Bulletin of the American Physical Society
APS March Meeting 2015
Volume 60, Number 1
Monday–Friday, March 2–6, 2015; San Antonio, Texas
Session W48: Physics of Evolutionary and Population Dynamics III |
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Sponsoring Units: DBIO Chair: Jayajit DAS, The Ohio State University Room: 217C |
Thursday, March 5, 2015 2:30PM - 2:42PM |
W48.00001: The structure of infectious disease outbreaks across the animal-human interface Christopher R. Myers, David J. Schneider, Sarabjeet Singh Zoonotic infectious diseases that spill over from animal to human populations are responsible for some of the most devastating plagues to haunt humanity throughout its history, including the recent Ebola outbreak. Yet despite considerable efforts by epidemiologists to model specific zoonotic infections, much of the basic underlying structure of cross-species outbreaks has not been well-characterized. Motivated by these gaps and by recent efforts to develop classification schemes for characterizing the spectrum of zoonotic diseases, we have solved -- using techniques from multitype branching processes and queuing theory -- for the structure and statistics of outbreaks resulting from cross-species spillover, characterizing outbreak sizes, probabilities and first-passage times. In the case of human outbreaks driven by epidemics in animal populations, we find a novel multicritical point at which outbreak size scaling that is different than in a single population. When human outbreaks are driven by an endemic disease in an animal reservoir, we find variable exponents characterizing outbreak size and duration that depend upon the rate of cross-species spillover. [Preview Abstract] |
Thursday, March 5, 2015 2:42PM - 2:54PM |
W48.00002: The spatial and metabolic profiles of microbial populations non-monotonically impact the growth of antibiotic resistant mutants Karishma Kaushik, Nalin Ratnayeke, Parag Katira, Vernita Gordon Spatial heterogeneity in the distribution of antibiotic is known to accelerate the development of genetic antibiotic resistance. However, the effect of the structure of the microbial population is less well studied. Microbial population structure is a type of spatial structure defined by composition, cell density, and spatial organization of cell types. As our cell types, we use antibiotic-resistant and antibiotic-susceptible (wild-type)\textit{ Pseudomonas aeruginosa} along with \textit{S. aureus} and \textit{B. cepacia,} both co-pathogens with \textit{P. aeruginosa}. In spatially-mixed systems, composed of wild-type cells and antibiotic-resistant mutants, we find that increasing cell density reduces the probability of antibiotic-resistant mutant survival in the presence of antibiotic. Using spatially-structured systems, we show that inhibition is mediated by a low-molecular weight, universal, alkaline by-product of bacterial catabolism of amino acids. We demonstrate that for organisms capable of growing on either amino acids or sugars, the nutrient environment provides a switch to activate or de-activate inhibition. Finally, we show that small spatial fluctuations in initial population density can shield mutants from the combined effect of antibiotic and the inhibitory factor [Preview Abstract] |
Thursday, March 5, 2015 2:54PM - 3:06PM |
W48.00003: Evolution of Super-Reciprocity in Noisy Iterated Games Masoud Mirmomeni, Arend Hintze, Christoph Adami In the classical Iterated Prisoners Dilemma (IPD), direct reciprocity is a form of communication leading to altruistic behavior. However, if players use stochastic strategies, a secondary form of cooperation in which players alternate in receiving the Temptation (T) and Sucker (S) rewards can emerge (super-reciprocity). This reciprocal behavior will become evolutionary dominant if the reward (T) is increased above a certain threshold, but is inherently more risky than primary cooperation since it relies on trust between players in two consecutive iterations of the game. Here, we investigate how different environmental conditions such as mutation rate, environmental noise, and reward T affect the evolution of reciprocity. Super-reciprocal strategies rely on the synchronization of two genes and are thus much more sensitive to environmental changes that affect the accuracy of players prediction of opponents' future moves. We find that increasing the environmental noise or mutation rate is deleterious to super-reciprocity, while increasing T stabilizes its evolution. Conversely, in environments that are highly predictable and where there is no payoff advantage to engage in reciprocal cooperation, basic cooperation via reciprocal communication remains the strategy of choice. [Preview Abstract] |
Thursday, March 5, 2015 3:06PM - 3:42PM |
W48.00004: An optimal energy dissipation strategy of the MinCDE oscillator in regulating symmetric bacterial cell division Invited Speaker: Ganhui Lan Sustained molecular oscillations are ubiquitous in biology. The obtained oscillatory patterns provide vital functions as timekeepers, pacemakers and spacemarkers. Control-theory type models have been introduced to explain how specific oscillatory behaviors stem from protein interaction feedbacks, whereas the energy dissipation through the oscillating processes and its role in the regulatory function remain elusive. Here we developed a general framework to assess oscillator's regulation performance at different dissipation levels. Using Escherichia coli MinCDE oscillator as model system, we showed that, unlike stationary regulators' monotonic performance-to-cost relation, excess dissipation at certain steps in the oscillating process damages the oscillator's regulatory performance. We further discovered that ATP hydrolysis energy has to be strategically assigned to the MinE-aided MinD release and the MinD immobilization steps for optimal performance, and higher energy budget improves the robustness of the oscillator. These results unfold a novel mode that living systems trade energy for regulatory function. [Preview Abstract] |
Thursday, March 5, 2015 3:42PM - 3:54PM |
W48.00005: Quantitative evolutionary dynamics of one million barcoded lineages Jamie Blundell, Sasha Levy, Sandeep Venkataram, Dmitri Petrov, Daniel Fisher, Gavin Sherlock Evolution of large asexual cell populations underlies $\approx 30\%$ of deaths worldwide, including those caused by bacteria, parasites, and cancer. However, the dynamics underlying these evolutionary processes remain poorly understood because they involve many competing beneficial lineages, most of which never rise above extremely low frequencies. To observe these normally hidden evolutionary dynamics, we constructed a sequencing-based ultra high-resolution lineage tracking system that can monitor the relative frequencies of $\approx 500,000$ lineages simultaneously. We find that the spectrum of fitness effects of beneficial mutations is far from exponential and not even monotonic. Early adaptation is a predictable consequence of this distribution and is strikingly reproducible, but the initial small-effect mutations are soon outcompeted by rarer large-effect mutations that result in variability between replicates. Our results suggest that early evolutionary dynamics may be deterministic for a period of time before stochastic effects become important. The interplay between deterministic and stochastic effects is controlled in large part by the distribution of mutation rates to each fitness effect, which high-resolution lineage tracking is uniquely suited to measure. [Preview Abstract] |
Thursday, March 5, 2015 3:54PM - 4:06PM |
W48.00006: Noise-stabilized Turing Patterns in a Synthetic Biofilm K. Michael Martini, David Karig, Ting Lu, Nigel Goldenfeld, Ron Weiss Deterministic Turing instabilities have been proposed to be a major source of pattern formation in biology, but have been hard to document rigorously, in part because of the requirement for a large ratio of the inhibitor to activator diffusion coefficient. A recently developed theory of stochastic Turing patterns predicts that stochastic or noise-stabilized Turing patterns occur over a larger region of parameter space and do not require as large a separation of diffusion rates. We apply this theory to a biofilm whose signaling molecules have been forward-engineered to exhibit activation and inhibition. Outside of the range of deterministic Turing patterns, we observe noise-stabilized patterns that exhibit a power spectrum power law tail with exponent $-2.3\pm.4$ consistent with theory. Our results are the first report of a spatial pattern in gene expression stabilized by copy number fluctuations. [Preview Abstract] |
Thursday, March 5, 2015 4:06PM - 4:18PM |
W48.00007: Limits on energy dissipation qualitatively change kinetic proofreading in single cells Jayajit Das Cell signaling events, composed of biochemical reactions, usually occur in the absence of the detailed balance condition and continuously dissipate energy. Consequently, when energy supply is limited, specific chemical modification steps might not occur due to the lack of energy to support those reactions. How does the absence of such modification steps, that are intrinsically stochastic in nature, affect single cell signaling kinetics? I address this question in the context of a kinetic proofreading scheme used in a simple model of early time T cell signaling. I show, using exact analytical calculations and numerical simulations, that the amount of energy dissipation needed to execute a desired discrimination scheme depends on whether the decision is made at the transient state or in the steady state of the kinetics. Using a modified Gillespie algorithm for simulating biochemical reactions in energy limited conditions, I show that restricting energy dissipation leads to poorer discrimination in single cells for weak and low affinity ligands. Furthermore, restricting energy dissipation produced substantially larger intrinsic cell-to-cell variations of proteins with qualitatively different distributions than the system with unlimited supply of energy. [Preview Abstract] |
Thursday, March 5, 2015 4:18PM - 4:54PM |
W48.00008: Decision theory for immune ligand recognition Invited Speaker: Paul Francois Variability in the chemical composition of the extra-cellular environment can significantly degrade the ability of cells to detect rare cognate ligands. Using concepts from statistical detection theory, we formalize the generic problem of detection of small concentrations of ligands in a fluctuating background of biochemically similar ligands binding to the same receptors. We discover that in contrast to expectations arising from considerations of signal amplification, inhibitory interactions between receptors can improve detection performance in the presence of substantial environmental variability, providing an adaptive interpretation to the phenomenon of ligand antagonism. Our results suggest that the structure of signalling pathways responsible for chemodetection in fluctuating and heterogeneous environments might be optimized with respect to the statistics and dynamics of environmental composition. Our formalism stresses the importance of characterizing non-specific interactions to understand function in signalling pathways. [Preview Abstract] |
Thursday, March 5, 2015 4:54PM - 5:06PM |
W48.00009: Phylogetic Tree from the Tangled Nature Model and Its Community Structure Osman Canko, Ferhat Taskin, Kamil Argin In the evolutionary biology, taxonomy and origination of species are a widely emphasized subject. An estimation of the evolutionary tree can be done via available DNA sequence data. The calculation of tree are made by well-known and frequently used methods such as maximum likelihood and neighbor-joining. In order to inquire the results of these methods, an evolutionary tree is pursued computationally by a mathematical model, called Tangled Nature. A relatively small genome space is investigated due to computational burden and it is found that actual and predicted tree are in a reasonably good agreement in terms of shape. Moreover, speciation and emerged community structure of food-web are investigated by modularity. [Preview Abstract] |
Thursday, March 5, 2015 5:06PM - 5:18PM |
W48.00010: A Stability Investigation of Dynamically Evolved Tangled Nature Model Ferhat Taskin, Osman Canko, Kamil Argin An individual based Tangled Nature model has non-stationary macro-dynamics of evolutionary ecology. System travels among the multi-space minimum through saddle point and stays in a valley, called quasi-steady states (qSS). We have compared the stability of sequential qSS by perturbation. To investigate stability of community, the perturbed and unperturbed systems are compared by their center of mass properties. Our primary results exhibit that the angle and distance between two center of mass shows a delayed response to perturbation for aged system. We have observed that the system evolves dynamically to the more stable states and shows robustness to external shocks with passing time. [Preview Abstract] |
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