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DNA molecular dynamics

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https://www.readbyqxmd.com/read/28526790/post-epizootic-persistence-of-asymptomatic-mycoplasma-conjunctivae-infection-in-iberian-ibex
#1
Xavier Fernández-Aguilar, Oscar Cabezón, José Enrique Granados, Joachim Frey, Emmanuel Serrano, Roser Velarde, Francisco Javier Cano-Manuel, Gregorio Mentaberre, Arián Ráez-Bravo, Paulino Fandos, Jorge Ramón López-Olvera
The susceptibility of Iberian ibex (Capra pyrenaica) to Mycoplasma conjunctivae ocular infection and the changes in their interaction over time were studied in terms of clinical outcome, molecular detection and IgG immune response in a captive population that underwent a severe infectious keratoconjunctivitis (IKC) outbreak. Mycoplasma conjunctivae was detected for the first time in the Iberian ibexes coinciding with the IKC outbreak. Its prevalence had a decreasing trend in 2013 that was consistent with the clinical resolution (August 35...
May 19, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28523538/mecp2-a-modulator-of-neuronal-chromatin-organization-involved-in-rett-syndrome
#2
Alexia Martínez de Paz, Juan Ausió
From an epigenetic perspective, the genomic chromatin organization of neurons exhibits unique features when compared to somatic cells. Methyl CpG binding protein 2 (MeCP2), through its ability to bind to methylated DNA, seems to be a major player in regulating such unusual organization. An important contribution to this uniqueness stems from the intrinsically disordered nature of this highly abundant chromosomal protein in neurons. Upon its binding to methylated/hydroxymethylated DNA, MeCP2 is able to recruit a plethora of interacting protein and RNA partners...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28522396/ultrafast-spectroscopy-on-dna-cleavage-by-endonuclease-in-molecular-crowding
#3
Priya Singh, Susobhan Choudhury, Shreyasi Dutta, Aniruddha Adhikari, Siddhartha Bhattacharya, Debasish Pal, Samir Kumar Pal
The jam-packed intracellular environments differ the activity of a biological macromolecule from that in laboratory environments (in vitro) through a number of mechanisms called molecular crowding related to structure, function and dynamics of the macromolecule. Here, we have explored the structure, function and dynamics of a model enzyme protein DNase I in molecular crowing of polyethylene glycol (PEG; MW 3350). We have used steady state and picosecond resolved dynamics of a well-known intercalator ethidium bromide (EB) in a 20-mer double-stranded DNA (dsDNA) to monitor the DNA-cleavage by the enzyme in absence and presence PEG...
May 15, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28518222/the-effect-of-initial-molecular-profile-on-response-to-recombinant-interferon-%C3%AE-rifn%C3%AE-treatment-in-early-myelofibrosis
#4
Richard T Silver, Ariella C Barel, Elena Lascu, Ellen K Ritchie, Gail J Roboz, Paul J Christos, Attilio Orazi, Duane C Hassane, Wayne Tam, Nicholas C P Cross
BACKGROUND: Although recombinant interferon-α (rIFNα) effectively treats patients with early myelofibrosis, the effect of driver and high molecular risk (HMR) mutations has not been considered. In this phase 2 study, for the first time, the authors correlate response to rIFNα treatment with driver and HMR mutations. METHODS: Patients were diagnosed using World Health Organization or International Working Group for Myeloproliferative Neoplasms Research and Treatment criteria...
May 18, 2017: Cancer
https://www.readbyqxmd.com/read/28514955/label-free-biosensing-of-salmonella-enterica-serovars-at-single-cell-level
#5
Bin Wang, Bosoon Park, Bingqian Xu, Yongkuk Kwon
BACKGROUND: The emerging nanotechnologies have greatly facilitated the development of label-free biosensors. The atomic force microscopy (AFM) has been used to study the molecular mechanism of the reactions for protein and aptamers. The surface plasmon resonance (SPR) have been used in fast detections of various pathogens such as bacteria. This study used both AFM and SPR to investigate the complex reactions between aptamers and outer membrane proteins (OMPs) on the surface of S. typhimurium...
May 17, 2017: Journal of Nanobiotechnology
https://www.readbyqxmd.com/read/28510357/kif11-silencing-and-inhibition-induces-chromosome-instability-that-may-contribute-to-cancer
#6
Yasamin Asbaghi, Laura L Thompson, Zelda Lichtensztejn, Kirk J McManus
Understanding the aberrant pathways that contribute to oncogenesis and identifying the altered genes involved in these pathways is a critical first step to develop effective strategies to better combat cancer. Chromosome instability (CIN) is an aberrant phenotype that occurs in ∼80% of all cancer types and is associated with aggressive tumors, the acquisition of multi-drug resistance and poor patient prognosis. Despite these associations however, the aberrant genes and molecular defects underlying CIN remain poorly understood...
May 16, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28510225/controlling-gene-expression-by-dna-mechanics-emerging-insights-and-challenges
#7
REVIEW
David Levens, Laura Baranello, Fedor Kouzine
Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein machinery to coalesce at the transcription start sites of genes in a spatial and temporal-specific manner. However, this is a highly dynamic process in which molecular motors such as RNA polymerase II (RNAPII), helicases, and other transcription factors, alter the level of mechanical force in DNA, rather than simply a set of static DNA-protein interactions...
September 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28510218/controlling-gene-expression-by-dna-mechanics-emerging-insights-and-challenges
#8
REVIEW
David Levens, Laura Baranello, Fedor Kouzine
Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein machinery to coalesce at the transcription start sites of genes in a spatial and temporal-specific manner. However, this is a highly dynamic process in which molecular motors such as RNA polymerase II (RNAPII), helicases, and other transcription factors, alter the level of mechanical force in DNA, rather than simply a set of static DNA-protein interactions...
November 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28510023/protein-rna-interactions-structural-biology-and-computational-modeling-techniques
#9
REVIEW
Susan Jones
RNA-binding proteins are functionally diverse within cells, being involved in RNA-metabolism, translation, DNA damage repair, and gene regulation at both the transcriptional and post-transcriptional levels. Much has been learnt about their interactions with RNAs through structure determination techniques and computational modeling. This review gives an overview of the structural data currently available for protein-RNA complexes, and discusses the technical issues facing structural biologists working to solve their structures...
December 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28506988/dmrt1-induces-the-male-pathway-in-a-turtle-with-temperature-dependent-sex-determination
#10
Chutian Ge, Jian Ye, Haiyan Zhang, Yi Zhang, Wei Sun, Yapeng Sang, Blanche Capel, Guoying Qian
The molecular mechanism underlying temperature-dependent sex determination (TSD) has been a long-standing mystery; in particular, the thermo-sensitive genetic triggers for gonadal sex differentiation are largely unknown. Here, we characterized a conserved DM domain gene, Dmrt1, in the red-eared slider turtle Trachemys scripta (T. scripta), which exhibits TSD. We found that Dmrt1 has a temperature-dependent, sexually dimorphic expression pattern, preceding gonadal sex differentiation, and is capable of responding rapidly to temperature shifts and aromatase inhibitor treatment...
May 15, 2017: Development
https://www.readbyqxmd.com/read/28505860/nonmonotonic-dna-length-dependent-mobility-in-pluronic-gels
#11
Seungyong You, Ling Wei, Sachin Shanbhag, David H Van Winkle
Two-dimensional electrophoresis was used to analyze the mobility of DNA fragments in micellar gels of pluronic F127 (EO_{100}PO_{70}EO_{100}) and pluronic P123 (EO_{20}PO_{70}EO_{20}). The 20-3500 base pair DNA fragments were separated by size first in agarose gels, and then in pluronic gels at room temperature. In agarose gels, the DNA mobility decreases monotonically with increasing DNA length. In pluronic gels, however, the mobility varies nonmonotonically according to fragment lengths that are strongly correlated with the diameter of the spherical micelles...
April 2017: Physical Review. E
https://www.readbyqxmd.com/read/28505598/interlocked-dna-topologies-for-nanotechnology
#12
REVIEW
Julián Valero, Finn Lohmann, Michael Famulok
Interlocked molecular architectures are well known in supramolecular chemistry and are widely used for various applications like sensors, molecular machines and logic gates. The use of DNA for constructing these interlocked structures has increased significantly within the current decade. Because of Watson-Crick base pairing rules, DNA is an excellent material for the self-assembly of well-defined interlocked nanoarchitectures. These DNA nanostructures exhibit sufficient stability, good solubility in aqueous media, biocompatibility, and can be easily combined with other biomolecules in bio-hybrid nano-assemblies...
May 12, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28504168/binding-efficacy-and-kinetics-of-chitosan-with-dna-duplex-the-effects-of-deacetylation-degree-and-nucleotide-sequences
#13
Yanmei Yang, Meng Guo, Rui Qian, Chang Liu, Xumin Zong, Yong-Qiang Li, Weifeng Li
The binding process of DNA duplex with various types of chitosan polymers were studied at atomic level through molecular dynamics simulations. The interaction kinetics and binding strength, complex morphology and DNA structure evolution were systematically accessed. The binding efficacy of chitosan to DNA reduces (both in complexation speed and binding strength) when deacetylation degree is decreased, because protonated amine groups on chitosan backbone are more prone to bind with DNA, especially the phosphate oxygen, through coulomb interaction...
August 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28497562/different-aggregation-states-of-a-nuclear-localization-signal-tagged-25-kda-c-terminal-fragment-of-tar-rna-dna-binding-protein-43%C3%A2-kda
#14
Akira Kitamura, Sachiko Yuno, Hideki Muto, Masataka Kinjo
The mechanism and cause of motor neuronal cell death in amyotrophic lateral sclerosis (ALS), a devastating neurodegenerative disorder, are unknown; gain of function of oligomers and aggregation of misfolded proteins, including carboxyl-terminal fragments (CTFs) of TAR RNA/DNA-binding protein 43 kDa (TDP-43), have been proposed as important causative factors in the onset of ALS. We recently reported that a nuclear localization signal (NLS)-tagged 25-kDa CTF of TDP-43 (TDP25) could decrease the cell-death proportion compared with that promoted by TDP25...
May 12, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28497129/molecular-modeling-of-the-ahr-structure-and-interactions-can-shed-light-on-ligand-dependent-activation-and-transformation-mechanisms
#15
Laura Bonati, Dario Corrada, Sara Giani Tagliabue, Stefano Motta
Molecular modeling has given important contributions to elucidation of the main stages in the AhR signal transduction pathway. Despite the lack of experimentally determined structures of the AhR functional domains, information derived from homologous systems has been exploited for modeling their structure and interactions. Homology models of the AhR PASB domain have provided information on the binding cavity and contributed to elucidate species-specific differences in ligand binding. Molecular Docking simulations of the ligand binding process have given insights into differences in binding of diverse agonists, antagonists, and selective AhR modulators, and their application to virtual screening of large databases of compounds have allowed identification of novel AhR ligands...
February 2017: Current Opinion in Toxicology
https://www.readbyqxmd.com/read/28491150/dynamic-silencing-of-somatic-l1-retrotransposon-insertions-reflects-the-developmental-and-cellular-contexts-of-their-genomic-integration
#16
Manoj Kannan, Jingfeng Li, Sarah E Fritz, Kathryn E Husarek, Jonathan C Sanford, Teresa L Sullivan, Pawan Kumar Tiwary, Wenfeng An, Jef D Boeke, David E Symer
BACKGROUND: The ongoing mobilization of mammalian transposable elements (TEs) contributes to natural genetic variation. To survey the epigenetic control and expression of reporter genes inserted by L1 retrotransposition in diverse cellular and genomic contexts, we engineered highly sensitive, real-time L1 retrotransposon reporter constructs. RESULTS: Here we describe different patterns of expression and epigenetic controls of newly inserted sequences retrotransposed by L1 in various somatic cells and tissues including cultured human cancer cells, mouse embryonic stem cells, and tissues of pseudofounder transgenic mice and their progeny...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28488874/an-optically-modulated-self-assembled-resonance-energy-transfer-pass-gate
#17
Craig D LaBoda, Alvin R Lebeck, Chris L Dwyer
We demonstrate an optically controlled molecular-scale pass gate that uses the photoinduced dark states of fluorescent molecules to modulate the flow of excitons. The device consists of four fluorophores spatially arranged on a self-assembled DNA nanostructure. Together, they form a resonance energy transfer (RET) network resembling a standard transistor with a source, channel, drain, and gate. When the gate fluorophore is directly excited, the device is toggled on. Excitons flow freely from the source to the drain, producing strong output fluorescence...
May 10, 2017: Nano Letters
https://www.readbyqxmd.com/read/28487885/novel-de-novo-variant-in-ebf3-is-likely-to-impact-dna-binding-in-a-patient-with-a-neurodevelopmental-disorder-and-expanded-phenotypes-patient-report-in-silico-functional-assessment-and-review-of-published-cases
#18
Patrick R Blackburn, Sarah S Barnett, Michael T Zimmermann, Margot A Cousin, Charu Kaiwar, Filippo Pinto E Vairo, Zhiyv Niu, Matthew J Ferber, Raul A Urrutia, Duygu Selcen, Eric W Klee, Pavel N Pichurin
Pathogenic variants in EBF3 were recently described in three back-to-back publications in association with a novel neurodevelopmental disorder characterized by intellectual disability, speech delay, ataxia, and facial dysmorphisms. In this report, we describe an additional patient carrying a de novo missense variant in EBF3 (c.487C>T, p.(Arg163Trp)) that falls within a conserved residue in the zinc knuckle motif of the DNA binding domain. Without a solved structure of the DNA binding domain, we generated a homology-based atomic model and performed molecular dynamics simulations for EBF3, which predicted decreased DNA affinity for p...
May 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28486920/mitochondria-a-novel-therapeutic-target-in-diabetic-nephropathy
#19
Shikun Yang, Yachun Han, Jun Liu, Panai Song, Xiaoxuan Xu, Li Zhao, Chun Hu, Li Xiao, Fuyou Liu, Hao Zhang, Lin Sun
Diabetic nephropathy (DN) is an important diabetic microvascular complication, and it is becoming the leading cause of end-stage renal disease worldwide. Unfortunately, there are no effective therapies to treat established DN. Therefore, new therapeutic targets are urgently required. Accumulating studies indicate that mitochondrial dysfunction is central to the pathogenesis of DN, such as elevated oxidative stress induced by disorders of the mitochondrial respiratory chain complex and mitochondrial dynamic disorders...
May 9, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28482831/molecular-dynamics-simulation-of-the-opposite-base-preference-and-interactions-in-the-active-site-of-formamidopyrimidine-dna-glycosylase
#20
Alexander V Popov, Anton V Endutkin, Yuri N Vorobjev, Dmitry O Zharkov
BACKGROUND: Formamidopyrimidine-DNA glycosylase (Fpg) removes abundant pre-mutagenic 8-oxoguanine (oxoG) bases from DNA through nucleophilic attack of its N-terminal proline at C1' of the damaged nucleotide. Since oxoG efficiently pairs with both C and A, Fpg must excise oxoG from pairs with C but not with A, otherwise a mutation occurs. The crystal structures of several Fpg-DNA complexes have been solved, yet no structure with A opposite the lesion is available. RESULTS: Here we use molecular dynamic simulation to model interactions in the pre-catalytic complex of Lactococcus lactis Fpg with DNA containing oxoG opposite C or A, the latter in either syn or anti conformation...
May 8, 2017: BMC Structural Biology
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