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
Friday, December 14, 2012
Thursday, November 15, 2012
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:
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
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
Wednesday, October 24, 2012
“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
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
Saturday, September 15, 2012
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
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
Wednesday, August 15, 2012
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
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
Monday, July 16, 2012
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
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
Friday, June 15, 2012
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
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
Subscribe to:
Posts (Atom)