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https://www.readbyqxmd.com/read/29342326/mixed-fluorotryptophan-substitutions-at-the-same-residue-expand-the-versatility-of-%C3%A2-%C3%A2-f-protein-nmr-spectroscopy
#1
Calem Kenward, Kyungsoo Shin, Jan Rainey
The strategy of applying fluorine NMR to characterize ligand binding to a membrane protein prepared with mixtures of tryptophans substituted with F at different positions on the indole ring was tested. The ¹⁹F NMR behavior of 4-, 5-, 6-, and 7-fluorotryptophan were directly compared as a function of both micellar environment and fragment size for two overlapping apelin receptor (AR/APJ) segments - one with a single transmembrane (TM) helix and two tryptophan residues, the other with three TM helices and two additional tryptophan residues...
January 17, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29341745/born-oppenheimer-dynamics-electronic-friction-and-the-inclusion-of-electron-electron-interactions
#2
Wenjie Dou, Gaohan Miao, Joseph E Subotnik
We present a universal expression for the electronic friction as felt by a set of classical nuclear degrees of freedom (DOFs) coupled to a manifold of quantum electronic DOFs; no assumptions are made regarding the nature of the electronic Hamiltonian and electron-electron repulsions are allowed. Our derivation is based on a quantum-classical Liouville equation for the coupled electronic-nuclear motion, followed by an adiabatic approximation whereby electronic transitions are assumed to equilibrate faster than nuclear movement...
July 28, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29339785/the-lncrna-gata6-as-epigenetically-regulates-endothelial-gene-expression-via-interaction-with-loxl2
#3
Philipp Neumann, Nicolas Jaé, Andrea Knau, Simone F Glaser, Youssef Fouani, Oliver Rossbach, Marcus Krüger, David John, Albrecht Bindereif, Phillip Grote, Reinier A Boon, Stefanie Dimmeler
Impaired or excessive growth of endothelial cells contributes to several diseases. However, the functional involvement of regulatory long non-coding RNAs in these processes is not well defined. Here, we show that the long non-coding antisense transcript of GATA6 (GATA6-AS) interacts with the epigenetic regulator LOXL2 to regulate endothelial gene expression via changes in histone methylation. Using RNA deep sequencing, we find that GATA6-AS is upregulated in endothelial cells during hypoxia. Silencing of GATA6-AS diminishes TGF-β2-induced endothelial-mesenchymal transition in vitro and promotes formation of blood vessels in mice...
January 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29337929/integrated-analyses-reveal-overexpressed-notch1-promoting-porcine-satellite-cells-proliferation-through-regulating-the-cell-cycle
#4
Yiren Jiao, Bo Huang, Yu Chen, Guangliang Hong, Jian Xu, Chingyuan Hu, Chong Wang
Notch signaling as a conserved cell fate regulator is involved in the regulation of cell quiescence, proliferation, differentiation and postnatal tissue regeneration. However, how Notch signaling regulates porcine satellite cells (PSCs) has not been elucidated. We stably transfected Notch1 intracellular domain (N1ICD) into PSCs to analyze the gene expression profile and miRNA-seq. The analysis of the gene expression profile identified 295 differentially-expressed genes (DEGs) in proliferating-N1ICD PSCs (P-N1ICD) and nine DEGs on differentiating-N1ICD PSCs (D-N1ICD), compared with that in control groups (P-Control and D-Control, respectively)...
January 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29337275/the-o-%C3%AE-linked-n-acetylglucosaminylation-of-the-lamin-b-receptor-and-its-impact-on-dna-binding-and-phosphorylation
#5
Caroline Smet-Nocca, Adeline Page, François-Xavier Cantrelle, Eleni Nikolakaki, Isabelle Landrieu, Thomas Giannakouros
Lamin B Receptor (LBR) is an integral protein of the interphase inner nuclear membrane that is implicated in chromatin anchorage to the nuclear envelope. Phosphorylation of a stretch of arginine-serine (RS) dipeptides in the amino-terminal nucleoplasmic domain of LBR regulates the interactions of the receptor with other nuclear proteins, DNA and RNA and thus modulates tethering of heterochromatin to the nuclear envelope. While phosphorylation has been extensively studied, very little is known about other post-translational modifications of the protein...
January 11, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29337196/nicorandil-and-theophylline-can-protect-experimental-rats-against-complete-freund-s-adjuvant-induced-rheumatoid-arthritis-through-modulation-of-jak-stat-rankl-signaling-pathway
#6
Ahmed Gaafar Ahmed Gaafar, Basim Anwar Shehata Messiha, Ahmed Mohamed Labib Abdelkafy
Signaling pathways are interesting fields of study of pathogenesis and treatment trials. We elucidated the possible protective effects of nicorandil (15mg/kg/day) and theophylline (20mg/kg/day) on experimentally-induced RA, focusing on the role of JAK (Janus Kinase) / STAT (Signal Transducer and Activator of Transcription) / RANKL (Receptor Activator of Nuclear factor-Kappa B Ligand) / cytokine signaling pathway. Four sets of experiments were performed. First, effect of test agents on normal animals was evaluated...
January 11, 2018: European Journal of Pharmacology
https://www.readbyqxmd.com/read/29334619/comparisons-between-a-new-point-kernel-based-scheme-and-the-infinite-plane-source-assumption-method-for-radiation-calculation-of-deposited-airborne-radionuclides-from-nuclear-power-plants
#7
Xiaole Zhang, George Efthimiou, Yan Wang, Meng Huang
Radiation from the deposited radionuclides is indispensable information for environmental impact assessment of nuclear power plants and emergency management during nuclear accidents. Ground shine estimation is related to multiple physical processes, including atmospheric dispersion, deposition, soil and air radiation shielding. It still remains unclear that whether the normally adopted "infinite plane" source assumption for the ground shine calculation is accurate enough, especially for the area with highly heterogeneous deposition distribution near the release point...
January 12, 2018: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/29330200/pwwp-domain-interactor-of-polycombs11-interacts-with-polycomb-group-proteins-and-histones-and-regulates-arabidopsis-flowering-and-development
#8
Mareike L Hohenstatt, Pawel Mikulski, Olga Komarynets, Constanze Klose, Ina Kycia, Albert Jeltsch, Sara Farrona, Daniel Schubert
Polycomb-group (PcG) proteins mediate epigenetic gene regulation by setting H3K27me3 via Polycomb Repressive Complex 2 (PRC2). In plants, it is largely unclear how PcG proteins are recruited to their target genes. Here, we identified the PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 (PWO1) protein, which interacts with all three Arabidopsis thaliana PRC2 histone methyltransferases and is required for maintaining full H3 occupancy at several Arabidopsis genes. PWO1 localizes and recruits CURLY LEAF to nuclear speckles in Nicotiana benthamiana nuclei, suggesting a role in spatial organization of PcG regulation...
January 12, 2018: Plant Cell
https://www.readbyqxmd.com/read/29330189/targeted-synthesis-and-characterization-of-a-gene-cluster-encoding-nad-p-h-dependent-3%C3%AE-3%C3%AE-and-12%C3%AE-hydroxysteroid-dehydrogenases-from-eggerthella-cag-298-a-gut-metagenomic-sequence
#9
Sean M Mythen, Saravanan Devendran, Celia Méndez-García, Isaac Cann, Jason M Ridlon
Gut metagenomic sequences provide a rich source of microbial genes, the majority of which are annotated by homology or unknown. Genes and gene pathways that encode enzymes catalyzing biotransformation of host bile acids are important to identify in gut metagenomic sequences due to the importance of bile acids on gut microbiome structure and host physiology. Hydroxysteroid dehydrogenases (HSDH) are pyridine nucleotide-dependent enzymes with stereo-specificity and regio-specificity for bile acid and steroid hydroxyl groups...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29326982/discovery-of-slow-magnetic-fluctuations-and-critical-slowing-down-in-the-pseudogap-phase-of-yba2cu3o-y
#10
Jian Zhang, Zhaofeng Ding, Cheng Tan, Kevin Huang, Oscar O Bernal, Pei-Chun Ho, Gerald D Morris, Adrian D Hillier, Pabitra K Biswas, Stephen P Cottrell, Hui Xiang, Xin Yao, Douglas E MacLaughlin, Lei Shu
The origin of the pseudogap region below a temperature T* is at the heart of the mysteries of cuprate high-temperature superconductors. Unusual properties of the pseudogap phase, such as broken time-reversal and inversion symmetry are observed in several symmetry-sensitive experiments: polarized neutron diffraction, optical birefringence, dichroic angle-resolved photoemission spectroscopy, second harmonic generation, and polar Kerr effect. These properties suggest that the pseudogap region is a genuine thermodynamic phase and are predicted by theories invoking ordered loop currents or other forms of intra-unit-cell (IUC) magnetic order...
January 2018: Science Advances
https://www.readbyqxmd.com/read/29326354/accuracy-of-dose-calibrators-for-gallium-68-pet-imaging-unexpected-findings-in-a-multi-centre-clinical-pre-trial-assessment
#11
Dale L Bailey, Michael S Hofman, Nicholas J Forwood, Graeme J O'Keefe, Andrew M Scott, Winifred M van Wyngaardt, Bonnie Howe, Olga Kovacev, Roslyn J Francis
AIMS: We report the discovery of a systematic miscalibration during the work-up process for site validation of a multi-centre clinical PET imaging trial using 68Ga, which manifested as a consistent and reproducible underestimation in the quantitative accuracy (assessed by SUV) of a range of PET cameras from different manufacturers at a number of different facilities around Australia. METHODS: Sites were asked to follow a strict preparation protocol to create a radioactive phantom with 68Ga to be imaged using a standard clinical protocol prior to commencing imaging in the trial...
January 11, 2018: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
https://www.readbyqxmd.com/read/29325077/integrating-restriction-site-associated-dna-sequencing-rad-seq-with-morphological-cladistic-analysis-clarifies-evolutionary-relationships-among-major-species-groups-of-bee-orchids
#12
Richard M Bateman, Gábor Sramkó, Ovidiu Paun
Background and Aims: Bee orchids (Ophrys) have become the most popular model system for studying reproduction via insect-mediated pseudo-copulation and for exploring the consequent, putatively adaptive, evolutionary radiations. However, despite intensive past research, both the phylogenetic structure and species diversity within the genus remain highly contentious. Here, we integrate next-generation sequencing and morphological cladistic techniques to clarify the phylogeny of the genus...
January 9, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29319797/an-in-silico-comparison-of-protocols-for-dated-phylogenomics
#13
Rupert A Collins, Tomas Hrbek
In the age of genome-scale DNA sequencing, choice of molecular marker arguably remains an important decision in planning a phylogenetic study. Using published genomes from 23 primate species, we make a standardized comparison of four of the most frequently used protocols in phylogenomics, viz., targeted sequence-enrichment using ultraconserved element and exon-capture probes, and restriction-site-associated DNA sequencing (RADseq and ddRADseq). Here, we present a procedure to perform in silico extractions from genomes and create directly comparable data sets for each class of marker...
January 8, 2018: Systematic Biology
https://www.readbyqxmd.com/read/29319143/prognostic-factors-of-breast-cancer-survival-in-the-islamic-republic-of-iran-an-additive-empirical-bayesian-approach
#14
Samane Nematolahi, Abbas Rezaianzadeh, Najaf Zare, Majid Akrami, Sedighe Tahmasebi
Breast cancer is a public health challenge in the Islamic Republic of Iran. Relatively few studies have dealt with large dataset and advanced statistical methods. Therefore, we aimed to investigate the role of prognostic factors on breast cancer survival using Additive Empirical Bayesian model with large data set. Breast cancer data set included 1574 women diagnosed with breast cancer from 2002 to 2012 that registered from Cancer Registry in Fars Province, Islamic Republic of Iran. Overall survival rates at 2, 3, 5 and 10 years were 0...
January 2, 2018: Eastern Mediterranean Health Journal, la Revue de Santé de la Méditerranée Orientale
https://www.readbyqxmd.com/read/29317769/phylogenomic-perspective-on-the-relationships-and-evolutionary-history-of-the-major-otocephalan-lineages
#15
Wei Dai, Ming Zou, Liandong Yang, Kang Du, Weitao Chen, Yanjun Shen, Richard L Mayden, Shunping He
The phylogeny of otocephalan fishes is the subject of broad controversy based on morphological and molecular evidence. The primary unresolved issue pertaining to this lineage relates to the origin of Characiphysi, especially the paraphyly of Characiformes. The considerable uncertainty associated with this lineage has precluded a greater understanding of the origin and evolution of the clade. Herein, a phylogenomic approach was applied to resolve this debate. By analyzing 10 sets of transcriptomic data generated in this study and 12 sets of high-throughput data available in public databases, we obtained 1,110 single-copy orthologous genes (935,265 sites for analysis) from 22 actinopterygians, including 14 otocephalan fishes from six orders: Clupeiformes, Gonorynchiformes, Cypriniformes, Siluriformes, Characiformes, and Gymnotiformes...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29317431/suppression-of-activated-foxo-transcription-factors-in-the-heart-prolongs-survival-in-a-mouse-model-of-laminopathies
#16
Gaelle Auguste, Priyatansh Gurha, Raffaella Lombardi, Cristian Coarfa, James T Willerson, Ali J Marian
Rationale: Mutations in the LMNA gene, encoding nuclear inner membrane protein Lamin A/C, cause distinct phenotypes, collectively referred to as laminopathies. Heart failure, conduction defects, and arrhythmias are the common causes of death in laminopathies. Objective: To identify and therapeutically target the responsible mechanism(s) for cardiac phenotype in laminopathies. Methods and Results: Whole heart RNA sequencing was performed prior to the onset of cardiac dysfunction in the Lmna-/- and matched control mice...
January 9, 2018: Circulation Research
https://www.readbyqxmd.com/read/29316156/tailored-environments-to-study-motile-cells-and-pathogens
#17
REVIEW
Julianne Mendi Muthinja, Johanna Ripp, Timothy Krüger, Andrea Imle, Tamás Haraszti, Oliver T Fackler, Joachim P Spatz, Markus Engstler, Friedrich Frischknecht
Motile cells and pathogens migrate in complex environments and yet are mostly studied on simple 2D substrates. In order to mimic the diverse environments of motile cells a set of assays including substrates of defined elasticity, microfluidics, micropatterns, organotypic cultures and 3D gels have been developed. We briefly introduce these and then focus on the use of micro-patterned pillar arrays, which help to bridge the gap between 2D and 3D. These structures are made from polydimethylsiloxane, a moldable plastic and their use has revealed new insights into mechanoperception in Caenorhabditis elegans, gliding motility of Plasmodium, swimming of trypanosomes and nuclear stability in cancer cells...
January 7, 2018: Cellular Microbiology
https://www.readbyqxmd.com/read/29313254/aligned-electrospun-fibers-for-neural-patterning
#18
Erfan Soliman, Fabio Bianchi, James N Sleigh, Julian H George, M Zameel Cader, Zhanfeng Cui, Hua Ye
OBJECTIVES: To test a 3D approach for neural network formation, alignment, and patterning that is reproducible and sufficiently stable to allow for easy manipulation. RESULTS: A novel cell culture system was designed by engineering a method for the directional growth of neurons. This uses NG108-15 neuroblastoma x glioma hybrid cells cultured on suspended and aligned electrospun fibers. These fiber networks improved cellular directionality, with alignment angle standard deviations significantly lower on fibers than on regular culture surfaces...
January 8, 2018: Biotechnology Letters
https://www.readbyqxmd.com/read/29310337/simulation-of-expected-childhood-and-adolescent-thyroid-cancer-cases-in-japan-using-a-cancer-progression-model-based-on-the-national-cancer-registry-application-to-the-first-round-thyroid-examination-of-the-fukushima-health-management-survey
#19
Hideto Takahashi, Kunihiko Takahashi, Hiroki Shimura, Seiji Yasumura, Satoru Suzuki, Akira Ohtsuru, Sanae Midorikawa, Tetsuya Ohira, Hitoshi Ohto, Shunichi Yamashita, Kenji Kamiya
During the 4 years following the nuclear power plant accident of 2011, 39 males and 77 females were diagnosed with or suspected of having cancer based on the first-round thyroid examination of the Fukushima Health Management Survey (FHMS) targeting residents aged <19 years in Fukushima. Prior comparisons between the observed data and Japan's National Cancer Registry (NCR) data suggested that this incidence might be excessive, but such comparisons are problematic because they need not only to adjust index unit (prevalence proportion vs incidence rate), but also examine characteristics (complete enumeration mass screening for the aged 0 to 18 years vs detections in clinical settings for all the residents) and sensitivity of the examinations...
December 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29305243/colonization-and-diversification-of-the-white-browed-shortwing-aves-muscicapidae-brachypteryx-montana-in-the-philippines
#20
Christopher C Kyriazis, Bushra Alam, Mark Wjodyla, Shannon Hackett, Peter Hosner, Herman L Mays, Lawrence R Heaney, Sushma Reddy
Molecular phylogenetic approaches have greatly improved our knowledge of the pattern and process of biological diversification across the globe; however, many regions remain poorly documented, even for well-studied vertebrate groups. The Philippine archipelago, one of the least-studied 'biodiversity hotspots', is an ideal natural laboratory for investigating the mechanisms driving diversification in an insular and geologically dynamic setting. We investigated the history and geography of diversification of the Philippine populations of a widespread montane bird, the White-browed Shortwing (Brachypteryx montana)...
January 2, 2018: Molecular Phylogenetics and Evolution
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