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D C Krakauer

Publications and source records attributed to D C Krakauer.

26 records · Page 2Linked to original sources
PubMed1998

Prion's progress: patterns and rates of molecular evolution in relation to spongiform disease.

Modification of the cellular prion protein has been correlated with the acquisition of several neurodegenerative diseases, including kuru, scrapie, bovine spongiform encephalopathy (BSE), and Creutzfeldt-Jakob disease (CJD). Sequence conservation and amino acid identity are known to influence the efficacy of interspecific transmission. We analyzed patterns of interspecific genetic variation with a view toward identifying features related to disease transmission. The reconstructed gene trees and amino acid tree were compared with the species tree, and all discordances observed were related to the species barrier of disease transmission. The rates of synonymous substitution, nonsynonymous substitution, and nucleotide content were determined for the protein-coding gene. Substitutions implicated in each of the prion diseases were found to occur in regions of the protein that are least variable across all species-opposite to the pattern of variability expected from interaction with an infectious pathogen. Amino acid residues related to the species barrier form a single cluster associated with the first alpha-helical domain of the protein. Residues related to sporadic and hereditary human prion disease form two separate clusters, associated with the second and third alpha-helical domains. Taken together, these results are consistent with the view that prion diseases arise from accidents in protein folding, rather than infection with an undiscovered virus-like particle. We speculate that the differences in disease phenotype between transmissable and hereditary forms could result from interactions between different parts of the protein during propagation.

Animals↗
PubMed1998

Effect of immune activation on the dynamics of human immunodeficiency virus replication and on the distribution of viral quasispecies.

Virus replication in a human immunodeficiency virus (HIV)-infected individual, as determined by the steady-state level of plasma viremia, reflects a complex balance of viral and host factors. We have previously demonstrated that immunization of HIV-infected individuals with the common recall antigen, tetanus toxoid, disrupts this steady state, resulting in transient bursts of plasma viremia after immunization. The present study defines the viral genetic basis for the transient bursts in viremia after immune activation. Tetanus immunization was associated with dramatic and generally reversible shifts in the composition of plasma viral quasispecies. The viral bursts in most cases reflected a nonspecific increase in viral replication secondary to an expanded pool of susceptible CD4(+) T cells. An exception to this was in a patient who harbored viruses of differing tropisms (syncytium inducing and non-syncytium inducing [NSI]). In this situation, immunization appeared to select for the replication of NSI viruses. In one of three patients, the data suggested that immune activation resulted in the appearance in plasma of virus induced from latently infected cells. These findings illustrate certain mechanisms whereby antigenic stimulation may influence the dynamics of HIV replication, including the relative expression of different viral variants.

Amino Acid Sequence↗
PubMed1997

The evolution of virus-induced apoptosis.

Viruses from several different families are able to exploit their host's cell death programmes so as to maximize viral fitness. Consideration of the evolution of such strategies has lead to the suggestion that the virus should inhibit apoptosis, in order to prolong the life of the cell and thereby maximize the number of progeny virions. The host, on the other hand, should stimulate apoptosis thereby inhibiting viral growth and blocking viral spread. For example, the function of the latent membrane protein I (LMPI) of the Epstein-Barr virus and the bcl-2 homologue gene A179L of African swine fever virus is to inhibit apoptosis. However, in other cases it is the virus that stimulates cell death or the host that benefits from inhibiting apoptosis, such as in fatal alphavirus encephalitis. This has been explained by assuming that virus-induced apoptosis in non-regenerating cells would be detrimental to the host. We present a mathematical framework for understanding virus-induced apoptosis which accounts for these two opposite solutions to virus infection with respect to the mode of virus replication and the life cycle of the target cell.

Apoptosis↗
PubMed1996

Selection by somatic signals: the advertisement of phenotypic state through costly intercellular signals.

We develop a model of intercellular signalling, to explore the possibility that the signals exchanged between cells within a body may be subject to many of the same evolutionary pressures as signals exchanged between individuals whose genetic interests conflict. Evolutionary signalling theory maintains that signals, to be reliable indicators of need, intention or quality must be more costly than would be required merely to transmit a message. Cost guarantees that poor quality individuals are less able to display the high magnitude signals produced by the higher quality individuals. Receivers have been favoured by natural selection to attend only to the costliest signals, and thereby acquire honest information from the signaller. Hence the extravagant, costly ornamentation found among males of many species, ensures that females can accurately choose among them on the basis of their qualities. However, because somatic cells are normally perfectly genetically related, and are often denied access to the germ line, there will be minimal genetic conflicts of interest. This appears to imply that reliable intercellular signals should be produced without the need for cost to ensure their reliability. Nevertheless, we show that whenever cells vary in their phenotypic qualities in ways relevant to the fitness of the body, and given that there exists a class of cell that remains "ignorant' of its phenotypic state, costly intercellular signalling will evolve as a form of quality control. Specifically, we show that given variation in the cell population, signal cost will aid the identification and removal of cells that over-represent their true phenotypic state, and which therefore could lower fitness. Cells that under-represent their state are simply outcompeted by other cells. The cells of a body employ signals in a variety of intercellular interactions, including the development of the nervous system, the formation of neuromuscular junctions, and during the establishment of the immune repetoire. In each of these cases, cells may employ costly signals to advertise their phenotypic quality to other cells, and we review the evidence in support of this hypothesis: in effect, the cells may possess a molecular counterpart to the peacock's tail.

Animals↗
PubMed1995

The evolution of exploitation and honesty in animal communication: a model using artificial neural networks.

Conflicts of interest arise between signaller and receiver in most kinds of biological communication. Some authors have argued that this conflict is likely to give rise to deceit and exploitation, as receivers lag behind in the coevolutionary 'arms race' with signallers. Others have argued that such manipulation is likely to be short-lived and that receivers can avoid being deceived by paying attention to signals that are costly and hence 'unfakeable.' These two views have been hard to reconcile. Here, we present results from simulations of signal evolution using artificial neural networks, which demonstrate that honesty can coexist with a degree of exploitation. Signal cost ensures that receivers are able to obtain some honest information, but is unable to prevent exploitative signalling strategies from gaining short-term benefits. Although any one receiver bias that is open to exploitation will subsist for only a short period of time once signallers begin to take advantage of it, new preferences of this kind are constantly regenerated through selection and random drift. Hidden preferences and sensory exploitation are thus likely to have an enduring influence on the evolution of honest, costly signals. At the same time, honesty and cost are prerequisites for the evolution of exploitation. When signalling is cost-free, selection cannot act to maintain honesty, and receivers rapidly evolve to ignore signals. This leads to a reduction in the extent of hidden preference, and a consequent loss of potential for exploitation.

Animal Communication↗
PubMedDate not supplied

Genetic instability and the evolution of angiogenic tumor cell lines (review).

Advanced tumor growth requires the formation of new blood vessels (angiogenesis). Whether new blood vessels are formed or not depends on a balance between angiogenesis inhibitors and promoters. Host tissue, as well as tumor cells, express inhibitory factors preventing angiogenesis. During cancer progression, tumor cell lines evolve which produce factors promoting the angiogenic switch. We use mathematical models in order to examine the conditions required for angiogenic cell lines to emerge and hence for the disease to progress. We find that genetic instability, defined as a much elevated mutation rate of somatic cells, is required for the emergence of angiogenic tumor cells. This is because a high mutation rate ensures that within a short period of time, a sufficiently high number of angiogenic cells are generated. This founder population of mutant cells is large enough to overcome the inhibitory factors produced by the tissue thereby inducing the angiogenic switch through the production of promoters. In the absence of genetic instability, angiogenic cells cannot fix, even if the relevant mutations are generated at low levels in the tumor cell population. This is because angiogenic promoters will not be sufficiently abundant to counter the influence of inhibitory factors. In this context, the inhibition of angiogenesis can be viewed as a host defense ensuring that the tumor need be genetically unstable if it is to grow and progress beyond a certain size limit. We observe that genetic instability is of value early in tumorigenesis but becomes a liability later. This is because instability decreases the fitness of the angiogenic tumor once it has become established.

Animals↗