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Fontana, Walter

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Fontana

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Walter

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Fontana, Walter
Author's Publications: search.filters.isAuthorOfPublication.2d95fa82-cf9d-4f92-b4f4-f119b9c7aec7

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Now showing 1 - 7 of 7
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    The C. elegans Lifespan Machine
    (2013) Stroustrup, Nicholas Edward; Ulmschneider, Bryne E.; Nash, Zachary M.; López Moyado, Isaac F.; Apfeld, Javier; Fontana, Walter
    The measurement of lifespan pervades aging research. Because lifespan results from complex interactions between genetic, environmental and stochastic factors, it varies widely even among isogenic individuals. The action of molecular mechanisms on lifespan is therefore visible only through their statistical effects on populations. Survival assays in C. elegans provided critical insights into evolutionarily conserved determinants of aging. To enable the rapid acquisition of survival curves at arbitrary statistical resolution, we developed a scalable imaging and analysis platform to observe nematodes over multiple weeks across square meters of agar surface at 8 μm resolution. The method generates a permanent visual record of individual deaths from which survival curves are constructed and validated, producing data consistent with the manual method for several mutants in both standard and stressful environments. Our approach allows rapid, detailed reverse-genetic and chemical screens for effects on survival and enables quantitative investigations into the statistical structure of aging.
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    An Insulin-to-Insulin Regulatory Network Orchestrates Phenotypic Specificity in Development and Physiology
    (Public Library of Science, 2014) Fernandes de Abreu, Diana Andrea; Caballero, Antonio; Fardel, Pascal; Stroustrup, Nicholas Edward; Chen, Zhunan; Lee, KyungHwa; Keyes, William D.; Nash, Zachary M.; López-Moyado, Isaac F.; Vaggi, Federico; Cornils, Astrid; Regenass, Martin; Neagu, Anca; Ostojic, Ivan; Liu, Chang; Cho, Yongmin; Sifoglu, Deniz; Shen, Yu Serena; Fontana, Walter; Lu, Hang; Csikasz-Nagy, Attila; Murphy, Coleen T.; Antebi, Adam; Blanc, Eric; Apfeld, Javier; Zhang, Yun; Alcedo, Joy; Ch'ng, QueeLim
    Insulin-like peptides (ILPs) play highly conserved roles in development and physiology. Most animal genomes encode multiple ILPs. Here we identify mechanisms for how the forty Caenorhabditis elegans ILPs coordinate diverse processes, including development, reproduction, longevity and several specific stress responses. Our systematic studies identify an ILP-based combinatorial code for these phenotypes characterized by substantial functional specificity and diversity rather than global redundancy. Notably, we show that ILPs regulate each other transcriptionally, uncovering an ILP-to-ILP regulatory network that underlies the combinatorial phenotypic coding by the ILP family. Extensive analyses of genetic interactions among ILPs reveal how their signals are integrated. A combined analysis of these functional and regulatory ILP interactions identifies local genetic circuits that act in parallel and interact by crosstalk, feedback and compensation. This organization provides emergent mechanisms for phenotypic specificity and graded regulation for the combinatorial phenotypic coding we observe. Our findings also provide insights into how large hormonal networks regulate diverse traits.
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    Lifespan-on-a-Chip: Microfluidic Chambers for Performing Lifelong Observation of C. elegans
    (Royal Society of Chemistry, 2010) Hulme, S. Elizabeth; Shevkoplyas, Sergey S.; McGuigan, Alison P.; Apfeld, Javier; Fontana, Walter; Whitesides, George
    This article describes the fabrication of a microfluidic device for the liquid culture of many individual nematode worms (Caenorhabditis elegans) in separate chambers. Each chamber houses a single worm from the fourth larval stage until death, and enables examination of a population of individual worms for their entire adult lifespans. Adjacent to the chambers, the device includes microfluidic worm clamps, which enable periodic, temporary immobilization of each worm. The device made it possible to track changes in body size and locomotion in individual worms throughout their lifespans. This ability to perform longitudinal measurements within the device enabled the identification of age-related phenotypic changes that correlate with lifespan in C. elegans.
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    Regulated spatial organization and sensitivity of cytosolic protein oxidation in Caenorhabditis elegans
    (2014) Romero-Aristizabal, Catalina; Marks, Debora; Fontana, Walter; Apfeld, Javier
    Cells adjust their behavior in response to redox events by regulating protein activity through the reversible formation of disulfide bridges between cysteine thiols. However, the spatial and temporal control of these modifications remains poorly understood in multicellular organisms. Here, we measured the protein thiol-disulfide balance in live C. elegans using a genetically-encoded redox sensor and found that it is specific to tissues and patterned spatially within a tissue. Insulin signaling regulates the sensor's oxidation at both of these levels. Unexpectedly, we found that isogenic individuals exhibit large differences in the sensor's thiol-disulfide balance. This variation contrasts with the general view that glutathione acts as the main cellular redox buffer. Indeed, our work suggests that glutathione converts small changes in its oxidation level into large changes in its redox potential. We therefore propose that glutathione facilitates the sensitive control of the thioldisulfide balance of target proteins in response to cellular redox events.
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    Combinatorial Complexity and Compositional Drift in Protein Interaction Networks
    (Public Library of Science, 2012) Deeds, Eric J.; Krivine, Jean; Feret, Jérôme; Danos, Vincent; Fontana, Walter
    The assembly of molecular machines and transient signaling complexes does not typically occur under circumstances in which the appropriate proteins are isolated from all others present in the cell. Rather, assembly must proceed in the context of large-scale protein-protein interaction (PPI) networks that are characterized both by conflict and combinatorial complexity. Conflict refers to the fact that protein interfaces can often bind many different partners in a mutually exclusive way, while combinatorial complexity refers to the explosion in the number of distinct complexes that can be formed by a network of binding possibilities. Using computational models, we explore the consequences of these characteristics for the global dynamics of a PPI network based on highly curated yeast two-hybrid data. The limited molecular context represented in this data-type translates formally into an assumption of independent binding sites for each protein. The challenge of avoiding the explicit enumeration of the astronomically many possibilities for complex formation is met by a rule-based approach to kinetic modeling. Despite imposing global biophysical constraints, we find that initially identical simulations rapidly diverge in the space of molecular possibilities, eventually sampling disjoint sets of large complexes. We refer to this phenomenon as “compositional drift”. Since interaction data in PPI networks lack detailed information about geometric and biological constraints, our study does not represent a quantitative description of cellular dynamics. Rather, our work brings to light a fundamental problem (the control of compositional drift) that must be solved by mechanisms of assembly in the context of large networks. In cases where drift is not (or cannot be) completely controlled by the cell, this phenomenon could constitute a novel source of phenotypic heterogeneity in cell populations.
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    The Stochastic Behavior of a Molecular Switching Circuit with Feedback
    (BioMed Central, 2007) Krishnamurthy, Supriya; Smith, Eric; Krakauer, David; Fontana, Walter
    Background: Using a statistical physics approach, we study the stochastic switching behavior of a model circuit of multisite phosphorylation and dephosphorylation with feedback. The circuit consists of a kinase and phosphatase acting on multiple sites of a substrate that, contingent on its modification state, catalyzes its own phosphorylation and, in a symmetric scenario, dephosphorylation. The symmetric case is viewed as a cartoon of conflicting feedback that could result from antagonistic pathways impinging on the state of a shared component. Results: Multisite phosphorylation is sufficient for bistable behavior under feedback even when catalysis is linear in substrate concentration, which is the case we consider. We compute the phase diagram, fluctuation spectrum and large-deviation properties related to switch memory within a statistical mechanics framework. Bistability occurs as either a first-order or second-order non-equilibrium phase transition, depending on the network symmetries and the ratio of phosphatase to kinase numbers. In the second-order case, the circuit never leaves the bistable regime upon increasing the number of substrate molecules at constant kinase to phosphatase ratio. Conclusion: The number of substrate molecules is a key parameter controlling both the onset of the bistable regime, fluctuation intensity, and the residence time in a switched state. The relevance of the concept of memory depends on the degree of switch symmetry, as memory presupposes information to be remembered, which is highest for equal residence times in the switched states. Reviewers: This article was reviewed by Artem Novozhilov (nominated by Eugene Koonin), Sergei Maslov, and Ned Wingreen.
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    Age-Dependence and Aging-Dependence: Neuronal Loss and Lifespan in a C. elegans Model of Parkinson’s Disease
    (MDPI, 2017) Apfeld, Javier; Fontana, Walter
    It is often assumed, but not established, that the major neurodegenerative diseases, such as Parkinson’s disease, are not just age-dependent (their incidence changes with time) but actually aging-dependent (their incidence is coupled to the process that determines lifespan). To determine a dependence on the aging process requires the joint probability distribution of disease onset and lifespan. For human Parkinson’s disease, such a joint distribution is not available, because the disease cuts lifespan short. To acquire a joint distribution, we resorted to an established C. elegans model of Parkinson’s disease in which the loss of dopaminergic neurons is not fatal. We find that lifespan is not correlated with the loss of individual neurons. Therefore, neuronal loss is age-dependent and aging-independent. We also find that a lifespan-extending intervention into insulin/IGF1 signaling accelerates the loss of specific dopaminergic neurons, while leaving death and neuronal loss times uncorrelated. This suggests that distinct and compartmentalized instances of the same genetically encoded insulin/IGF1 signaling machinery act independently to control neurodegeneration and lifespan in C. elegans. Although the human context might well be different, our study calls attention to the need to maintain a rigorous distinction between age-dependence and aging-dependence.