Biomedical subjects

Carole J Proctor

Publications and source records attributed to Carole J Proctor.

9 recordsLinked to original sources

PubMed2006

Tools for the SBML Community.

MOTIVATION: SBML is quickly becoming the standard format to exchange biochemical models. The tools presented in this paper are loosely-coupled, and are intended to be incorporated into SBML aware applications. The rationale for this is to reduce the amount of repeated work carried out within the community and to create tools that offer a greater number of features to the end-user. AVAILABILITY: All tools described are available from http://www.basis.ncl.ac.uk/software and are licensed under GNU General Public License.

Biochemistry↗

PubMed2005

Antipredator vigilance in birds: modelling the 'edge' effect.

Many animals spend a large proportion of their time either foraging for food or watching out for predators (antipredator vigilance). There have been many theoretical and empirical studies investigating the trade-off between these two activities, especially in birds. Previous models of antipredator vigilance assume that all birds within the group spend the same amount of time feeding. However, many empirical studies have shown that individuals on the edge of flocks are more vigilant. Here we describe a vigilance model which investigates the effect of position on the birds' strategies by dividing the feeding area into an inner and outer region. The model examines how various parameters such as food availability and predation risk affect the strategies of individual birds according to whether they are in the inner or outer region. Our model predicts that birds in the outer group are always more vigilant than those in the inner region. Birds in the centre receive a higher payoff in each of the wide range of scenarios that we have considered, and so our model also indicates why dominant birds would choose to feed in the centre of the group; a prediction in accord with several empirical studies.

Algorithms↗

PubMed2005

Modelling the actions of chaperones and their role in ageing.

Many molecular chaperones are also known as heat shock proteins because they are synthesised in increased amounts after brief exposure of cells to elevated temperatures. They have many cellular functions and are involved in the folding of nascent proteins, the re-folding of denatured proteins, the prevention of protein aggregation, and assisting the targeting of proteins for degradation by the proteasome and lysosomes. They also have a role in apoptosis and are involved in modulating signals for immune and inflammatory responses. Stress-induced transcription of heat shock proteins requires the activation of heat shock factor (HSF). Under normal conditions, HSF is bound to heat shock proteins resulting in feedback repression. During stress, cellular proteins undergo denaturation and sequester heat shock proteins bound to HSF, which is then able to become transcriptionally active. The induction of heat shock proteins is impaired with age and there is also a decline in chaperone function. Aberrant/damaged proteins accumulate with age and are implicated in several important age-related conditions (e.g. Alzheimer's disease, Parkinson's disease, and cataract). Therefore, the balance between damaged proteins and available free chaperones may be greatly disturbed during ageing. We have developed a mathematical model to describe the heat shock system. The aim of the model is two-fold: to explore the heat shock system and its implications in ageing; and to demonstrate how to build a model of a biological system using our simulation system (biology of ageing e-science integration and simulation (BASIS)).

Animals↗

PubMed2004

A mathematical model of ageing in yeast.

Budding yeast, Saccharomyces cerevisiae, is commonly used as a system to study cellular ageing. Yeast mother cells are capable of only a limited number of divisions before they undergo senescence, whereas newly formed daughters usually have their replicative age "reset" to zero. Accumulation of extrachromosomal ribosomal DNA circles (ERCs) appears to be an important contributor to ageing in yeast, and we describe a mathematical model that we developed to examine this process. We show that an age-related accumulation of ERCs readily explains the observed features of yeast ageing but that in order to match the experimental survival curves quantitatively, it is necessary that the probability of ERC formation increases with the age of the cell. This implies that some other mechanism(s), in addition to ERC accumulation, must underlie yeast ageing. We also demonstrate that the model can be used to gain insight into how an extra copy of the Sir2 gene might extend lifespan and we show how the model makes novel, testable predictions about patterns of age-specific mortality in yeast populations.

Aging↗

PubMed2003

A communication-based spatial model of antipredator vigilance.

Many animals spend their lives performing two often mutually exclusive tasks: feeding and watching out for predators (anti-predator vigilance). There have been many theoretical and empirical studies investigating this trade-off, especially for birds. An important characteristic of a flock of real birds is the area occupied by the flock. Individuals feeding close together experience increased competition so that the feeding rate decreases. Widely spaced individuals may suffer a loss in vigilance efficiency, since communication between individuals is more difficult, such that the predation risk increases. A vigilance model is developed which allows birds to control their spacing (and so the area of the flock) as well as their vigilance rate. The best strategy for the birds is found under a variety of environmental conditions, under the assumption that each individual acts selfishly to maximize its own fitness.

Animal Communication↗

PubMed2003

Somatic mutations and ageing in silico.

Considerable evidence points to an accumulation of somatic mutations in older cells and organisms but the causal role of mutations in the ageing process is still unclear. In addition to demonstrating that mutations accumulate, it is important to address the question of whether they do so at a sufficient rate and with a dynamic profile that is consistent with them playing a causative role. We describe the development of in silico models that can be used to explore the role of somatic mutations in ageing and which form a part of a growing effort to build predictive mathematical and computer models that can help unravel the complexity of the functional genomics of ageing. Our models address, in particular, how mutations affect populations of dividing cells like human fibroblasts, in which the challenge to the somatic mutation theory is greatest, since selection at the cellular level will tend to suppress the accumulation of mutations.

Aging↗

PubMed2003

Towards an e-biology of ageing: integrating theory and data.

Ageing is a highly complex process; it involves interactions between numerous biochemical and cellular mechanisms that affect many tissues in an organism. Although work on the biology of ageing is now advancing quickly, this inherent complexity means that information remains highly fragmented. We describe how a new web-based modelling initiative is seeking to integrate data and hypotheses from diverse biological sources.

Aging↗

PubMed2003

Modelling cellular senescence as a result of telomere state.

Telomeres in mammalian cells end in large duplex T loops. These loops protect the single-strand overhangs from degradation and/or interactions with signalling proteins. This protection is sometimes referred to as capping. At each cell division, telomeres shorten and there is a general consensus that telomere shortening triggers cell cycle exit. However, the exact mechanism by which telomere shortening causes cell cycle arrest is not known. Mathematical models of telomere shortening have been developed to help us understand the processes involved. Until now most models have assumed that the trigger for cell cycle arrest is the first telomere or a group of telomeres reaching a critically short length. However, there is evidence that cells stop cycling over a wide range of telomere lengths. This suggests that telomere length per se may not in fact be the trigger for cellular senescence. In this paper we develop a model which examines the hypothesis that uncapping of a telomere is the main trigger. By letting the probability of uncapping depend upon telomere length, we show that the hypothesized model provides a good fit to experimental data.

Cell Division↗

PubMed2002

Modelling telomere shortening and the role of oxidative stress.

Extensive evidence supports the idea that progressive telomere loss contributes to the phenomenon of cell replicative senescence, but the mechanisms responsible for telomere loss are still unclear. In addition to the widely recognized end-replication problem, there is evidence that oxidative stress plays a major role in determining the rate of loss of telomeric DNA, and the action of a C-strand-specific exonuclease is also suggested to be important. We describe a mathematical model which examines the different contributions of these mechanisms to telomere loss and its role in triggering cell senescence. The model allows us to make quantitative predictions about the rates of telomere loss resulting from these alternative mechanisms, and their interactions. By varying the key parameters of the model, it is possible to examine the extent to which the different hypotheses are compatible with quantitative and qualitative features of the experimental data. For example, the model predicts that under low levels of oxidative stress, the main mechanisms of telomere shortening are the end-replication problem plus C-strand processing. However, when levels of oxidative stress are higher, as in cell cultures grown under normoxic or hyperoxic conditions, the model predicts that single strand breaks make an important contribution to telomere loss and their inclusion within the model is necessary to explain the data. We suggest that theoretical models of this kind are valuable tools to bridge the gap between the verbal statements of hypotheses and their rigorous experimental test.

Humans↗