Wednesday, December 3, 2014

Dr. Xiaodan Ruan Defended (successfully)

I am very happy that Xiaodan has successfully defended her PhD. It has been a pleasure to work with her over the past years. Xiaodan’s research topic was on the effect of lake N fixation on watershed N export. I still remember when she identified the question. We were looking at cyanobacteria from the Charles River under the microscope. Xiaodan noticed quite a few heterocysts (N fixing cells) in Anabaena. I initially dismissed this as unimportant, because the Charles River is generally believed to be P-limited (thats another point to discuss sometime). Anyway, she said, OK, but what will happen to all that N when it discharges to Boston Harbor and Massachusetts Bay? That was the initial question that eventually developed into a PhD thesis. Congratulations, Xiaodan!

Thursday, November 6, 2014

NEWEA Microconstituents Conference Report

Last week, I and several students in my Surface Water Quality Modeling class attended the NEWEA Microconstituents speciality conference at Bentley University. Microconstituents (aka emerging contaminants, pharmaceuticals and personal care products) are an important new problem we face as environmental engineers and this conference provided a good introduction to this topic. I made a presentation entitled “Where the Pipe Ends: Antibiotics and Antibiotic Resistance in the Ambient Environment”. You know, water quality models have evolved in step with environmental problems: Dissolved Oxygen (Streeter-Phelps) > Pathogens > Eutrophication > Toxics (e.g. PCBs) > Heavy metals > Harmful algae (e.g. cyanobacteria) > Pharmaceuticals and Personal Care Products (PPCPs). The development of models for antibiotic resistance is a natural next step for water quality modeling. Here are some pictures from the event:

Friday, September 12, 2014

Non-Darwinian evolution produces biogeography in model ocean microbe population

I am very happy that our paper on agent-based modeling of global ocean microbe evolution is now published. This study shows that neutral evolution and dispersal limitation can lead to substantial biogeography in ocean microbe populations. In a nutshell: Microbes evolve faster than the ocean circulation can mix them. I expect these results will receive a lot of attention, and I look forward to the discussion. In this post I want to highlight another aspect of the paper I am excited about, focused more on modeling technology.

You know, when I start my research program here at Northeastern about 10 years ago, I set out to develop models that are consistent with the quantity and types of observations we generate today. So I went to the literature and started looking at what people are measuring. I ran across papers by Ed DeLong and Craig Venter that presented metagenomics observations. My initial reaction of excitement quickly turned to despair when I realized that the quantity of information generated by modern observational tools now greatly surpasses what we can get out of models. In this model we simulate individual microbes, each with a full 1 Mbp genome. That approach constitutes one possible direction towards closing this gap. In some ways, our model application turns the table again, at least in terms of information quantity. For example, one of our simulations (Fig. 1B in the paper, “start uniform” simulation) includes 2.9e8 mutations and thus unique genomes, for a total of 290 Tbp, which is far larger than metagenomics datasets (e.g. GOS has 6.3 Gbp) or what is currently in GenBank (160 Gbp, Feb. 2014). I have an opening for an undergraduate research assistant to upload this data to GenBank (joke).

Here are links to the paper, a perspective article, some news features and an animation (which has been approved for going viral).

Thursday, September 4, 2014

Here we go …

Our fall semester is starting this week. This semester I am teaching my graduate Surface Water Quality Modeling course. I always enjoy this class, because the topic is very close to my research. The nature of graduate education is changing: For the first time I have more “online” than “inclass” students. Here is a link to the syllabus.

Wednesday, August 20, 2014

New project: Analysis of cyanobacteria sensor data

I am pleased to announce the start of a new project entitled “Robust Identification and Model Validation for a Class of Nonlinear Dynamic Systems and Applications”. This is a collaboration with Mario Sznaier and Octavia Camps from ECE, sponsored by NSF. In this project we will develop and apply data-driven models to high-volume environmental parameters (e.g. from cyanobacteria sensors) that hopefully will help us understand and manage water quality problems, including harmful algal blooms (HABs), in the Charles River and other water bodies. Here is a picture of a sensor buoy (courtesy GLEON) and a link to the project abstract.

Monday, July 28, 2014

2nd Public Swim in Charles River

On Saturday I jumped into the Charles River … again. This is a now annual event organized by the Charles River Conservancy. Last year there was one swim day. This year there were two scheduled, but the first one had to be cancelled because of a cyanobacteria bloom. Hopefully next year we will have even more and eventually a permanent beach or dock. Here is a link to CRCs web site:

Wednesday, July 2, 2014

Summer Sampling Under Way

Our summer sampling program has started. This year, PhD student Frank Schellenger and YSP students Mia Kobs and Mindy Wu are exploring the role of phosphorus loading from lakefront septic systems to lakes. An interesting aspect of this problem is the time dimension. Because phosphate sorbs strongly onto the solids in the ground a lot of it remains there and does not reach the lake. But P is conservative, so it will get there (“break through”) eventually. When do we expect this to happen? Here is a picture of Frank, Mia and Mindy at the lake and a link to more pictures.

Thursday, June 19, 2014

Tufts Conference Report

This week we have the UCOWR/NIWR/CUAHSI Conference at Tufts. The theme is “Water Systems, Science, and Society under Global Change”. We have two presentations: I will give a talk on Neil’s Lake Taihu model and Xiaodan will present her work on Lake Loading/Export modeling.

Here is a link to the conference: 

Friday, May 30, 2014

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:

… 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.

Friday, May 23, 2014

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:

Monday, May 19, 2014

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:

Tuesday, May 6, 2014

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:

Friday, May 2, 2014

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:

Friday, April 11, 2014

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:

Monday, February 24, 2014

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: