Promise and Challenges in Systems Microbiology Workshop Summary (2004) / Chapter Skim
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2 Workshop Proceedings
2 Workshop Proceedings
Pages 3-26
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From page 3... ...
Other microorganisms play a role in the breakdown of pollutants but Lovicy explained that Geobacter is special in that it dominates many microbial communities in subsurface environments in which oxygen is absent but iron oxides are abundant. Molecular studies, which avoid culture bias, have demonstrated that geobacters account for about half the microbial community in environments in which metal reduction is important.
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From page 4... ...
Geobacters can serve as biopowered antenna grids or play a role in novel biosensing devices. They can convert such waste organic matter as sewage sludge, domestic wastes, and industrial organic wastes to electricity; and they can convert renewable biomass to electricity instead of ethanol.
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From page 5... ...
oxides that serve as their primary electron acceptor in subsurface environments. Although geobacters were believed to be nonmotile, inspection of the preliminary genome sequence revealed genes for flagella slender outgrowth of cells used for swimming and other forms of locomotion and that suggested that the microorganisms might be motile after all, at least under some conditions.
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From page 6... ...
This exquisite architecture of symbiotic processes lies at the core of Leadbetter's work. Specifically, his research focuses on the intricate dynamics of the hindgut community of the California, or Pacific, dampwood termite, Zootermopsis angusticollis, and on the mutualistic symbiosis formed between the termite and the microorganisms .
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From page 7... ...
After discussing the peculiarities of the hindgut environment, Leadbetter introduced a number of microbial communities that live in the hindgut and presented an array of biochemical processes that are carried out by them. He then described aspects of one of the processes, called acetogenesis the process of generating organic carbon in the form of acetate from inorganic carbon catalyzed by bacteria which is the focus of his research at the California Institute of Technology.
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If the host fails, it's all over. Or if the microbial community fails the host, it's really all over." New generations of microorganisms have been passed from termite to termite in this manner for more than 12 million years.
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Including research on microbial communities in system-based studies could provide a broader perspective on controls of biological processes and how they operate in and among .
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A tidal salt marsh is an example of a whole intact ecosystem with multiple variables with respect to the flow of water in and out of the system. A system can be on the molecular scale.
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Geabacter and Termite Hindgut as Mode! Systems The workshop planners chose Geobacter and termite hindgut organisms as extreme cases of single-organism and multiorganism systems for comparison and to maintain the focus of discussion.
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He added, however, that existing simulation technology is inadequate because biological dynamics are stiff and stochastic with lots of random variables and multiple scales. Processes in biological systems occur in different time scales, and fast dynamics coexist with slow dynamics.
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Without knowledge of the governing principles, scientists may never truly understand how a system functions even if all its components are known. Most of the governing principles are related to efficient energy flow, particularly resistance to fluctuations, Doyle explained.
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Computation infrastructure for modeling must be able to integrate dynamic measurements of multiple scales. Workshop participants agreed that the flood of data from high-throughput techniques makes it clear that biological research needs to move forward in a more quantitative manner than it has in the past.
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The day and night cycle and seasonality may be the governing principles for some processes and have minimal effect on others. Doyle thought that that was a good example because it is the changes that result from the two cycles that make a big difference in New Yorkers' response strategies.
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From page 16... ...
Lovicy reasoned that once the geobacters' preferred electron acceptor is depleted, the next preferred one is sulfate; the sulfur reducers flourish because of the abundant amount of acetate that is available for their consumption. Doyle pointed out that although Lovicy constructed a mode!
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A day and night cycle and maybe seasonality can be included to improve understanding of the underlying architecture of the community. But every system is different.
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From page 18... ...
A systems approach to research in microorganisms and microbial communities requires novel experimental tools for detecting and measuring biochemical processes such as gene expression, metabolic activity, and protein production across the entire system, whether the system is defined as a genome, a cell, or a cell culture. To make sense of information generated from measurements of systemwide activity, assays must be repeated continually, each time monitoring the system under a different set of conditions.
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From page 19... ...
for developing an especially creative strategy for generating research about cystic fibrosis. "The Foundation makes metric chips available for about $150 if you write to them with a short proposal and say, 'I'm going to study this particular aspect of Pseudomonas aeruginosa.
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Tames Frederickson (Pacific Northwest National Laboratory) emphasized the importance of basic biological research.
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There has been some effort by software engineers to connect databases and to create a distributed system whereby researchers can view their own annotation in a central searchable system. Any new database would be registered to the central system so that researchers can query the central system and obtain information from different databases.
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From page 22... ...
is important because the people who wire up the lines are different from the people who decide where the structures go. In the past, when engineers built an airplane, the specifications called for running a hydraulic line directly through a big piece of metal, which, of course, cannot be done.
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From page 23... ...
We can take money away from single investigators and dump it into large collaborative interdisciplinary projects, but it's not going to have the same impact." Dennis went on to say that NSF has a new Frontiers in Integrated Biological Research program that provides $1 million a year for 5 years. Many researchers believe that such funding is insufficient to meet the goals at hand and that pulling together a large team for a short period like 5 years is not realistic.
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One suggested strategy involved transforming graduate-level microbiology courses into one integrative microbiology course to make room for quantitative courses, but this strategy was unpopular with the biologists in the group. Lovicy objected to universities' reducing their offering of microbiology courses.
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We don't do a good job of teaching people to collaborate." Future scientists may be encouraged to collaborate through carefully designed programs at the undergraduate and graduate levels, but postdoctoral researchers may be encouraged by the funding of projects that force them to work across disciplines with biologists, mathematicians, and computer scientists. Experienced scientists can look for new short courses specially designed to share knowledge across disciplines.
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From page 26... ...
Biochemistry, organic and inorganic chemistry, physics, economics, and other disciplines all play roles. CONCLUDING REMARKS In the final discussion, Donohue cautioned that the value of basic biological research and benchwork such as genome sequencing, which Lovicy had described earlier as the too!
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