Glycolytic reprogramming in cancer cells: PKM2 dimer predominance induced by pulsatile PFK-1 activity.

abstract：:In recent years, by using modern imaging techniques, scientists have found evidence of collaboration between different types of stem cells (SCs), and proposed a bi-compartmental organization of the SC niche. Here we create a class of stochastic models to simulate the dynamics of such a heterogeneous SC niche. We consi...

journal_title：Physical biology

authors： Shahriyari L,Komarova NL

更新日期：2015-07-31 00:00:00

abstract：:Motile biological cells in tissue often display the phenomenon of durotaxis, i.e. they tend to move towards stiffer parts of substrate tissue. The mechanism for this behavior is not completely understood. We consider simplified models for durotaxis based on the classic persistent random walker scheme. We show that eve...

journal_title：Physical biology

authors： Doering CR,Mao X,Sander LM

更新日期：2018-09-11 00:00:00

abstract：:In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. coli in stationary growth conditions from which we infer the ...

journal_title：Physical biology

authors： De Martino D

更新日期：2016-01-29 00:00:00

abstract：:A cluster of neural crest cells (NCCs) may chemotax up a shallow external gradient to which a single cell is unresponsive. To explain this intriguing 'group advantage', we propose a chemo-mechanical model based on the signaling proteins Rac1 and RhoA. We represent each cell as a polygon with nodes connected by elastic...

journal_title：Physical biology

authors： Merchant B,Feng JJ

更新日期：2020-03-10 00:00:00

abstract：:The single-molecule fluorescence technique is becoming a general and mature tool to probe interactions and dynamics of biomolecules with ultra high precision and accuracy. However, nonspecific adsorption of biomolecules to the flow cells remains a major experimental riddle for the study of many complex biological syst...

journal_title：Physical biology

authors： Pan H,Xia Y,Qin M,Cao Y,Wang W

更新日期：2015-06-29 00:00:00

abstract：:Gene-regulation networks contain recurring elementary circuits termed network motifs. It is of interest to understand under which environmental conditions each motif might be selected. To address this, we study one of the most significant network motifs, a three-gene circuit called the coherent feed-forward loop (FFL)...

journal_title：Physical biology

authors： Dekel E,Mangan S,Alon U

更新日期：2005-06-01 00:00:00

abstract：:Cancer may result from localized failure of instructive cues that normally orchestrate cell behaviors toward the patterning needs of the organism. Steady-state gradients of transmembrane voltage (V(mem)) in non-neural cells are instructive, epigenetic signals that regulate pattern formation during embryogenesis and mo...

journal_title：Physical biology

authors： Lobikin M,Chernet B,Lobo D,Levin M

更新日期：2012-12-01 00:00:00

abstract：:Bidirectional cargo transport by molecular motors in cells is a complex phenomenon in which the cargo (usually a vesicle) alternately moves in retrograde and anterograde directions. In this case, teams of oppositely pulling motors (e.g., kinesin and dynein) bind to the cargo, simultaneously, and 'coordinate' their act...

journal_title：Physical biology

authors： Bhat D,Gopalakrishnan M

更新日期：2012-08-01 00:00:00

abstract：:The controlling factors that underlie the growth of tumors have often been hard to identify because of the presence in this system of a large number of intracellular biochemical parameters. Here, we propose a simplifying framework to identify the key physical parameters that govern the early growth of tumors. We model...

journal_title：Physical biology

authors： Remy G,Cluzel P

更新日期：2016-04-04 00:00:00

abstract：:A model of ligand-induced intracellular calcium (Ca2+) responses incorporating phospholipase C (PLC) and protein kinase C (PKC) is developed for the purpose of understanding the mechanisms underlying the observed temporal patterns of intracellular calcium (Ca(i)2+) under sustained agonist stimulation. Some studies hav...

journal_title：Physical biology

authors： Kang M,Othmer HG

更新日期：2007-12-13 00:00:00

abstract：:Successful biological development via spatial regulation of cell differentiation relies on the action of multiple signaling molecules that are known as morphogens. It is now well-established that signaling molecules create non-uniform concentration profiles, morphogen gradients, that activate different genes, leading ...

journal_title：Physical biology

authors： Teimouri H,Kolomeisky AB

更新日期：2015-04-17 00:00:00

abstract：:Recently, major progress has been made to develop computational models to predict and explain the mechanisms and behaviors of gene regulation. Here, we review progress on how these mechanisms and behaviors have been interpreted with analog models, where cell properties continuously modulate transcription, and digital ...

journal_title：Physical biology

authors： Munsky B,Neuert G

更新日期：2015-06-18 00:00:00

abstract：:In addition to serving as structural elements and as tracks for motor proteins, microtubules use chemical energy derived from the hydrolysis of GTP to generate forces when growing and shrinking. These forces are used to push or pull on organelles such as chromosomes and the mitotic spindle. If an array of microtubules...

journal_title：Physical biology

authors： Howard J

更新日期：2006-02-28 00:00:00

abstract：:The asymmetric cell division cycle in Caulobacter crescentus is controlled by an elaborate molecular mechanism governing the production, activation and spatial localization of a host of interacting proteins. In previous work, we proposed a deterministic mathematical model for the spatiotemporal dynamics of six major r...

journal_title：Physical biology

authors： Li F,Subramanian K,Chen M,Tyson JJ,Cao Y

更新日期：2016-06-25 00:00:00

abstract：:The morphological symmetry of the division process of Escherichia coli is well-known. Recent studies verified that, in optimal growth conditions, most divisions are symmetric, although there are exceptions. We investigate whether such morphological asymmetries in division introduce functional asymmetries between siste...

journal_title：Physical biology

authors： Gupta A,Lloyd-Price J,Oliveira SM,Yli-Harja O,Muthukrishnan AB,Ribeiro AS

更新日期：2014-11-10 00:00:00

abstract：:The importance of the tumor microenvironment in cancer progression is undisputed, yet the significance of biophysical forces in the microenvironment remains poorly understood. Interstitial fluid flow is a nearly ubiquitous and physiologically relevant biophysical force that is elevated in tumors because of tumor-assoc...

journal_title：Physical biology

authors： Shieh AC,Swartz MA

更新日期：2011-02-01 00:00:00

abstract：:Gravity or ultracentrifuge settling of colloidal particles and macromolecules usually involves several disperse species, either because natural and industrial colloids display a large size polydispersity, or because additives are put in on purpose to allow for density-based fractionation of the suspension. Such 'macro...

journal_title：Physical biology

authors： Piazza R,Buzzaccaro S,Secchi E,Parola A

更新日期：2013-08-01 00:00:00

abstract：: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. ...

journal_title：Physical biology

authors： Fang X,Wang J

更新日期：2017-02-16 00:00:00

abstract：:A central question in eukaryotic cell biology asks, during cell division, how is the growth and distribution of organelles regulated to ensure each daughter cell receives an appropriate amount. For vacuoles in budding yeast, there are well described organelle-to-cell size scaling trends as well as inheritance mechanis...

journal_title：Physical biology

authors： Chadwick WL,Biswas SK,Bianco S,Chan YM

更新日期：2020-10-09 00:00:00

abstract：:We present a new particle tracking software algorithm designed to accurately track the motion of low-contrast particles against a background with large variations in light levels. The method is based on a polynomial fit of the intensity around each feature point, weighted by a Gaussian function of the distance from th...

journal_title：Physical biology

authors： Rogers SS,Waigh TA,Zhao X,Lu JR

更新日期：2007-10-09 00:00:00

abstract：:The one-cell amphibian embryo is modeled as a rigid spherical shell containing equal volumes of two immiscible fluids with different densities and viscosities and a surface tension between them. The fluids represent denser yolk in the bottom hemisphere and clearer cytoplasm and the germinal vesicle in the top hemisphe...

journal_title：Physical biology

authors： Nouri C,Luppes R,Veldman AE,Tuszynski JA,Gordon R

更新日期：2008-04-10 00:00:00

abstract：:A two-dimensional model is proposed for intercellular calcium (Ca(2 +)) waves with Ca(2 +)-induced IP(3) regeneration and the diffusion of IP(3) through gap junctions. Many experimental observations in glial cells, i.e. responding to local mechanical stimulation, glutamate application, mechanical stimulation followed ...

journal_title：Physical biology

authors： Wei F,Shuai J

更新日期：2011-04-01 00:00:00

abstract：:A vast literature has explored the genetic interactions among the cellular components regulating gene expression in many organisms. Early on, in the absence of any biochemical definition, regulatory modules were conceived using the strict formalism of genetics to designate the modifiers of phenotype as either cis- or ...

journal_title：Physical biology

authors： Levens D,Benham CJ

更新日期：2011-06-01 00:00:00

abstract：:The DFT:B3LYP (6-31G** basis set) method, including the hyperfine and spin-orbit couplings (HFC and SOC, respectively), is used to study the separation of two complementary trinucleotide sequences, (dC-dG-dA)-(dG-dC-dT), upon the action of two Mg(2+) cofactors (a simplified model). The computations reveal a crossing o...

journal_title：Physical biology

authors： Tulub AA,Stefanov VE

更新日期：2015-12-10 00:00:00

abstract：:Monolayer expansion has generated great interest as a model system to study collective cell migration. During such an expansion the culture front often develops 'fingers', which we have recently modeled using a proposed feedback between the curvature of the monolayer's leading edge and the outward motility of the edge...

journal_title：Physical biology

authors： Tarle V,Gauquelin E,Vedula SRK,D'Alessandro J,Lim CT,Ladoux B,Gov NS

更新日期：2017-05-03 00:00:00

abstract：:To address the issue of extracting useful information from large data-set of large scale networks of neurons, we propose an algorithm that involves both algebraic-statistical and topological tools. We investigate the electrical behavior of in vitro cortical assemblies both during spontaneous and stimulus-evoked activi...

journal_title：Physical biology

authors： Pirino V,Riccomagno E,Martinoia S,Massobrio P

更新日期：2015-01-05 00:00:00

abstract：:How do the cells in our body reconfigure their shape to achieve complex tasks like migration and mitosis, yet maintain their shape in response to forces exerted by, for instance, blood flow and muscle action? Cell shape control is defined by a delicate mechanical balance between active force generation and passive mat...

journal_title：Physical biology

authors： Mulla Y,Aufderhorst-Roberts A,Koenderink GH

更新日期：2018-04-30 00:00:00

abstract：:Protein-protein interactions are central to biology and, in this 'post-genomic era', prediction of these interactions has become the goal of many computational efforts. Close inspection of even relatively simple biological regulatory circuitry reveals multiple levels of control of the contributing protein interactions...

journal_title：Physical biology

authors： Beckett D

更新日期：2005-06-01 00:00:00

abstract：:The mechanical behavior of living murine T-lymphocytes was assessed by atomic force microscopy (AFM). A robust experimental procedure was developed to overcome some features of lymphocytes, in particular their spherical shape and non-adherent character. The procedure included the immobilization of the lymphocytes on a...

journal_title：Physical biology

authors： Daza R,Cruces J,Arroyo-Hernández M,Marí-Buyé N,De la Fuente M,Plaza GR,Elices M,Pérez-Rigueiro J,Guinea GV

更新日期：2015-03-19 00:00:00

abstract：:When the author arrived in Berkeley, in the mid 1970s, to study Biophysics he soon felt as if he was engaging himself in a somewhat marginal activity. Biology was then entering another of its cyclical periods of annotation that was to culminate with the human genome project. Two decades later, however, at the end of t...

journal_title：Physical biology

authors： Bustamante CJ

更新日期：2014-10-08 00:00:00