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https://www.readbyqxmd.com/read/28212112/cancer-as-robust-intrinsic-state-shaped-by-evolution-a-key-issues-review
#1
Ruoshi Yuan, Xiaomei Zhu, Gaowei Wang, Site Li, Ping Ao
Cancer is a complex disease: its pathology cannot be properly understood in terms of independent players-genes, proteins, molecular pathways, or their simple combinations. This is similar to many-body physics of a condensed phase that many important properties are not determined by a single atom or molecule. The rapidly accumulating large 'omics' data also require a new mechanistic and global underpinning to organize for rationalizing cancer complexity. A unifying and quantitative theory was proposed by some of the present authors that cancer is a robust state formed by the endogenous molecular-cellular network, which is evolutionarily built for the developmental processes and physiological functions...
February 17, 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/28211194/a-field-reciprocal-transplant-experiment-reveals-asymmetric-costs-of-migration-between-lake-and-river-ecotypes-of-three-spined-sticklebacks-gasterosteus-aculeatus
#2
Joshka Kaufmann, Tobias L Lenz, Martin Kalbe, Manfred Milinski, Christophe Eizaguirre
Theory of local adaptation predicts that non-adapted migrants will suffer increased costs compared to local residents. Ultimately this process can result in the reduction of gene flow and culminate in speciation. Here, we experimentally investigated the relative fitness of migrants in foreign habitats, focusing on diverging lake and river ecotypes of three-spined sticklebacks. A reciprocal transplant experiment performed in the field revealed asymmetric costs of migration: while mortality of river fish was increased under lake conditions, lake migrants suffered from reduced growth relative to river residents...
February 17, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28208471/analysis-of-thermodiffusive-cellular-instabilities-in-continuum-combustion-fronts
#3
Hossein Azizi, Sebastian Gurevich, Nikolas Provatas
We explore numerically the morphological patterns of thermodiffusive instabilities in combustion fronts with a continuum fuel source, within a range of Lewis numbers and ignition temperatures, focusing on the cellular regime. For this purpose, we generalize the recent model of Brailovsky et al. to include distinct process kinetics and reactant heterogeneity. The generalized model is derived analytically and validated with other established models in the limit of infinite Lewis number for zero-order and first-order kinetics...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28205321/an-investigative-graduate-laboratory-course-for-teaching-modern-dna-techniques
#4
Alexandre de Lencastre, A Thomas Torello, Lani C Keller
This graduate-level DNA methods laboratory course is designed to model a discovery-based research project and engages students in both traditional DNA analysis methods and modern recombinant DNA cloning techniques. In the first part of the course, students clone the Drosophila ortholog of a human disease gene of their choosing using Gateway(®) cloning. In the second part of the course, students examine the expression of their gene of interest in human cell lines by reverse transcription PCR and learn how to analyze data from quantitative reverse transcription PCR (qRT-PCR) experiments...
February 16, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28202588/control-and-regulation-of-pathways-via-negative-feedback
#5
REVIEW
Herbert M Sauro
The biochemical networks found in living organisms include a huge variety of control mechanisms at multiple levels of organization. While the mechanistic and molecular details of many of these control mechanisms are understood, their exact role in driving cellular behaviour is not. For example, yeast glycolysis has been studied for almost 80 years but it is only recently that we have come to understand the systemic role of the multitude of feedback and feed-forward controls that exist in this pathway. In this article, control theory is discussed as an approach to dissect the control logic of complex pathways...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28195400/hypersonic-poration-a-new-versatile-cell-poration-method-to-enhance-cellular-uptake-using-a-piezoelectric-nano-electromechanical-device
#6
Zhixin Zhang, Yanyan Wang, Hongxiang Zhang, Zifan Tang, Wenpeng Liu, Yao Lu, Zefang Wang, Haitao Yang, Wei Pang, Hao Zhang, Daihua Zhang, Xuexin Duan
Efficient delivery of genes and therapeutic agents to the interior of the cell is critical for modern biotechnology. Herein, a new type of chemical-free cell poration method-hypersonic poration-is developed to improve the cellular uptake, especially the nucleus uptake. The hypersound (≈GHz) is generated by a designed piezoelectric nano-electromechanical resonator, which directly induces normal/shear stress and "molecular bombardment" effects on the bilayer membranes, and creates reversible temporal nanopores improving the membrane permeability...
February 13, 2017: Small
https://www.readbyqxmd.com/read/28186392/understanding-the-mtor-signaling-pathway-via-mathematical-modeling
#7
REVIEW
Nurgazy Sulaimanov, Martin Klose, Hauke Busch, Melanie Boerries
The mechanistic target of rapamycin (mTOR) is a central regulatory pathway that integrates a variety of environmental cues to control cellular growth and homeostasis by intricate molecular feedbacks. In spite of extensive knowledge about its components, the molecular understanding of how these function together in space and time remains poor and there is a need for Systems Biology approaches to perform systematic analyses. In this work, we review the recent progress how the combined efforts of mathematical models and quantitative experiments shed new light on our understanding of the mTOR signaling pathway...
February 10, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28185435/evidence-that-a-mitochondrial-death-spiral-underlies-antagonistic-pleiotropy
#8
REVIEW
Michael Stern
The antagonistic pleiotropy (AP) theory posits that aging occurs because alleles that are detrimental in older organisms are beneficial to growth early in life and thus are maintained in populations. Although genes of the insulin signaling pathway likely participate in AP, the insulin-regulated cellular correlates of AP have not been identified. The mitochondrial quality control process called mitochondrial autophagy (mitophagy), which is inhibited by insulin signaling, might represent a cellular correlate of AP...
February 9, 2017: Aging Cell
https://www.readbyqxmd.com/read/28182991/raman-scattering-based-multiconformational-analysis-for-probing-the-structural-differences-between-acetylcholine-and-acetylthiocholine
#9
Belén Hernández, Pascal Houzé, Fernando Pflüger, Sergei G Kruglik, Mahmoud Ghomi
Acetylcholine is the first discovered neurotransmitter that has received a great attention regarding its capability of binding to several cellular targets. The chemical composition of acetylcholine, including a positively charged trimethylammonium and a carbonyl group, as well as its conformational flexibility was pointed out as the key factors in the stabilization of its interactions. Here, the possibilities offered by a Raman scattering-based multiconformatioal analysis to access the most stable conformers of acetylcholine, is discussed...
January 27, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28177156/from-maxwell-s-equations-to-the-theory-of-current-source-density-analysis
#10
Sergey L Gratiy, Geir Halnes, Daniel Denman, Michael J Hawrylycz, Christof Koch, Gaute T Einevoll, Costas A Anastassiou
Despite the widespread use of current-source density (CSD) analysis of extracellular potential recordings in the brain, the physical mechanisms responsible for the generation of the signal are still debated. While the extracellular potential is thought to be exclusively generated by the transmembrane currents, recent studies suggest that extracellular diffusive, advective and displacement currents-traditionally neglected-may also contribute considerably towards extracellular potential recordings. Here, we first justify the application of the electro-quasistatic approximation of Maxwell's equations to describe the electromagnetic field of physiological origin...
February 8, 2017: European Journal of Neuroscience
https://www.readbyqxmd.com/read/28170349/physical-principles-of-filamentous-protein-self-assembly-kinetics
#11
Thomas Michaels, Xiaoxuan Liu, Georg Meisl, Tuomas P J Knowles
The polymerization of proteins and peptides into filamentous supramolecular structures is an elementary form of self-organization of key importance to the functioning biological systems, as in the case of actin biofilaments that compose the cellular cytoskeleton. Aberrant filamentous protein self-assembly, however, is associated with undesired effects and severe clinical disorders, such as Alzheimer's and Parkinson's diseases, which, at the molecular level, are associated with the formation of certain forms of filamentous protein aggregates known as amyloids...
February 7, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28165367/the-role-of-lipid-biomarkers-in-major-depression
#12
REVIEW
Amy Parekh, Demelza Smeeth, Yasmin Milner, Sandrine Thure
In the UK, the lifetime-documented prevalence of major depressive disorder (MDD) is currently 10%. Despite its increasing prevalence and devastating impact on quality of life, the pathophysiological mechanisms underpinning MDD remain to be fully elucidated. Current theories of neurobiological components remain incomplete and protein-centric, rendering pharmacological treatment options suboptimal. In this review, we highlight the pivotal role of lipids in intra- and inter-neuronal functioning, emphasising the potential use of lipids as biomarkers for MDD...
February 3, 2017: Healthcare (Basel, Switzerland)
https://www.readbyqxmd.com/read/28155924/structure-and-dysprosium-dopant-engineering-of-gadolinium-oxide-nanoparticles-for-enhanced-dual-modal-magnetic-resonance-and-fluorescence-imaging
#13
Jinchang Yin, Chaorui Li, Deqi Chen, Jiajun Yang, Huan Liu, Wenyong Hu, Yuanzhi Shao
We report a class of multi-functional core-shell nanoarchitectures, consisting of silica nanospheres as the core and Gd2O3:Dy(3+) nanocrystals as the ultra-thin shell, that enable unique multi-color living cell imaging and remarkable in vivo magnetic resonance imaging. These types of targeted cell imaging nanoarchitectures can be used as a variety of fluorescence nanoprobes due to the multi-color emissions of the Gd2O3:Dy(3+) nanophosphor. We also proposed a strategy of modulating core-shell structure design to achieve an enhanced magnetic resonance contrast ability of Gd2O3 nanoagents, and the classical Solomon-Bloembergen-Morgan theory was applied to explicate the mechanism underlying the enhancement...
February 3, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28155122/anisotropic-permeability-of-trabecular-bone-and-its-relationship-to-fabric-and-architecture-a-computational-study
#14
T C Kreipke, G L Niebur
Trabecular bone is a porous, mineralized tissue found in vertebral bodies, the metaphyses and epiphyses of long bones, and in the irregular and flat shaped bones. The pore space is filled with bone marrow, a highly cellular fluid. Together, the bone and marrow behave as a poroelastic solid. In poroelasticity theory, the permeability is the primary material property that governs the momentum transfer between the solid and fluid constituents. In the linearized theory, the permeability of a material depends on the shape and connectivity of the pores...
February 2, 2017: Annals of Biomedical Engineering
https://www.readbyqxmd.com/read/28153981/does-the-membrane-pacemaker-theory-of-metabolism-explain-the-size-dependence-of-metabolic-rate-in-marine-mussels
#15
Alexey Sukhotin, Natalia Fokina, Tatiana Ruokolainen, Christian Bock, Hans-Otto Pörtner, Gisela Lannig
According to the Membrane Pacemaker Theory of metabolism (MPT) allometric scaling of metabolic rate in animals is determined by the composition of cellular and mitochondrial membranes that changes with body size in a predictable manner. MPT has been elaborated from interspecific comparisons in mammals. It projects that the degree of unsaturation of membrane phospholipids decreases in larger organisms, thereby lowering ion permeability of the membranes and making cellular and thus whole animal metabolism more efficient...
February 2, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28153012/kinetic-stability-analysis-of-protein-assembly-on-the-center-manifold-around-the-critical-point
#16
Tatsuaki Tsuruyama
BACKGROUND: Non-linear kinetic analysis is a useful method for illustration of the dynamic behavior of cellular biological systems. To date, center manifold theory (CMT) has not been sufficiently applied for stability analysis of biological systems. The aim of this study is to demonstrate the application of CMT to kinetic analysis of protein assembly and disassembly, and to propose a novel framework for nonlinear multi-parametric analysis. We propose a protein assembly model with nonlinear kinetics provided by the fluctuation in monomer concentrations during their diffusion...
February 2, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28150175/macroscopic-coherent-structures-in-a-stochastic-neural-network-from-interface-dynamics-to-coarse-grained-bifurcation-analysis
#17
Daniele Avitable, Kyle C A Wedgwood
We study coarse pattern formation in a cellular automaton modelling a spatially-extended stochastic neural network. The model, originally proposed by Gong and Robinson (Phys Rev E 85(5):055,101(R), 2012), is known to support stationary and travelling bumps of localised activity. We pose the model on a ring and study the existence and stability of these patterns in various limits using a combination of analytical and numerical techniques. In a purely deterministic version of the model, posed on a continuum, we construct bumps and travelling waves analytically using standard interface methods from neural field theory...
February 1, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28140350/from-molecules-to-cellular-networks-past-and-future-outlook
#18
Xiaona Fang, Jin Wang
Cellular networks have been the focus of studies in modern systems biology. They are crucial in understanding cell functions and related diseases. We review some past progress in both the theory and experiments, and we also provide several future perspectives for the field.
February 16, 2017: Physical Biology
https://www.readbyqxmd.com/read/28130697/blobel-and-sabatini-s-beautiful-idea-visual-representations-of-the-conception-and-refinement-of-the-signal-hypothesis
#19
Michelle Lynne LaBonte
In 1971, Günter Blobel and David Sabatini proposed a novel and quite speculative schematic model to describe how proteins might reach the proper cellular location. According to their proposal, proteins destined to be secreted from the cell contain a "signal" to direct their release. Despite the fact that Blobel and Sabatini presented their signal hypothesis as a "beautiful idea" not grounded in experimental evidence, they received criticism from other scientists who opposed such speculation. Following the publication of the 1971 model, Blobel persisted in conducting experiments and revising the model to incorporate new data...
January 27, 2017: Journal of the History of Biology
https://www.readbyqxmd.com/read/28124714/clathrin-polymerization-exhibits-high-mechano-geometric-sensitivity
#20
Ehsan Irajizad, Nikhil Walani, Sarah L Veatch, Allen P Liu, Ashutosh Agrawal
How tension modulates cellular transport has become a topic of interest in the recent past. However, the effect of tension on clathrin assembly and vesicle growth remains less understood. Here, we use the classical Helfrich theory to predict the energetic cost that clathrin is required to pay to remodel the membrane at different stages of vesicle formation. Our study reveals that this energetic cost is highly sensitive to not only the tension in the membrane but also to the instantaneous geometry of the membrane during shape evolution...
January 26, 2017: Soft Matter
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