Bigelow OCB Meeting Report

I am at Bigelow Lab in Boothbay Harbor, Maine for a workshop on single cell analysis for marine plankton. This is a very exciting area where novel observational technologies are rapidly growing the gap between observations and modeling. There simply is no correlation between our conventional/operational models and modern data. Today I learned something new. I was already aware of the high phenotypic heterogeneity we see in clonal cultures, but single cell genomics are now revealing a high degree of genomic heterogeneity in clonal populations as well! Is this variability neutral? What is the ecological role? How do we model it? Workshop link: http://www.whoi.edu/page.do?pid=133296

… and now my wife is coming up and we will go on to Acadia National Park for some hiking and camping. Visiting this park has been a goal of mine since 2004, and now we are finally doing it. This blog is for professional topics only, so this trip must therefore be hereby marked "sampling" solely to indicate this fact.

Portland JASM Meeting Report

I am in Portland (OR) for the JASM meeting. We have two presentations. I am giving a talk on our global ocean simulation and Neil is talking about our Taihu model. Yesterday I was at a session on “molecular ecology” and (as usual) I was struck by how disconnected the conventional phytoplankton/biogeochemical modeling approach is from the types of observations that are being generated. This session may be an extreme example of this, but people are presenting DNA, RNA, etc. data. Whatever happened to chlorophyll a? We really need to change our models to keep up with the changes in observational technology.

Here are links to our abstracts:
http://www.sgmeet.com/jasm2014/viewabstract.asp?AbstractID=14671
http://www.sgmeet.com/jasm2014/viewabstract.asp?AbstractID=13586

Boston ASM Meeting Report

This week I am at the general meeting of the American Society of Microbiology (ASM) here in Boston. We are presenting two posters: One is about evolution of ocean microbes at the global scale (“Exploring the Contribution of Neutral Evolution to Biogeography in Global Surface Ocean Microbes Using Agent-Based Modeling”) and another is about aging in bacteria (“From Protein Damage to Cell Aging to Population Fitness in E. coli: Insights from a Multi-level Agent-based Model”). Today I was at a session on "bacterial quiescence", where people talk about phenotypic differentiation of a small fraction of the population, including dormancy, sporulation, lag phase, viable but not culturable (VBNC), not growing metabolically active (NGMA), constant activity stationary phase (CASP), etc. One thing that strikes me is that its all about the heterogeneity. Biology no longer assumes that bacterial populations are homogeneous. This is in stark contrast to our mathematical models, which still treat bacteria as if they were homogenous populations. We are going to need agent-/individual-based models to analyze these data.

Here are links to our abstracts:

http://www.abstractsonline.com/Plan/ViewAbstract.aspx?sKey=927cef45-9ff5-4914-ae99-407ebc5a6a8e&cKey=65246fe7-05b3-4770-9a85-479447a69412&mKey=%7b673511F0-C86B-432F-A387-058032B8500B%7d

http://www.abstractsonline.com/Plan/ViewAbstract.aspx?sKey=c0bdb80c-43a9-4ff2-8a77-3a83c68b0a21&cKey=7af49378-688e-4f12-9ac2-0707246f6ab4&mKey=%7b673511F0-C86B-432F-A387-058032B8500B%7d

Vienna Stochastic Biology Workshop Report

I am at IST Austria for a workshop on Stochastic Biology. This is really a nice place to be and I enjoy listening to science during the day and then going for a run and dinner in Vienna in the evening. Today I gave a presentation on Kami’s model of aging in E. coli, which (I think) was well-received. This workshop focuses on how stochastic intracellular mechanisms (e.g. gene expression) give rise to cellular behavior. I am interested in incorporating these mechanisms into my microbe models and then modeling populations of these to see how they affect population and ecosystem behavior. However, right now I am sitting here in the audience with mixed emotions. On the one hand, I feel like a kid in a candy store. All these novel observational and experimental techniques are producing very exciting data and I want to model it all. On the other hand, these tools are now so good that it sometimes is difficult to see what modeling can still contribute. If we can observe everything, why do we need models? Here is a link to the workshop: http://ist.ac.at/stochastic-biology/

On N loading and export from lakes

I am pleased to announce that Xiaodan Ruan’s paper (co-authored by Frank Schellenger and myself) has been published in ES&T. This paper is concerned with nitrogen export from watersheds, which is a worldwide problem (e.g. the Mississippi River “dead zone”, see picture below). Our findings have important implications for watershed management. Specifically, we present a model that suggests a certain reduction (e.g. 50%) in N loading (i.e. from fertilizer or other sources) will not translate into the same amount of reduction at the watershed outlet, because N fixation by cyanobacteria in lakes and reservoirs may counteract the reduction. We are presently running whole-watershed models for a number of systems to develop a quantitative estimate of this problem.
Here is a link to the paper: http://pubs.acs.org/doi/abs/10.1021/es405707n

Environmental Capstones

It’s that time of year again... Capstones! Please join us for the 2014 Environmental Capstone student presentations. This year, we have a variety of interesting projects, including relocating a village in Honduras, re-designing an urban slum in India, designing an eco-city in China, upgrading a wastewater treatment plant and solving a water distribution loss problem in Massachusetts. Five Capstone teams have been working hard with CEE and ChemE faculty (Dan Saulnier, Annalisa Onnis-Hayden, Matt Eckelman, Ron Willey) and mentors, and now it’s time to see what they came up with. Please join us! A flyer with more details is posted here: https://dl.dropboxusercontent.com/u/58018213/EnvCapstone2014.pdf

 

On a warm summer's evenin' …

… on a train bound for nowhere, I met up with the gambler …

I am pleased to announce our paper on bet hedging in yeast has been published. I am really excited about this paper. One point that I would like to highlight here is the tight integration of individual-based observations (IBO) with individual-based modeling (IBM). As an example, the figure below shows the distribution of Tsl1 (a protein involved in the synthesis of the stress protectant trehalose), as observed (by Levy et al., PLoS Bio, 2012) using green fluorescent protein (GFP) tagging and flow cytometry, and modeled using our agent-based model. Modern observational methods increasingly resolve population heterogeneity and individual/agent-based modeling is a natural way to analyze these data. This project has consumed much of my time in 2012/13. To give you some idea of the scope, the time from inception to completion (initial manuscript submission) was 12 month, and the project included reviewing 110 papers and approximately 2,200 model runs.

Links to the paper, movie and code:
http://www.biomedcentral.com/1752-0509/8/18 
http://youtu.be/W-3kxaZtJaY 
https://www.dropbox.com/s/rdmubyp04s2da37/Yeast_BMCSB_2014.zip