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https://www.readbyqxmd.com/read/29351737/identifying-genome-wide-immune-gene-variation-underlying-infectious-disease-in-wildlife-populations-a-next-generation-sequencing-approach-in-the-gopher-tortoise
#1
Jean P Elbers, Mary B Brown, Sabrina S Taylor
BACKGROUND: Infectious disease is the single greatest threat to taxa such as amphibians (chytrid fungus), bats (white nose syndrome), Tasmanian devils (devil facial tumor disease), and black-footed ferrets (canine distemper virus, plague). Although understanding the genetic basis to disease susceptibility is important for the long-term persistence of these groups, most research has been limited to major-histocompatibility and Toll-like receptor genes. To better understand the genetic basis of infectious disease susceptibility in a species of conservation concern, we sequenced all known/predicted immune response genes (i...
January 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29350933/reproducing-the-ensemble-average-polar-solvation-energy-of-a-protein-from-a-single-structure-gaussian-based-smooth-dielectric-function-for-macromolecular-modeling
#2
Arghya Chakravorty, Zhe Jia, Lin Li, Shan Zhao, Emil Alexov
Typically, the ensemble average polar component of solvation energy (∆G_polar^solv) of a macromolecule is computed using molecular dynamics (MD) or Monte Carlo (MC) simulations to generate conformational ensemble and then single/rigid conformation solvation energy calculation is performed on each of snapshots. The primary objective of this work is to demonstrate that Poisson-Boltzmann (PB) based approach using a Gaussian-based smooth dielectric function for macromolecular modeling previously developed by us (Li et al...
January 19, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29350911/a-programmable-dna-origami-platform-for-organizing-intrinsically-disordered-nucleoporins-within-nanopore-confinement
#3
Patrick D Ellis Fisher, Qi Shen, Bernice Akpinar, Luke K Davis, Kenny Kwok Hin Chung, David Baddeley, Andela Saric, Thomas J Melia, Bart W Hoogenboom, Chenxiang Lin, C Patrick Lusk
Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated, but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ~40 nm diameter transport channel contributes to their collective properties and function...
January 19, 2018: ACS Nano
https://www.readbyqxmd.com/read/29350909/dual-drug-delivery-system-based-on-biodegradable-organosilica-core-shell-architectures
#4
Jiang-Lan Li, Ying-Jia Cheng, Chi Zhang, Han Cheng, Jun Feng, Ren-Xi Zhuo, Xuan Zeng, Xian-Zheng Zhang
To overcome drug resistance, efficient cancer therapeutic strategies using combination of small-molecule drugs and macromolecule drugs are highly desired. However, due to their significant differences in molecular weight and size, it is difficult to load them simultaneously in one vector and to release them individually. Here, a biodegradable organosilica based core/shell-structured nanocapsule was designed and used as a dual stimuli-responsive drug vector to solve this problem. Biodegradable organosilica shell coated outside the macromolecule model drug "core" would be disrupted by high glutathione (GSH) levels inside tumor cells, resulting in the escape of the entrapped drugs...
January 19, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29348418/a-novel-modeling-in-mathematical-biology-for-classification-of-signal-peptides
#5
Asma Ehsan, Khalid Mahmood, Yaser Daanial Khan, Sher Afzal Khan, Kuo-Chen Chou
The molecular structure of macromolecules in living cells is ambiguous unless we classify them in a scientific manner. Signal peptides are of vital importance in determining the behavior of newly formed proteins towards their destined path in cellular and extracellular location in both eukaryotes and prokaryotes. In the present research work, a novel method is offered to foreknow the behavior of signal peptides and determine their cleavage site. The proposed model employs neural networks using isolated sets of prokaryote and eukaryote primary sequences...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348177/dasatinib-increases-endothelial-permeability-leading-to-pleural-effusion
#6
Carole Phan, Etienne-Marie Jutant, Ly Tu, Raphaël Thuillet, Andrei Seferian, David Montani, Alice Huertas, Jan van Bezu, Fabian Breijer, Anton Vonk Noordegraaf, Marc Humbert, Jurjan Aman, Christophe Guignabert
Pleural effusion is a frequent side-effect of dasatinib, a second-generation tyrosine kinase inhibitor used in the treatment of chronic myelogenous leukaemia. However, the underlying mechanisms remain unknown. We hypothesised that dasatinib alters endothelial integrity, resulting in increased pulmonary vascular endothelial permeability and pleural effusion.To test this, we established the first animal model of dasatinib-related pleural effusion, by treating rats with a daily regimen of high doses of dasatinib (10 mg·kg-1·day-1 for 8 weeks)...
January 2018: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
https://www.readbyqxmd.com/read/29348132/t2-relaxometry-mri-predicts-cerebral-palsy-in-preterm-infants
#7
L-W Chen, S-T Wang, C-C Huang, Y-F Tu, Y-S Tsai
BACKGROUND AND PURPOSE: T2-relaxometry brain MR imaging enables objective measurement of brain maturation based on the water-macromolecule ratio in white matter, but the outcome correlation is not established in preterm infants. Our study aimed to predict neurodevelopment with T2-relaxation values of brain MR imaging among preterm infants. MATERIALS AND METHODS: From January 1, 2012, to May 31, 2015, preterm infants who underwent both T2-relaxometry brain MR imaging and neurodevelopmental follow-up were retrospectively reviewed...
January 18, 2018: AJNR. American Journal of Neuroradiology
https://www.readbyqxmd.com/read/29347492/elucidating-fluctuating-diffusivity-in-center-of-mass-motion-of-polymer-models-with-time-averaged-mean-square-displacement-tensor
#8
Tomoshige Miyaguchi
There have been increasing reports that the diffusion coefficient of macromolecules depends on time and fluctuates randomly. Here a method is developed to elucidate this fluctuating diffusivity from trajectory data. Time-averaged mean-square displacement (MSD), a common tool in single-particle-tracking (SPT) experiments, is generalized to a second-order tensor with which both magnitude and orientation fluctuations of the diffusivity can be clearly detected. This method is used to analyze the center-of-mass motion of four fundamental polymer models: the Rouse model, the Zimm model, a reptation model, and a rigid rodlike polymer...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347475/micromechanical-model-for-protein-materials-from-macromolecules-to-macroscopic-fibers
#9
G Puglisi, D De Tommasi, M F Pantano, N M Pugno, G Saccomandi
We propose a model for the mechanical behavior of protein materials. Based on a limited number of experimental macromolecular parameters (persistence and contour length) we obtain the macroscopic behavior of keratin fibers (human, cow, and rabbit hair), taking into account the damage and residual stretches effects that are fundamental in many functions of life. We also show the capability of our approach to describe the main dissipation and permanent strain effects observed in the more complex spider silk fibers...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347432/lattice-diffusion-of-a-single-molecule-in-solution
#10
Francesca Ruggeri, Madhavi Krishnan
The ability to trap a single molecule in an electrostatic potential well in solution has opened up new possibilities for the use of molecular electrical charge to study macromolecular conformation and dynamics at the level of the single entity. Here we study the diffusion of a single macromolecule in a two-dimensional lattice of electrostatic traps in solution. We report the ability to measure both the size and effective electrical charge of a macromolecule by observing single-molecule transport trajectories, typically a few seconds in length, using fluorescence microscopy...
December 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347100/correcting-binding-parameters-for-interacting-ligand-lattice-systems
#11
Jordan Hervy, Dominique J Bicout
Binding of ligands to macromolecules is central to many functional and regulatory biological processes. Key parameters characterizing ligand-macromolecule interactions are the stoichiometry, inducing the number of ligands per macromolecule binding site, and the dissociation constant, quantifying the ligand-binding site affinity. Both these parameters can be obtained from analyses of classical saturation experiments using the standard binding equation that offers the great advantage of mathematical simplicity but becomes an approximation for situations of interest when a ligand binds and covers more than one single binding site on the macromolecule...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29345901/playing-with-the-molecules-of-life
#12
Douglas D Young, Peter G Schultz
Our understanding of the complex molecular processes of living organisms is growing exponentially. This knowledge, togeth-er with a powerful arsenal of tools for manipulating the structures of biological macromolecules, is allowing chemists to begin to harness and reprogram the remarkable machinery of life. Here we review one such example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins in ways previously unimaginable...
January 18, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29345714/from-discrete-to-continuous-description-of-spherical-surface-charge-distributions
#13
Anže Lošdorfer Božič
The importance of electrostatic interactions in soft matter and biological systems can often be traced to non-uniform charge effects, which are commonly described using a multipole expansion of the corresponding charge distribution. The standard approach when extracting the charge distribution of a given system is to treat the constituent charges as points. This can, however, lead to an overestimation of multipole moments of high order, such as dipole, quadrupole, and higher moments. Focusing on distributions of charges located on a spherical surface - characteristic of numerous biological macromolecules, such as globular proteins and viral capsids, as well as of inverse patchy colloids - we develop a novel way of representing spherical surface charge distributions based on the von Mises-Fisher distribution...
January 18, 2018: Soft Matter
https://www.readbyqxmd.com/read/29345406/helicobacter-pylori-infection-and-occurrence-of-celiac-disease-in-subjects-hla-dq2-dq8-positive-a-prospective-study
#14
Maria P Dore, Roberta Salis, Maria F Loria, Vincenzo Villanacci, Gabrio Bassotti, Giovanni M Pes
BACKGROUND: Celiac disease (CD) occurs in subjects positive for HLA-DQ2 and/or DQ8 gene loci at any age following ingestion of gluten-containing food. An increased permeability of the mucosa allows interactions between gliadin macromolecules and genetic factors. It has been observed that Helicobacter pylori has the ability to modulate the integrity of the duodenal epithelium. We aimed to determine whether H. pylori infection may enhance the occurrence of CD in genetically susceptible subjects...
January 18, 2018: Helicobacter
https://www.readbyqxmd.com/read/29344874/laser-capture-microdissection-based-rna-seq-of-barley-grain-tissues
#15
Ronny Brandt, Martin Mascher, Johannes Thiel
Spatiotemporal patterning throughout the plant body depends to a large degree on cell- and tissue-specific expression of genes. Subsequently, for a better understanding of cell and tissue differentiation processes during plant development it is important to conduct transcript analyses in individual cells or tissue types rather than in bulk tissues. Laser capture microdissection (LCM) provides a useful method for isolating specific cell types from complex tissue structures for downstream applications. Contrasting to mammalian cells, the texture of plant cells is more critical due to hard, cellulose-rich cell walls, large vacuoles, and air spaces which complicates tissue preparation and extraction of macromolecules, like DNA and RNA...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29343833/dopamine-d3-receptor-antagonist-reveals-a-cryptic-pocket-in-aminergic-gpcrs
#16
Noelia Ferruz, Stefan Doerr, Michelle A Vanase-Frawley, Yaozhong Zou, Xiaomin Chen, Eric S Marr, Robin T Nelson, Bethany L Kormos, Travis T Wager, Xinjun Hou, Anabella Villalobos, Simone Sciabola, Gianni De Fabritiis
The recent increase in the number of X-ray crystal structures of G-protein coupled receptors (GPCRs) has been enabling for structure-based drug design (SBDD) efforts. These structures have revealed that GPCRs are highly dynamic macromolecules whose function is dependent on their intrinsic flexibility. Unfortunately, the use of static structures to understand ligand binding can potentially be misleading, especially in systems with an inherently high degree of conformational flexibility. Here, we show that docking a set of dopamine D3 receptor compounds into the existing eticlopride-bound dopamine D3 receptor (D3R) X-ray crystal structure resulted in poses that were not consistent with results obtained from site-directed mutagenesis experiments...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29342092/metabolic-alterations-in-cancer-cells-and-the-emerging-role-of-oncometabolites-as-drivers-of-neoplastic-change
#17
REVIEW
Zhengqiu Zhou, Elochukwu Ibekwe, Yevgen Chornenkyy
The mitochondrion is an important organelle and provides energy for a plethora of intracellular reactions. Metabolic dysregulation has dire consequences for the cell, and alteration in metabolism has been identified in multiple disease states-cancer being one. Otto Warburg demonstrated that cancer cells, in the presence of oxygen, undergo glycolysis by reprogramming their metabolism-termed "aerobic glycolysis". Alterations in metabolism enable cancer cells to gain a growth advantage by obtaining precursors for macromolecule biosynthesis, such as nucleic acids and lipids...
January 17, 2018: Antioxidants (Basel, Switzerland)
https://www.readbyqxmd.com/read/29341916/effects-of-surfactant-based-permeation-enhancers-on-mannitol-permeability-histology-and-electrogenic-ion-transport-responses-in-excised-rat-colonic-mucosae
#18
Sam Maher, Joanne Heade, Fiona McCartney, Seona Waters, Sinéad B Bleiel, David J Brayden
Surfactant-based intestinal permeation enhancers (PEs) are constituents of several oral macromolecule formulations in clinical trials. This study examined the interaction of a test panel of surfactant-based PEs with isolated rat colonic mucosae mounted in Ussing chambers in an attempt to determine if increases in transepithelial permeability can be separated from induction of mucosal perturbation. The aim was to assess the effects of PEs on (i) apparent permeability coefficient (Papp) of [14C]-mannitol on (ii) histology score and (iii) short-circuit current (ΔIsc) responses to a cholinomimetic (carbachol, CCh)...
January 13, 2018: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/29341909/nanogel-dfo-conjugates-as-a-model-to-investigate-pharmacokinetics-biodistribution-and-iron-chelation-in-vivo
#19
Yan Wang, Zhi Liu, Tien-Min Lin, Shaurya Chanana, May P Xiong
Deferoxamine (DFO) to treat iron overload (IO) has been limited by toxicity issues and short circulation times and it would be desirable to prolong circulation to improve non-transferrin bound iron (NTBI) chelation. In addition, DFO is currently unable to efficiently target the large pool of iron in the liver and spleen. Nanogel-Deferoxamine conjugates (NG-DFO) can prove useful as a model to investigate the pharmacokinetic (PK) properties and biodistribution (BD) behavior of iron-chelating macromolecules and their overall effect on serum ferritin levels...
January 13, 2018: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/29341305/plasmid-templated-control-of-dna-cyclodextrin-nanoparticle-morphology-through-molecular-vector-design-for-effective-gene-delivery
#20
Laura Gallego-Yerga, Juan M Benito, Laura Blanco-Fernández, María Martínez-Negro, Itziar Vélaz, Emilio Aicart, Elena Junquera, Carmen Ortiz Mellet, Conchita Tros de Ilarduya, Jose M Garcia Fernandez
Engineering self-assembled superstructures through complexation of plasmid DNA (pDNA) and single-isomer nanometric size macromolecules (molecular nanoparticles) is a promising strategy for gene delivery. Notably, the functionality and overall architecture of the vector can be precisely moulded at the atomic level by chemical tailoring, enabling unprecedented opportunities for structure/self-assembling/pDNA delivery relationship studies. Beyond this notion, by judiciously preorganizing the functional elements in cyclodextrin (CD)-based molecular nanoparticles through covalent dimerization, here we demonstrate that the morphology of the resulting nanocomplexes (CDplexes) can be tuned, from spherical to ellipsoidal, rod-type or worm-like nanoparticles, which makes it possible to gain understanding of their shape-dependent transfection properties...
January 17, 2018: Chemistry: a European Journal
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