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Complex systems

Michael C Gundry, Lorenzo Brunetti, Angelique Lin, Allison E Mayle, Ayumi Kitano, Dimitrios Wagner, Joanne I Hsu, Kevin A Hoegenauer, Cliona M Rooney, Margaret A Goodell, Daisuke Nakada
Our understanding of the mechanisms that regulate hematopoietic stem/progenitor cells (HSPCs) has been advanced by the ability to genetically manipulate mice; however, germline modification is time consuming and expensive. Here, we describe fast, efficient, and cost-effective methods to directly modify the genomes of mouse and human HSPCs using the CRISPR/Cas9 system. Using plasmid and virus-free delivery of guide RNAs alone into Cas9-expressing HSPCs or Cas9-guide RNA ribonucleoprotein (RNP) complexes into wild-type cells, we have achieved extremely efficient gene disruption in primary HSPCs from mouse (>60%) and human (∼75%)...
October 25, 2016: Cell Reports
Katherine A Muratore, Heather M Grundhofer, Edgar A Arriaga
Macroautophagy is a cellular degradation process responsible for the clearance of excess intracellular cargo. Existing methods for bulk quantification of autophagy rely on organelle markers that bind to multiple autophagy organelle types, making it difficult to tease apart the subcellular mechanisms implicated in autophagy dysfunction in liver and other pathologies. To address this issue, methods based on individual organelle measurements are needed. Capillary electrophoresis with laser induced fluorescent detection (CE-LIF) was previously used to count and determine properties of individual autophagy organelles isolated from an LC3-GFP expressing cell line, but has never been used on autophagy organelles originating from a tissue sample...
October 26, 2016: Analytical Chemistry
Carlos Fernandez-Patron, Zamaneh Kassiri, Dickson Leung
Matrix metalloproteinase-2 (MMP-2) is a 72-kDa zinc- and calcium-dependent endopeptidase with intracellular and extracellular functions ranging from the modulation of extracellular matrix remodeling to cell growth and migration, angiogenesis, inflammation, and metabolism. An upregulation of MMP-2 activity has the potential to deregulate lipid metabolism through the cleavage of numerous metabolic mediators including plasma lipoproteins and cell surface receptors of lipoproteins. Paradoxically, MMP-2 deficiency induces inflammation and deregulates metabolism...
September 15, 2016: Comprehensive Physiology
André David Kovac, Maximilian Koall, Gordon Pipa, Hazem Toutounji
Delays are ubiquitous in biological systems, ranging from genetic regulatory networks and synaptic conductances, to predator/pray population interactions. The evidence is mounting, not only to the presence of delays as physical constraints in signal propagation speed, but also to their functional role in providing dynamical diversity to the systems that comprise them. The latter observation in biological systems inspired the recent development of a computational architecture that harnesses this dynamical diversity, by delay-coupling a single nonlinear element to itself...
2016: PloS One
Sulaf Alwassouf, Vasiliki Christodoulou, Laurence Bichaud, Pantelis Ntais, Apostolos Mazeris, Maria Antoniou, Remi N Charrel
Phleboviruses transmitted by sandflies are endemic in the Mediterranean area. The last decade has witnessed the description of an accumulating number of novel viruses. Although, the risk of exposure of vertebrates is globally assessed, detailed geographic knowledge is poor even in Greece and Cyprus where sandfly fever has been recognized for a long time and repeatedly. A total of 1,250 dogs from mainland Greece and Greek archipelago on one hand and 422 dogs from Cyprus on the other hand have been sampled and tested for neutralising antibodies against Toscana virus (TOSV), Sandfly fever Sicilian virus (SFSV), Arbia virus, and Adana virus i...
October 2016: PLoS Neglected Tropical Diseases
Alireza Mashaghi, Sergey Bezrukavnikov, David P Minde, Anne S Wentink, Roman Kityk, Beate Zachmann-Brand, Matthias P Mayer, Günter Kramer, Bernd Bukau, Sander J Tans
The Hsp70 system is a central hub of chaperone activity in all domains of life. Hsp70 performs a plethora of tasks, including folding assistance, protection against aggregation, protein trafficking, and enzyme activity regulation, and interacts with non-folded chains, as well as near-native, misfolded, and aggregated proteins. Hsp70 is thought to achieve its many physiological roles by binding peptide segments that extend from these different protein conformers within a groove that can be covered by an ATP-driven helical lid...
October 26, 2016: Nature
Samuel Stolpe, Michel A Kroes, Neil Webb, Tami Wisniewski
BACKGROUND: Diabetes care is associated with a considerable burden to the health care system in the United States, and measuring the quality of health care is an important development goal of the Department of Health and Human Services and the Centers for Medicare & Medicaid Services. Diabetes is a priority disease within the National Quality Strategy and should therefore remain a focus in the measurement of health care quality. Despite the importance of measuring quality in diabetes care management, no quality measure is currently associated with adherence to insulin treatment, and measuring adherence to insulin is known to be complicated...
November 2016: Journal of Managed Care & Specialty Pharmacy
Cannada Andrew Lewis, Justus Aaron Calvin, Edward F Valeev
We describe the Clustered Low Rank (CLR) framework for block-sparse and block-low-rank tensor representation and computation. The CLR framework exploits the tensor structure revealed by basis clustering; computational savings arise from low-rank compression of tensor blocks and performing block arithmetic in the low-rank form whenever beneficial. The precision is rigorously controlled by 2 parameters, avoiding ad-hoc heuristics, such as domains: one controls the CLR block rank truncation and the other controls screening of small contributions in arithmetic operations on CLR tensors to propagate sparsity through expressions...
October 26, 2016: Journal of Chemical Theory and Computation
Jeong Eun Hyeon, Sang Kyu Shin, Sung Ok Han
The utilization of scaffolds for enzyme immobilization involves advanced bionanotechnology applications in biorefinery fields, which can be achieved by optimizing the function of various enzymes. This review presents various current scaffolding techniques based on proteins, microbes and nanomaterials for enzyme immobilization, as well as the impact of these techniques on the biorefinery of lignocellulosic materials. Among them, architectural scaffolds have applied to useful strategies for protein engineering to improve the performance of immobilized enzymes in several industrial and research fields...
October 26, 2016: Biotechnology Journal
Toby M Michelena, Jeremy L Farrell, David A Winkler, Christine A Goodrich, Charles W Boylen, James W Sutherland, Sandra A Nierzwicki-Bauer
In 1990, the US Congress amended the Clean Air Act (CAA) to reduce regional-scale ecosystem degradation from SO x and NO x emissions which have been responsible for acid deposition in regions such as the Adirondack Mountains of New York State. An ecosystem assessment project was conducted from 1994 to 2012 by the Darrin Fresh Water Institute to determine the effect of these emission reduction policies on aquatic systems. The project investigated water chemistry and biota in 30 Adirondack lakes and ponded waters...
November 2016: Environmental Monitoring and Assessment
Si Cheng, Jie Sun, Junxing Yang, Jianqiang Lv, Feng Wu, Yanxing Lin, Lishan Liao, Yiyou Ye, Chenfu Cao, Liurong Fang, Qunyi Hua
A fast and ultrasensitive test-strip system combining quantum dots (QDs) with a lateral-flow immunoassay strip (LFIAS) was established for detection of Peste des petits ruminants virus (PPRV) antibody. The highly luminescent water-soluble carboxyl-functionalized QDs were used as the signal output and were conjugated to streptococcal protein G (SPG), which was capable of binding to immunoglobulin G (IgG) from many species through an amide bond to capture the target PPRV IgGs. The PPRV N protein, which was immobilized on the detection zone of the test strip, was expressed by transfecting recombinant Bacmid-PPRV-N with Lipofect into Sf9 insect cells...
October 25, 2016: Analytical and Bioanalytical Chemistry
Chao Zhang, Chendan Wang, Jianbo Ren, Xiangjie Guo, Keming Yun
Glutamate is not only a neurotransmitter but also an important neurotoxin in central nervous system (CNS). Chronic elevation of glutamate induces both neuronal and glial cell apoptosis. However, its effect on astrocytes is complex and still remains unclear. In this study, we investigated whether morphine, a common opioid ligand, could affect glutamate-induced apoptosis in astrocytes. Primary cultured astrocytes were incubated with glutamate in the presence/absence of morphine. It was found that morphine could reduce glutamate-induced apoptosis of astrocytes...
October 24, 2016: International Journal of Molecular Sciences
Colin Echeverría Aitken, Petra Beznosková, Vladislava Vlčkova, Wen-Ling Chiu, Fujun Zhou, Leoš Shivaya Valášek, Alan G Hinnebusch, Jon R Lorsch
Eukaryotic translation initiation factor 3 (eIF3) is a central player in recruitment of the pre-initiation complex (PIC) to mRNA. We probed the effects on mRNA recruitment of a library of S. cerevisiae eIF3 functional variants spanning its 5 essential subunits using an in vitro-reconstituted system. Mutations throughout eIF3 disrupt its interaction with the PIC and diminish its ability to accelerate recruitment to a native yeast mRNA. Alterations to the eIF3a CTD and eIF3b/i/g significantly slow mRNA recruitment, and mutations within eIF3b/i/g destabilize eIF2•GTP•Met-tRNAi binding to the PIC...
October 26, 2016: ELife
Jamie Ross, Fiona Stevenson, Rosa Lau, Elizabeth Murray
BACKGROUND: There is a significant potential for e-health to deliver cost-effective, quality health care, and spending on e-health systems by governments and healthcare systems is increasing worldwide. However, there remains a tension between the use of e-health in this way and implementation. Furthermore, the large body of reviews in the e-health implementation field, often based on one particular technology, setting or health condition make it difficult to access a comprehensive and comprehensible summary of available evidence to help plan and undertake implementation...
October 26, 2016: Implementation Science: IS
Enrico Franco, Mike Ristic, Marc Rea, Wladyslaw M W Gedroyc
PURPOSE: Percutaneous ablation under MRI-guidance allows treating otherwise inoperable liver tumors locally using a catheter probe. However, manually placing the probe is an error-prone and time consuming task that requires a considerable amount of training. The aim of this paper was to present a pneumatically actuated robotic instrument that can assist clinicians in MRI-guided percutaneous intervention of the liver and to assess its functionality in a clinical setting. The robot positions a needle-guide inside the MRI scanner bore and assists manual needle insertions outside the bore...
October 2016: Medical Physics
K Müller, S Datta, M Ahmad, J-H Choi, T Moore, L Pung, C Niebler, G E Gold, A Maier, R Fahrig
PURPOSE: In the last years, dual-energy CT imaging has shown clinical value, thanks to its ability to differentiate materials based on their atomic number and to exploit different properties of images acquired at two different energies. C-arm CT systems are used to guide procedures in the interventional suite. Until now, there are no commercially available systems that employ dual-energy material decomposition. This paper explores the feasibility of implementing a fast kV-switching technique on a clinically available angiographic system for acquiring dual-energy C-arm CT images...
October 2016: Medical Physics
Vaibhav Jain, Prabal K Maiti, Prasad V Bharatam
Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details...
September 28, 2016: Journal of Chemical Physics
Arne Luenser, Jörg Kussmann, Christian Ochsenfeld
We present a (sub)linear-scaling algorithm to determine indirect nuclear spin-spin coupling constants at the Hartree-Fock and Kohn-Sham density functional levels of theory. Employing efficient integral algorithms and sparse algebra routines, an overall (sub)linear scaling behavior can be obtained for systems with a non-vanishing HOMO-LUMO gap. Calculations on systems with over 1000 atoms and 20 000 basis functions illustrate the performance and accuracy of our reference implementation. Specifically, we demonstrate that linear algebra dominates the runtime of conventional algorithms for 10 000 basis functions and above...
September 28, 2016: Journal of Chemical Physics
S Orioli, P Faccioli
Renormalization Group (RG) theory provides the theoretical framework to define rigorous effective theories, i.e., systematic low-resolution approximations of arbitrary microscopic models. Markov state models are shown to be rigorous effective theories for Molecular Dynamics (MD). Based on this fact, we use real space RG to vary the resolution of the stochastic model and define an algorithm for clustering microstates into macrostates. The result is a lower dimensional stochastic model which, by construction, provides the optimal coarse-grained Markovian representation of the system's relaxation kinetics...
September 28, 2016: Journal of Chemical Physics
Tahereh Nemati Aram, Petrutza Anghel-Vasilescu, Asghar Asgari, Matthias Ernzerhof, Didier Mayou
We present a novel simple model to describe molecular photocells where the energy conversion process takes place by a single molecular donor-acceptor complex attached to electrodes. By applying quantum scattering theory, an open quantum system method, the coherent molecular photocell is described by a wave function. We analyze photon absorption, energy conversion, and quantum yield of a molecular photocell by considering the effects of electron-hole interaction and non-radiative recombination. We model the exciton creation, dissociation, and subsequent effects on quantum yield in the energy domain...
September 28, 2016: Journal of Chemical Physics
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