Thursday, March 12, 2015

Aging in bacteria

I am please to announce the publication of our paper on aging in bacteria “From protein damage to cell aging to population fitness in E. coli: Insights from a multi-level agent-based model” in Ecological Modelling. This paper explores the fitness benefit of asymmetric damage partitioning (aging) in E. coli using an ABM. Specifically, we find that aging is beneficial, but the magnitude of the benefit is very small, so its probably a side-effect of some other process (see discussion in paper for more)We think this paper is an important contribution to understanding the role of aging in bacteria. In this post I want to do some mixing of art and science. In 2013 I attended the Congress of European Microbiologists (FEMS) in Leipzig, Germany. In his keynote address, Johan Leveau related the artwork of Ursus Wehrli (“The Art of Tidying Up”, to microbiology. I was really impressed by this and decided to apply that concept to our model to point to the role of spatial organization in aging of bacteria. 

Link to paper:

Thursday, January 1, 2015

New graduate student in my group

On Monday morning, Gunes and I welcomed a new member of our family: Mario Emre Ferdinand Hellweger. We are still a bit tired and overwhelmed, but very happy that everyone is healthy and to begin this new chapter in our lives. (This blog is for official research business only, so this guy has to be named a research assistant solely to indicate this fact.)

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.