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 against since cheaters could reap the benefits without paying the cost. We have investigated the impact of niche specificity on tumour evolution using an individual based model of breast tumour growth, in which the carrying capacity of each cell consists of two components: an intrinsic, subclone-specific part and a contribution from all neighbouring cells. Analysis of the model shows that the ability of a mutant to invade a resident population depends strongly on the specificity. When specificity is low selection is mostly on growth rate, while high specificity shifts selection towards increased carrying capacity. Further, we show that the long-term evolution of the system can be predicted using adaptive dynamics. By comparing the results from a spatially structured versus well-mixed population we show that spatial structure restores selection for carrying capacity even at zero specificity, which poses a solution to the niche construction dilemma. Lastly, we show that an expanding population exhibits spatially variable selection pressure, where cells at the leading edge exhibit higher growth rate and lower carrying capacity than those at the centre of the tumour.
journal_name
Phys Bioljournal_title
Physical biologyauthors
Gerlee P,Anderson ARdoi
10.1088/1478-3975/12/5/056001subject
Has Abstractpub_date
2015-08-12 00:00:00pages
056001issue
5eissn
1478-3967issn
1478-3975journal_volume
12pub_type
杂志文章相关文献
PHYSICAL BIOLOGY文献大全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::Sequence-dependent DNA flexibility is an important structural property originating from the DNA 3D structure. In this paper, we investigate the DNA flexibility of the budding yeast (S. Cerevisiae) replication origins on a genome-wide scale using flexibility parameters from two different models, the trinucleotide and t...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/5/3/036012
更新日期:2008-09-29 00:00:00
abstract::The majority of chronic infections are caused by biofilms, which have higher levels of antibiotic resistance than planktonic growth. Violet-blue 405 nm light has recently emerged as a novel bactericide, but limited studies have been conducted on its effectiveness against biofilms. We found that in response to 405 nm l...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/ab759a
更新日期:2020-03-04 00:00:00
abstract::By combining optical tweezers-assisted dynamic force spectroscopy experiments with fluorescence activated cell sorting (FACS), we demonstrate a new approach to reducing the data variance in measuring receptor-ligand interactions on a single molecule level by ensuring similar coating densities. Therefore, the carboxyfl...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/4/046004
更新日期:2013-08-01 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::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
pub_type: 杂志文章
doi:10.1088/1478-3975/12/2/026006
更新日期:2015-04-17 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
pub_type: 杂志文章
doi:10.1088/1478-3975/9/6/065002
更新日期:2012-12-01 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::The translocation of molecules across cellular membranes or through synthetic nanopores is strongly affected by thermal fluctuations. In this work we study how the dynamics of a polymer in a noisy environment changes when the translocation process is driven by an oscillating electric field. An improved version of the ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/7/3/034001
更新日期:2010-08-04 00:00:00
abstract::Epigenetic mechanisms of silencing via heritable chromatin modifications play a major role in gene regulation and cell fate specification. We consider a model of epigenetic chromatin silencing in budding yeast and study the bifurcation diagram and characterize the bistable and the monostable regimes. The main focus of...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/3/036005
更新日期:2013-06-01 00:00:00
abstract::Oscillations play an important physiological role in a variety of biological systems. For example, respiration and carbohydrate synthesis are coupled to the circadian clock in cyanobacteria (Ishiura et al 1998 Science 281 1519) and ultradian oscillations with time periods of a few hours have been observed in immune re...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/6/3/036009
更新日期:2009-05-21 00:00:00
abstract::Mucociliary clearance and cough are the two main natural mucus draining methods in the bronchial tree. If they are affected by a pathology, they can become insufficient or even ineffective, then therapeutic draining of mucus plays a critical role to keep mucus levels in the lungs acceptable. The manipulations of physi...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/8/5/056006
更新日期:2011-10-01 00:00:00
abstract::Engineering artificial cells to mimic one or multiple fundamental cell biological functions is an emerging area of synthetic biology. Reconstituting functional modules from biological components in vitro is a challenging yet an important essence of bottom-up synthetic biology. Here we describe the concept of building ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/aa9768
更新日期:2017-12-06 00:00:00
abstract::Nucleosomes, which contain DNA and proteins, are the basic unit of eukaryotic chromatins. Polymers such as DNA and proteins are dynamic, and their conformational changes can lead to functional changes. Periodic dinucleotide patterns exist in nucleosomal DNA chains and play an important role in the nucleosome structure...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/8/6/066004
更新日期:2011-12-01 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::Neurofilaments are transported along axons stochastically in a stop-and-go manner, cycling between brief bouts of rapid movement and pauses that can vary from seconds to hours in length. Presently the only way to analyze neurofilament pausing experimentally on both long and short time scales is the pulse-escape method...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/11/2/026001
更新日期:2014-04-01 00:00:00
abstract::Thrombosis accounts for 80% of deaths in patients with diabetes mellitus. Diabetic patients demonstrate tortuous microvessels and larger than normal platelets. Large platelets are associated with increased platelet activation and thrombosis, but the physical effects of large platelets in the microscale processes of th...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/5/056003
更新日期:2013-10-01 00:00:00
abstract::Based on the experimental evidence that translating ribosomes stabilize the mRNAs, we introduce and study a theoretical model for the dynamic shielding of mRNA by ribosomes. We present an improved fitting of published decay assay data in E. coli and show that only one third of the decay patterns are exponential. Our n...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/4/046008
更新日期:2013-08-01 00:00:00
abstract::How cell collectives move and deposit subunits within a developing embryo is a question of outstanding interest. In many cases, a chemotactic mechanism is employed, where cells move up or down a previously generated attractive or repulsive gradient of signalling molecules. Recent studies revealed the existence of syst...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/8/4/045004
更新日期:2011-08-01 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::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...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/5/056011
更新日期:2013-10-01 00:00:00
abstract::A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms. The fact that different viruses adopt similar structural forms is an indication o...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/7/4/045001
更新日期:2010-12-09 00:00:00
abstract::Intermolecular interactions became an inherent part of the structure-function paradigm. Therefore, the generalized concept of protein stability and interactions should consider the balance of stabilizing forces working in different types of intermolecular interactions. We consider here two 'extremes' of protein intera...
journal_title:Physical biology
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/8/3/035002
更新日期:2011-06-01 00:00:00
abstract::Shelter-in-place and other confinement strategies implemented in the current COVID-19 pandemic have created stratified patterns of contacts between people: close contacts within households and more distant contacts between the households. The epidemic transmission dynamics is significantly modified as a consequence. W...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/abb209
更新日期:2020-10-21 00:00:00
abstract::We analyze theoretically the effects of excluded-volume interactions between motors on the dynamics of a cargo driven by multiple motors. The model considered shares much in common with others recently proposed in the literature, with the addition of direct interaction between motors and motor back steps. The cargo is...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/7/4/046009
更新日期:2010-11-22 00:00:00
abstract::Directed cell migration often involves at least two types of cell motility that include multicellular streaming and chain migration. However, what is unclear is how cell contact dynamics and the distinct microenvironments through which cells travel influence the selection of one migratory mode or the other. The embryo...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/3/035003
更新日期:2013-06-01 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
pub_type: 杂志文章
doi:10.1088/1478-3975/3/1/006
更新日期:2006-02-28 00:00:00
abstract::Tumor metastasis involves a progressive loss of tissue architecture and dissolution of structural boundaries between the epithelium and connective tissue. The basement membrane (BM), a specialized network of extracellular matrix proteins forms a barrier that physically restricts pre-invasive lesions such that they rem...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/9/6/065003
更新日期:2012-12-01 00:00:00
abstract::Efficient nucleotide import is critical to fuel the reverse DNA synthesis that takes place within the HIV-1 capsid. However, the mechanism by which the HIV-1 capsid imports nucleotides is presently unclear. In this work, we carry out a series of Brownian diffusion simulations to elucidate the nucleotide import process...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/abbf32
更新日期:2020-10-07 00:00:00
abstract::We present a simple two-state model to understand the size-dependent endocytosis of nanoparticles. Using this model, we elucidate the relevant energy terms required to understand the size-dependent uptake mechanism and verify it by correctly predicting the behavior at large and small particle sizes. In the absence of ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/8/4/046002
更新日期:2011-08-01 00:00:00