Abstract:
:Messenger RNA (mRNA) encodes a sequence of amino acids by using codons. For most amino acids, there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for changing the ribosome speed while keeping the amino acid sequence and hence the resulting protein. Recently, it has been noticed that the choice of the synonymous codon, via the resulting distribution of slow- and fast-translated codons, affects not only on the average speed of one ribosome translating the mRNA but also might have an effect on nearby ribosomes by affecting the appearance of 'traffic jams' where multiple ribosomes collide and form queues. To test this 'context effect' further, we here investigate the effect of the sequence of synonymous codons on the ribosome traffic by using a ribosome traffic model with codon-dependent rates, estimated from experiments. We compare the ribosome traffic on wild-type (WT) sequences and sequences where the synonymous codons were swapped randomly. By simulating translation of 87 genes, we demonstrate that the WT sequences, especially those with a high bias in codon usage, tend to have the ability to reduce ribosome collisions, hence optimizing the cellular investment in the translation apparatus. The magnitude of such reduction of the translation time might have a significant impact on the cellular growth rate and thereby have importance for the survival of the species.
journal_name
Phys Bioljournal_title
Physical biologyauthors
Mitarai N,Pedersen Sdoi
10.1088/1478-3975/10/5/056011subject
Has Abstractpub_date
2013-10-01 00:00:00pages
056011issue
5eissn
1478-3967issn
1478-3975journal_volume
10pub_type
杂志文章相关文献
PHYSICAL BIOLOGY文献大全abstract::In many bacterial species, the protein FtsZ forms a cytoskeletal ring that marks the future division site and scaffolds the division machinery. In rod-shaped bacteria, most frequently membrane-attached FtsZ rings or ring fragments are reported and occasionally helices. By contrast, axial FtsZ clusters have never been ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/9/1/016009
更新日期:2012-02-01 00:00:00
abstract::The tripartite synapse denotes the junction of a pre- and postsynaptic neuron modulated by a synaptic astrocyte. Enhanced transmission probability and frequency of the postsynaptic current-events are among the significant effects of the astrocyte on the synapse as experimentally characterized by several groups. In thi...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/4/1/001
更新日期:2007-01-09 00:00:00
abstract::Based on recent experimental data, we design a model for neuronal membrane potentials that incorporates the influence of the surrounding glia (dressed neurons). A neurotransmitter released into the synaptic cleft triggers a Ca(2+) response in nearby glial cells that spreads as a Ca(2+) wave and interacts with other sy...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3967/1/1/004
更新日期:2004-06-01 00:00:00
abstract::Recent advances in clinical medicine have elucidated two significantly different subtypes of glioblastoma which carry very different prognoses, both defined by mutations in isocitrate dehydrogenase-1 (IDH-1). The mechanistic consequences of this mutation have not yet been fully clarified, with conflicting opinions exi...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/8/1/015016
更新日期:2011-02-01 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
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/aa5b6a
更新日期:2017-02-16 00:00:00
abstract::We propose a reaction model for the palytoxin-sodium-potassium (PTX-Na(+)/K(+)) pump complex. The model, which is similar to the Albers-Post model for Na(+)/K(+)-ATPase, is used to elucidate the effect of PTX on Na(+)/K(+)-ATPase during the enzyme interactions with Na(+) and/or K(+) ions. Conformational substates and ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/5/3/036005
更新日期:2008-07-29 00:00:00
abstract::A DNA triplex is formed through binding of a third strand to the major groove of a duplex. Due to the high charge density of a DNA triplex, metal ions are critical for its stability. We recently developed the tightly bound ion (TBI) model for ion-nucleic acids interactions. The model accounts for the potential correla...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/8/6/066006
更新日期:2011-12-01 00:00:00
abstract::The maintenance of tissue integrity is essential for the life of multicellular organisms. Healing of a skin wound is a paradigm for how various cell types localize and repair tissue perturbations in an orchestrated fashion. To investigate biophysical mechanisms associated with wound localization, we focus on a model s...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/aa6b67
更新日期:2017-06-28 00:00:00
abstract::Cancer cells are known to modify their micro-environment such that it can sustain a larger population, or, in ecological terms, they construct a niche which increases the carrying capacity of the population. It has however been argued that niche construction, which benefits all cells in the tumour, would be selected a...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/12/5/056001
更新日期:2015-08-12 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
pub_type: 杂志文章
doi:10.1088/1478-3975/ab71f1
更新日期:2020-03-10 00:00:00
abstract::The spatial patterning of three cell fates in a row of competent cells is exemplified by vulva development in the nematode Caenorhabditis elegans. The intercellular signaling network that underlies fate specification is well understood, yet quantitative aspects remain to be elucidated. Quantitative models of the netwo...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/9/4/045001
更新日期:2012-08-01 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
pub_type: 杂志文章
doi:10.1088/1478-3975/4/4/009
更新日期:2007-12-13 00:00:00
abstract::Several viruses exploit clathrin-mediated endocytosis to gain entry into host cells. This process is also used extensively in biomedical applications to deliver nanoparticles (NPs) to diseased cells. The internalization of these nano-objects is controlled by the assembly of a clathrin-containing protein coat on the cy...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/13/1/016005
更新日期:2016-02-12 00:00:00
abstract::Staphylococcus aureus is an important pathogen, giving rise to antimicrobial resistance in cell strains such as Methicillin Resistant S. aureus (MRSA). Here we report an image analysis framework for automated detection and image segmentation of cells in S. aureus cell clusters, and explicit identification of their cel...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/13/5/055002
更新日期:2016-10-17 00:00:00
abstract::Self-organization processes in multicellular aggregates of bacteria and amoebae offer fascinating insights into the evolution of cooperation and differentiation of cells. During myxobacterial development a variety of spatio-temporal patterns emerges such as counterpropagating waves of cell density that are known as ri...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/3/2/006
更新日期:2006-06-23 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
pub_type: 杂志文章
doi:10.1088/1478-3975/4/3/008
更新日期:2007-10-09 00:00:00
abstract::Modeling the spatiotemporal dynamics of biochemical reaction systems at single-molecule resolution has become feasible with the increase of computing power and is applied especially to cellular signal transduction. For an association reaction the two molecules have to be in contact. Hence, a physically faithful model ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/4/046005
更新日期:2013-08-01 00:00:00
abstract::The glycolytic enzyme pyruvate kinase M2 (PKM2) exists in both catalytically inactive dimeric and active tetrameric forms. In cancer cells, PKM2 dimer predominance contributes to tumor growth by triggering glycolytic reprogramming. However, the mechanism that promotes PKM2 dimer predominance over tetramer in cancer ce...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/ab3f5a
更新日期:2019-09-18 00:00:00
abstract::Increasing numbers of physicists engage in research activities that address biological questions from physics perspectives or strive to develop physics insights from active biological processes. The on-going development and success of such activities morph our ways of thinking about what it is to 'do biophysics' and a...
journal_title:Physical biology
pub_type: 社论
doi:10.1088/1478-3975/aaca0a
更新日期:2018-07-06 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
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/8/3/035011
更新日期:2011-06-01 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
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/8/1/015012
更新日期:2011-02-01 00:00:00
abstract::Cells moving on a two dimensional substrate generate motion by polymerizing actin filament networks inside a flat membrane protrusion. New filaments are generated by branching off existing ones, giving rise to branched network structures. We investigate the force-extension relation of branched filaments, grafted on an...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/12/4/046007
更新日期:2015-06-04 00:00:00
abstract::Gene expression is an intrinsically noisy process, typically, producing mRNAs and proteins in bursts. An important description of such stochastic processes can be done in terms of the mean first passage time (MFPT), i.e., the time taken by mRNAs/proteins to reach a particular threshold. We study the role of burstiness...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/13/3/036004
更新日期:2016-05-20 00:00:00
abstract::Cell signaling is achieved predominantly by reversible phosphorylation-dephosphorylation reaction cascades. Up until now, circuits conferring adaptation have all required the presence of a cascade with some type of closed topology: negative-feedback loop with a buffering node, or incoherent feed-forward loop with a pr...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/8/4/046005
更新日期:2011-08-01 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
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/12/4/045004
更新日期:2015-06-18 00:00:00
abstract::We propose a three-dimensional mechanical model of embryonic tissue dynamics. Mechanically coupled adherent cells are represented as particles interconnected with elastic beams which can exert non-central forces and torques. Tissue plasticity is modeled by a stochastic process consisting of a connectivity change (addi...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/12/1/016005
更新日期:2014-12-15 00:00:00
abstract::When motile cells come into contact with one another their motion is often considerably altered. In a process termed contact inhibition of locomotion (CIL) cells reshape and redirect their movement as a result of cell-cell contact. Here we describe a mathematical model that demonstrates that CIL alone is sufficient to...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/4/046002
更新日期:2013-08-01 00:00:00
abstract::The detection of gravity plays a fundamental role during the growth and evolution of plants. Although progress has been made in our understanding of the molecular, cellular and physical mechanisms involved in the gravity detection, a coherent scenario consistent with all the observations is still lacking. In this spec...
journal_title:Physical biology
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/aa6876
更新日期:2017-05-23 00:00:00
abstract::This comment argues against the view that cancer cells produce less entropy than normal cells as stated in a recent paper by Marín and Sabater. The basic principle of estimation of entropy production rate in a living cell is discussed, emphasizing the fact that entropy production depends on both the amount of heat exc...
journal_title:Physical biology
pub_type: 评论,杂志文章
doi:10.1088/1478-3975/aa8eab
更新日期:2018-02-08 00:00:00
abstract::How interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image an...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/abd0db
更新日期:2020-12-04 00:00:00