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https://www.readbyqxmd.com/read/28940798/protein-structure-prediction-using-rosetta-in-casp12
#1
Sergey Ovchinnikov, Hahnbeom Park, David Kim, Frank DiMaio, David Baker
We describe several notable aspects of our structure predictions using Rosetta in CASP12 in the free modeling (FM) and refinement (TR) categories. First, we had previously generated (and published) models for most large protein families lacking experimentally determined structures using Rosetta guided by co-evolution based contact predictions, and for several targets these models proved better starting points for comparative modeling than any known crystal structure-our model database thus starts to fulfill one of the goals of the original protein structure initiative...
September 22, 2017: Proteins
https://www.readbyqxmd.com/read/28940598/amine-oxidase-from-euphorbia-characias-kinetic-and-structural-characterization
#2
Francesca Pintus, Annalaura Sabatucci, Mauro Maccarrone, Enrico Dainese, Rosaria Medda
This minireview focuses on a plant copper/TPQ amine oxidase isolated from the latex of the shrub Euphorbia characias (ELAO). This enzyme has been investigated in terms of both molecular structure and kinetic mechanism. The characterization of this enzyme allowed us to identify specific amino acids and domains that play a key role in modulating substrate access into the active site of not only for ELAO but also for other plant and mammalian amine oxidases. As mammalian amine oxidases are implicated in several physiological and pathological conditions, the deep structural characterization of their active site accession mechanisms could be the starting point for the development of enzyme modulators with high therapeutic potential...
September 20, 2017: Biotechnology and Applied Biochemistry
https://www.readbyqxmd.com/read/28940334/uncovering-a-third-dissolved-phase-129-xe-resonance-in-the-human-lung-quantifying-spectroscopic-features-in-healthy-subjects-and-patients-with-idiopathic-pulmonary-fibrosis
#3
Scott H Robertson, Rohan S Virgincar, Elianna A Bier, Mu He, Geoffrey M Schrank, Rose Marie Smigla, Craig Rackley, H Page McAdams, Bastiaan Driehuys
PURPOSE: The purpose of this work was to accurately characterize the spectral properties of hyperpolarized (129) Xe in patients with idiopathic pulmonary fibrosis (IPF) compared to healthy volunteers. METHODS: Subjects underwent hyperpolarized (129) Xe breath-hold spectroscopy, during which 38 dissolved-phase free induction decays (FIDs) were acquired after reaching steady state (echo time/repetition time = 0.875/50 ms; bandwidth = 8.06 kHz; flip angle≈22 °)...
October 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28939121/discovery-of-novel-1-2-4-triazolo-4-3-a-quinoxaline-aminophenyl-derivatives-as-bet-inhibitors-for-cancer-treatment
#4
Imran Ali, Jooyun Lee, Areum Go, Gildon Choi, Kwangho Lee
Bromodomain and extra-terminal (BET) proteins, a class of epigenetic reader domains has emerged as a promising new target class for small molecule drug discovery for the treatment of cancer, inflammatory, and autoimmune diseases. Starting from in silico screening campaign, herein we report the discovery of novel BET inhibitors based on [1,2,4]triazolo[4,3-a]quinoxaline scaffold and their biological evaluation. The hit compound was optimized using the medicinal chemistry approach to the lead compound with excellent inhibitory activities against BRD4 in the binding assay...
September 14, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28935667/upregulation-of-herv-k-is-linked-to-immunity-and-inflammation-in-pulmonary-arterial-hypertension
#5
Toshie Saito, Kazuya Miyagawa, Shih-Yu Chen, Rasa Tamosiuniene, Lingli Wang, Orr Sharp, Erik Samayoa, Daisuke Harada, Jan-Renier A J Moonen, Aiqin Cao, Pin-I Chen, Jan K Hennigs, Mingxia Gu, Caiyun G Li, Ryan D Leib, Dan Li, Christopher M Adams, Patricia A Del Rosario, Matthew A Bill, Francois Haddad, Jose G Montoya, William Robinson, Wendy J Fantl, Garry P Nolan, Roham T Zamanian, Mark R Nicolls, Charles Y Chiu, Maria E Ariza, Marlene Rabinovitch
Background -Immune dysregulation has been linked to occlusive vascular remodeling in pulmonary arterial hypertension (PAH) that is hereditary, idiopathic or associated with other conditions. Circulating autoantibodies, lung perivascular lymphoid tissue and elevated cytokines have been related to PAH pathogenesis but without clear understanding of how these abnormalities are initiated, perpetuated and connected in the progression of disease. We therefore set out to identify specific target antigens in PAH lung immune complexes as a starting point toward resolving these issues to better inform future application of immunomodulatory therapies...
September 21, 2017: Circulation
https://www.readbyqxmd.com/read/28933666/regulation-of-proliferation-in-developing-human-tooth-germs-by-msx-muscle-segment-homeodomain-proteins-and-cyclin-dependent-kinase-inhibitor-p19-ink4d
#6
Darko Kero, Katarina Vukojevic, Petra Stazic, Danijela Sundov, Snjezana Mardesic Brakus, Mirna Saraga-Babic
Before the secretion of hard dental tissues, tooth germs undergo several distinctive stages of development (dental lamina, bud, cap and bell). Every stage is characterized by specific proliferation patterns, which is regulated by various morphogens, growth factors and homeodomain proteins. The role of MSX homeodomain proteins in odontogenesis is rather complex. Expression domains of genes encoding for murine Msx1/2 during development are observed in tissues containing highly proliferative progenitor cells. Arrest of tooth development in Msx knockout mice can be attributed to impaired proliferation of progenitor cells...
September 21, 2017: Organogenesis
https://www.readbyqxmd.com/read/28932246/implementation-and-evaluation-of-an-intervention-for-children-in-afghanistan-at-risk-for-substance-use-or-actively-using-psychoactive-substances
#7
Abdul Subor Momand, Elizabeth Mattfeld, Brian Morales, Manzoor Ul Haq, Thom Browne, Kevin E O'Grady, Hendrée E Jones
The present study examined the impact of a novel intervention for children at risk for substance use or actively using substances that was provided to 783 children between 4 and 18 years of age in Afghanistan. They received the Child Intervention for Living Drug-free (CHILD) protocol while in outpatient or residential treatment. CHILD included age-appropriate literacy and numeracy, drug education, basic living safety, and communication and trauma coping skills. A battery of measures examined multiple child health domains at treatment's start and end and 12 weeks later...
2017: International Journal of Pediatrics
https://www.readbyqxmd.com/read/28929974/reconstruction-and-visualization-of-large-scale-volumetric-models-of-neocortical-circuits-for-physically-plausible-in-silico-optical-studies
#8
Marwan Abdellah, Juan Hernando, Nicolas Antille, Stefan Eilemann, Henry Markram, Felix Schürmann
BACKGROUND: We present a software workflow capable of building large scale, highly detailed and realistic volumetric models of neocortical circuits from the morphological skeletons of their digitally reconstructed neurons. The limitations of the existing approaches for creating those models are explained, and then, a multi-stage pipeline is discussed to overcome those limitations. Starting from the neuronal morphologies, we create smooth piecewise watertight polygonal models that can be efficiently utilized to synthesize continuous and plausible volumetric models of the neurons with solid voxelization...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28926259/dual-photochemical-reaction-pathway-in-flavin-based-photoreceptor-lov-domain-a-combined-quantum-mechanics-molecular-mechanics-investigation
#9
Setsuko Nakagawa, Oliver Weingart, Christel M Marian
The primary photochemical reaction of the light, oxygen, and voltage (LOV) domain of the blue-light photo-sensor YtvA of Bacillus subtilis were investigated using high-level QM(DFT/MRCI)/MM methods. After blue-light excitation, the Sγ atom of the reactive cysteine forms a covalent bond with the C4a of the flavin mononucleotide (FMN) ring. Two conformations for the side chain of reactive cysteine with occupancies of 70% (conf A) and 30% (conf B) are observed in the X-ray crystallographic structures of the YtvA-LOV (Möglich, A...
September 19, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28924313/tobacco-use-among-serving-army-personnel-an-epidemiological-study
#10
Atul Puthia, A K Yadav, Atul Kotwal
BACKGROUND: India has consequential burden of tobacco related disease and death. Though there are surveys conducted at national and regional level yet the information about tobacco consumption among army personnel is scarce. Thus an epidemiological study was conducted to estimate the prevalence and assess determinants of tobacco consumption amongst army personnel. METHODS: A community based cross sectional study was conducted using simple random sampling to enroll 380 personnel...
April 2017: Medical Journal, Armed Forces India
https://www.readbyqxmd.com/read/28919577/some-properties-of-three-%C3%AE-b-crystallin-mutants-carrying-point-substitutions-in-the-c-terminal-domain-and-associated-with-congenital-diseases
#11
Evgenia S Gerasimovich, Sergei V Strelkov, Nikolai B Gusev
Physico-chemical properties of G154S, R157H and A171T mutants of αB-crystallin (HspB5) associated with congenital human diseases including certain myopathies and cataract were investigated. Oligomers formed by G154S and A171T mutants have the size and apparent molecular weight indistinguishable from those of the wild-type HspB5, whereas the size of oligomers formed by R157H mutant is slightly smaller. All mutants are less thermostable and start to aggregate at a lower temperature than the wild-type protein...
September 14, 2017: Biochimie
https://www.readbyqxmd.com/read/28919361/molecular-characterisation-ontogeny-and-expression-analysis-of-melanoma-differentiation-associated-factor-5-mda5-from-asian-seabass-lates-calcarifer
#12
Anutosh Paria, M Makesh, Aparna Chaudhari, C S Purushothaman, K V Rajendran
MDA5 is the pivotal member of the retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) and is reported to play a crucial role in type I IFN-mediated responses against pathogen-associated molecular patterns (PAMPs), especially nucleic acids. In this study, we have identified and cloned the full-length cDNA sequence of MDA5, which comprises 3398 nucleotides and encodes for a putative protein of 978 AA length, in Asian seabass, Lates calcarifer. From the putative amino acid sequence of AsMDA5, four different conserved domains could be predicted: two N-terminal CARD domains, a DExDc domain, a HELICc domain and a C-terminal RIG-1_C-RD domain...
September 15, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28915267/cooling-induces-phase-separation-in-membranes-derived-from-isolated-cns-myelin
#13
Julio M Pusterla, Emanuel Schneck, Sérgio S Funari, Bruno Démé, Motomu Tanaka, Rafael G Oliveira
Purified myelin membranes (PMMs) are the starting material for biochemical analyses such as the isolation of detergent-insoluble glycosphingolipid-rich domains (DIGs), which are believed to be representatives of functional lipid rafts. The normal DIGs isolation protocol involves the extraction of lipids under moderate cooling. Here, we thus address the influence of cooling on the structure of PMMs and its sub-fractions. Thermodynamic and structural aspects of periodic, multilamellar PMMs are examined between 4°C and 45°C and in various biologically relevant aqueous solutions...
2017: PloS One
https://www.readbyqxmd.com/read/28914313/cohesiveness-and-flowability-of-particulated-solid-and-semi-solid-food-systems
#14
Aarti B Tobin, Peggy Heunemann, Judith Wemmer, Jason R Stokes, Timothy Nicholson, Erich J Windhab, Peter Fischer
Cohesiveness and flowability of particulated food systems is of particular interest in the oral processing and swallowing of food products, especially for people suffering from dysphagia. Although cohesiveness of a bolus is an essential parameter in swallowing, a robust technique for objective measurement of cohesiveness of particulated semi- or soft-solids is still lacking. In our approach the ring shear tester is used to measure the cohesiveness and flowability of a model particulated food system based on fresh green pea powders and pastes with controlled moisture content...
September 15, 2017: Food & Function
https://www.readbyqxmd.com/read/28913775/complete-mitochondrial-genome-of-taharana-fasciana-insecta-hemiptera-cicadellidae-and-comparison-with-other-cicadellidae-insects
#15
Jiajia Wang, Hu Li, Renhuai Dai
Here, we describe the first complete mitochondrial genome (mitogenome) sequence of the leafhopper Taharana fasciana (Coelidiinae). The mitogenome sequence contains 15,161 bp with an A + T content of 77.9%. It includes 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding (A + T-rich) region; in addition, a repeat region is also present (GenBank accession no. KY886913). These genes/regions are in the same order as in the inferred insect ancestral mitogenome. All protein-coding genes have ATN as the start codon, and TAA or single T as the stop codons, except the gene ND3, which ends with TAG...
September 14, 2017: Genetica
https://www.readbyqxmd.com/read/28913593/interaction-of-arabidopsis-tga3-and-wrky53-transcription-factors-on-cestrum-yellow-leaf-curling-virus-cmylcv-promoter-mediates-salicylic-acid-dependent-gene-expression-in-planta
#16
Shayan Sarkar, Abhimanyu Das, Prashant Khandagale, Indu B Maiti, Sudip Chattopadhyay, Nrisingha Dey
This paper highlighted a salicylic acid-inducible Caulimoviral promoter fragment from Cestrum yellow leaf curling virus (CmYLCV). Interaction of Arabidopsis transcription factors TGA3 and WRKY53 on CmYLCV promoter resulted in the enhancement of the promoter activity via NPR1-dependent salicylic acid signaling. Several transcriptional promoters isolated from plant-infecting Caulimoviruses are being presently used worldwide as efficient tools for plant gene expression. The CmYLCV promoter has been isolated from the Cestrum yellow leaf curling virus (Caulimoviruses) and characterized more than 12 years ago; also we have earlier reported a near-constitutive, pathogen-inducible CmYLCV promoter fragment (-329 to +137 from transcription start site; TSS) that enhances stronger (3×) expression than the previously reported fragments; all these fragments are highly efficient in monocot and dicot plants (Sahoo et al...
September 14, 2017: Planta
https://www.readbyqxmd.com/read/28913422/ultratransparent-and-stretchable-graphene-electrodes
#17
Nan Liu, Alex Chortos, Ting Lei, Lihua Jin, Taeho Roy Kim, Won-Gyu Bae, Chenxin Zhu, Sihong Wang, Raphael Pfattner, Xiyuan Chen, Robert Sinclair, Zhenan Bao
Two-dimensional materials, such as graphene, are attractive for both conventional semiconductor applications and nascent applications in flexible electronics. However, the high tensile strength of graphene results in fracturing at low strain, making it challenging to take advantage of its extraordinary electronic properties in stretchable electronics. To enable excellent strain-dependent performance of transparent graphene conductors, we created graphene nanoscrolls in between stacked graphene layers, referred to as multilayer graphene/graphene scrolls (MGGs)...
September 2017: Science Advances
https://www.readbyqxmd.com/read/28911863/the-crystal-structure-of-the-pyrococcus-abyssi-mono-functional-methyltransferase-patrm5b
#18
Jialiang Wu, Qian Jia, Saibin Wu, Hui Zeng, Yujie Sun, Caiyan Wang, Ruiguang Ge, Wei Xie
The wyosine hypermodification found exclusively at G37 of tRNA(Phe) in eukaryotes and archaea is a very complicated process involving multiple steps and enzymes, and the derivatives are essential for the maintenance of the reading frame during translation. In the archaea Pyrococcus abyssi, two key enzymes from the Trm5 family, named PaTrm5a and PaTrm5b respectively, start the process by forming N1-methylated guanosine (m(1)G37). In addition, PaTrm5a catalyzes the further methylation of C7 on 4-demethylwyosine (imG-14) to produce isowyosine (imG2) at the same position...
September 11, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28911209/intracellular-activation-of-ovastacin-mediates-pre-fertilization-hardening-of-the-zona-pellucida
#19
Hagen Körschgen, Michael Kuske, Konstantin Karmilin, Irene Yiallouros, Melanie Balbach, Julia Floehr, Dagmar Wachten, Willi Jahnen-Dechent, Walter Stöcker
STUDY QUESTION: How and where is pro-ovastacin activated and how does active ovastacin regulate zona pellucida hardening (ZPH) and successful fertilization? STUDY FINDING: Ovastacin is partially active before exocytosis and pre-hardens the zona pellucida (ZP) before fertilization. WHAT IS KNOWN ALREADY: The metalloproteinase ovastacin is stored in cortical granules, it cleaves zona pellucida protein 2 (ZP2) upon fertilization and thereby destroys the ZP sperm ligand and triggers ZPH...
September 1, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/28910574/o-glcnacylation-of-boundary-element-associated-factor-beaf-32-in-drosophila-melanogaster-correlates-with-active-histone-marks-at-the-promoters-of-its-target-genes
#20
Debaditya De, Satish Kallappagoudar, Jae-Min Lim, Rashmi U Pathak, Rakesh K Mishra
Boundary Element-Associated Factor 32 (BEAF 32) is a sequence specific DNA binding protein involved in functioning of chromatin domain boundaries in Drosophila. Several studies also show it to be involved in transcriptional regulation of a large number of genes, many of which are annotated to have cell cycle, development and differentiation related function. Since post-translational modifications (PTMs) of proteins add to their functional capacity, we investigated the PTMs on BEAF 32. The protein is known to be phosphorylated and O-GlcNAcylated...
September 14, 2017: Nucleus
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