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https://www.readbyqxmd.com/read/28735107/integrative-modelling-of-cellular-assemblies
#1
REVIEW
Agnel Praveen Joseph, Guido Polles, Frank Alber, Maya Topf
A wide variety of experimental techniques can be used for understanding the precise molecular mechanisms underlying the activities of cellular assemblies. The inherent limitations of a single experimental technique often requires integration of data from complementary approaches to gain sufficient insights into the assembly structure and function. Here, we review popular computational approaches for integrative modelling of cellular assemblies, including protein complexes and genomic assemblies. We provide recent examples of integrative models generated for such assemblies by different experimental techniques, especially including data from 3D electron microscopy (3D-EM) and chromosome conformation capture experiments, respectively...
July 20, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28735027/translation-of-an-injectable-triple-interpenetrating-network-hydrogel-for-intervertebral-disc-regeneration-in-a-goat-model
#2
Sarah E Gullbrand, Thomas P Schaer, Prateek Agarwal, Justin R Bendigo, George R Dodge, Weiliam Chen, Dawn M Elliott, Robert L Mauck, Neil R Malhotra, Lachlan J Smith
Degeneration of the intervertebral discs is a progressive cascade of cellular, compositional and structural changes that is frequently associated with low back pain. As the first signs of disc degeneration typically arise in the disc's central nucleus pulposus (NP), augmentation of the NP via hydrogel injection represents a promising strategy to treat early to mid-stage degeneration. The purpose of this study was to establish the translational feasibility of a triple interpenetrating network hydrogel composed of dextran, chitosan, and teleostean (DCT) for augmentation of the degenerative NP in a preclinical goat model...
July 19, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28735012/fgwas-functional-genome-wide-association-analysis
#3
Chao Huang, Paul Thompson, Yalin Wang, Yang Yu, Jingwen Zhang, Dehan Kong, Rivka R Colen, Rebecca C Knickmeyer, Hongtu Zhu
Functional phenotypes (e.g., subcortical surface representation), which commonly arise in imaging genetic studies, have been used to detect putative genes for complexly inherited neuropsychiatric and neurodegenerative disorders. However, existing statistical methods largely ignore the functional features (e.g., functional smoothness and correlation). The aim of this paper is to develop a functional genome-wide association analysis (FGWAS) framework to efficiently carry out whole-genome analyses of functional phenotypes...
July 19, 2017: NeuroImage
https://www.readbyqxmd.com/read/28735008/trehalose-induced-structural-modulation-of-bovine-serum-albumin-at-ambient-temperature
#4
Ahana Das, Pijush Basak, Rudradip Pattanayak, Turban Kar, Rajib Majumder, Debadrita Pal, Anindita Bhattacharya, Maitree Bhattacharyya, Samudra Prosad Banik
Trehalose is a well-known protein stabilizing osmolyte. The present study has been designed to understand the interaction of trehalose with BSA at ambient temperature. Steady state fluorescence and life-time analysis along with CD, DLS and ITC have been employed to show that trehalose causes surface-associated structural perturbation of BSA to promote its compaction. Trehalose at 0.1M concentration resulted in increased solvent exposure of one of the two tryptophans of BSA with a 5nm redshift in emission and enhanced susceptibility to acrylamide quenching with an increase in KSV from 2...
July 19, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28734777/inhibitor-mechanisms-in-the-s1-binding-site-of-the-dopamine-transporter-defined-by-multi-site-molecular-tethering-of-photoactive-cocaine-analogs
#5
Danielle Krout, Akula Bala Pramod, Rejwi Acharya Dahal, Michael J Tomlinson, Babita Sharma, James D Foster, Mu-Fa Zou, Comfort Boatang, Amy Hauck Newman, John R Lever, Roxanne A Vaughan, L Keith Henry
Dopamine transporter (DAT) blockers like cocaine and many other abused and therapeutic drugs bind and stabilize an inactive form of the transporter inhibiting reuptake of extracellular dopamine (DA). The resulting increases in DA lead to the ability of these drugs to induce psychomotor alterations and addiction, but paradoxical findings in animal models indicate that not all DAT antagonists induce cocaine-like behavioral outcomes. How this occurs is not known, but one possibility is that uptake inhibitors may bind at multiple locations or in different poses to stabilize distinct conformational transporter states associated with differential neurochemical endpoints...
July 19, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28734534/elbow-vascularized-composite-allotransplantation-surgical-anatomy-and-technique
#6
Zvi Steinberger, Heng Xu, Nikolas H Kazmers, Stephanie Thibaudeau, Russel G Huffman, L Scott Levin
BACKGROUND: Elbow reconstruction with vascularized composite allotransplantation (VCA) may hold promise in treating end-stage arthritis as no current treatment is both functional and durable. We describe the vascular and gross anatomy of the elbow in the context of VCA procurement and propose a step-by-step surgical technique for human elbow VCA. METHODS: We injected latex in the arterial tree of 16 fresh adult cadaveric upper extremities. We identified and measured arteries and nerves and their branch points relative to the medial epicondyle...
August 2017: Journal of Shoulder and Elbow Surgery
https://www.readbyqxmd.com/read/28734296/spherical-harmonics-analysis-of-surface-density-fluctuations-of-spherical-ionic-sds-and-nonionic-c12e8-micelles-a-molecular-dynamics-study
#7
Noriyuki Yoshii, Yuki Nimura, Kazushi Fujimoto, Susumu Okazaki
The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (C12E8) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734294/the-standard-mean-field-treatment-of-inter-particle-attraction-in-classical-dft-is-better-than-one-might-expect
#8
Andrew J Archer, Blesson Chacko, Robert Evans
In classical density functional theory (DFT), the part of the Helmholtz free energy functional arising from attractive inter-particle interactions is often treated in a mean-field or van der Waals approximation. On the face of it, this is a somewhat crude treatment as the resulting functional generates the simple random phase approximation (RPA) for the bulk fluid pair direct correlation function. We explain why using standard mean-field DFT to describe inhomogeneous fluid structure and thermodynamics is more accurate than one might expect based on this observation...
July 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28734212/treatment-of-refractory-contaminants-by-sludge-derived-biochar-persulfate-system-via-both-adsorption-and-advanced-oxidation-process
#9
Jia Wang, Zhuwei Liao, Jerosha Ifthikar, Lerong Shi, Yunan Du, Jingyi Zhu, Shuang Xi, Zhuqi Chen, Zhulei Chen
A novel strategy for the removal of refractory organic contaminants was realized through sludge-derived biochar (SDBC)/persulfate (PS) system via both adsorption and advanced oxidation process under ambient conditions. SDBC was prepared by one single step of slow pyrolysis of municipal sewage sludge, appeared a porous structure, and contained abundant oxygen-containing functional groups as well as amorphous Fe species. Large surface area and porous structure of SDBC benefitted the adsorption and enrichment of contaminants, while oxygen-containing functional groups and Fe species on the surface were considered as reactive components for the activation of PS...
July 17, 2017: Chemosphere
https://www.readbyqxmd.com/read/28734207/in-silico-designing-of-therapeutic-protein-enriched-with-branched-chain-amino-acids-for-the-dietary-treatment-of-chronic-liver-disease
#10
Sunil L, Prasanna Vasu
Leucine, isoleucine, and valine are three essential branched-chain amino acids (BCAA) account for 40-45% of total essential amino acids. BCAA stimulates protein synthesis primarily in skeletal muscles, and it can directly transport to circulatory blood stream bypassing the liver. Hence, a protein enriched with BCAA is an important therapeutic target for the dietary treatment of chronic liver disease. The present study is to design a synthetic protein enriched with BCAA and the challenge is to maximize the BCAA content, keeping the balanced ratio of leucine, isoleucine, valine - 2: 1: 1...
July 12, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28733928/structural-neurodegeneration-correlates-with-early-diabetic-retinopathy
#11
Ulrik Frydkjaer-Olsen, Rasmus Soegaard Hansen, Tunde Peto, Jakob Grauslund
PURPOSE: To examine differences in structural and functional neurodegenerative measurements between patients with no and early diabetic retinopathy (DR). METHODS: In this cross-sectional study, we examined 103 patients with type 2 diabetes mellitus. In 7-field fundus photographs acquired with Topcon TRC-NW6S, a single, certified grader determined the presence of DR according to the Early Treatment Diabetic Retinopathy Study (ETDRS) scale. Retinal neurodegeneration was evaluated by Topcon 3D OCT-2000 spectral domain optical coherence tomography (OCT) and by a RETI-scan multifocal electroretinography (mf-ERG) system in rings 1-6...
July 21, 2017: International Ophthalmology
https://www.readbyqxmd.com/read/28733922/effect-of-collagen-fibre-orientation-on-intervertebral-disc-torsion-mechanics
#12
Bo Yang, Grace D O'Connell
The intervertebral disc is a complex fibro-cartilaginous material, consisting of a pressurized nucleus pulposus surrounded by the annulus fibrosus, which has an angle-ply structure. Disc injury and degeneration are noted by significant changes in tissue structure and function, which significantly alters stress distribution and disc joint stiffness. Differences in fibre orientation are thought to contribute to changes in disc torsion mechanics. Therefore, the objective of this study was to evaluate the effect of collagen fibre orientation on internal disc mechanics under compression combined with axial rotation...
July 21, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/28733882/prediction-of-the-lowest-charge-transfer-excited-state-energy-at-the-donor-acceptor-interface-in-a-condensed-phase-using-ground-state-dft-calculations-with-generalized-kohn-sham-functionals
#13
Shaohui Zheng, Mengyue Xiao, Yongping Tian, Xue Chen
Knowledge of the charge (electron) transfer process at the donor-acceptor interface is required to understand the working mechanisms of different organic photovoltaic materials. Investigating the lowest charge-transfer state in organic donor-acceptor solar cells is important as it allows the destruction/formation of excitons and polarons to be studied, and is directly related to the open circuit voltage. By performing low-cost and feasible calculations of ground-state electronic structures using the Mulliken rule as well as the optimally tuned range-separated hybrid (OTRSH) density functional and a regular long-range corrected functional, the lowest charge-transfer (CT) state energies of a series of dimers containing functionalized anthracene (the donor) and tetracyanoethylene (the acceptor) were obtained...
August 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28733783/perianth-organs-in-nymphaeaceae-comparative-study-on-epidermal-and-structural-characters
#14
Lucía Melisa Zini, Beatriz Gloria Galati, María Silvia Ferrucci
The perianth organs of six species of Nymphaeaceae, representing Euryale, Nymphaea and Victoria, were studied on the basis of macroscopical, micromorphological, and anatomical characters. The aims were to determine whether perianth is differentiated among tepal whorls considering the presence of sepaloid and petaloid characters, and to evaluate the occurrence of both features in individual tepals. Selected perianth series were examined macroscopically, with light microscopy, and scanning electron microscopy...
July 21, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/28733670/brd3-and-brd4-bet-bromodomain-proteins-differentially-regulate-skeletal-myogenesis
#15
Thomas C Roberts, Usue Etxaniz, Alessandra Dall'Agnese, Shwu-Yuan Wu, Cheng-Ming Chiang, Paul E Brennan, Matthew J A Wood, Pier Lorenzo Puri
Myogenic differentiation proceeds through a highly coordinated cascade of gene activation that necessitates epigenomic changes in chromatin structure. Using a screen of small molecule epigenetic probes we identified three compounds which inhibited myogenic differentiation in C2C12 myoblasts; (+)-JQ1, PFI-1, and Bromosporine. These molecules target Bromodomain and Extra Terminal domain (BET) proteins, which are epigenetic readers of acetylated histone lysine tail residues. BETi-mediated anti-myogenic effects were also observed in a model of MYOD1-mediated myogenic conversion of human fibroblasts, and in primary mouse and human myoblasts...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733162/patterning-the-eye-a-role-for-the-cell-cycle
#16
Nicholas E Baker
Although highly regulated cell cycle behavior accompanies specification of cell types in the Drosophila retina, no evidence has previously existed that cell cycle phase influences cell fate choice. Meserve and Duronio have now used genetic techniques to trace the fate of a sub-population of cells that accumulate in G2-phase of the cell cycle, discovering that they contribute to a particular fate, the precursor of the sensory inter-ommatidial bristles. Meserve and Duronio further show that G2 cells have an advantage acquiring inter-ommatidial bristle fate...
July 18, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28733037/efficient-probabilistic-finite-element-analysis-of-a-lumbar-motion-segment
#17
Dana J Coombs, Paul J Rullkoetter, Peter J Laz
Finite element models of the lumbar spine are useful in assessing biomechanics and performance of implants. Models are often developed using the anatomy of an individual subject. Average mechanical property values for the annulus and other soft tissue structures are typically utilized from the literature, as data for the same subject are not available. However, these properties can have significant variability. While probabilistic methods enable the impact of soft tissue property variability on spine mechanics to be assessed, they often require lengthy computation times...
July 11, 2017: Journal of Biomechanics
https://www.readbyqxmd.com/read/28733025/revisiting-historical-khoe-san-skeletal-remains-in-european-collections-a-search-for-identity-through-craniometric-analysis
#18
D Botha, M Steyn, Y Scholtz, I Ribot
As the identity of a large number of Khoe-San skeletal material in European collections recently came into question during its documentation, a re-evaluation of the remains by employing a non-invasive method such as craniometrics was done to investigate the biological affinity. For this purpose, gene flow and population diversity present within the group, as well as between the study sample (N=63) and other modern and historic population groups from southern, central and east Africa were explored. Available comparative groups included the historic Khoe-San from Riet River (N=31), the Sotho-Tswana from southern Africa (N=61), the Basuku from central Africa (N=66) and the Bahutu (N=53) and Teita (N=24) from east Africa...
June 28, 2017: Homo: Internationale Zeitschrift Für die Vergleichende Forschung Am Menschen
https://www.readbyqxmd.com/read/28732249/evaluating-alzheimer-s-disease-biomarkers-as-mediators-of-age-related-cognitive-decline
#19
Timothy J Hohman, Doug Tommet, Shawn Marks, Joey Contreras, Rich Jones, Dan Mungas
Age-related changes in cognition are partially mediated by the presence of neuropathology and neurodegeneration. This manuscript evaluates the degree to which biomarkers of Alzheimer's disease, (AD) neuropathology and longitudinal changes in brain structure, account for age-related differences in cognition. Data from the AD Neuroimaging Initiative (n = 1012) were analyzed, including individuals with normal cognition and mild cognitive impairment. Parallel process mixed effects regression models characterized longitudinal trajectories of cognitive variables and time-varying changes in brain volumes...
July 4, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28732246/inspiration-from-heart-development-biomimetic-development-of-functional-human-cardiac-organoids
#20
Dylan J Richards, Robert C Coyle, Yu Tan, Jia Jia, Kerri Wong, Katelynn Toomer, Donald R Menick, Ying Mei
Recent progress in human organoids has provided 3D tissue systems to model human development, diseases, as well as develop cell delivery systems for regenerative therapies. While direct differentiation of human embryoid bodies holds great promise for cardiac organoid production, intramyocardial cell organization during heart development provides biological foundation to fabricate human cardiac organoids with defined cell types. Inspired by the intramyocardial organization events in coronary vasculogenesis, where a diverse, yet defined, mixture of cardiac cell types self-organizes into functional myocardium in the absence of blood flow, we have developed a defined method to produce scaffold-free human cardiac organoids that structurally and functionally resembled the lumenized vascular network in the developing myocardium, supported hiPSC-CM development and possessed fundamental cardiac tissue-level functions...
July 12, 2017: Biomaterials
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