Quantification system for the viral dynamics of a highly pathogenic simian/human immunodeficiency virus based on an in vitro experiment and a mathematical model

<p>Abstract</p> <p>Background</p> <p>Developing a quantitative understanding of viral kinetics is useful for determining the pathogenesis and transmissibility of the virus, predicting the course of disease, and evaluating the effects of antiviral therapy. The availability of data in clinical, animal, and cell culture studies, however, has been quite limited. Many studies of virus infection kinetics have been based solely on measures of total or infectious virus count. Here, we introduce a new mathematical model which tracks both infectious and total viral load, as well as the fraction of infected and uninfected cells within a cell culture, and apply it to analyze time-course data of an SHIV infection <it>in vitro</it>.</p> <p>Results</p> <p>We infected HSC-F cells with SHIV-KS661 and measured the concentration of Nef<it>-</it>negative (target) and Nef<it>-</it>positive (infected) HSC-F cells, the total viral load, and the infectious viral load daily for nine days. The experiments were repeated at four different MOIs, and the model was fitted to the full dataset simultaneously. Our analysis allowed us to extract an infected cell half-life of 14.1 h, a half-life of SHIV-KS661 infectiousness of 17.9 h, a virus burst size of 22.1 thousand RNA copies or 0.19 TCID₅₀, and a basic reproductive number of 62.8. Furthermore, we calculated that SHIV-KS661 virus-infected cells produce at least 1 infectious virion for every 350 virions produced.</p> <p>Conclusions</p> <p>Our method, combining <it>in vitro </it>experiments and a mathematical model, provides detailed quantitative insights into the kinetics of the SHIV infection which could be used to significantly improve the understanding of SHIV and HIV-1 pathogenesis. The method could also be applied to other viral infections and used to improve the <it>in vitro </it>determination of the effect and efficacy of antiviral compounds.</p

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Response surface methods of fitting stochastic biological models : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Statistics at Massey University

PLEASE NOTE Page ii is missing from the original copyResponse surface methods are discussed, with emphasis on the particular experimentation problems encountered in their use. A brief outline of simulation and modelling is given. This includes an indication of the role of randomness. Two specific uses of computer simulation of biological phenomena are considered. The first is fitting growth curves to some cell growth data. This was done largely to develop techniques. The second and more significant use is in fitting stochastic selection values to some genotypic frequency data. To date, only deterministic estimates have been found from this data. Attention is given to the careful design of simulation experiments, in order to reduce the number of simulation runs needed. Response surface methods were used and proved to be efficient experimentation techniques

Stem cell proliferation and differentiation: a multitype branching process model

The body contains many cellular systems that require the continuous production of new, fully functional, differentiated cells to replace cells lacking or having limited self-renewal capabilities that die or are damaged during the lifetime of an individual. Such systems include the epidermis, the epithelial lining of the gut, and the blood. For example, erythrocytes (red blood cells) lack nuclei and thus are incapable of self-replication. They have a life span in the circulation of about 120 days. Mature granulocytes, which also lack proliferative capacity, have a much shorter life span - typically 12 hours, though this may be reduced to only two or three hours in times of serious tissue infection. Perhaps a more familiar example is the outermost layer of the skin. This layer is composed of fully mature, dead epidermal cells that must be replaced by the descendants of stem cells lodged in lower layers of the epidermis (cf. Alberts et al. , 1983). In total, to supply the normal steady-state demands of cells, an average human must produce approximately 3. 7 x 1011 cells a day throughout life (Dexter and Spooncer, 1987). Common to each of these cellular systems is a primitive (undifferentiated) stem cell which replenishes cells through the production of offspring, some of which proliferate and gradually differentiate until mature, fully functional cells are produced

Kinetics of Influenza A Virus Infection in Humans

Currently, little is known about the viral kinetics of influenza A during infection within an individual. We utilize a series of mathematical models of increasing complexity, which incorporate target cell limitation and the innate interferon response, to examine influenza A virus kinetics in the upper respiratory tracts of experimentally infected adults. The models were fit to data from an experimental H1N1 influenza A/Hong Kong/123/77 infection and suggest that it is important to include the eclipse phase of the viral life cycle in viral dynamic models. Doing so, we estimate that after a delay of ∼6 h, infected cells begin producing influenza virus and continue to do so for ∼5 h. The average lifetime of infected cells is ∼11 h, and the half-life of free infectious virus is ∼3 h. We calculated the basic reproductive number, R(0), which indicated that a single infected cell could produce ∼22 new productive infections. This suggests that antiviral treatments have a large hurdle to overcome in moderating symptoms and limiting infectiousness and that treatment has to be initiated as early as possible. For about 50% of patients, the curve of viral titer versus time has two peaks. This bimodal behavior can be explained by incorporating the antiviral effects of interferon into the model. Our model also compared well to an additional data set on viral titer after experimental infection and treatment with the neuraminidase inhibitor zanamivir, which suggests that such models may prove useful in estimating the efficacies of different antiviral therapies for influenza A infection

On Deviations from the Maximum in a Stochastic Process

17 pages, 1 article*On Deviations from the Maximum in a Stochastic Process* (Macken, Catherine A.; Taylor, Howard M.) 17 page