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https://www.readbyqxmd.com/read/27914045/achievements-and-challenges-in-computational-protein-design
#1
Ilan Samish
Computational protein design (CPD), a yet evolving field, includes computer-aided engineering for partial or full de novo designs of proteins of interest. Designs are defined by a requested structure, function, or working environment. This chapter describes the birth and maturation of the field by presenting 101 CPD examples in a chronological order emphasizing achievements and pending challenges. Integrating these aspects presents the plethora of CPD approaches with the hope of providing a "CPD 101". These reflect on the broader structural bioinformatics and computational biophysics field and include: (1) integration of knowledge-based and energy-based methods, (2) hierarchical designated approach towards local, regional, and global motifs and the integration of high- and low-resolution design schemes that fit each such region, (3) systematic differential approaches towards different protein regions, (4) identification of key hot-spot residues and the relative effect of remote regions, (5) assessment of shape-complementarity, electrostatics and solvation effects, (6) integration of thermal plasticity and functional dynamics, (7) negative design, (8) systematic integration of experimental approaches, (9) objective cross-assessment of methods, and (10) successful ranking of potential designs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913358/conformational-sampling-of-a-biomolecular-rugged-energy-landscape
#2
Jakub Rydzewski, Rafal Jakubowski, Giuseppe Nicosia, Wieslaw Nowak
The protein structure refinement using conformational sampling is important in hitherto protein studies. In this paper we examined the protein structure refinement by means of potential energy minimization using immune computing as a method of sampling conformations. The method was tested on the x-ray structure and 30 decoys of the mutant of [Leu]Enkephalin, a paradigmatic example of the biomolecular multiple-minima problem. In order to score the refined conformations, we used a standard potential energy function with the OPLSAA force field...
December 1, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27906355/control-of-the-two-photon-fluorescence-of-quantum-dots-coupled-to-silver-nanowires
#3
Weijie Mai, Xiaokang Song, Ping Jiang, Wenzhong Wang, Li Yu, Jiasen Zhang
Plasmon-based fluorescence modulation has led to important advances in various fields and has paved the way toward promising scientific research aimed at enabling new applications. However, the modulation of fluorescence properties based on both localized surface plasmon (LSP) and cavity modes of propagating surface plasmon polaritons (SPPs) are rarely reported. Here, we raster scanned a hybrid nanowire (HNW) with quantum dots (QDs) adsorbed onto a Ag nanowire (NW) and obtained two-photon fluorescence (TPF) maps of the intensity and decay rate...
November 28, 2016: Optics Express
https://www.readbyqxmd.com/read/27906313/experimental-study-on-the-transition-of-plasmonic-resonance-modes-in-double-ring-dimers-by-conductive-junctions-in-the-terahertz-regime
#4
Huifang Zhang, Chun Li, Caihong Zhang, Xueqian Zhang, Jianqiang Gu, Biaobing Jin, Jiaguang Han, Weili Zhang
Plasmonic dimers that made from two subwavelength particles have drawn much attention in the recent years, which are quite promising in local field enhancement, sensing, high frequency conductance probing and electron tunneling. In this work, we experimentally investigate the mode transition effect of different plasmonic resonances in double-ring dimers when introducing conductive junction at the dimer gap in the terahertz regime. Without the junction, the dimers support a single dipolar bonding dimer plasmonic (BDP) mode...
November 28, 2016: Optics Express
https://www.readbyqxmd.com/read/27905668/subconjunctival-antimicrobial-poloxamer-gel-for-treatment-of-corneal-ulceration-in-stranded-california-sea-lions-zalophus-californianus
#5
Claire A Simeone, Carmen M H Colitz, Kathleen M Colegrove, Cara L Field, Carlos Rios, Heather L Chandler, Shawn P Johnson
OBJECTIVE: Corneal ulcers are commonly encountered in pinnipeds. Prolonged oral antibiotics and topical ophthalmic solutions may not be practical to administer, and novel treatment techniques are desired. Thermodynamic gels are a potential solution because they hold antimicrobials at the site of injection, slowly releasing drug. This study investigated the clinical efficacy of antibiotic-impregnated poloxamer gel in management of corneal ulceration. ANIMAL STUDIED: Twenty-six California sea lions undergoing rehabilitation at The Marine Mammal Center...
December 1, 2016: Veterinary Ophthalmology
https://www.readbyqxmd.com/read/27905555/the-complex-nature-of-calcium-cation-interactions-with-phospholipid-bilayers
#6
Adéla Melcrová, Sarka Pokorna, Saranya Pullanchery, Miriam Kohagen, Piotr Jurkiewicz, Martin Hof, Pavel Jungwirth, Paul S Cremer, Lukasz Cwiklik
Understanding interactions of calcium with lipid membranes at the molecular level is of great importance in light of their involvement in calcium signaling, association of proteins with cellular membranes, and membrane fusion. We quantify these interactions in detail by employing a combination of spectroscopic methods with atomistic molecular dynamics simulations. Namely, time-resolved fluorescent spectroscopy of lipid vesicles and vibrational sum frequency spectroscopy of lipid monolayers are used to characterize local binding sites of calcium in zwitterionic and anionic model lipid assemblies, while dynamic light scattering and zeta potential measurements are employed for macroscopic characterization of lipid vesicles in calcium-containing environments...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27903266/environmental-determinants-of-malaria-transmission-in-african-villages
#7
Noriko Endo, Elfatih A B Eltahir
BACKGROUND: Malaria transmission is complex, involving a range of hydroclimatological, biological, and environmental processes. The high degree of non-linearity in these processes makes it difficult to predict and intervene against malaria. This study seeks both to define a minimal number of malaria transmission determinants, and to provide a theoretical basis for sustainable environmental manipulation to prevent malaria transmission. METHODS: Using a field-tested mechanistic malaria model, HYDREMATS, a theoretical study was conducted under hypothetical conditions...
December 1, 2016: Malaria Journal
https://www.readbyqxmd.com/read/27901081/driving-a-superconductor-to-insulator-transition-with-random-gauge-fields
#8
H Q Nguyen, S M Hollen, J Shainline, J M Xu, J M Valles
Typically the disorder that alters the interference of particle waves to produce Anderson localization is potential scattering from randomly placed impurities. Here we show that disorder in the form of random gauge fields that act directly on particle phases can also drive localization. We present evidence of a superfluid bose glass to insulator transition at a critical level of this gauge field disorder in a nano-patterned array of amorphous Bi islands. This transition shows signs of metallic transport near the critical point characterized by a resistance , indicative of a quantum phase transition...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900646/the-potential-of-omics-technologies-in-lyme-disease-biomarker-discovery-and-early-detection
#9
REVIEW
Alaa Badawi
Lyme borreliosis (LB) is the most prevalent arthropod-borne infectious disease in North America and many countries of the temperate Northern Hemisphere. It is associated with local and systemic manifestations and has persistent post-treatment health complications in some individuals. Innate and acquired immunity-related inflammation is likely to play a critical role in both host defense against Borrelia burgdorferi and disease severity. Large-scale analytical approaches to quantify gene expression (transcriptomics), proteins (proteomics) and metabolites (metabolomics) in LB have recently emerged with a potential to advance the development of disease biomarkers in early, disseminated and posttreatment disease stages...
November 29, 2016: Infectious Diseases and Therapy
https://www.readbyqxmd.com/read/27899890/causal-role-of-thalamic-interneurons-in-brain-state-transitions-a-study-using-a-neural-mass-model-implementing-synaptic-kinetics
#10
Basabdatta Sen Bhattacharya, Thomas P Bond, Louise O'Hare, Daniel Turner, Simon J Durrant
Experimental studies on the Lateral Geniculate Nucleus (LGN) of mammals and rodents show that the inhibitory interneurons (IN) receive around 47.1% of their afferents from the retinal spiking neurons, and constitute around 20-25% of the LGN cell population. However, there is a definite gap in knowledge about the role and impact of IN on thalamocortical dynamics in both experimental and model-based research. We use a neural mass computational model of the LGN with three neural populations viz. IN, thalamocortical relay (TCR), thalamic reticular nucleus (TRN), to study the causality of IN on LGN oscillations and state-transitions...
2016: Frontiers in Computational Neuroscience
https://www.readbyqxmd.com/read/27898704/genetic-structure-and-potential-environmental-determinants-of-local-genetic-diversity-in-japanese-honeybees-apis-cerana-japonica
#11
Teruyoshi Nagamitsu, Mika Yasuda, Fuki Saito-Morooka, Maki N Inoue, Mio Nishiyama, Koichi Goka, Shinji Sugiura, Kaoru Maeto, Kimiko Okabe, Hisatomo Taki
Declines in honeybee populations have been a recent concern. Although causes of the declines remain unclear, environmental factors may be responsible. We focused on the potential environmental determinants of local populations of wild honeybees, Apis cerana japonica, in Japan. This subspecies has little genetic variation in terms of its mitochondrial DNA sequences, and genetic variations at nuclear loci are as yet unknown. We estimated the genetic structure and environmental determinants of local genetic diversity in nuclear microsatellite genotypes of fathers and mothers, inferred from workers collected at 139 sites...
2016: PloS One
https://www.readbyqxmd.com/read/27897668/global-enhancement-but-local-suppression-in-feature-based-attention
#12
Norman Forschack, Søren K Andersen, Matthias M Müller
A key property of feature-based attention is global facilitation of the attended feature throughout the visual field. Previously, we presented superimposed red and blue randomly moving dot kinematograms (RDKs) flickering at a different frequency each to elicit frequency-specific steady-state visual evoked potentials (SSVEPs) that allowed us to analyze neural dynamics in early visual cortex when participants shifted attention to one of the two colors. Results showed amplification of the attended and suppression of the unattended color as measured by SSVEP amplitudes...
November 29, 2016: Journal of Cognitive Neuroscience
https://www.readbyqxmd.com/read/27895575/can-animal-models-contribute-to-understanding-tinnitus-heterogeneity-in-humans
#13
REVIEW
Jos J Eggermont
The brain activity of humans with tinnitus of various etiologies is typically studied with electro- and magneto-encephalography and functional magnetic resonance imaging-based imaging techniques. Consequently, they measure population responses and mostly from the neocortex. The latter also underlies changes in neural networks that may be attributed to tinnitus. However, factors not strictly related to tinnitus such as hearing loss and hyperacusis, as well as other co-occurring disorders play a prominent role in these changes...
2016: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/27891080/enhanced-burst-suppression-and-disruption-of-local-field-potential-synchrony-in-a-mouse-model-of-focal-cortical-dysplasia-exhibiting-spike-wave-seizures
#14
Anthony J Williams, Chen Zhou, Qian-Quan Sun
Focal cortical dysplasias (FCDs) are a common cause of brain seizures and are often associated with intractable epilepsy. Here we evaluated aberrant brain neurophysiology in an in vivo mouse model of FCD induced by neonatal freeze lesions (FLs) to the right cortical hemisphere (near S1). Linear multi-electrode arrays were used to record extracellular potentials from cortical and subcortical brain regions near the FL in anesthetized mice (5-13 months old) followed by 24 h cortical electroencephalogram (EEG) recordings...
2016: Frontiers in Neural Circuits
https://www.readbyqxmd.com/read/27889678/early-hippocampal-hyperexcitability-in-ps2app-mice-role-of-mutant-ps2-and-app
#15
Roberto Fontana, Mario Agostini, Emanuele Murana, Mufti Mahmud, Elena Scremin, Maria Rubega, Giovanni Sparacino, Stefano Vassanelli, Cristina Fasolato
Alterations of brain network activity are observable in Alzheimer's disease (AD) together with the occurrence of mild cognitive impairment, before overt pathology. However, in humans as well in AD mouse models, identification of early biomarkers of network dysfunction is still at its beginning. We performed in vivo recordings of local field potential activity in the dentate gyrus of PS2APP mice expressing the human amyloid precursor protein (APP) Swedish mutation and the presenilin-2 (PS2) N141I. From a frequency-domain analysis, we uncovered network hyper-synchronicity as early as 3 months, when intracellular accumulation of amyloid beta was also observable...
November 5, 2016: Neurobiology of Aging
https://www.readbyqxmd.com/read/27889627/subthalamic-oscillations-and-phase-amplitude-coupling-are-greater-in-the-more-affected-hemisphere-in-parkinson-s-disease
#16
Lauren A Shreve, Anca Velisar, Mahsa Malekmohammadi, Mandy Miller Koop, Megan Trager, Emma J Quinn, Bruce C Hill, Zack Blumenfeld, Camilla Kilbane, Alessandra Mantovani, Jaimie M Henderson, Helen Brontë-Stewart
OBJECTIVE: Determine the incidence of resting state oscillations in alpha/beta, high frequency (HFO) bands, and their phase amplitude coupling (PAC) in a large cohort in Parkinson's disease (PD). METHODS: Intra-operative local field potentials (LFPs) from subthalamic nucleus (STN) were recorded from 100 PD subjects, data from 74 subjects were included in the analysis. RESULTS: Alpha/beta oscillations were evident in >99%, HFO in 87% and PAC in 98% of cases...
November 10, 2016: Clinical Neurophysiology: Official Journal of the International Federation of Clinical Neurophysiology
https://www.readbyqxmd.com/read/27885655/a-landscape-scale-field-experiment-reveals-the-importance-of-dispersal-in-a-resource-limited-metacommunity
#17
Jill Lancaster, Barbara J Downes
Dispersal may play a strong role in driving species diversity across landscapes. Theoretically, dispersal permits species to remain extant within a metacommunity, even if they are periodically excluded from some local communities. Field tests of dispersal effects are difficult, and most non-experimental data suggest that environmental conditions play the predominant role in setting species diversity. However, most such studies cannot differentiate between patterns caused primarily by dispersal constraints vs abiotic factors vs biotic constraints (e...
November 25, 2016: Ecology
https://www.readbyqxmd.com/read/27884774/esponsive-multifunctional-drug-delivery-nanoparticles-for-elastic-matrix-regenerative-repair
#18
Balakrishnan Sivaraman, Ganesh Swaminathan, Lee Moore, Jonathan Fox, Dhruv Seshadri, Shataakshi Dahal, Ivan Stoilov, Maciej Zborowski, Robert Mecham, Anand Ramamurthi
: Arresting or regressing growth of abdominal aortic aneurysms (AAAs), localized expansions of the abdominal aorta are contingent on inhibiting chronically overexpressed matrix metalloproteases (MMPs)-2 and -9 that disrupt elastic matrix within the aortic wall, concurrent with providing a stimulus to augmenting inherently poor auto-regeneration of these matrix structures. In a recent study we demonstrated that localized, controlled and sustained delivery of doxycycline (DOX; a tetracycline-based antibiotic) from poly(lactic-co-glycolic acid) nanoparticles (PLGA NPs), enhances elastic matrix deposition and MMP-inhibition at a fraction of the therapeutically effective oral dose...
November 21, 2016: Acta Biomaterialia
https://www.readbyqxmd.com/read/27877113/the-effects-of-realistic-synaptic-distribution-and-3d-geometry-on-signal-integration-and-extracellular-field-generation-of-hippocampal-pyramidal-cells-and-inhibitory-neurons
#19
Attila I Gulyás, Tamás F Freund, Szabolcs Káli
In vivo and in vitro multichannel field and somatic intracellular recordings are frequently used to study mechanisms of network pattern generation. When interpreting these data, neurons are often implicitly considered as electrotonically compact cylinders with a homogeneous distribution of excitatory and inhibitory inputs. However, the actual distributions of dendritic length, diameter, and the densities of excitatory and inhibitory input are non-uniform and cell type-specific. We first review quantitative data on the dendritic structure and synaptic input and output distribution of pyramidal cells (PCs) and interneurons in the hippocampal CA1 area...
2016: Frontiers in Neural Circuits
https://www.readbyqxmd.com/read/27874845/collaboration-and-emotions-to-the-test-the-experience-of-file-volunteers-in-hospices
#20
Giulia Mascagni
BACKGROUND AND AIMS: This study seeks to provide an in-depth analysis of care-based interaction in the experiences of volunteers working in lenitherapy (pain therapy) through the case study of hospices in Florence, Italy. METHOD: A qualitative method of data collection was chosen: the field research made use of open-ended questionnaires distributed to trained but unspecialised volunteers (V = 32) and to volunteers with hospital-based medical expertise (PV = 35) acting for the Italian Lenitherapy Foundation (FILe) and operating in hospices within the ex-ASL (Local Health Unit) of Florence...
November 22, 2016: Acta Bio-medica: Atenei Parmensis
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