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https://www.readbyqxmd.com/read/28335516/marine-diterpenes-molecular-modeling-of-thrombin-inhibitors-with-potential-biotechnological-application-as-an-antithrombotic
#1
Rebeca Cristina Costa Pereira, André Luiz Lourenço, Luciana Terra, Paula Alvarez Abreu, Valéria Laneuville Teixeira, Helena Carla Castro
Thrombosis related diseases are among the main causes of death and incapacity in the world. Despite the existence of antithrombotic agents available for therapy, they still present adverse effects like hemorrhagic risks which justify the search for new options. Recently, pachydictyol A, isopachydictyol A, and dichotomanol, three diterpenes isolated from Brazilian marine brown alga Dictyota menstrualis were identified as potent antithrombotic molecules through inhibition of thrombin, a key enzyme of coagulation cascade and a platelet agonist...
March 20, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28335505/porcine-epidemic-diarrhea-virus-induces-autophagy-to-benefit-its-replication
#2
Xiaozhen Guo, Mengjia Zhang, Xiaoqian Zhang, Xin Tan, Hengke Guo, Wei Zeng, Guokai Yan, Atta Muhammad Memon, Zhonghua Li, Yinxing Zhu, Bingzhou Zhang, Xugang Ku, Meizhou Wu, Shengxian Fan, Qigai He
The new porcine epidemic diarrhea (PED) has caused devastating economic losses to the swine industry worldwide. Despite extensive research on the relationship between autophagy and virus infection, the concrete role of autophagy in porcine epidemic diarrhea virus (PEDV) infection has not been reported. In this study, autophagy was demonstrated to be triggered by the effective replication of PEDV through transmission electron microscopy, confocal microscopy, and Western blot analysis. Moreover, autophagy was confirmed to benefit PEDV replication by using autophagy regulators and RNA interference...
March 19, 2017: Viruses
https://www.readbyqxmd.com/read/28335297/rotation-of-magnetization-derived-from-brownian-relaxation-in-magnetic-fluids-of-different-viscosity-evaluated-by-dynamic-hysteresis-measurements-over-a-wide-frequency-range
#3
Satoshi Ota, Ryoichi Kitaguchi, Ryoji Takeda, Tsutomu Yamada, Yasushi Takemura
The dependence of magnetic relaxation on particle parameters, such as the size and anisotropy, has been conventionally discussed. In addition, the influences of external conditions, such as the intensity and frequency of the applied field, the surrounding viscosity, and the temperature on the magnetic relaxation have been researched. According to one of the basic theories regarding magnetic relaxation, the faster type of relaxation dominates the process. However, in this study, we reveal that Brownian and Néel relaxations coexist and that Brownian relaxation can occur after Néel relaxation despite having a longer relaxation time...
September 10, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335200/structural-and-magnetic-response-in-bimetallic-core-shell-magnetic-nanoparticles
#4
Adeela Nairan, Usman Khan, Munawar Iqbal, Maaz Khan, Khalid Javed, Saira Riaz, Shahzad Naseem, Xiufeng Han
Bimagnetic monodisperse CoFe₂O₄/Fe₃O₄ core/shell nanoparticles have been prepared by solution evaporation route. To demonstrate preferential coating of iron oxide onto the surface of ferrite nanoparticles X-ray diffraction (XRD), High resolution transmission electron microscope (HR-TEM) and Raman spectroscopy have been performed. XRD analysis using Rietveld refinement technique confirms single phase nanoparticles with average seed size of about 18 nm and thickness of shell is 3 nm, which corroborates with transmission electron microscopy (TEM) analysis...
April 14, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28334976/a-sensitivity-analysis-of-rna-folding-nearest-neighbor-parameters-identifies-a-subset-of-free-energy-parameters-with-the-greatest-impact-on-rna-secondary-structure-prediction
#5
Jeffrey Zuber, Hongying Sun, Xiaoju Zhang, Iain McFadyen, David H Mathews
Nearest neighbor parameters for estimating the folding energy changes of RNA secondary structures are used in structure prediction and analysis. Despite their widespread application, a comprehensive analysis of the impact of each parameter on the precision of calculations had not been conducted. To identify the parameters with greatest impact, a sensitivity analysis was performed on the 291 parameters that compose the 2004 version of the free energy nearest neighbor rules. Perturbed parameter sets were generated by perturbing each parameter independently...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334864/coordination-among-tertiary-base-pairs-results-in-an-efficient-frameshift-stimulating-rna-pseudoknot
#6
Yu-Ting Chen, Kai-Chun Chang, Hao-Teng Hu, Yi-Lan Chen, You-Hsin Lin, Chiung-Fang Hsu, Cheng-Fu Chang, Kung-Yao Chang, Jin-Der Wen
Frameshifting is an essential process that regulates protein synthesis in many viruses. The ribosome may slip backward when encountering a frameshift motif on the messenger RNA, which usually contains a pseudoknot structure involving tertiary base pair interactions. Due to the lack of detailed molecular explanations, previous studies investigating which features of the pseudoknot are important to stimulate frameshifting have presented diverse conclusions. Here we constructed a bimolecular pseudoknot to dissect the interior tertiary base pairs and used single-molecule approaches to assess the structure targeted by ribosomes...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334829/structure-of-the-sac3-rna-binding-m-region-in-the-saccharomyces-cerevisiae-trex-2-complex
#7
James M B Gordon, Shintaro Aibara, Murray Stewart
Transcription-export complex 2 (TREX-2, or THSC) facilitates localization of actively transcribing genes such as GAL1 to the nuclear periphery, contributes to the generation of export-competent mRNPs and influences gene expression through interactions with Mediator. TREX-2 is based on a Sac3 scaffold to which Thp1, Sem1, Cdc31 and Sus1 bind and consists of three modules: the N-region (Sac3∼1-100), which binds mRNA export factor Mex67:Mtr2; the M-region, in which Thp1 and Sem1 bind to Sac3∼100-550; and the CID region in which Cdc31 and two Sus1 chains bind to Sac3∼720-805...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334827/yeast-hrq1-shares-structural-and-functional-homology-with-the-disease-linked-human-recq4-helicase
#8
Cody M Rogers, Joseph Che-Yen Wang, Hiroki Noguchi, Tsuyoshi Imasaki, Yuichiro Takagi, Matthew L Bochman
The five human RecQ helicases participate in multiple processes required to maintain genome integrity. Of these, the disease-linked RecQ4 is the least studied because it poses many technical challenges. We previously demonstrated that the yeast Hrq1 helicase displays similar functions to RecQ4 in vivo, and here, we report the biochemical and structural characterization of these enzymes. In vitro, Hrq1 and RecQ4 are DNA-stimulated ATPases and robust helicases. Further, these activities were sensitive to DNA sequence and structure, with the helicases preferentially unwinding D-loops...
February 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334819/comparative-analyses-of-the-thermodynamic-rna-binding-signatures-of-different-types-of-rna-recognition-motifs
#9
Brighton Samatanga, Antoine Cléry, Pierre Barraud, Frédéric H-T Allain, Ilian Jelesarov
RNA recognition motifs (RRMs) are structurally versatile domains important in regulation of alternative splicing. Structural mechanisms of sequence-specific recognition of single-stranded RNAs (ssRNAs) by RRMs are well understood. The thermodynamic strategies are however unclear. Therefore, we utilized microcalorimetry and semi-empirical analyses to comparatively analyze the cognate ssRNA binding thermodynamics of four different RRM domains, each with a different RNA binding mode. The different binding modes are: canonical binding to the β-sheet surface; canonical binding with involvement of N- and C-termini; binding to conserved loops; and binding to an α-helix...
February 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334755/tracking-fluctuation-hotspots-on-the-yeast-ribosome-through-the-elongation-cycle
#10
Suna P Gulay, Sujal Bista, Amitabh Varshney, Serdal Kirmizialtin, Karissa Y Sanbonmatsu, Jonathan D Dinman
Chemical modification was used to quantitatively determine the flexibility of nearly the entire rRNA component of the yeast ribosome through 8 discrete stages of translational elongation, revealing novel observations at the gross and fine-scales. These include (i) the bulk transfer of energy through the intersubunit bridges from the large to the small subunit after peptidyltransfer, (ii) differences in the interaction of the sarcin ricin loop with the two elongation factors and (iii) networked information exchange pathways that may functionally facilitate intra- and intersubunit coordination, including the 5...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334742/recognition-but-no-repair-of-abasic-site-in-single-stranded-dna-by-human-ribosomal-us3-protein-residing-within-intact-40s-subunit
#11
Anastasia S Grosheva, Dmitry O Zharkov, Joachim Stahl, Alexander V Gopanenko, Alexey E Tupikin, Marsel R Kabilov, Dmitri M Graifer, Galina G Karpova
Isolated human ribosomal protein uS3 has extra-ribosomal functions including those related to base excision DNA repair, e.g. AP lyase activity that nicks double-stranded (ds) DNA 3΄ to the abasic (AP) site. However, the ability of uS3 residing within ribosome to recognize and cleave damaged DNA has never been addressed. Here, we compare interactions of single-stranded (ss) DNA and dsDNA bearing AP site with human ribosome-bound uS3 and with the isolated protein, whose interactions with ssDNA were not yet studied...
January 30, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334722/even-a-moderate-fluid-removal-rate-during-individualised-haemodialysis-session-times-is-associated-with-decreased-patient-survival
#12
Charles Chazot, Cyril Vo-Van, Christie Lorriaux, Patrik Deleaval, Brice Mayor, Jean-Marc Hurot, Guillaume Jean
BACKGROUND: Several studies report that fluid removal rate (FRR) above 10-13 mL/h/kg is associated with increased mortality in haemodialysis (HD) patients. AIM: The aims of this study are to assess the influence of moderate FRR on survival in a cohort of prevalent dialysis patients with various dialysis session times and to challenge the FRR thresholds associated with increased mortality risk reported previously. METHODS: Interdialytic weight gain (IDWG) and FRR (calculated from ultrafiltration [UF], target weight, and session time prescriptions) were studied in 190 prevalent dialysis patients (female: 42%, mean age: 69...
March 24, 2017: Blood Purification
https://www.readbyqxmd.com/read/28334695/how-the-embryonic-chick-brain-twists
#13
Zi Chen, Qiaohang Guo, Eric Dai, Nickolas Forsch, Larry A Taber
During early development, the tubular embryonic chick brain undergoes a combination of progressive ventral bending and rightward torsion, one of the earliest organ-level left-right asymmetry events in development. Existing evidence suggests that bending is caused by differential growth, but the mechanism for the predominantly rightward torsion of the embryonic brain tube remains poorly understood. Here, we show through a combination of in vitro experiments, a physical model of the embryonic morphology and mechanics analysis that the vitelline membrane (VM) exerts an external load on the brain that drives torsion...
November 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28334424/frequency-and-function-in-the-basal-ganglia-the-origins-of-beta-and-gamma-band-activity
#14
Alexander Blenkinsop, Sean Anderson, Kevin Gurney
Neural oscillations in the basal ganglia are well studied yet remain poorly understood. Behavioural correlates of spectral activity are well described, yet a quantitative hypothesis linking time domain dynamics and spectral properties to basal ganglia function has been lacking. We show, for the first time, that a unified description is possible by interpreting previously ignored structure in data describing GPi responses to cortical stimulation. These data were used to expose a pair of distinctive neuronal responses to the stimulation...
March 23, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28334034/contrasting-effects-of-visiting-urban-green-space-and-the-countryside-on-biodiversity-knowledge-and-conservation-support
#15
Deborah F Coldwell, Karl L Evans
Conservation policy frequently assumes that increasing people's exposure to green-space enhances their knowledge of the natural world and desire to protect it. Urban development is, however, considered to be driving declining connectedness to nature. Despite this the evidence base supporting the assumption that visiting green-spaces promotes biodiversity knowledge and conservation support, and the impacts of urbanization on these relationships, is surprisingly limited. Using data from door-to-door surveys of nearly 300 residents in three pairs of small and large urban areas in England we demonstrate that people who visit green-space more regularly have higher biodiversity knowledge and support for conservation (measured using scales of pro-environmental behavior)...
2017: PloS One
https://www.readbyqxmd.com/read/28333640/integrated-hifu-drive-system-on-a-chip-for-cmut-based-catheter-ablation-system
#16
Omid Farhanieh, Ali Sahafi, Rupak Bardhan Roy, Arif Sanli Ergun, Ayhan Bozkurt
Conventional High Intensity Focused Ultrasound (HIFU) is a therapeutic modality which is extracorporeally administered. In applications where a relatively small HIFU lesion is required, an intravascular HIFU probe can be deployed to the ablation site. In this paper, we demonstrate the design and implementation a fully integrated HIFU drive system on a chip to be placed on a 6 Fr catheter probe. An 8-element capacitive micromachined ultrasound transducer (CMUT) ring array of 2 mm diameter has been used as the ultrasound source...
March 20, 2017: IEEE Transactions on Biomedical Circuits and Systems
https://www.readbyqxmd.com/read/28333434/measurement-of-in-vivo-protein-binding-affinities-in-a-signaling-network-with-mass-spectrometry
#17
Mumun Gencoglu, Alexander Schmidt, Attila Becskei
Protein interaction networks play a key role in signal processing. Despite the progress in identifying the interactions, the quantification of their strengths lags behind. Here we present an approach to quantify the in vivo binding of proteins to their binding partners in signaling-transcriptional networks, by the pairwise genetic isolation of each interaction and by varying the concentration of the interacting components over time. The absolute quantification of the protein concentrations was performed with targeted mass spectrometry...
March 23, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28333377/circadian-rhythms-in-adipose-tissue-physiology
#18
Jana-Thabea Kiehn, Anthony H Tsang, Isabel Heyde, Brinja Leinweber, Isa Kolbe, Alexei Leliavski, Anthony H Tsang
The different types of adipose tissues fulfill a wide range of biological functions-from energy storage to hormone secretion and thermogenesis-many of which show pronounced variations over the course of the day. Such 24-h rhythms in physiology and behavior are coordinated by endogenous circadian clocks found in all tissues and cells, including adipocytes. At the molecular level, these clocks are based on interlocked transcriptional-translational feedback loops comprised of a set of clock genes/proteins. Tissue-specific clock-controlled transcriptional programs translate time-of-day information into physiologically relevant signals...
March 16, 2017: Comprehensive Physiology
https://www.readbyqxmd.com/read/28333205/convergence-of-domain-architecture-structure-and-ligand-affinity-in-animal-and-plant-rna-binding-proteins
#19
Raquel Dias, Austin Manny, Oralia Kolaczkowski, Bryan Kolaczkowski
Reconstruction of ancestral protein sequences using phylogenetic methods is a powerful technique for directly examining the evolution of molecular function. Although ancestral sequence reconstruction (ASR) is itself very efficient, downstream functional and structural studies necessary to characterize when and how changes in molecular function occurred are often costly and time-consuming, currently limiting ASR studies to examining a relatively small number of discrete functional shifts. As a result, we have very little direct information about how molecular function evolves across large protein families...
February 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28333133/fidelity-of-classwide-resistant-hiv-2-reverse-transcriptase-and-differential-contribution-of-k65r-to-the-accuracy-of-hiv-1-and-hiv-2-reverse-transcriptases
#20
Mar Álvarez, Alba Sebastián-Martín, Guillermo García-Marquina, Luis Menéndez-Arias
Nucleoside reverse transcriptase (RT) inhibitors constitute the backbone of current therapies against human immunodeficiency virus type 1 and type 2 (HIV-1 and HIV-2, respectively). However, mutational pathways leading to the development of nucleoside analogue resistance are different in both types of HIV. In HIV-2, resistance to all approved nucleoside analogues is conferred by the combination of RT substitutions K65R, Q151M and M184V. Nucleotide incorporation kinetic analyses of mutant and wild-type (WT) HIV-2 RTs show that the triple-mutant has decreased catalytic efficiency due to the presence of M184V...
March 23, 2017: Scientific Reports
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