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https://www.readbyqxmd.com/read/28107736/crystal-structures-binding-interactions-and-adme-evaluation-of-brain-penetrant-n-substituted-indazole-5-carboxamides-as-subnanomolar-selective-monoamine-oxidase-b-and-dual-mao-a-b-inhibitors
#1
Nikolay T Tzvetkov, Hans-Georg Stammler, Beate Neumann, Silvia Hristova, Liudmil Antonov, Marcus Gastreich
The pharmacological and physicochemical analysis of structurally optimized N-alkyl-substituted indazole-5-carboxamides, developed as potential drug and radioligand candidates for the treatment and diagnosis of Parkinson's disease (PD) and other neurological disorders, is reported. Recent efforts have been focused on the development of subnanomolar potent, selective MAO-B (N1-alkyl-substituted compounds 12a-14a and 15) and dual active MAO-A/B (N2-methylated compounds 12b-14b) inhibitors with nanomolar potency towards MAO-B and moderately active against MAO-A enzyme, respectively...
January 11, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28107711/the-influence-of-dissolved-si-on-ni-precipitate-formation-at-the-kaolinite-water-interface-kinetics-drs-and-exafs-analysis
#2
Xiaoli Tan, Ge Liu, Huiyang Mei, Ming Fang, Xuemei Ren, Changlun Chen
Unraveling the formation process of Ni precipitates at molecular scale is important for understanding the fate and mobility of Ni species in the real environment. Dissolved Si presents in the natural environment ubiquitously, which can alter Ni sorption as well as incorporation into neoformed precipitates. Batch experiments show that the dissolved Si leads to a rapid increase in the Ni sorption rate and interferes with the formation of Ni precipitates. The results of diffuse reflectance spectroscopy (DRS) and extended X-ray absorption fine structure (EXAFS) spectroscopy analyses suggest that the nucleation of a (Ni,Al) phyllosilicate phase involves a kaolinite-like local structure...
January 16, 2017: Chemosphere
https://www.readbyqxmd.com/read/28107365/parenclitic-network-analysis-of-methylation-data-for-cancer-identification
#3
Alexander Karsakov, Thomas Bartlett, Artem Ryblov, Iosif Meyerov, Mikhail Ivanchenko, Alexey Zaikin
We make use of ideas from the theory of complex networks to implement a machine learning classification of human DNA methylation data, that carry signatures of cancer development. The data were obtained from patients with various kinds of cancers and represented as parenclictic networks, wherein nodes correspond to genes, and edges are weighted according to pairwise variation from control group subjects. We demonstrate that for the 10 types of cancer under study, it is possible to obtain a high performance of binary classification between cancer-positive and negative samples based on network measures...
2017: PloS One
https://www.readbyqxmd.com/read/28107207/dynamic-mechanical-interactions-between-neighboring-airspaces-determine-cyclic-opening-and-closure-in-injured-lung
#4
Ludovic Broche, Gaetano Perchiazzi, Liisa Porra, Angela Tannoia, Mariangela Pellegrini, Savino Derosa, Alessandra Sindaco, João Batista Borges, Loïc Degrugilliers, Anders Larsson, Göran Hedenstierna, Anthony S Wexler, Alberto Bravin, Sylvia Verbanck, Bradford J Smith, Jason H T Bates, Sam Bayat
OBJECTIVES: Positive pressure ventilation exposes the lung to mechanical stresses that can exacerbate injury. The exact mechanism of this pathologic process remains elusive. The goal of this study was to describe recruitment/derecruitment at acinar length scales over short-time frames and test the hypothesis that mechanical interdependence between neighboring lung units determines the spatial and temporal distributions of recruitment/derecruitment, using a computational model. DESIGN: Experimental animal study...
January 19, 2017: Critical Care Medicine
https://www.readbyqxmd.com/read/28107098/early-initiation-of-breastfeeding-among-maya-mothers-in-the-western-highlands-of-guatemala
#5
Natalie N Atyeo, Tahvi D Frank, Emma F Vail, William A L Sperduto, David L Boyd
BACKGROUND: Guatemala exhibits the sixth highest rate of child stunting worldwide, and stunting disproportionately affects Guatemala indigenous communities. In a country struggling to combat this result of malnutrition, early child nutrition is especially critical. Specifically, early initiation of breastfeeding is important for the development of newborn infants. Understanding beliefs and practices related to early initiation of breastfeeding in Maya Guatemala may provide an avenue to guide nutrition interventions in indigenous communities...
January 1, 2017: Journal of Human Lactation: Official Journal of International Lactation Consultant Association
https://www.readbyqxmd.com/read/28107009/nmr-and-computation-reveal-a-pressure-sensitive-folded-conformation-of-trp-cage
#6
Soichiro Kitazawa, Martin J Fossat, Scott A McCallum, Angel E Garcia, Catherine Ann Royer
Beyond defining the structure and stability of folded states of proteins, primary amino acid sequences determine all of the features of their conformational landscapes. Characterizing how sequence modulates the population of protein excited states or folding pathways requires atomic level detailed structural and energetic information. Such insight is essential for improving protein design strategies, as well as for interpreting protein evolution. Here, high pressure NMR and molecular dynamics simulations were combined to probe the conformational landscape of a small model protein, the tryptophan cage variant, Tc5b...
January 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28106980/structural-snapshots-of-an-engineered-cystathionine-%C3%AE-lyase-reveal-the-critical-role-of-electrostatic-interactions-in-the-active-site
#7
Wupeng Yan, Everett M Stone, Yan Jessie Zhang
Enzyme therapeutics that can degrade L-methionine (L-Met) are of great interest as numerous malignancies are exquisitely sensitive to L-Met depletion. To exhaust the pool of the methionine in human serum, we previously engineered an L-Met degrading enzyme based on the human cystathionine-γ-lyase scaffold (hCGL-NLV) in order to circumvent immunogenicity and stability issues observed in the preclinical application of bacterial derived methionine-γ-lyases (MGL). To gain further insights into structure/activity relationships governing the chemistry of the hCGL-NLV lead molecule, we undertook a biophysical characterization campaign that captured crystal structures (2...
January 20, 2017: Biochemistry
https://www.readbyqxmd.com/read/28106929/conformational-analysis-of-an-antibacterial-cyclodepsipeptide-active-against-m-tuberculosis-by-a-combined-roe-and-rdc-analysis
#8
Maic Fredersdorf, Michael Kurz, Armin Bauer, Marc-Olivier Ebert, Carla Rigling, Laurie Lannes, Christina Thiele
Griselimycin (GM) and methylgriselimycin (MGM), naturally produced by microorganisms of the genus Streptomyces, are cyclic depsipeptides composed of ten amino acids. They exhibit antibacterial activity against mycobacterium species by inhibiting the sliding clamp of prokaryotic DNA polymerase III and are therefore considered as potential anti-tuberculosis drugs. The difference between both peptides is the presence of L -(R)-4-methylproline in MGM instead of L -proline in GM at position 8 of the amino acid sequence...
January 20, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28106879/bacterial-community-segmentation-facilitates-the-prediction-of-ecosystem-function-along-the-coast-of-the-western-antarctic-peninsula
#9
Jeff S Bowman, Linda A Amaral-Zettler, Jeremy J Rich, Catherine M Luria, Hugh W Ducklow
Bacterial community structure can be combined with observations of ecophysiological data to build predictive models of microbial ecosystem function. These models are useful for understanding how function might change in response to a changing environment. Here we use five spring-summer seasons of bacterial community structure and flow cytometry data from a productive coastal site along the western Antarctic Peninsula to construct models of bacterial production (BP), an ecosystem function that heterotrophic bacteria provide...
January 20, 2017: ISME Journal
https://www.readbyqxmd.com/read/28106786/sulfolobus-acidocaldarius-udg-can-remove-du-from-the-rna-backbone-insight-into-the-specific-recognition-of-uracil-linked-with-deoxyribose
#10
Gang-Shun Yi, Wei-Wei Wang, Wei-Guo Cao, Feng-Ping Wang, Xi-Peng Liu
Sulfolobus acidocaldarius encodes family 4 and 5 uracil-DNA glycosylase (UDG). Two recombinant S. acidocaldarius UDGs (SacUDG) were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU) base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond...
January 18, 2017: Genes
https://www.readbyqxmd.com/read/28106444/symmetry-reduction-in-the-quantum-kagome-antiferromagnet-herbertsmithite
#11
A Zorko, M Herak, M Gomilšek, J van Tol, M Velázquez, P Khuntia, F Bert, P Mendels
Employing complementary torque magnetometry and electron spin resonance on single crystals of herbertsmithite, the closest realization to date of a quantum kagome antiferromagnet featuring a spin-liquid ground state, we provide novel insight into different contributions to its magnetism. At low temperatures, two distinct types of defects with different magnetic couplings to the kagome spins are found. Surprisingly, their magnetic response contradicts the threefold symmetry of the ideal kagome lattice, suggesting the presence of a global structural distortion that may be related to the establishment of the spin-liquid ground state...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28106434/observation-of-mollow-triplets-with-tunable-interactions-in-double-lambda-systems-of-individual-hole-spins
#12
K G Lagoudakis, K A Fischer, T Sarmiento, P L McMahon, M Radulaski, J L Zhang, Y Kelaita, C Dory, K Müller, J Vučković
Although individual spins in quantum dots have been studied extensively as qubits, their investigation under strong resonant driving in the scope of accessing Mollow physics is still an open question. Here, we have grown high quality positively charged quantum dots embedded in a planar microcavity that enable enhanced light-matter interactions. Under a strong magnetic field in the Voigt configuration, individual positively charged quantum dots provide a double lambda level structure. Using a combination of above-band and resonant excitation, we observe the formation of Mollow triplets on all optical transitions...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28106424/quasiparticle-scattering-off-defects-and-possible-bound-states-in-charge-ordered-yba_-2-cu_-3-o_-y
#13
R Zhou, M Hirata, T Wu, I Vinograd, H Mayaffre, S Krämer, M Horvatić, C Berthier, A P Reyes, P L Kuhns, R Liang, W N Hardy, D A Bonn, M-H Julien
We report the NMR observation of a skewed distribution of ^{17}O Knight shifts when a magnetic field quenches superconductivity and induces long-range charge-density-wave (CDW) order in YBa_{2}Cu_{3}O_{y}. This distribution is explained by an inhomogeneous pattern of the local density of states N(E_{F}) arising from quasiparticle scattering off, yet unidentified, defects in the CDW state. We argue that the effect is most likely related to the formation of quasiparticle bound states, as is known to occur, under specific circumstances, in some metals and superconductors (but not in the CDW state, in general, except for very few cases in 1D materials)...
January 6, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28106383/synthesis-chemistry-and-electronic-structures-of-group-9-metallaboranes
#14
Rosmita Borthakur, Sourav Kar, Subrat Kumar Barik, Somnath Bhattacharya, Gargi Kundu, Babu Varghese, Sundargopal Ghosh
Dimetallaoctaborane(12) of Ru, Co, and Rh have been well-characterized by a range of spectroscopic techniques and X-ray diffraction studies. Thus, reinvestigation of the Ir-system became of interest. As a result, a slight modification in the reaction conditions enabled us to isolate the missing Ir analogue of octaborane(12), [(Cp*Ir)2B6H10], 1. Compound 1 adapts a geometry similar to that of its parent octaborane(12) and Ru, Co, and Rh analogues. In [M2B6H10+x](M = Ru, x = 2; M = Co and Rh, x = 0), there exist two M-H-B protons...
January 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28106223/next-generation-of-network-medicine-interdisciplinary-signaling-approaches
#15
REVIEW
Tamas Korcsmaros, Maria Victoria Schneider, Giulio Superti-Furga
In the last decade, network approaches have transformed our understanding of biological systems. Network analyses and visualizations have allowed us to identify essential molecules and modules in biological systems, and improved our understanding of how changes in cellular processes can lead to complex diseases, such as cancer, infectious and neurodegenerative diseases. "Network medicine" involves unbiased large-scale network-based analyses of diverse data describing interactions between genes, diseases, phenotypes, drug targets, drug transport, drug side-effects, disease trajectories and more...
January 20, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28106073/high-resolution-cryo-em-structure-of-the-proteasome-in-complex-with-adp-alfx
#16
Zhanyu Ding, Zhenglin Fu, Cong Xu, Yifan Wang, Yanxing Wang, Junrui Li, Liangliang Kong, Jinhuan Chen, Na Li, Rongguang Zhang, Yao Cong
The 26S proteasome is an ATP-dependent dynamic 2.5 MDa protease that regulates numerous essential cellular functions through degradation of ubiquitinated substrates. Here we present a near-atomic-resolution cryo-EM map of the S. cerevisiae 26S proteasome in complex with ADP-AlFx. Our biochemical and structural data reveal that the proteasome-ADP-AlFx is in an activated state, displaying a distinct conformational configuration especially in the AAA-ATPase motor region. Noteworthy, this map demonstrates an asymmetric nucleotide binding pattern with four consecutive AAA-ATPase subunits bound with nucleotide...
January 20, 2017: Cell Research
https://www.readbyqxmd.com/read/28106069/identification-of-novel-cellular-clusters-define-a-specialized-area-in-the-cerebellar-periventricular-zone
#17
María Alejandra González-González, Gabriela B Gómez-González, Marymar Becerra-González, Ataúlfo Martínez-Torres
The periventricular zone of cerebellum is a germinative niche during the embryonic development, nevertheless its structural organization and functional implications in adult have not been widely studied. Here we disclose the presence of two novel clusters of cells in that area. The first one was named the subventricular cellular cluster (SVCC) and is composed of cells that express glial and neuronal markers. The second was named the ventromedial cord (VMC) and appears as a streak of biciliated cells with microvillosities facing the ventricle, that includes GFAP(+) and nestin(+) cells organized along the periventricular vasculature...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28105940/integrated-single-cell-data-analysis-reveals-cell-specific-networks-and-novel-coactivation-markers
#18
Shila Ghazanfar, Adam J Bisogni, John T Ormerod, David M Lin, Jean Y H Yang
BACKGROUND: Large scale single cell transcriptome profiling has exploded in recent years and has enabled unprecedented insight into the behavior of individual cells. Identifying genes with high levels of expression using data from single cell RNA sequencing can be useful to characterize very active genes and cells in which this occurs. In particular single cell RNA-Seq allows for cell-specific characterization of high gene expression, as well as gene coexpression. RESULTS: We offer a versatile modeling framework to identify transcriptional states as well as structures of coactivation for different neuronal cell types across multiple datasets...
December 5, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28105914/homology-modeling-and-molecular-dynamics-provide-structural-insights-into-tospovirus-nucleoprotein
#19
Rayane Nunes Lima, Muhammad Faheem, João Alexandre Ribeiro Gonçalves Barbosa, Marcelo Depólo Polêto, Hugo Verli, Fernando Lucas Melo, Renato Oliveira Resende
BACKGROUND: Tospovirus is a plant-infecting genus within the family Bunyaviridae, which also includes four animal-infecting genera: Hantavirus, Nairovirus, Phlebovirus and Orthobunyavirus. Compared to these members, the structures of Tospovirus proteins still are poorly understood. Despite multiple studies have attempted to identify candidate N protein regions involved in RNA binding and protein multimerization for tospovirus using yeast two-hybrid systems (Y2HS) and site-directed mutagenesis, the tospovirus ribonucleocapsids (RNPs) remains largely uncharacterized at the molecular level and the lack of structural information prevents detailed insight into these interactions...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105856/evaluation-of-in-silico-tools-to-predict-the-skin-sensitization-potential-of-chemicals
#20
G R Verheyen, E Braeken, K Van Deun, S Van Miert
Public domain and commercial in silico tools were compared for their performance in predicting the skin sensitization potential of chemicals. The packages were either statistical based (Vega, CASE Ultra) or rule based (OECD Toolbox, Toxtree, Derek Nexus). In practice, several of these in silico tools are used in gap filling and read-across, but here their use was limited to make predictions based on presence/absence of structural features associated to sensitization. The top 400 ranking substances of the ATSDR 2011 Priority List of Hazardous Substances were selected as a starting point...
January 20, 2017: SAR and QSAR in Environmental Research
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