Off to Israel & Geosyntec Seminar

Hi Everyone:

Ok, so I am off to Israel today. I am part of a delegation of about 50 people that are traveling as part of the “Massachusetts Water Innovation Mission to Israel”. We will visit some of the water infrastructure and meet with professionals and academics. I hope to learn more about water resources in this stressed region, and also make some connections for future research collaborations. If you want to learn more about this trip, you can read this article in Xconomy: http://goo.gl/ahpCZ.

I also presented a research seminar at Geosyntec Consultants, an environmental engineering and science company: http://www.geosyntec.com/UI/Default.aspx
I gave an overview of my research program and talked about a recent project looking at intraspecific nutrient heterogeneity. You can get my slides from here: https://www.dropbox.com/sh/81tv7ozuyu6a05x/oidkXVDlVg/2012/Geosyntec_Charles_Quota_Heterogeneity.pptx

Best regards,
Ferdi

New paper: 3rd in the “in silico series”

Hello People!

I am excited to announce the paper “Escherichia coli adapts to tetracycline resistance plasmid (pBR322) by mutating endogenous potassium transport: in silico hypothesis testing” to be published in FEMS Microbiology Ecology.http://onlinelibrary.wiley.com/doi/10.1111/1574-6941.12019/abstract

This is the third paper in my “in silico series”. The other two papers in the series are:

Carrying photosynthesis genes increases ecological fitness of cyanophage in silicohttp://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.01866.x/full

and

Resonating circadian clocks enhance fitness in cyanobacteria in silicohttp://www.sciencedirect.com/science/article/pii/S0304380010001602

Take a quick look at the model schematic in each paper (below). I think they nicely capture the spirit of the series. Specifically, all show cells with intracellular mechanisms (resolved down to the level of individual genes) [systems biology] and populations made up of individual cells [systems ecology]. This approach [systems bioecology] explicitly investigates the role of genes in the fitness of microbes.

Prochlorococcus model:



Synechococcus model: 

E. coli model: 

For this paper, you may also like ...

… the source code:https://www.dropbox.com/sh/mgj7glkfgohljxg/9f73m3eldl

… the movie:http://youtu.be/Dt0-YEMtTiA

… the poster:https://www.dropbox.com/sh/81tv7ozuyu6a05x/7Vfkk1l2nS/2012/ISME_Tetracycline_Resistance.pdf

The fourth paper planned for the series is the yeast bet hedging one I am presently developing.

Do you have any interesting problems that can be investigated with this approach? I am always interested in talking and collaborating. Drop me a line!

Best regards,
Ferdi

“Urban Water” Faculty Position Opening in CEE

Hello World,

The Northeastern CEE department is searching for a new faculty member in the area of urban water. Here is the add description:

Northeastern University seeks faculty candidates for tenured or tenure-track appointments at the assistant, associate, or full professor level in the Department of Civil and Environmental Engineering and in conjunction with interdisciplinary positions across the campus. The department is in the midst of a significant, multi-year expansion in size and scope, including faculty, facilities, and programs within several disciplines and across disciplinary boundaries. The successful candidate will be expected to demonstrate a proven ability to sustain a research program with an emphasis on interdisciplinary and translational research, teach both undergraduate and graduate classes, and be an active, recognized leader in the discipline. Applicants with a distinguished record and vision in environmental engineering and related fields will be considered for the CDM Endowed Professorship in Civil Engineering . We invite applications from individuals who can contribute to areas of civil and environmental engineering related to Urban Water and Environmental Systems Engineering. Other related interdisciplinary positions are also available via separate application and are described at http://www.civ.neu.edu/civilsearch.

https://neu.peopleadmin.com/postings/21971

Please pass this along to anyone you think may be interested, and contact me if you have any questions.

Best regards,
Ferdi

ISME Report and Dimensions Grant

Hello People:

So last month I was at ISME in Copenhagen. It was nice to see some friends, and also listen to presentations from people I know from the literature. The main thing I took away from the conference is that individual-based observations (IBO) (e.g. single cell genomics, NanoSIMS, etc.) are really taking off. It seems that every session I visited had at least one presentation with some sort of IBO. To me, as an individual-based modeler (IBM), I see a lot of potential to make progress using IBMs. “IBMs for IBOs” is a main motivation for using IBM (e.g. Hellweger and Bucci, 2009),

I am glad to announce that I will be busy with a new NSF project with Hans Paerl (UNC), Steve Wilhelm (UTK), Greg Boyer (SUNY Syracuse), Wayne Gardner (UT Austin) and Mark McCarthy (U Guelph) entitled “Dimensions: Collaborative Research: Anthropogenic nutrient input drives genetic, functional and taxonomic biodiversity in hypereutrophic Lake Taihu, China”. I am very excited to work with a great team on an important problem. Here is a blurb on the CEE web site: http://www.civ.neu.edu/news/index.html#hellweger2

This semester I am teaching Hydrology and am working on my yeast bet hedging model.

Best regards,
Ferdi

Off to ISME, then vacation...

Hi Everyone:

Today, I am off to Copenhagen for a meeting of the International Society of Microbial Ecology (ISME). I am presenting a poster entitled “adaptation of bacteria to ameliorate the metabolic burden of carrying antibiotic resistance genes (a systems bioecology modeling analysis)”. I am really looking forward to this meeting. There are a lot of interesting presentations and “roundtable discussions”. You can learn more about the conference here: http://www.isme-microbes.org/isme14/

When I get back its time to do some vacation with family. On the agenda is a 4-day stretch of the Appalachian Trail (AT) in Vermont. It will be an adventure...

Then its full speed into the semester. I am teaching two graduate classes: Hydrology and Surface Water Quality Modeling. My goal for research for the Fall semester will be to finish the yeast bet hedging model (see my previous post)...

Farvel (goodbye in Danish),
Ferdi

Take a chance on me..., Cyanobacteria ecology & Web site updates

Hi Friends:

The last couple of weeks I have been immersed in a new project, which is about bet hedging in yeast. It all started with a very exciting paper I read by Levy et al:
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001325
There is a tremendous amount of data in that paper, but the most interesting findings (from my perspective) is that they see a correlation between age, growth rate and stress resistance. The idea they put forward is that old cells are best candidates for being stress resistant persistors, because they contribute relatively less to the population growth anyway. I am working on developing a model to investigate this question. This is one of the most joyful times for me, when I learn about a new problem, read up on the literature, start coding the model, etc... I feel like I am back in graduate school.

Our summer Charles River work has started again. This year, PhD student Xiaodan Ruan, RETs Judy Luber-Narod and Jalal Ghaemghami, and YSPs Nicholas King and Jackie Ly will be focusing on understanding the ecology of toxic cyanobacteria in the river. Last year’s research was hampered a bit because we did not get a significant bloom. This year we already had a big bloom and temperatures are high, so we expect to get more (bad for the river, good for research).

Some updates on my web page: As you can see on my homepage (www.systemsbioecology.org), I make use of other sites to host my stuff. For example, I have a YouTube channel for all my videos, and my blog is here at Blogspot. I have found this strategy to be quite useful, and I now also started using Dropbox to host my files for Talks, CV and Models.

Best regards,
Ferdi

Continuing Education

Hi Friends:

My efforts to further my skills continue. Tomorrow I am off to Iceland to take a 1-week short course on Systems Biology modeling, taught by Bernhard Pallson and co-workers. My efforts in this area motivated by trends in two areas, which I believe will soon converge. First, ecological models (Systems Ecology) are increasingly resolving intracellular workings of microbes. Second, microbe models (Systems Biology) are increasingly used to ask ecological questions, or put into ecological context. These fields are combining, in what can be called Systems BioEcology. I envision models of lakes or oceans, teeming with systems biology - enabled agents, acting, interacting, LIVING! I am very excited to learn more about Systems Biology models.

On other fronts, check out this nice article on our capstone project: http://www.northeastern.edu/news/2012/06/watercapstone/

Bless bless (goodbye in Icelandic),
Ferdi

EPA Merit Award for Charles River Research

Hi Friends: Greetings from Istanbul (vacation). This month I am happy to share with you that the EPA has decided to recognize the research our team has done over the past eight years on the water quality of the Charles River. They awarded me the Environmental Merit Award. See an article on the NU web page here: http://www.northeastern.edu/news/2012/04/swimming-in-that-dirty-water/ I am very pleased about this and it made me think back to when I interviewed to join the faculty here in 2004. In my seminar I said I would develop a research program focusing on the water quality of the Charles, with a special focus on swimming. This award makes me feel that I am making good on that promise. But we are not done and will not stop until we can swim! In 2004 we started by looking at E. coli, but in the past couple of years our focus has increasingly shifted towards cyanobacteria. This summer we have a pretty intensive sampling and analysis effort, including daily sampling at multiple locations, doing cell counts, nutrients, N fixation and other parameters. Take care, Ferdi

2012 Environmental Capstones

Please join us for the 2012 Environmental Capstone student presentations. This year, the class is focusing on designing a "shovel-ready" drinking water system for the village of Bbanda, Uganda. The project includes pumping of groundwater, tank storage, and distribution to a number of tap stands. This is a very exciting project, because Northeastern's Engineers Without Borders (EWB) student group is planning to actually implement this design starting later this year. Three Capstone teams are working in competition to come up with the best design. The details are posted here: http://www1.coe.neu.edu/~ferdi/files/EnvCapstone2012.pdf

Happy St. Patrick's Day

Hi People:

I am please to announce that our “EBPR paper” is up on the ES&T website:
http://dx.doi.org/10.1021/es204052p

This paper is the “brother” of the “quota paper” I discussed in my January 2012 post. Both papers focus on heterogeneity in internal nutrients, and provide (the first ever?) comparison of individual-based observations and modeling of internal nutrients. The quota paper focuses on phytoplankton and the measurements were made using SXRF (by Ben Twining at Bigelow). The EBPR paper focuses on wastewater bacteria and the measurements were made using Raman (by April Gu here at NU).

On the personal front, I have been able to take some R&R. This winter (which looks to be pretty much over by now) I went up to Killington for skiing twice [although the weekends picked turned out to be freezers 1/14 & 2/11] and climbed up Mt Washington [luckily on a not-so-windy day].

Now my PhD student Neil and I are off to UW Milwaukee for a couple of days to talk with John Berges & Co. about death in phytoplankton...

Take care,
Ferdi

I am learning...

Hi Friends:

In the past couple of weeks I have found myself in an increasingly rare situation of having some time on my hands. I am using this opportunity to continue to educate myself. Specifically, I am learning about genome-scale modeling, which today is often referred to as “systems biology modeling”. Although I have not done anything at the genome scale, I do use systems biology concepts (i.e. complex systems, bottom-up simulation, emerging properties) in my research. I therefore feel I should know more about these genome scale models. Also, I may do this in future projects. So, I am going through the book “Systems Biology: Simulation of Dynamic Network States” and associated narrated slides by Bernhard Palsson. I find the narrated slides quite useful. Here is the link: http://systemsbiology.ucsd.edu/Publications/Books/SB2LectureSlides

I am tempted to set up one of those models on my computer and play with it. We will see how far I get before other obligations take over...

Take care,
Ferdi

January 2012 News

Hi Friends:

OK, so after an ambitious start over a year ago, I haven’t written much here. But my New Year’s resolution is to update this blog at least once a month. I even created a recurring reminder in my Google calendar...

The recent news I would like to highlight this month is the publication of the “quota paper”, which wraps up an NSF project on agent-based modeling of phytoplankton. In fact, the subject of the paper - heterogeneity in internal nutrient content of phytoplankton - is what got me started on agent-based modeling in the first place, several years ago. With the help of my collaborator - Ben Twining - we now have observations and simulations of P quota heterogeneity, and the results are quite interesting (I think).

You can access the paper from this link:
http://www.springerlink.com/content/bhpj205346h87617/

Also, there is a video that goes along with it, and you can get it here:
http://youtu.be/9qnj2ZYCR1s

OK that’s it for now (until next month),
Ferdi