A5054236642- Evolution and Genetic Dynamics
- HIV Research and Treatment
- HIV/AIDS drug development and treatment
- HIV/AIDS Research and Interventions
- Mathematical and Theoretical Epidemiology and Ecology Models
- Evolutionary Game Theory and Cooperation
- Antibiotic Resistance in Bacteria
- COVID-19 epidemiological studies
- Antibiotic Use and Resistance
- Immune Cell Function and Interaction
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Antibiotics Pharmacokinetics and Efficacy
- T-cell and B-cell Immunology
- Plant Virus Research Studies
- Hepatitis C virus research
- Vibrio bacteria research studies
- Plant and animal studies
- Reproductive tract infections research
- Microbial Community Ecology and Physiology
- Pharmaceutical and Antibiotic Environmental Impacts
- Gene Regulatory Network Analysis
- SARS-CoV-2 and COVID-19 Research
- Bacteriophages and microbial interactions
- SARS-CoV-2 detection and testing
ETH Zurich
2016-2025
Collegium Helveticum
2023
Board of the Swiss Federal Institutes of Technology
2004-2022
Massachusetts Institute of Technology
2017
Rothamsted Research
2017
Agricultural Development Advisory Service (United Kingdom)
2017
Google (United States)
2016
University of Lausanne
2015
Swiss Integrative Center for Human Health
2015
École Polytechnique Fédérale de Lausanne
2000-2006
Although cytotoxic T lymphocytes (CTLs) are thought to be involved in the control of human immunodeficiency virus–type 1 (HIV-1) infection, it has not been possible demonstrate a direct relation between CTL activity and plasma RNA viral load. Human leukocyte antigen–peptide tetrameric complexes offer specific means directly quantitate circulating CTLs ex vivo. With use complexes, significant inverse correlation was observed HIV-specific frequency In contrast, no association detected...
Heterotrophic organisms generally face a trade-off between rate and yield of adenosine triphosphate (ATP) production. This may result in an evolutionary dilemma, because cells with higher but lower ATP production gain selective advantage when competing for shared energy resources. Using analysis model simulations biochemical observations, we show that low high can be viewed as form cooperative resource use evolve spatially structured environments. Furthermore, argue the respiration have...
Treatment of chronic hepatitis B virus (HBV) infections with the reverse transcriptase inhibitor lamivudine leads to a rapid decline in plasma viremia and provides estimates for crucial kinetic constants HBV replication. We find that persistently infected patients, particles are cleared from half-life approximately 1.0 day, which implies 50% daily turnover free population. Total viral release into periphery is 10(11) per day. Although we have no direct measurement cell mass, can estimate...
Livestock antibiotic resistance Most use is for livestock, and it growing with the increase in global demand meat. It unclear what antibiotics means occurrence of drug animals risk to humans. Van Boeckel et al. describe burden antimicrobial on basis systematic reviews over past 20 years (see Perspective by Moore). There a clear number resistant bacterial strains occurring chickens pigs. The current study provides much-needed baseline model low- middle-income countries “one health”...
ABSTRACT Human immunodeficiency virus (HIV)-specific T-cell responses are thought to play a key role in viral load decline during primary infection and determining the subsequent set point. The requirements for this effect unknown, partly because comprehensive analysis of total HIV-specific CD4 + CD8 all HIV-encoded epitopes has not been accomplished. To assess these responses, we used cytokine flow cytometry overlapping peptide pools encompassing products HIV-1 genome study 23 highly active...
Consider user fees and regulatory caps on veterinary use
The recent development of potent antiviral drugs not only has raised hopes for effective treatment infections with HIV or the hepatitis B virus, but also led to important quantitative insights into viral dynamics in vivo . Interpretation experimental data depends upon mathematical models that describe nonlinear interaction between virus and host cell populations. Here we discuss emerging understanding population dynamics, role immune system limiting abundance, drug resistance, question...
Phylogenetic trees can be used to infer the processes that generated them. Here, we introduce a model, Bayesian birth–death skyline plot, which explicitly estimates rate of transmission, recovery, and sampling thus allows inference effective reproductive number directly from genetic data. Our method these parameters vary through time in piecewise fashion is implemented within B EAST 2 software framework. The powerful alternative existing coalescent providing insight into differing roles...
Estimation of the effective reproductive number Rt is important for detecting changes in disease transmission over time. During Coronavirus Disease 2019 (COVID-19) pandemic, policy makers and public health officials are using to assess effectiveness interventions inform policy. However, estimation from available data presents several challenges, with critical implications interpretation course pandemic. The purpose this document summarize these illustrate them examples synthetic data, and,...
The spread of bacteria resistant to antimicrobial agents calls for population-wide treatment strategies delay or reverse the trend toward antibiotic resistance. Here we propose new criteria evaluation effects protocols directly transmitted bacterial infections and discuss different usage patterns single multiple therapy. A mathematical model suggests that long-term benefit drug from introduction until a high frequency resistance precludes its use is almost independent pattern use. When more...
The Prisoner's Dilemma (PD) is a widely employed metaphor for problems associated with the evolution of cooperative behavior. We have recently proposed an alternative approach to PD, by exploring "spatial games" in which players--who are either pure cooperators, C, or defectors, D--interact neighbors some spatial array; each generation, players add up scores from all encounters, and next generation given cell retained its previous owner taken over neighbor, depending on who has largest...
Anti-viral drug treatment of human immunodeficiency virus type I (HIV-1) and hepatitis B (HBV) infections causes rapid reduction in plasma load. Viral decline occurs several phases provides information on important kinetic constants replication vivo pharmacodynamical properties. We develop a mathematical model that takes into account the intracellular phase viral life-cycle, defined as time between infection cell production new particles. derive analytic solutions for dynamics following with...
Hematopoietic stem cells (HSCs) maintain blood production. How often mouse HSCs divide and whether each HSC contributes simultaneously, sequentially, or repetitively to hematopoiesis remains be determined. We track division of 5-(and-6)-carboxyfluorescein diacetate succinimidyl ester (CFSE)–labeled in vivo. found that, steady-state mice, bone marrow capable reconstituting lifelong are within both fast-cycling (undergoing five more divisions 7 wk) quiescent zero 12–14 lineage marker–negative...
Epidemiological processes leave a fingerprint in the pattern of genetic structure virus populations. Here, we provide new method to infer epidemiological parameters directly from viral sequence data. The is based on phylogenetic analysis using birth-death model (BDM) rather than commonly used coalescent as for transmission pathogen. Using BDM has advantage that and death rates are estimated independently therefore enables first time estimation basic reproductive number pathogen only data,...
Combination therapy is rarely used to counter the evolution of resistance in bacterial infections. Expansion use combination requires knowledge how drugs interact at inhibitory concentrations. More than 50 years ago, it was noted that, if bactericidal are most potent with actively dividing cells, then inhibition growth induced by a bacteriostatic drug should result an overall reduction efficacy when drug. Our goal here investigate this hypothesis systematically. We first constructed...
The effective reproductive number R e is a key indicator of the growth an epidemic. Since start SARS-CoV-2 pandemic, many methods and online dashboards have sprung up to monitor this through time. However, these are not always thoroughly tested, correctly placed in time, or overly confident during high incidence periods. Here, we present method for timely estimation , applied COVID-19 epidemic data from 170 countries. We evaluate on simulated data, intuitive web interface interactive...
Studies of lymphocyte turnover in animal models have implications for understanding the mechanism cell killing and extent regeneration human immunodeficiency virus infection. Quantitative analyses sequential changes bromodeoxyuridine labeling CD4 CD8 T lymphocytes not only revealed normal proliferation death rates these populations uninfected macaques, but also showed a substantial increase associated with simian (SIV) Faster delabeling memory naı̈ve subpopulations as well NK (natural...
Little is known of the changes in human immunodeficiency virus type 1 (HIV-1)-specific effector cytotoxic T lymphocytes (CTL) after potent antiretroviral therapy. Using HLA/peptide tetrameric complexes, we show that starting treatment, there are early rapid fluctuations HIV-1-specific CTL response which last to 2 weeks. These followed by an exponential decay (median half-life, 45 days) continues while viremia remains undetectable. data have implications for immunological control drug-resistant virus.
We extend our exploration of the dynamics spatial evolutionary games [Nowak & May 1992, 1993] in three distinct but related ways. analyse, first, deterministic versus stochastic rules; second, discrete continuous time (see Hubermann Glance [1993]); and, third, different geometries interaction regular and random arrays. show that effects can change some intuitive concepts game theory: (i) equilibria among strategies are no longer necessarily characterised by equal average payoffs; (ii)...
Reproductive strategies such as sexual reproduction and recombination that involve the shuffling of parental genomes for production offspring are ubiquitous in nature. However, their evolutionary benefit remains unclear. Many theories have identified potential benefits, but progress is hampered by scarcity relevant data. One class based on assumption mutations affecting fitness exhibit negative epistasis. Retroviruses recombine frequently thus provide a unique opportunity to test these...