal (lineage). In this paper we test to what extent coupled chemical and physical fields can underlie the cell's positional information during development. We choose the root apical meristem of Arabidopsis thaliana to model the emergence of cellular patterns...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28415169/understanding-the-origin-of-liquid-crystal-ordering-of-ultrashort-double-stranded-dna
#14
Suman Saurabh, Yves Lansac, Yun Hee Jang, Matthew A Glaser, Noel A Clark, Prabal K Maiti
Recent experiments have shown that short double-stranded DNA (dsDNA) fragments having six- to 20-base pairs exhibit various liquid crystalline phases. This violates the condition of minimum molecular shape anisotropy that analytical theories demand for liquid crystalline ordering. It has been hypothesized that the liquid crystalline ordering is the result of end-to-end stacking of dsDNA to form long supramolecular columns which satisfy the shape anisotropy criterion necessary for ordering. To probe the thermodynamic feasibility of this process, we perform molecular dynamics simulations on ultrashort (four base pair long) dsDNA fragments, quantify the strong end-to-end attraction between them, and demonstrate that the nematic ordering of the self-assembled stacked columns is retained for a large range of temperature and salt concentration...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28414239/a-novel-sample-preparation-for-shotgun-proteomics-characterization-of-hcps-in-antibodies
#15
Lihua Huang, Ning Wang, Charles E Mitchell, Tammy J Brownlee, Steven R Maple, Michael R De Felippis
Residual host cell proteins (HCPs) in biopharmaceuticals derived from recombinant DNA technology can present potential safety risks to patients or compromise product stability. Thus, the downstream purification process is designed to demonstrate robust removal of these impurities. ELISA using polyclonal anti-HCP antibodies as reagents for capture, detection and quantitation purposes is most commonly used to monitor HCP removal during process development but this technique has limitations. More recently, LC-MS for residual HCP characterization has emerged as a powerful tool to support purification process development...
April 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28410882/epo-reprograms-the-epigenome-of-erythroid-cells
#16
Andrea A Perreault, Mary Lauren Benton, Mark J Koury, Stephen J Brandt, Bryan J Venters
The hormone erythropoietin (Epo) is required for erythropoiesis, yet its molecular mechanism of action remains poorly understood, particularly in regards to chromatin dynamics. To investigate how Epo modulates the erythroid epigenome, we performed epigenetic profiling using an ex vivo murine cell system that undergoes synchronous erythroid maturation in response to Epo stimulation. Our findings define the repertoire of Epo-modulated enhancers, illuminating a new facet of Epo signaling. First, a large number of enhancers rapidly responded to Epo stimulation, revealing a cis-regulatory network of Epo-responsive enhancers...
April 11, 2017: Experimental Hematology
https://www.readbyqxmd.com/read/28410371/determining-the-role-of-missense-mutations-in-the-pou-domain-of-hnf1a-that-reduce-the-dna-binding-affinity-a-computational-approach
#17
Sneha P, Thirumal Kumar D, George Priya Doss C, Siva R, Hatem Zayed
Maturity-onset diabetes of the young type 3 (MODY3) is a non-ketotic form of diabetes associated with poor insulin secretion. Over the past years, several studies have reported the association of missense mutations in the Hepatocyte Nuclear Factor 1 Alpha (HNF1A) with MODY3. Missense mutations in the POU homeodomain (POUH) of HNF1A hinder binding to the DNA, thereby leading to a dysfunctional protein. Missense mutations of the HNF1A were retrieved from public databases and subjected to a three-step computational mutational analysis to identify the underlying mechanism...
2017: PloS One
https://www.readbyqxmd.com/read/28409126/genomics-and-comparative-genomic-analyses-provide-insight-into-the-taxonomy-and-pathogenic-potential-of-novel-emmonsia-pathogens
#18
Ying Yang, Qiang Ye, Kang Li, Zongwei Li, Xiaochen Bo, Zhen Li, Yingchun Xu, Shengqi Wang, Peng Wang, Huipeng Chen, Junzhi Wang
Over the last 50 years, newly described species of Emmonsia-like fungi have been implicated globally as sources of systemic human mycosis (emmonsiosis). Their ability to convert into yeast-like cells capable of replication and extra-pulmonary dissemination during the course of infection differentiates them from classical Emmonsia species. Immunocompromised patients are at highest risk of emmonsiosis and exhibit high mortality rates. In order to investigate the molecular basis for pathogenicity of the newly described Emmonsia species, genomic sequencing and comparative genomic analyses of Emmonsia sp...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28406400/the-rnf168-paralog-rnf169-defines-a-new-class-of-ubiquitylated-histone-reader-involved-in-the-response-to-dna-damage
#19
Julianne Kitevski-LeBlanc, Amélie Fradet-Turcotte, Predrag Kukic, Marcus D Wilson, Guillem Portella, Tairan Yuwen, Stephanie Panier, Shili Duan, Marella D Canny, Hugo van Ingen, Cheryl H Arrowsmith, John L Rubinstein, Michele Vendruscolo, Daniel Durocher, Lewis E Kay
Site-specific histone ubiquitylation plays a central role in orchestrating the response to DNA double-strand breaks (DSBs). DSBs elicit a cascade of events controlled by the ubiquitin ligase RNF168, which promotes the accumulation of repair factors such as 53BP1 and BRCA1 on the chromatin flanking the break site. RNF168 also promotes its own accumulation, and that of its paralog RNF169, but how they recognize ubiquitylated chromatin is unknown. Using methyl-TROSY solution NMR spectroscopy and molecular dynamics simulations, we present an atomic resolution model of human RNF169 binding to a ubiquitylated nucleosome, and validate it by electron cryomicroscopy...
April 13, 2017: ELife
https://www.readbyqxmd.com/read/28404508/model-based-analyses-reveal-insular-population-diversification-and-cryptic-frog-species-in-the-ischnocnema-parva-complex-in-the-atlantic-forest-of-brazil
#20
Marcelo Gehara, Adriane Barth, Eliana Faria de Oliveira, Marco Antonio Costa, Célio Fernando Baptista Haddad, Miguel Vences
The Atlantic Forest (AF) of Brazil has long been recognized as a biodiversity conservation hotspot. Despite decades of studies the species inventory of this biome continues to increase with the discovery of cryptic diversity and the description of new species. Different diversification mechanisms have been proposed to explain the diversity in the region, including models of forest dynamics, barriers to gene flow and dispersal. Also, sea level change is thought to have influenced coastal diversification and isolated populations on continental islands...
April 9, 2017: Molecular Phylogenetics and Evolution
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