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https://www.readbyqxmd.com/read/28343137/synthesis-of-novel-muramic-acid-derivatives-and-their-interaction-with-lysozyme-action-of-lysozyme-revisited
#1
Manas Jana, Anirban Ghosh, Abhishek Santra, Rajiv Kumar Kar, Anup Kumar Misra, Anirban Bhunia
HYPOTHESIS: The interaction of lysozyme with the N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) unit of peptidoglycan (PGN) polymer of the bacterial cell wall is of immense importance to understand the mechanism of lysozyme on PGN. EXPERIMENTS: The synthesis of three novel NAM derivatives containing fused oxazinone ring to the NAM moiety has been achieved. The synthesized compounds were evaluated for their potential as a glycomimetic acceptor of lysozyme using different biophysical and computational methods such as (1)H NMR, STD NMR, DOSY and Molecular docking...
March 16, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28342833/a-high-density-cho-s-transient-transfection-system-comparison-of-expicho-and-expi293
#2
Nina K Jain, Susan Barkowski-Clark, Richard Altman, Krista Johnson, Fang Sun, Jonathan Zmuda, Chao Yan Liu, Adriana Kita, Ryan Schulz, Alyssa Neill, Robert Ballinger, Rekha Patel, Jian Liu, Alinafe Mpanda, Brian Huta, Henry Chiou, Walter Voegtli, Tadas Panavas
Chinese Hamster Ovary (CHO) cells are the principal mammalian host used for stable cell line generation and biotherapeutic protein production. Until recently, production of milligrams to grams of protein in CHO transient systems was challenging. As such, Human Embryonic Kidney (HEK293) cells are the most common mammalian cell type used for transient transfection. The post-translational modifications (PTMs) of a protein are dictated in part by the cell line used for expression, and changes in PTMs have been shown to affect both the activity and biophysical properties of proteins...
March 22, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28341344/propofol-affinity-to-mitochondrial-membranes-does-not-alter-mitochondrial-function
#3
Luís M Félix, Fernando Correia, Pedro A Pinto, Sónia P Campos, Telma Fernandes, Romeu Videira, M Manuel Oliveira, Francisco P Peixoto, Luís M Antunes
The molecular mechanisms of hepatotoxicity after propofol anaesthesia have not been fully elucidated, although there is a relation with mitochondrial dysfunction. The action of propofol on mitochondrial hepatic functions in a rat model was evaluated by infusion for 4h with 25 and 62.5mg/kg/h propofol or 3.125ml/kg/h (vehicle). Liver mitochondrial respiratory rates were evaluated as well as mitochondrial transmembrane potential (ΔΨ), calcium fluxes, mitochondrial enzymatic activities (Complex I - V) and oxidative stress biomarkers (superoxide dismutase, catalase, glutathione reductase, glutathione S-transferase, lipid peroxidation and the oxidized/reduced glutathione ratio)...
March 21, 2017: European Journal of Pharmacology
https://www.readbyqxmd.com/read/28340485/an-approach-for-liposome-immobilization-using-sterically-stabilized-micelles-ssms-as-a-precursor-for-bio-layer-interferometry-based-interaction-studies
#4
Jakob Wallner, Gabriele Lhota, Markus Schosserer, Karola Vorauer-Uhl
Non-fluidic bio-layer interferometry (BLI) has rapidly become a standard tool for monitoring almost all biomolecular interactions in a label-free, real-time and high-throughput manner. High-efficiency screening methods which measure the kinetics of liposomes with a variety of compounds require the immobilization of liposomes. In this work, a method is described for immobilizing liposomes for interaction studies, based on the biophysical principles of this biosensor platform. The immobilization approach includes the loading of DSPE-PEG(2000)-biotin containing sterically stabilized micelles (SSMs) which are restructured in a buffer change step, resulting in an accessible substrate for liposome immobilization...
March 12, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28340330/same-same-but-different-the-evolution-of-tbp-in-archaea-and-their-eukaryotic-offspring
#5
Fabian Blombach, Dina Grohmann
Transcription factors TBP and TF(II)B assemble with RNA polymerase at the promoter DNA forming the initiation complex. Despite a high degree of conservation, the molecular binding mechanisms of archaeal and eukaryotic TBP and TF(II)B differ significantly. Based on recent biophysical data, we speculate how the mechanisms co-evolved with transcription regulation and TBP multiplicity.
February 8, 2017: Transcription
https://www.readbyqxmd.com/read/28339206/utilizing-electron-spin-echo-envelope-modulation-to-distinguish-between-the-local-secondary-structures-of-an-%C3%AE-helix-and-an-amphipathic-310-helical-peptide
#6
Lauren Bottorf, Sophia Rafferty, Indra Dev Sahu, Robert M McCarrick, Gary A Lorigan
Electron Spin Echo Envelope Modulation (ESEEM) spectroscopy was used to distinguish between the local secondary structures of an α-helix and a 310-helix. Previously, we have shown that ESEEM spectroscopy in combination with site-directed spin labeling (SDSL) and 2H-labeled amino acids (i) can probe the local secondary structure of α-helices, resulting in an obvious deuterium modulation pattern, where i+4 positions generally show larger 2H ESEEM peak intensities than i+3 positions. Here, we have hypothesized that due to the unique turn periodicities of an α-helix (3...
March 24, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28338845/computational-psychiatry-and-the-challenge-of-schizophrenia
#7
John H Krystal, John D Murray, Adam M Chekroud, Philip R Corlett, Genevieve Yang, Xiao-Jing Wang, Alan Anticevic
Schizophrenia research is plagued by enormous challenges in integrating and analyzing large datasets and difficulties developing formal theories related to the etiology, pathophysiology, and treatment of this disorder. Computational psychiatry provides a path to enhance analyses of these large and complex datasets and to promote the development and refinement of formal models for features of this disorder. This presentation introduces the reader to the notion of computational psychiatry and describes discovery-oriented and theory-driven applications to schizophrenia involving machine learning, reinforcement learning theory, and biophysically-informed neural circuit models...
March 8, 2017: Schizophrenia Bulletin
https://www.readbyqxmd.com/read/28338825/modular-organization-of-residue-level-contacts-shape-the-selection-pressure-on-individual-amino-acid-sites-of-ribosomal-proteins
#8
Saurav Mallik, Sudip Kundu
Understanding the molecular evolution of macromolecular complexes in the light of their structure, assembly and stability is of central importance. Here we address how the modular organization of native molecular contacts shapes the selection pressure on individual residue sites of ribosomal complexes. The bacterial ribosomal complex is represented as a residue contact network where nodes represent amino acid/nucleotide residues and edges represent their van der Waals interactions. We find statistically overrepresented native amino acid-nucleotide contacts (OaantC, one amino acid contacts one or multiple nucleotides, inter-nucleotide contacts are disregarded)...
February 22, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338083/microvasculature-on-a-chip-study-of-the-endothelial-surface-layer-and-the-flow-structure-of-red-blood-cells
#9
Daria Tsvirkun, Alexei Grichine, Alain Duperray, Chaouqi Misbah, Lionel Bureau
Microvasculatures-on-a-chip, i.e. in vitro models that mimic important features of microvessel networks, have gained increasing interest in recent years. Such devices have allowed investigating pathophysiological situations involving abnormal biophysical interactions between blood cells and vessel walls. Still, a central question remains regarding the presence, in such biomimetic systems, of the endothelial glycocalyx. The latter is a glycosaminoglycans-rich surface layer exposed to blood flow, which plays a crucial role in regulating the interactions between circulating cells and the endothelium...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28337984/lipid-dependent-conformational-dynamics-underlie-the-functional-versatility-of-t-cell-receptor
#10
Xingdong Guo, Chengsong Yan, Hua Li, Wenmao Huang, Xiaoshan Shi, Min Huang, Yingfang Wang, Weiling Pan, Mingjun Cai, Lunyi Li, Wei Wu, Yibing Bai, Chi Zhang, Zhijun Liu, Xinyan Wang, Xiaohui F Zhang, Chun Tang, Hongda Wang, Wanli Liu, Bo Ouyang, Catherine C Wong, Yi Cao, Chenqi Xu
T-cell receptor-CD3 complex (TCR) is a versatile signaling machine that can initiate antigen-specific immune responses based on various biochemical changes of CD3 cytoplasmic domains, but the underlying structural basis remains elusive. Here we developed biophysical approaches to study the conformational dynamics of CD3ε cytoplasmic domain (CD3εCD). At the single-molecule level, we found that CD3εCD could have multiple conformational states with different openness of three functional motifs, i.e., ITAM, BRS and PRS...
March 24, 2017: Cell Research
https://www.readbyqxmd.com/read/28337496/sugar-coated-proteins-the-importance-of-degree-of-polymerisation-of-oligo-galacturonic-acid-on-protein-binding-and-aggregation
#11
Amy Y Xu, Laurence D Melton, Timothy M Ryan, Jitendra P Mata, Geoffrey B Jameson, Agata Rekas, Martin A K Williams, Duncan J McGillivray
We have simplified the structural heterogeneity of protein-polysaccharide binding by investigating protein binding to oligosaccharides. The interactions between bovine beta-lactoglobulin A (βLgA) and oligo-galacturonic acids (OGAs) with various numbers of sugar residues have been investigated with a range of biophysical techniques. We show that the βLgA-OGA interaction is critically dependent on the length of the oligosaccharide. Isothermal titration calorimetry results suggest that a minimum length of 7 or 8 sugar residues is required in order to exhibit appreciable exothermic interactions with βLgA - shorter oligosaccharides show no enthalpic interactions at any concentration ratio...
March 24, 2017: Soft Matter
https://www.readbyqxmd.com/read/28337211/nutritional-biophysical-and-physiological-characteristics-of-wild-rocket-genotypes-as-affected-by-soilless-cultivation-system-salinity-level-of-nutrient-solution-and-growing-period
#12
Anna Bonasia, Corrado Lazzizera, Antonio Elia, Giulia Conversa
With the aim of defining the best management of nutrient solution (NS) in a soilless system for obtaining high quality baby-leaf rocket, the present study focuses on two wild rocket genotypes ("Nature" and "Naturelle"), grown in a greenhouse under two Southern Italy growing conditions-autumn-winter (AW) and winter-spring (WS)-using two soilless cultivation systems (SCS)-at two electrical conductivity values (EC) of NS. The SCSs used were the Floating System (FS) and Ebb and Flow System (EFS) and the EC values were 2...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28335464/a-geographic-information-assisted-temporal-mixture-analysis-for-addressing-the-issue-of-endmember-class-and-endmember-spectra-variability
#13
Wenliang Li, Changshan Wu
Spectral mixture analysis (SMA) is a common approach for parameterizing biophysical fractions of urban environment and widely applied in many fields. For successful SMA, the selection of endmember class and corresponding spectra has been assumed as the most important step. Thanks to the spatial heterogeneity of natural and urban landscapes, the variability of endmember class and corresponding spectra has been widely considered as the profound error source in SMA. To address the challenging problems, we proposed a geographic information-assisted temporal mixture analysis (GATMA)...
March 18, 2017: Sensors
https://www.readbyqxmd.com/read/28334800/optimization-of-a-novel-biophysical-model-using-large-scale-in-vivo-antisense-hybridization-data-displays-improved-prediction-capabilities-of-structurally-accessible-rna-regions
#14
Jorge Vazquez-Anderson, Mia K Mihailovic, Kevin C Baldridge, Kristofer G Reyes, Katie Haning, Seung Hee Cho, Paul Amador, Warren B Powell, Lydia M Contreras
Current approaches to design efficient antisense RNAs (asRNAs) rely primarily on a thermodynamic understanding of RNA-RNA interactions. However, these approaches depend on structure predictions and have limited accuracy, arguably due to overlooking important cellular environment factors. In this work, we develop a biophysical model to describe asRNA-RNA hybridization that incorporates in vivo factors using large-scale experimental hybridization data for three model RNAs: a group I intron, CsrB and a tRNA. A unique element of our model is the estimation of the availability of the target region to interact with a given asRNA using a differential entropic consideration of suboptimal structures...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334762/missense-uros-mutations-causing-congenital-erythropoietic-porphyria-reduce-uros-homeostasis-that-can-be-rescued-by-proteasome-inhibition
#15
Jean-Marc Blouin, Ganeko Bernardo-Seisdedos, Emma Sasso, Julie Esteve, Cécile Ged, Magalie Lalanne, Arantza Sanz-Parra, Pedro Urquiza, Hubert de Verneuil, Oscar Millet, Emmanuel Richard
Congenital erythropoietic porphyria (CEP) is an inborn error of heme biosynthesis characterized by uroporphyrinogen III synthase (UROS) deficiency resulting in deleterious porphyrin accumulation in blood cells responsible for hemolytic anemia and cutaneous photosensitivity. We analyzed here the molecular basis of UROS impairment associated with twenty nine UROS missense mutations actually described in CEP patients. Using a computational and biophysical joint approach we predicted that most disease-causing mutations would affect UROS folding and stability...
February 21, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334404/calcium-homeostasis-modulator-1-like-currents-in-rat-fungiform-taste-cells-expressing-amiloride-sensitive-sodium-currents
#16
Albertino Bigiani
Salt reception by taste cells is still the less understood transduction process occurring in taste buds, the peripheral sensory organs for the detection of food chemicals. Although there is evidence suggesting that the epithelial sodium channel (ENaC) works as sodium receptor, yet it is not clear how salt-detecting cells signal the relevant information to nerve endings. Taste cells responding to sweet, bitter, and umami substances release ATP as neurotransmitter through a nonvesicular mechanism. Three different channel proteins have been proposed as conduit for ATP secretion: pannexin channels, connexin hemichannels, and calcium homeostasis modulator 1 (CALHM1) channels...
March 10, 2017: Chemical Senses
https://www.readbyqxmd.com/read/28333587/variational-latent-gaussian-process-for-recovering-single-trial-dynamics-from-population-spike-trains
#17
Yuan Zhao, Il Memming Park
When governed by underlying low-dimensional dynamics, the interdependence of simultaneously recorded populations of neurons can be explained by a small number of shared factors, or a low-dimensional trajectory. Recovering these latent trajectories, particularly from single-trial population recordings, may help us understand the dynamics that drive neural computation. However, due to the biophysical constraints and noise in the spike trains, inferring trajectories from data is a challenging statistical problem in general...
March 23, 2017: Neural Computation
https://www.readbyqxmd.com/read/28332571/profiling-protein-expression-in-circulating-tumour-cells-using-microfluidic-western-blotting
#18
Elly Sinkala, Elodie Sollier-Christen, Corinne Renier, Elisabet Rosàs-Canyelles, James Che, Kyra Heirich, Todd A Duncombe, Julea Vlassakis, Kevin A Yamauchi, Haiyan Huang, Stefanie S Jeffrey, Amy E Herr
Circulating tumour cells (CTCs) are rare tumour cells found in the circulatory system of certain cancer patients. The clinical and functional significance of CTCs is still under investigation. Protein profiling of CTCs would complement the recent advances in enumeration, transcriptomic and genomic characterization of these rare cells and help define their characteristics. Here we describe a microfluidic western blot for an eight-plex protein panel for individual CTCs derived from estrogen receptor-positive (ER+) breast cancer patients...
March 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28331218/identification-of-a-novel-heterozygous-mutation-of-the-aggrecan-gene-in-a-family-with-idiopathic-short-stature-and-multiple-intervertebral-disc-herniation
#19
Sumito Dateki, Akiko Nakatomi, Satoshi Watanabe, Hitomi Shimizu, Yukiko Inoue, Hideo Baba, Koh-Ichiro Yoshiura, Hiroyuki Moriuchi
Aggrecan is a critical proteoglycan component of the extracellular matrix of the growth plates and articular cartilage and has a key role in the biophysical and biomechanical properties of cartilage. Recently, heterozygous mutations in the ACAN gene, which encodes aggrecan, have been identified in patients with short stature and accelerated bone age. We herein report another family with a heterozygous ACAN mutation associated with idiopathic short stature along with accelerated bone age and early-onset herniation of the lumbar discs at the levels of L1/2 through L5/S1...
March 23, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28331000/biophysical-studies-of-cholesterol-effects-on-chromatin
#20
Isabel T G Silva, Vinicius Fernandes, Caio Souza, Werner Treptow, Guilherme Martins Santos
Changes in chromatin structure regulate gene expression and genome maintenance. Molecules that bind to the nucleosome, the complex of DNA and histone proteins, are key modulators of chromatin structure. Previous work indicated that cholesterol, a ubiquitous cellular lipid, may bind to chromatin in vivo, suggesting a potential function for lipids in modulating chromatin architecture. However, the molecular mechanisms of cholesterol action on chromatin structure have remained unclear. Here, we explored the biophysical impact of cholesterol on nucleosome and chromatin fibers reconstituted in vitro and characterized in silico the cholesterol binding to nucleosome...
March 22, 2017: Journal of Lipid Research
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