Biomedical subjects

L M Wahl

Publications and source records attributed to L M Wahl.

At least 19 recordsLinked to original sources

PubMed2007

Costs versus benefits: best possible and best practical treatment regimens for HIV.

Current HIV therapy, although highly effective, may cause very serious side effects, making adherence to the prescribed regimen difficult. Mathematical modeling may be used to evaluate alternative treatment regimens by weighing the positive results of treatment, such as higher levels of helper T cells, against the negative consequences, such as side effects and the possibility of resistance mutations. Although estimating the weights assigned to these factors is difficult, current clinical practice offers insight by defining situations in which therapy is considered "worthwhile". We therefore use clinical practice, along with the probability that a drug-resistant mutation is present at the start of therapy, to suggest methods of rationally estimating these weights. In our underlying model, we use ordinary differential equations to describe the time course of in-host HIV infection, and include populations of both activated CD4(+) T cells and CD8(+) T cells. We then determine the best possible treatment regimen, assuming that the effectiveness of the drug can be continually adjusted, and the best practical treatment regimen, evaluating all patterns of a block of days "on" therapy followed by a block of days "off" therapy. We find that when the tolerance for drug-resistant mutations is low, high drug concentrations which maintain low infected cell populations are optimal. In contrast, if the tolerance for drug-resistant mutations is fairly high, the optimal treatment involves periods of reduced drug exposure which consequently boost the immune response through increased antigen exposure. We elucidate the dependence of the optimal treatment regimen on the pharmacokinetic parameters of specific antiviral agents.

Anti-HIV Agents↗

PubMed2006

Functionally important residues in the peptidyl-prolyl isomerase Pin1 revealed by unigenic evolution.

Pin1 is a phosphorylation-dependent member of the parvulin family of peptidyl-prolyl isomerases exhibiting functional conservation between yeast and man. To perform an unbiased analysis of the regions of Pin1 essential for its functions, we generated libraries of randomly mutated forms of the human Pin1 cDNA and identified functional Pin1 alleles by their ability to complement the Pin1 homolog Ess1 in Saccharomyces cerevisiae. We isolated an extensive collection of functional mutant Pin1 clones harboring a total of 356 amino acid substitutions. Surprisingly, many residues previously thought to be critical in Pin1 were found to be altered in this collection of functional mutants. In fact, only 17 residues were completely conserved in these mutants and in Pin1 sequences from other eukaryotic organisms, with only two of these conserved residues located within the WW domain of Pin1. Examination of invariant residues provided new insights regarding a phosphate-binding loop that distinguishes a phosphorylation-dependent peptidyl-prolyl isomerase such as Pin1 from other parvulins. In addition, these studies led to an investigation of residues involved in catalysis including C113 that was previously implicated as the catalytic nucleophile. We demonstrate that substitution of C113 with D does not compromise Pin1 function in vivo nor does this substitution abolish catalytic activity in purified recombinant Pin1. These findings are consistent with the prospect that the function of residue 113 may not be that of a nucleophile, thus raising questions about the model of nucleophilic catalysis. Accordingly, an alternative catalytic mechanism for Pin1 is postulated.

Amino Acid Sequence↗

PubMed2006

Dynamics of recurrent viral infection.

In chronic viral infection, low levels of viral replication and infectious particle production are maintained over long periods, punctuated by brief bursts of high viral production and release. We apply well-established principles of modelling virus dynamics to the study of chronic viral infection, demonstrating that a model which incorporates the distinct contributions of cytotoxic T lymphocytes (CTLs) and antibodies exhibits long periods of quiescence followed by brief bursts of viral production. This suggests that for recurrent viral infections, no special mechanism or exogenous trigger is necessary to provoke an episode of reactivation; rather, the system may naturally cycle through recurrent episodes at intervals which can be many years long. We also find that exogenous factors which cause small fluctuations in the natural course of the infection can trigger a recurrent episode. Our model predicts that longer periods between recurrences are associated with more severe viral episodes. Four factors move the system towards less frequent, more severe episodes: decreased viral infectivity, decreased CTL efficacy, decreased memory T cell response and increased antibody efficacy.

Antibodies, Viral↗

PubMed2006

Improving estimates of the basic reproductive ratio: using both the mean and the dispersal of transition times.

In both within-host and epidemiological models of pathogen dynamics, the basic reproductive ratio, R(0), is a powerful tool for gauging the risk associated with an emerging pathogen, or for estimating the magnitude of required control measures. Techniques for estimating R(0), either from incidence data or in-host clinical measures, often rely on estimates of mean transition times, that is, the mean time before recovery, death or quarantine occurs. In many cases, however, either data or intuition may provide additional information about the dispersal of these transition times about the mean, even if the precise form of the underlying probability distribution remains unknown. For example, we may know that recovery typically occurs within a few days of the mean recovery time. In this paper we elucidate common situations in which R(0) is sensitive to the dispersal of transition times about their respective means. We then provide simple correction factors that may be applied to improve estimates of R(0) when not only the mean but also the standard deviation of transition times out of the infectious state can be estimated.

Disease Outbreaks↗

PubMed2005

Perspectives on the basic reproductive ratio.

The basic reproductive ratio, R0, is defined as the expected number of secondary infections arising from a single individual during his or her entire infectious period, in a population of susceptibles. This concept is fundamental to the study of epidemiology and within-host pathogen dynamics. Most importantly, R0 often serves as a threshold parameter that predicts whether an infection will spread. Related parameters which share this threshold behaviour, however, may or may not give the true value of R0. In this paper we give a brief overview of common methods of formulating R0 and surrogate threshold parameters from deterministic, non-structured models. We also review common means of estimating R0 from epidemiological data. Finally, we survey the recent use of R0 in assessing emerging diseases, such as severe acute respiratory syndrome and avian influenza, a number of recent livestock diseases, and vector-borne diseases malaria, dengue and West Nile virus.

Animals↗

PubMed2005

Using information theory to search for co-evolving residues in proteins.

MOTIVATION: Some functionally important protein residues are easily detected since they correspond to conserved columns in a multiple sequence alignment (MSA). However important residues may also mutate, with compensatory mutations occurring elsewhere in the protein, which serve to preserve or restore functionality. It is difficult to distinguish these co-evolving sites from other non-conserved sites. RESULTS: We used Mutual Information (MI) to identify co-evolving positions. Using in silico evolved MSAs, we examined the effects of the number of sequences, the size of amino acid alphabet and the mutation rate on two sources of background MI: finite sample size effects and phylogenetic influence. We then assessed the performance of various normalizations of MI in enhancing detection of co-evolving positions and found that normalization by the pair entropy was optimal. Real protein alignments were analyzed and co-evolving isolated pairs were often found to be in contact with each other. AVAILABILITY: All data and program files can be found at http://www.biochem.uwo.ca/cgi-bin/CDD/index.cgi

Amino Acid Sequence↗

PubMed2004

Drug resistance in an immunological model of HIV-1 infection with impulsive drug effects.

We consider an SIR-type model of immunological behaviour for HIV dynamics, including the effects of reverse transcriptase inhibitors and other drugs which prevent cellular infection. We use impulsive differential equations to model drug behaviour. We classify different regimes according to whether the drug efficacy is negligible, intermediate or high. We consider two strains of the virus: a wild-type strain that can be controlled by both intermediate and high drug concentrations, and a mutant strain that can only be controlled by high drug concentrations. Drug regimes may take trajectories through one, two or all three regimes, depending on the dosage and the dosing schedule. We demonstrate that drug resistance arises at both intermediate and high drug levels. At low drug levels resistance does not emerge, but the total T cell count is proven to be significantly lower than in the disease-free state. At intermediate drug levels, drug resistance is guaranteed to emerge. At high drug levels, either the drug-resistant strain will dominate or, in the absence of longer-lived reservoirs of infected cells, both viral sub-populations will be cleared. In the latter case the immune system is maintained by a population of T cells which have absorbed sufficient quantities of the drug to prevent infection by even the drug-resistant strain. We provide estimates of a range of dosages and dosing schedules which would, if physiologically tolerable, theoretically eliminate free virus in this system. Our results predict that to control viral load, decreasing the interval between doses is more effective than increasing the dose.

Anti-HIV Agents↗

PubMed2004

Distinct effects of protease and reverse transcriptase inhibition in an immunological model of HIV-1 infection with impulsive drug effects.

We present an immunological model that considers the dynamics of CD4+ T cells interacting with free virions, reverse transcriptase inhibiting drugs and protease inhibiting drugs. We divide the T cells into multiple classes and use impulsive differential equations to describe the drug activity. As expected, we find that insufficient dosing of either drug corresponds to high viral load and a large population of infectious T cells. The model further predicts that, in the absence of physiological limits on tolerable drug concentrations, sufficiently frequent dosing with the reverse transcriptase inhibitor alone could theoretically maintain the CD4+ T cell count arbitrarily close to the T cell count in the uninfected immune system. However, for frequent dosing of the protease inhibitor alone, the limiting T cell populations may not be enough to maintain the immune system. Furthermore, frequent dosing of both drugs has the same net effect on the T cell population as frequent dosing of the reverse transcriptase inhibitor only. Thus, the two drug classes can have fundamentally different effects on the long-term dynamics and the reverse transcriptase inhibitor, in particular, plays a crucial role in maintaining the immune system. We also provide estimates for the dosing intervals of each drug that could theoretically sustain the T cell population at a desired level.

CD4 Lymphocyte Count↗

PubMed2004

Fixation probability favors increased fecundity over reduced generation time.

The cornerstone of population genetics is a probabilistic understanding of the ultimate fate--survival or extinction--of rare mutations. If a mutation is beneficial, it enables its carrier to reproduce faster than native wild-type individuals. In classic derivations and in the considerable body of research that has followed, "faster" has been defined mathematically to mean "able to produce more surviving offspring per generation." Many organisms, however, may increase their reproductive rate by producing the same number of offspring in a shorter generation time: a mutant bacterium, for example, may complete the cell cycle and produce two offspring more quickly than the wild type. We find that the ultimate fixation probability of a mutation conferring a shorter generation time differs from that of a mutation conferring more offspring by a factor of 2 ln(2)-nearly 40%. This predicts a reduction in the overall substitution rate for any mutation that decreases the generation time: fixation probability is biased toward increased offspring number.

Amino Acid Substitution↗

PubMed2002

Evolving the division of labour: generalists, specialists and task allocation.

The evolutionary dynamics of specialization, in the context of the division of labour, are investigated. Individuals associate in groups in which benefits are shared and costs borne individually; each individual is either a generalist who can perform all the necessary tasks, a specialist who performs a sub-set of the necessary tasks, or a parasite who contributes nothing to the group. The implications of the model are explored analytically and through both numerical and Monte Carlo methods. These methods demonstrate the evolution of populations towards stable arrangements of specialists and generalists. The fittest populations are those that divide tasks fairly and associate in large, highly specialized groups. Generalists have a distinct advantage in small groups, but the presence of generalists, ironically, lowers group fitness. Parasites are able to invade both specialized and non-specialized populations. A basic model for the continuous division of labour is also presented, demonstrating a tendency for populations to evolve increasingly unfair divisions of labour. This last result implies that an evolutionary ratchet favours disparity between the workload of specialist populations.

Animals↗

PubMed2001

Genomic-scale measurement of mRNA turnover and the mechanisms of action of the anti-cancer drug flavopiridol.

BACKGROUND: Flavopiridol, a flavonoid currently in cancer clinical trials, inhibits cyclin-dependent kinases (CDKs) by competitively blocking their ATP-binding pocket. However, the mechanism of action of flavopiridol as an anti-cancer agent has not been fully elucidated. RESULTS: Using DNA microarrays, we found that flavopiridol inhibited gene expression broadly, in contrast to two other CDK inhibitors, roscovitine and 9-nitropaullone. The gene expression profile of flavopiridol closely resembled the profiles of two transcription inhibitors, actinomycin D and 5,6-dichloro-1-beta-D-ribofuranosyl-benzimidazole (DRB), suggesting that flavopiridol inhibits transcription globally. We were therefore able to use flavopiridol to measure mRNA turnover rates comprehensively and we found that different functional classes of genes had distinct distributions of mRNA turnover rates. In particular, genes encoding apoptosis regulators frequently had very short half-lives, as did several genes encoding key cell-cycle regulators. Strikingly, genes that were transcriptionally inducible were disproportionately represented in the class of genes with rapid mRNA turnover. CONCLUSIONS: The present genomic-scale measurement of mRNA turnover uncovered a regulatory logic that links gene function with mRNA half-life. The observation that transcriptionally inducible genes often have short mRNA half-lives demonstrates that cells have a coordinated strategy to rapidly modulate the mRNA levels of these genes. In addition, the present results suggest that flavopiridol may be more effective against types of cancer that are highly dependent on genes with unstable mRNAs.

Antineoplastic Agents↗

PubMed2001

Monocyte membrane type 1-matrix metalloproteinase. Prostaglandin-dependent regulation and role in metalloproteinase-2 activation.

Membrane type 1-matrix metalloproteinase (MT1-MMP)-mediated activation of MMP-2 is thought to be important in the proteolysis of extracellular matrix in pathological events in which monocytes/macrophages are found. Here we report on the induction and regulation of human monocyte MT1-MMP and its role in MMP-2 activation. Activation of monocytes by lipopolysaccharide resulted in the induction of MT1-MMP mRNA and protein that was suppressed by inhibitors of prostaglandin synthesis (indomethacin), adenylyl cyclase (SQ 22536), and protein kinase A (Rp-cAMPs). Suppression of MT1-MMP by indomethacin and SQ 22536 was reversed by prostaglandin E(2) and dibutyryl cyclic AMP, respectively, demonstrating that induction of monocyte MT1-MMP is regulated through a prostaglandin-cAMP pathway. Functional analysis revealed that pro-MMP-2 in the supernatants from human bone marrow stromal fibroblasts, normal male-derived fibroblasts and melanoma cells (A2058) was converted to active MMP-2 when cultured with activated but not control monocytes. Antibodies against MT1-MMP blocked the activation of MMP-2. Tissue inhibitor of metalloproteinase-2 regulation of MMP-2 activation was shown through the addition of varying amounts of recombinant tissue inhibitor of metalloproteinase-2 with pro-MMP-2 to MT1-MMP-expressing monocytes. These findings demonstrate that activated monocytes express functionally active MT1-MMP that may play a significant role in the activation of MMP-2 produced by other cells and as such influence developmental and pathological conditions.

Adenine↗

PubMed2001

The probability that beneficial mutations are lost in populations with periodic bottlenecks.

Population bottlenecks affect the dynamics of evolution, increasing the probability that beneficial mutations will be lost. Recent protocols for the experimental study of evolution involve repeated bottlenecks-when fresh media are inoculated during serial transfer or when chemostat tubes are changed. Unlike population reductions caused by stochastic environmental factors, these bottlenecks occur at known, regular intervals and with a fixed dilution ratio. We derive the ultimate probability of extinction for a beneficial mutation in a periodically bottlenecked population, using both discrete and continuous approaches. We show that both approaches yield the same approximation for extinction probability. From this, we derive an approximate expression for an effective population size.

Biological Evolution↗

PubMed2001

Pregnancy-specific glycoproteins function as immunomodulators by inducing secretion of IL-10, IL-6 and TGF-beta1 by human monocytes.

PROBLEM: Low levels of pregnancy-specific glycoproteins (PSGs) in maternal serum have been correlated with complications of pregnancy. We investigated the ability of human PSGs to regulate in vitro production of cytokines. METHOD OF STUDY: Human monocytes and murine RAW 264.7 cells were treated with recombinant PSG1, PSG6, PSG11, or a truncated PSG6 consisting of only the N-terminal domain (PSG6N). Cytokine production in response to PSG-treatment was measured by ELISA and/or reverse transcriptase-PCR. RESULTS: All PSGs tested induced secretion of interleukin (IL)-10, IL-6 and transforming growth factor (TGF)-beta1 by both human and murine cells, but not IL-1beta, tumor necrosis factor (TNF)-alpha or IL-12. The N-terminal domain of PSG6 was sufficient for induction of monocyte cytokine secretion. Induction of IL-10 and IL-6 was preceded by an increase in the specific mRNAs. CONCLUSIONS: PSG1, PSG6, PSG6N, and PSG11 induce dose-dependent secretion of anti-inflammatory cytokines by human monocytes. Human and murine PSGs exhibit cross-species activity. Our results are consistent with a role for PSGs in modulation of the innate immune system.

Adjuvants, Immunologic↗

PubMed2001

Raloxifene-mediated increase in matrix metalloproteinase-1 production by activated monocytes.

Matrix metalloproteinases (MMPs), proteolytic enzymes produced by monocytes, may contribute to atherosclerotic arterial wall remodeling and to plaque rupture. Because estrogen influences the synthesis of MMPs, we examined the effect of raloxifene, a selective estrogen receptor modulator, on monocyte MMP production. Human primary blood monocytes treated with raloxifene (10 micromol/L) in the presence of lipopolysaccharide (LPS) or tumor necrosis factor-alpha and granulocyte-macrophage colony-stimulating factor induced a 2- to 3-fold increase in MMP-1 production by monocytes. The enhancement of MMP-1 production by raloxifene in LPS-activated monocytes occurred through a cyclooxygenase-2- and prostaglandin E(2)-independent mechanism. Additionally, compared with monocytes acquired during the placebo phase, peripheral blood monocytes from 5 of 6 healthy postmenopausal women treated with raloxifene (60 mg daily for 1 month) in a clinical trial produced significantly higher levels of MMP-1 when the monocytes were activated with LPS. Furthermore, serum obtained during the raloxifene phase from 4 of these subjects, when added to control monocytes, significantly enhanced LPS-induced MMP-1 production compared with that from serum obtained during the placebo phase. In summary, raloxifene increases the production of MMP-1 in activated monocytes; this effect may be favorable in atherosclerotic arterial wall remodeling but unfavorable for plaque stability.

Arteriosclerosis↗

PubMed2000

Divergent effects of hormone therapy on serum markers of inflammation in postmenopausal women with coronary artery disease on appropriate medical management.

OBJECTIVES: The goal of our study was to determine whether hormone therapy alters markers of inflammation in postmenopausal women with chronic stable coronary artery disease (CAD) on appropriate medical management. BACKGROUND: Hormone therapy reduces some markers of inflammation associated with atherosclerosis risk (cell adhesion molecules) but increases levels of another marker of inflammation--C-reactive protein-in healthy postmenopausal women. METHODS: Ten women (average age 66 years; range 59 to 76 years) with CAD on medical management (including aspirin [9], statin lipid-lowering therapy [7], angiotensin-converting enzyme inhibitors [3]) were randomly assigned to conjugated equine estrogens 0.625 mg (combined with medroxyprogesterone acetate 2.5 mg daily in five women with uterus intact) or placebo(s) daily for one month with crossover to the alternate therapy after one month off of hormone treatment in a double-blind study. At the end of each treatment phase, the following markers of inflammation were measured in serum: interleukin-6, C-reactive protein, E-selectin, intercellular adhesion molecule-1, vascular cell adhesion molecule-1 and matrix metalloproteinase-9. RESULTS: Hormone therapy significantly lowered serum levels of cell adhesion molecules E-selectin (46.9+/-18.3 vs. 56.3+/-20.6 ng/mL, p = 0.006), intercellular adhesion molecule-1 (282+/-74 vs. 304+/-78 ng/mL, p = 0.013) and vascular cell adhesion molecule-1 (605+/-218 vs. 657+/-214 ng/mL, p = 0.01) but increased levels of matrix metalloproteinase-9 (648+/-349 vs. 501+/-285 ng/mL, p = 0.02). Interleukin-6 (4.33+/-4.78 vs. 3.04+/-1.47 pg/mL, p = 0.283) and C-reactive protein (0.88+/-1.13 vs. 0.61+/-0.50 mg/dL, p = 0.358) were not significantly elevated on hormone therapy compared with placebo values. CONCLUSIONS: Hormone therapy has divergent effects on serum markers of inflammation in women with CAD. Reduction in levels of cell adhesion molecules may reduce attachment of white blood cells to the vessel wall, but increases in matrix metalloproteinase-9 within the vessel wall could digest and weaken fibrous caps of vulnerable plaques, thus provoking thrombosis.

Aged↗

PubMed2000

Adherence and drug resistance: predictions for therapy outcome.

We combine standard pharmacokinetics with an established model of viral replication to predict the outcome of therapy as a function of adherence to the drug regimen. We consider two types of treatment failure: failure to eliminate the wild-type virus, and the emergence of drug-resistant virus. Specifically, we determine the conditions under which resistance dominates as a result of imperfect adherence. We derive this result for both single- and triple-drug therapies, with attention to conditions which favour the emergence of viral strains that are resistant to one or more drugs in a cocktail. Our analysis provides quantitative estimates of the degree of adherence necessary to prevent resistance. We derive results specific to the treatment of human immunodeficiency virus infection, but emphasize that our method is applicable to a range of viral or other infections treated by chemotherapy.

Anti-HIV Agents↗

PubMed2000

Immunization with a novel HIV-1-Tat multiple-peptide conjugate induces effective immune response in mice.

We report here a novel, highly immunogenic synthetic, multiple-peptide conjugate comprising functional domains Tat(21-40) and Tat(53-68) from HIV-1 group M plus Tat(9-20) from HIV-1 group O of the HIV-Tat protein (HIV-1-Tat-MPC). Vaccination of mice with HIV-1-Tat-MPC induced an effective immune response to all three functional domains. The anti-HIV-1-Tat-MPC antibodies efficiently inhibited Tat-induced viral activation in monocytes infected with HIV(Ba-L) as well as with various clinical HIV-1 isolates, and reduced Tat-mediated cytopathicity in infected cells by 60-75%. Our results indicate that anti-HIV-1-Tat-MPC antibodies inhibit viral pathogenesis, possibly by blocking functional determinants of Tat and disrupting autocrine and paracrine actions of secreted Tat protein. This epitope-specific, synthetic Tat construct may, therefore, provide a subunit AIDS vaccine candidate for inducing an effective immunoprophylaxis response to reduce progression of HIV infection.

AIDS Vaccines↗