Bulletin of the American Physical Society
APS March Meeting 2018
Volume 63, Number 1
Monday–Friday, March 5–9, 2018; Los Angeles, California
Session S49: Evolutionary Dynamics of Genomes IFocus
|
Hide Abstracts |
Sponsoring Units: DBIO GSNP Chair: Edo Kussell, New York University Room: LACC 511A |
Thursday, March 8, 2018 11:15AM - 11:51AM |
S49.00001: Exploratory adaptation in gene regulatory networks Invited Speaker: Naama Brenner Biological systems exhibit well-defined and repeatable responses, but can also explore, improvise and generate new functionality in the face of unforeseen conditions. At the level of populations, exploration can be implemented by variation and selection. At the level of the single cell or organism, exploratory behavior has been observed experimentally, but a theory or organizing principle is not well developed. |
Thursday, March 8, 2018 11:51AM - 12:03PM |
S49.00002: Inferring natural influenza transmission bottleneck sizes from sequencing data Daniel Weissman, Ashley Sobel Leonard, Benjamin Greenbaum, Elodie Ghedin, Katia Koelle Pathogen populations typically go through a bottleneck when they pass from host to host. These bottlenecks control the genetic diversity (and therefore evolutionary potential) of single infections and determines the extent to which multiple pathogen types can reliably co-transmit. They are, however, essentially impossible to measure directly in nature. We introduce a simple method for inferring bottleneck sizes from sequences of pathogen populations. Applying this method to data from influenza A virus transmission chains, we find dramatic differences between different populations, with some consistently having bottlenecks of hundreds of viruses while others are consistently bottlenecked to a single virus. We consider several possible explanations for this difference and suggest how they could be tested. |
Thursday, March 8, 2018 12:03PM - 12:15PM |
S49.00003: Spatial constraints on evolutionary dynamics Gabor Balazsi, Vincent Destefano, Michael Cortes Standard evolutionary dynamics assumes well-mixed populations without spatial structure or constraints. However, growing cell populations may often have spatial limitations. For example, epithelial cell growth may be restricted to the surfaces of luminal organs. We investigate the population structure and evolution of such spatially constrained cell populations compared to well-mixed ones. |
Thursday, March 8, 2018 12:15PM - 12:27PM |
S49.00004: Standing Variation of Beneficial Mutations is Sufficient for Maintenance of Anisogamy Caroline Holmes, Ilya Nemenman, Daniel Weissman The advantages of sexual reproduction are well known. However, the benefits of having a population with anisogamous sexual reproduction (i.e., with males and females) is less clear. We propose that some of the benefits of anisogamous reproduction may come from the differences in the maximum number of offspring produced by anisogamous females, isogamous females, and anisogamous males. Only the anisogamous males are virtually unlimited in total number of potential offspring, which allows for a more rapid spread of beneficial alleles through the population. We show that in some parameter regimes this effect alone is sufficient to maintain anisogamy in computational experiments. We end with proposals for experimental verification of our theory. |
Thursday, March 8, 2018 12:27PM - 1:03PM |
S49.00005: Negative feedback as a facilitator of gene network evolution Invited Speaker: Murat Acar Despite the examples of protein evolution via mutations in coding sequences, we have very limited understanding on gene network evolution via changes in cis-regulatory elements. Using the galactose network as a model, we studied how the regulatory promoters of the network contribute to the evolved network activity between two yeast species. In Saccharomyces cerevisiae, we combinatorially replaced all regulatory network promoters by their counterparts from Saccharomyces paradoxus, measured the resulting network inducibility profiles, and modeled the results. Lowering relative strength of GAL80-mediated negative feedback by replacing GAL80 promoter was necessary and sufficient to have high network inducibility levels as in S. paradoxus. This was achieved by increasing OFF-to-ON phenotypic switching rates. Competitions performed among strains with or without the GAL80 promoter replacement showed strong relationships between network inducibility and fitness. Our results support the hypothesis that gene network activity can evolve by optimizing the strength of negative-feedback regulation. |
Thursday, March 8, 2018 1:03PM - 1:15PM |
S49.00006: Competition During Reprogramming Gives Rise to Deterministically Elite Clones. Sophie McGibbon-Gardner, Nika Shakiba, Peter Zandstra, Sidhartha Goyal Cellular reprogramming is a source of induced pluripotent stem cells, but this process remains incompletely understood. The current theory of equipotency during reprogramming, in which all cells are equally inducible, argues that clone size distributions arise only from stochasticity in the system. However, large variability is seen in experiments. Our null, stochastic model, does not agree with barcoding experiments and shows that the equipotency theory may not be correct. To better explain these distributions we introduce multiple populations with different reprogramming parameters. Reprogramming is driven by a few dominant clones, a feature that will be captured by this mixed population model. Furthermore, barcoding experiments show correlation in clone sizes in repeated trails, indicating that there is heterogeneity in the reprogramming potential of clones. We will develop a stochastic model informed by experimental evidence that the cells that are derived from the neural crest have a proliferative advantage. This approach also introduces heritable reprogramming potential into our model. An accurate model of the reprogramming process can inform our understanding of the path to pluripotency, and increase the yield of reprogramming protocols. |
Thursday, March 8, 2018 1:15PM - 1:27PM |
S49.00007: Regulation of gene exchange in bacterial outer membrane vesicles James Boedicker, Frances Tran Recent experimental work has revealed the ability of bacteria to produce and uptake extracellular vesicles. Such vesicle exchange enables cells to exchange biomolecules, including genetic material, which enables horizontal gene transfer between bacteria. Many of the biophysical mechanisms and parameters that control the production and uptake of such extracellular vesicles have not been explored. |
Thursday, March 8, 2018 1:27PM - 1:39PM |
S49.00008: Highly multiplexed imaging of microbial diversity Hao Shi, Iwijn De Vlaminck Next generation sequencing technologies have greatly accelerated discoveries and understanding of phylogenetic diversity in natural microbial communities. However, the spatial structure of these communities is difficult to measure, primarily due to spectral overlap associated with fluorescence imaging. We have previously developed High Phylogenetic Resolution Fluorescence In-situ Hybridization (HiPR-FISH), a highly multiplexed FISH method that can overcome the multiplexity limitations of fluorescence imaging, and enable studies of the spatial organization of microbial communities at their full diversity. In this talk, we will present results that demonstrate the multiplexity capability of HiPR-FISH on five synthetic communities of E. coli encoded as different 10-bit binary words, with 63 binary words per community. We will also discuss identification errors associated with spectra classification using basic machine learning algorithms. Finally, we will show preliminary results from application of HiPR-FISH on microbial communities from a few model organisms. |
Thursday, March 8, 2018 1:39PM - 2:15PM |
S49.00009: Bacteria are different – the dynamics of genome content Invited Speaker: William Hanage Bacteria show startling variation in the composition of their genomes, such that isolates of the same named species may vary by as much as 10% of the genes present, which are termed the ‘accessory’ genome. This is often thought to be a consequence of natural selection, both on the organisms, and the genes themselves, which may behave as selfish actors. However much of the observed variation may be explained by a simple, neutral model that allows bacteria to take up DNA from other members of the same species, which is often observed in nature. This may be used to estimate ecological overlap of species clusters, by the amount they have diverged. Finally, there is evidence that negative frequency dependent selection on a subset of genes may explain features of population structure, and be useful in predicting population dynamics in response to vaccination. |
(Author Not Attending)
|
S49.00010: Comparison of Weak Magnetic Field Effects on the Antibiotic Susceptibility of Common Bacteria Kevin Do, Abdullah Albalawi, Samina Masood We present a study of weak magnetic field effects on the antibiotic susceptibility of several common bacterial species. The growth curves of bacterial samples exposed to both static and time varying magnetic field configurations were compared to control samples, all of which were grown for a few days in controlled conditions. At the 12-hour mark, half of the samples were treated with different concentrations of erythromycin. The interaction of antibiotics with bacteria in the presence of magnetic fields is investigated. |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700