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 

Living the dream: Desperately Seeking Agent 5503216

Our latest project involves modeling individual microbes, each with a full genome, in the global ocean over 10k+ years. This is a really exciting problem and I wake up every day thinking about it. We are currently in the model development phase and are struggling with keeping track of the microbes in the model. Microbe 5503216 shows up in the population at time 317.34 years, but not at time 318.35, yet it doesn't register as dying in between these two times. Where did it go? In my experience, and those of my students, this is common problem and there is no alternative, but to hunt the cell down. So thats what I am working on these days. Its the same thing I did many years ago when I developed my first agent-based model of phytoplankton. So my life hasn't changed a bit... I love it!

Muddy River Restoration Project Visit

Last week our Hydro class visited the Muddy River Restoration Project construction site. This project includes “daylighting” of a previously buried section of the river. These types of projects are happening across the country and they highlight a change in our attitude towards urban water systems. In the old days, we polluted rivers and hid them under the ground. Now we protect, cherish and enjoy them as part of our urban environment. This visit was very interesting to me because, this project has been the subject of a previous Senior Design Capstone class (which helped inform some of the design) and also research (see link to paper below). Here is a picture of Mike Andryuk, a former student and now an engineer with the US Army Corps of Engineers, telling us about the site.

http://www.nae.usace.army.mil/Missions/ProjectsTopics/MuddyRiver.aspx
http://www.muddyrivermmoc.org/
http://www.sciencedirect.com/science/article/pii/S0269749111000923

Vision: Microbial Individual-Based Ecology (µIBE)

I am pleased to announce the publication of our opinion article in PNAS. This paper represents a milestone in our continuing crusade to change modeling of microbial ecology. You know, we used to (and often still do) model microbes as if they are chemical molecules. This approach does not allow us to account for their heterogeneity and it limits how much complexity we can include. Also, and this is the main point of this specific paper, it prohibits us from using any of the individual-based observations (IBOs) generated using novel single-cell observational and experimental techniques. Microbial ecologists are drowning in a flood of IBOs and, just as with systems biology years ago, new analysis tools are needed. Individual-based models (IBMs) to the rescue! This paper lays out our vision for combining IBMs and IBOs, which leads to microbial individual-based ecology (µIBE). Here are links to the paper and a couple of news coverages:

http://www.pnas.org/content/110/45/18027.full
http://www.northeastern.edu/news/2013/11/hey-bacteria-are-individuals-too/
http://www.nimbios.org/wordpress/2013/11/06/modeling-of-microbial-world-comes-of-age/

Prof. Vanni Bucci Seminar

My former PhD student Vanni Bucci, now Assistant Professor in Biology at U. Mass. Dartmouth, will be back on campus to give a seminar about his research. The talk will be October 10th - 6:15-7:30pm - 346 Curry Student Center. This event is organized by the NU NEWEA (New England Water Environment Association) student group. PIZZA WILL BE SERVED!! Title and abstract are below.

Ecological modeling from metagenomics: predicting multi-species microbial dynamics relevant to Clostridium di fficile infection

The intestinal microbiota is a microbial ecosystem of crucial importance to human health. Understanding how the microbiota confers resistance against enteric pathogens and how antibiotics disrupt that resistance is key to the prevention and cure of intestinal infections. In this talk I will present recent work to infer microbiota ecology directly from time-resolved metagenomics and predict its temporal dynamics. Data from recent experiments on antibiotic-mediated Clostridium diffi cile infection are analyzed to quantify microbial interactions, commensal-pathogen interactions, and the effect of the antibiotic on the community. Numerical simulations and linear stability analysis confirm that the microbiota is multistable and that antibiotic perturbations and C. di fficile inoculation can produce catastrophic shifts that persist even after removal of the perturbations. Importantly, we identify a subnetwork of bacterial groups implicated in protection against C. diffi cile, which is common to mice as well as hospitalized cancer patients.

UMass Dartmouth SMAST Visit

Last week Neil Fredrick and I visited the School of Marine Science and Technology (SMAST) at U. Mass. Dartmouth. I gave a seminar and we had some very good discussions about science and research with SMAST faculty. One thing we were very excited about was meeting Dr. Changsheng Chen, who is the developer of the FVCOM model, which we are using for our Lake Taihu project. Dr. Chen gave us some useful advice on our model and also showed us his  Northeast Coastal Ocean Forecast System (NECOFS). I spent a couple of hours playing with this system today. For someone interested in surface water quality, its really interesting technology. I made the plot below, which shows the currents at 8am today, outgoing tide. A while back, Boston discharged its wastewater at Moon Island (red circle). Then, they constructed two treatment plants, at Nut Island (green circle) and Deer Island (yellow circle). Seems like a good (or better) choice considering the currents. Now Boston has just one treatment plant at Deer Island, but the outfall is 9 miles offshore. Here is the link to the system:
http://porpoise1.smast.umassd.edu:8080/fvcomwms/

New paper: Mechanisms of Heterogeneity in Phytoplankton

I am pleased to announce the publication of our paper “Use of Agent-Based Modeling To Explore the Mechanisms of Intracellular Phosphorus Heterogeneity in Cultured Phytoplankton“ by Neil Fredrick et al. in Applied & Environmental Microbiology. I want to use this post to highlight an important point that has real consequences for our biogeochemical models. This paper is related to a previous one where we looked at the nutrient content heterogeneity in a field population. One of the main conclusions from that research was that microscale patchiness leads to large heterogeneity. This process is related to zooplankton excretion and thus does not operate in laboratory experiments. This means the heterogeneity in laboratory experiments is much lower than in the field, and that, considering the effect of heterogeneity, means that parameters estimated from the lab are not applicable to the field. Specifically, the maximum growth rate in the Droop quota model should be reduced by a factor of about 0.7. Here is a side-by-side comparison of the laboratory and field results:

Here are links to the “lab” and “field” papers.
http://aem.asm.org/content/79/14/4359.short
http://link.springer.com/article/10.1007/s10452-011-9384-6
And if you want to try the model, here it is:
http://www.systemsbioecology.org/files/QuotaHeterogeneity/QuotaHeterogeneity.html