Thursday, April 28, 2016

Anabaena Paper Published

I am pleased to report that the Anabaena model paper is now published in Environmental Microbiology.

In this paper we present a dynamic, mechanistic, gene level model of Anabaena – nitrogen interaction. This model is unique and constitutes a significant step in the area of microbial ecology, where models are typically based on concepts developed over 50 years ago (i.e., Monod kinetics), do not include modern biology and do not make predictions commensurate with modern observational technologies (e.g., transcript levels). The model development process is also novel in the context of microbial ecology. It builds on a large database of empirical observations, data from 55 papers (269 experiments) were digitized and used for model-data comparison (i.e. a meta-analysis). The model helps to interpret the observations. For example, application to isotope tracing experiments suggests a role for an N storage pool, consistent with recent observations. We use the model to explore an important question about the efficacy of reducing nitrogen to control lake eutrophication. Beyond these results we propose that our approach constitutes a way to summarize observations that has significant advantages over the traditional review paper when the amount of observations is large. We believe this paper makes a significant contribution to the biology and ecology of Anabaena and presents a novel approach that is of interest to researchers in other areas of microbiology and ecology.

I want to use this post to lay out some of the thoughts I have about possible follow-on projects for this model. The overall “master plan” for the Anabaena model is shown in the figure below, and some more details follow. Please contact me, if you are interested in collaborating on any of these projects.

Anabaena Lab: This is done now. To give you some idea of the effort involved: The Anabaena Lab model took much of my time over the course of a year. I think on average about 4h/day.

Anabaena Lab Validation: This is a validation exercise. It would involve taking additional papers that were not used in the model development and comparing the model to those. The present model was developed and compared to experiments from 55 papers. This exercise may include about 10 papers. I already have these papers identified. This would be a good MS thesis project for a student. Along with this paper, I would like to publish the source code and user guide of the model as well.

Anabaena Field: The present model can be applied to a real lake. Since it only includes Anabaena, this lake would have to be dominated by Anabaena. If everything goes smoothly, this could also be a good MS thesis project.

Microcystis Toxin Lab: This would involve taking the present model and adapting it to Microcystis. The basic structure would be the same, except that Microcystis does not fix N. This is easily handled in the model by “knocking out” nifH and associated genes. Then the model would need to be calibrated to observations of Microcystis. Then, the toxin production genes and pathways would have to be programmed and calibrated/validated. This will require more work, comparable to the Anabaena Lab project, and a good PhD thesis topic.

Anabaena Energy Lab: The present model does not explicitly track intracellular energy (i.e. in terms of ATP or equivalent) and tie it to growth. For example, the cost of fixing one N2 vs. taking up and reducing one NO3 is not explicitly considered in the model. I could, for example, simply increase the NifH rate and then the cells would grow faster on N2 than NO3. This change would make the model more mechanistically detailed and correct. This will require more work, comparable to the Anabaena Lab project, again a good PhD topic.

Microcystis Field: Once the Microcystis model is coded we could apply it to a real lake. Again, this would require that the lake is dominated by Microcystis. Of course, it is unlikely that we would find such a system anywhere [this is a Taihu insider joke].

Anabaena/Microcystis Lab Competition: This came out of some discussion and ideas we had about light energy and competition between these species.

Anabaena/Microcystis Competition Field: Finally, the whole model can be used to explore the competition between these two species in the field.

Link to the paper:

Link to the YouTUBE movie:



Friday, April 15, 2016

Environmental Capstones

It’s that time of year again... Capstones! Please join us for the 2016 Environmental Capstone student presentations. This year, we have a variety of interesting projects, including designing refugee camps in Haiti and Greece, a floodwall to protect the Logan Airport power station from hurricanes, a water management system at the Blue Hills Ski Area, a dam on the Charles River, an off-the-grid home, a solar system for an industrial client, a food waste composting system for the Town of Melrose and a wastewater treatment plant for the Northeastern University campus. Nine Capstone teams have been working hard all semester 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/EnvCapstone2016s.pdf



Tuesday, April 5, 2016

Freeman Lecture

Please join us for the annual John R Freeman Lecture, which will be held at Northeastern this year. This year’s speaker will be Prof. John H Lienhard V from MIT and he will be talking about desalination. The problem of freshwater availability is growing with the increase in population across the globe, and desalination is one important solution. The event will be on April 11 in room 20 WVF. It starts with a reception (free food) at 6pm and then the lecture at 7pm.
http://web.mit.edu/freeman-bsces/index.html
http://web.mit.edu/freeman-bsces/2016%20John%20R%20Freeman%20Flyer.pdf


Sunday, March 20, 2016

@ASM Conference Report

I am at DCA on my way back to Boston. We just finished a conference on single-cell analyses and agent-based modeling at the ASM headquarters in Washington DC. This is an excellent venue. It was great to be among so many like-minded people and I really enjoyed the presentations and discussions. Here are the slides from my opening remarks and presentation and a copy of the program.

Intro Slides
https://www.dropbox.com/s/3gg5t3fuyzd4hud/atASM_ConferenceIntroduction.pptx?dl=0
Anabaena Slides
https://www.dropbox.com/s/i6x0vhjryo7rng3/atASM_AnabaenaNitrogen.pptx?dl=0
Conference Program
https://www.dropbox.com/s/p2sis3yl4our2f4/atASM%20Conf%20Program.pdf?dl=0


Tuesday, December 15, 2015

Google Presents River Stories Live

Last week I was at Google in Cambridge, where we had an event celebrating the recently published River Stories book and the new Google Trekker image library of the river. I participated in a panel discussion with other River Stories authors where we shared some of our thoughts about the river.



GOOGLE “RIVERVIEW”
https://www.google.com/maps/@42.3575123,-71.0740046,3a,75y,314.04h,87.94t/data=!3m6!1e1!3m4!1sb-z3Splk3JGU0HwJ6CCQZw!2e0!7i13312!8i6656

ENTIRE EVENT ON YOUTUBE
https://youtu.be/iw2Y5JUh2QU

PICTURES
https://www.facebook.com/media/set/?set=a.10153741663224449.1073741921.94705844448&type=3

RIVERSTORIES BOOK
http://www.thecharles.org/news-and-events/publications/river-stories/

Wednesday, December 9, 2015

Dr. Indrani Ghosh named in Top 10 Young Professionals by ENR

ENR editors select young professionals who have “advanced into leadership roles at design and construction firms, and are making an impact in [New England].” Congratulations to my former PhD student Indrani Ghosh, Team Leader of the Sustainability Group at Kleinfelder, who was named as one of the Engineering News-Record’s (ENR) Top 10 Young Professionals. Indrani has established herself as a leader in reframing the engineering design process to include climate change impacts. Congratulations Indrani!

Friday, November 20, 2015

Agent-Based Modeling Class

Please consider taking my ABM class in the Spring 2016 Semester

What is ABM? Agent-based modeling (ABM) is a growing technology that is finding application in many areas from environmental chemistry to microbial ecology to transportation engineering to social sciences and business. It is a "systems" or "bottom-up" approach for understanding how complex systems behave. Individual low-level elements of the system (e.g. bacteria, cars) are simulated and the system-level behavior (e.g. population density, traffic congestion) emerges as a result of the cumulative action and interaction of these low-level entities. This is different from the traditional "top-down" approach where system-level state variables are modified directly using differential equations.

Course overview. The course is geared towards a multi-disciplinary audience, and open to students from engineering, environmental science, biology and chemistry, sociology, business and others. Topics include introduction and motivation of ABM, basic principles, comparison to other methods (e.g. cellular automata, individual-based modeling), available software, computational strategies (e.g. up-scaling, agent accounting), model development, model calibration and testing, and model application.  A number of case studies from the literature in various disciplines will be reviewed and discussed. A major part of the course will be a hands-on term project. Students are encouraged to explore the use of ABM for their own research interests for the term project. The project will be implemented using the NetLogo ABM framework. NetLogo models can be served as Java Applets on the Internet and the students will be required to submit their final papers as web pages, which will be published on the course web page. The text will be "Agent-based and Individual-based Modeling: A Practical Introduction" by Grimm and Railsback (2011).