mBiosphere

Big Changes in the Big Easy: ASM2011 "Not your father's microbiology meeting"

Responding to input and requests from membership, ASM has planned some big changes for the General Meeting in New Orleans this spring, including a significant reduction in the number of scientific sessions and the debut of a two-track system that underscores the distinctions between the medical and general microbiology segments of the meeting. A commentary appearing in mBio this week summarizes the recommendations of a committee tasked with overhauling the 100-year-old meeting and the rationale for the changes in store.

“We are at a time in the history of biology where microbiology should be front and center,” says Margaret McFall-Ngai, Chair of the ASM General Meeting and a member of the task force. “We have to have a meeting that integrates microbiology and demonstrates how microbiology interfaces with other aspects of science. If we were to stay the same we would miss a huge opportunity.”

"This is not your father's microbiology meeting," jokes McFall-Ngai.

McFall-Ngai and the rest of the task force were charged with evaluating the organization of the meeting and helping to chart its future course. In addition to McFall-Ngai, task force members included the Chair, Jeff Miller, Vice-Chair of the General Meeting Arturo Casadevall, ASM President Bonnie Bassler, Roberto Kolter, Stan Maloy, and Lucia Rothman-Denes.

Perhaps the first change repeat attendees will notice is the start day: the 2011 opening session will take place on Saturday evening instead of Sunday. Three full days of scientific sessions will follow the opening session, ending on Tuesday evening – a half day shorter than the old program, which went from Sunday to Thursday afternoon.

Another obvious change is the move to a two-track system that includes a “medical microbiology track”, which caters to the needs of the clinical community, and the “general microbiology track”, which encompasses the rest of the sessions. Arturo Casadevall is adamant that the two-track system doesn’t represent a schism, but rather that it reflects the fact that the two groups look for different things when attending a meeting.

“They have different needs. In medical microbiology, they have a need to go to a meeting to get [continuing education] updates, whereas the scientists don’t really have that requirement as a part of their job,” says Casadevall. Even in the past, he says, the General Meeting was pretty neatly divided between the two themes, each with its own sessions. “What we have done is we have just consolidated everything into two tracks.”

McFall-Ngai says the two-track system should not limit movement or cross-talk at the meeting. “We have made sure that the timing of each session, and each presentation within each session, and so on, are completely in lock step. Somebody who is very integrative can go back and forth across the two tracks. There will be no timing problems.”

The total number of scientific sessions will also be cut in response to requests from attendees at past meetings who complained that there was too much overlap among simultaneous sessions and too many sessions to attend, says McFall-Ngai.

McFall-Ngai and Casadevall agree that the General Meeting faces competition from other, smaller microbiology meetings that it did not face a generation ago, and many of the changes made to ASM2011 are aimed at enhancing the chief strength of the meeting: integrative science.

“Why would I come to the General Meeting?” says McFall-Ngai. “Because I want to put my work in the context of the larger field of microbiology. If the General Meeting were of such a format as it has been in the past where we looked at very focused topics, any given individual might come and go to a series of sessions that might be better represented at a Gordon conference or small ASM conference.”

“One of the major functions of the General Meeting is to integrate across the entire spectrum of microbiology. We have asked the division chairs and reps to make an effort to increase participation and think about these issues of integrating across the topics,” she says.

McFall-Ngai says it isn’t always easy for humans to embrace change, and the former format of the General Meeting has some inertia among the membership, but she is confident that the differences will make for a better experience for attendees. Speaking for the organizing committee, McFall-Ngai extends an invitation to ASM’s membership to come to New Orleans in May to participate in the meeting in its new incarnation.

“We’re going back to a town that’s had some challenges and struggles and I’m enthusiastic about supporting their economy and bringing the meeting to New Orleans again.”  

ASM's General Meeting website: http://gm.asm.org/

Bioluminescent E. coli leaves a glowing path in the bloodstream

Many urinary tract infections (UTIs) can be cleared up with a big bottle of cranberry juice, but when these infections go bad, they can be really, really bad. Uropathogenic E. coli is the leading cause of uncomplicated UTIs, and if left untreated it can proceed right up the urinary tract to the kidneys and sometimes even into the bloodstream. Although the results are usually devastating for patients, the specifics of what E. coli does once it reaches the bloodstream are mostly unknown.

The solution to this problem might just be inside a glowing mouse. In a new study published in mBio, scientists apply a bioluminescent reporter gene in E. coli to learn more about the where and what of the bacterium’s activities during bacteremia. After injecting mice with the bioluminescent strain of uropathogenic E. coli, the researchers used biophotonic imaging – which, incredibly, detects light from the bacteria right through the skin of live mice – to monitor the infection over the next 48 hours. The imaging revealed that E. coli moved all around the mice, but appeared to localize in discrete sites. Comparing these results with infections with various E. coli strains that lacked genes for suspected virulence factors in the blood stream enabled the authors to either confirm or reject the role those genes might play in virulence. The authors speculate that this model of bacteremia could be used to identify other, new bloodstream virulence factors in the future.

Pandemic flu still has a few tricks up its sleeve

The ruckus over swine flu may have passed, but scientists and public health authorities are still keeping tabs on the virus and on how it might evolve in the coming months and years. The authors of an article published in mBio this week took a close look at how the virus might recombine with the seasonal flu virus and found that given the opportunity, pandemic flu might yet provide some serious public health problems. When the two viruses were combined for several generations in human airway cell cultures, they reassorted their genes and produced a pandemic strain that was more virulent than it began, but only when the pandemic strain started out as numerically dominant. The study demonstrates that the emergence of a pandemic H1N1 strain of higher virulence is possible.

Keeping the fungi away: did warm bodies put mammals on top in evolutionary history?

Did a warm body put mammals at the head of the evolutionary rat race? Aviv Bergman and Arturo Casadevall present evidence in an Observation piece in mBio this week that the warm mammalian body is no accident and our relatively high body temperature could represent the perfect evolutionary compromise between metabolic costs and the increased fitness that comes with resistance to fungal diseases.

Using a computer model, Bergman and Casadevall pitted the cost of maintaining excess metabolic rates that keep mammalian body temperature high against the benefits of evading those nasty fungal infections. Their calculations show that the ideal body temperature to minimize costs and maximize fitness falls at 36.7°C – very close to the average mammalian body temperature. To Bergman and Casadevall, this supports the idea that overcoming susceptibility to fungal disease was a key to mammals’ success during the Tertiary geologic period, a time when mammals supplanted reptiles as the dominant land-based vertebrates.

ZAP! Manipulating Bacterial Metabolism With an Electrode

Humans have been getting microbes to do our bidding for millennia by taking their inherent processes (or engineered new processes) and applying them to making foods, drinks, drugs, biofuels, and other products. In most approaches, we feed them the right ingredients and wait for the good stuff to come out the other side. A study appearing in the latest issue of mBio reveals an electrifying new way to get what we want from bacteria: researchers manipulated bacterial metabolism by pulling excess electrons out of the mix and into an electrode.

Flynn et al. developed their system to coax an ethanol-making transformation out of Shewanella oneidensis. Using genes from Escherichia coli and Zymomonas mobilis, they created a custom plasmid that enabled S. oneidensis to convert glycerol to ethanol, but since the fermentation to ethanol is an unbalanced one, they needed to go one step further. By sticking an electrode into the reaction to draw off two electrons for every glycerol molecule, they were able to make the reaction favorable, thus making two valuable products in one step: ethanol and electricity.

“There’s been intense interest in microbe-electrode interactions for at least a decade now, and a lot of the interest has come from trying to produce electricity from waste organic matter,” says Derek Lovley, Distinguished Professor in the Department of Microbiology at the University of Massachusetts and a member of mBio’s Board of Editors. Lovley says the approach Flynn et al used is novel because instead of using the electrode solely for the purpose of generating electricity, they used it to coax a product out of the bacterium.

“This shows one of the alternatives – that you can use electrodes to manipulate microbial metabolism. It’s a proof of concept study, but it gives the idea that you could use the electrode to influence other complex fermentations,” says Lovley.

The authors assert that using electrode-interfaced bacteria expands the landscape of possibilities for metabolic engineering and synthetic biology strategies for producing biofuels and other materials.

Lovley agrees. “It was a very clever approach, and it helps open our eyes to how we might use microbes and electrodes for other practical applications,” he says.

Down with cooperation! Better to make methanogens do all the work

Mutually-beneficial cooperation is a high ideal, but for bacteria and archaea, working together isn’t always a good solution. Now a team at Pennsylvania State University has worked out a system that could work better than inter-domain cooperation: by putting genes from a bacterium into an archaeon, they got the archaeon to do all the work on its own. The study appears in the latest issue of mBio.

To transform organic materials to methane usually calls for the skills of a consortium of bacteria and archaea, but these multi-species food chains are fragile and require painstaking care and feeding. To get around these problems and make a useful product, Lessner et al. placed MekB, a broad- specificity esterase gene from the bacterium Pseudomonas veronii, on a plasmid and put the plasmid in the archaeon Methanosarcina acetivorans. They then fused the gene to a constitutive M. acetivorans promoter. The “Franken-archaeon” put its new gene to good use: it completely converted an industrial solvent and a naturally occurring compound to methane and carbon dioxide. (I wonder if the lab was filled with hysterical cries of “It’s alive!!!” that day?)

“I think this is interesting at two levels,” says Derek Lovley, Distinguished Professor in the Department of Microbiology at the University of Massachusetts and a member of mBio’s Board of Editors. He continues, “One is the practical level, which was you can make methane, a useful fuel. Two is that they show you could expand the range of compounds that a methanogen could make methane from.”

The practical aspects of this work are hard to miss: methane is a valuable biofuel that has some significant advantages over the more well-known ethanol. By expanding the list of substrates for making methane, the engineered pathway created by Lessner et al. could simplify the whole food chain problem and lead to more efficient conversion of complex biomass to methane.

Lovley points out the implications for making other products as well. “They show that maybe you could get more complex substrates to be metabolized in a single organism if you just were to introduce the appropriate genes,” so that industrial process that took many steps might only take one, says Lovley. 

Ground zero in a fight for interdisciplinary knowledge: microbiology and immunology

This week in mBio, our Editor in Chief and a member of the Board of Editors weigh in on the relationship between two natural allies in medicine: microbiology and immunology. The two disciplines have a long history that stretches back to when they each emerged in the late 1800s, and since then they have sometimes been closely connected, sometimes not. Christine Biron and Arturo Casadevall outline a brief history of how the disciplines have intertwined in Departments of Microbiology and Immunology at universities and medical schools over the years, and argue that some of the greatest breakthroughs in medicine have arisen from close collaboration between the two. They contend that since each field has something the other lacks, their integration is important for advancing understanding of the immune system and microbes. 

And in a first for our journal, Biron and Casadevall have included a cartoon to illustrate their point about the sometimes distant relationship between the disciplines. 

 
But why a spider and a fish...? 

Open-access Publishing: Reaching Beyond Academia?

Who benefits when scientists publish articles in open-access journals like mBio? I talked recently with someone who thinks a lot about open-access publishing, and he had some surprising things to say. He tells me that publishing an article in an open-access journal earns it the same number of citations as publishing in a “traditional” subscription journal, but open-access articles are also downloaded more often, which may result in greater readership and a broader reach.

Phil Davis, a postdoctoral associate at Cornell University, studies the use and dissemination of open-access content, applying scientific methods to scientific publishing. He says open-access science publishing seems to be on the upswing, with fee-for publishing journals like the PloS family of journals and mBio gaining recognition. Some would argue that unfettered access to scientific findings online is a uniformly positive development for research, and that scientists can only benefit from having their work freely available to all.

But Davis isn’t satisfied with what he sees as unproven platitudes about the benefits of open-access and argues that regardless of what you might believe about open access publishing, you’ve got to back up those assertions with measurements and facts.

While earning his Ph.D. at Cornell, Davis tested the notion of scientific impact – how often articles are viewed and cited – in an experiment in which he randomly assigned articles to either open-access (which were freely available on the publisher’s website), or subscription access. He says articles published as open-access were cited just as often as the subscription-access articles, but the kicker is that they were downloaded more frequently. So, presumably, the open-access articles were read by more people than the pay-for-access articles (that’s my interpretation). Davis was interviewed about his work for an article on "Free Journals" in the August 20 issue of Science magazine.

Davis takes this download disparity as evidence that open-access articles have the potential to reach beyond the usual consumers of scientific research findings (researchers at major universities and research institutes) to other people interested in the science who don’t have the benefit of institutional journal subscriptions.

Davis sees this as an important benefit. “When we count citations, we are measuring only the effect of one user community – scientific authors.  There are many other communities that consume, but do not contribute to, the scientific literature,” he says.  These communities may include lecturers, practitioners, industry researchers, students, and the lay public, says Davis.

Davis has published his work under such provocative titles as, “Open Access: Increased Citations Not Guaranteed”, and “Do Open-Access articles really have a greater research impact?”. Do his publication list and his enthusiasm for scrutinizing the issues indicate he doesn’t support open-access publishing? “Not at all,” he says.

“Science is based on the principles of openness and sharing. Science is a public domain,” says Davis. “But we need to make sure that the publishing process has integrity, we need to make sure that the best possible science is published.”