Click for "Microbes After Hours" videos
Host: Jeff Fox with special guests, Julia Yeomans and Vikas Berry.
Julia Yeomans of Oxford University in the United Kingdom and chemical engineer
Vikas Berry of the University of Illinois, Chicago, talk with Jeff Fox about their separate, but in some ways similar, research efforts in which they use bacteria to perturb and probe the physical properties of simple machines, in one case, and unusual materials, in the other.
Yeomans and her collaborators are developing models of miniature windfarms in which 64 rotors are arrayed regularly within a symmetric lattice, to which actively swimming bacteria are added. Under appropriate constraints, the bacteria spontaneously organize in such a way that they induce neighboring rotors to spin in opposite directions. Single rotors would be "kicked around randomly," the researchers say, but the arrayed rotors form "a regular pattern." Yeomans says, "Nature is brilliant at creating tiny engines, and there is enormous potential if we can understand how to exploit similar designs."
Berry and his collaborators aligned rod-shaped gram-positive bacteria and then vacuum-shrunk a graphene sheet over them, thus forming nanoscale ripples into the otherwise smooth graphene surface. "The current across the graphene wrinkles is less than the current along them," says Berry. "We envision that with graphene one could make the smallest wavelength wrinkles in the world—about 2 nanometers. The structure is different, and the fundamental electronic properties are new."
Right click to download MMP017 (35 MB .mp3, 48 minutes).
This story was featured in the September 2016 issue of Microbe Magazine.
Tweet Jeff your questions about this episode or just say hi!
Host: Jeff Fox with special guest, Emma Wilson.
Emma H. Wilson of the University of California, Riverside, talks with Jeff Fox about efforts, with her collaborators to determine more precisely how Toxoplasma gondii parasites disrupt the mammalian brain—in this case, the brains of mice. This same parasite infects about one-third of the human population, but is held in check by the immune system unless those host defense mechanisms become impaired.
Wilson and her collaborators find that these parasites interfere with the cycling of the neurotransmitter glutamate within the central nervous system, blocking its uptake by astrocytes, widely distributed cells within brains that are intertwine with and thus work very closely with neurons, which are the main cells for transmitting nerve impulses throughout the central nervous system.
Some damaging effects of the parasites can be reversed by treating the mice with a drug—in this case, it happens to be an antibacterial drug but here acts by a separate mechanism-- that helps to restore the glutamate transport protein in astrocytes. In this way, it partly corrects that glutamate imbalance within the brain.
Right click to download MMP016 (27 MB .mp3, 37.5 minutes).
This story was featured in the August 2016 issue of Microbe Magazine.
Tweet me your questions about this episode or just to say hi!
Host: Jeff Fox with special guests, Carolyn Shore and Ruben Tommasi.
Carolyn Shore of Pew Charitable Trusts in Washington, D.C., and Ruben Tommasi of Entasis Therapeutics in Waltham, Massachusetts, talk with Jeff Fox about what’s needed to identify and develop new antimicrobial agents to treat infections caused by bacterial pathogens, with an emphasis on gram-negative bacterial pathogens.
According to that recent report from Pew Charitable Trust, which is based in Philadelphia, the challenges facing developers of such antibiotics fall into four main categories: developing a better understanding of the workings of gram-negative bacterial pathogens, a shortage of candidate drugs whose chemical design focuses on bacterial pathogens, an assessment of non-traditional efforts to control microbial infections, and an overview of what’s needed in terms of expertise and of sharing information among investigators in this field to meet these challenges.
Right click to download MMP015 (27 MB .mp3, 37.5 minutes).
This story was featured in the July 2016 issue of Microbe Magazine.
Tweet me your questions about this episode or just say hi!
Host: Jeff Fox with special guests, Gemma Reguera and Geoffrey Gadd.
Gemma Reguera of Michigan State University in East Lansing and Geoffrey Gadd of the University of Dundee in Scotland talk with Jeff Fox about their efforts, to probe some of the electrical properties of materials produced naturally by specific microorganisms. Thus, Geobacter bacteria make protein filaments, called pili, that act as nanowires, transporting 1 billion electrons per second, according to Reguera and her collaborators. Analytic evidence suggests that the electrons move along these proteins by a thermally activated, multistep hopping mechanism, enabling these bacteria to draw electrons from the extracellular milieu.
Meanwhile, the fungus Neurospora crassa can transform manganese into a mineral composite with favorable electrochemical properties. The fungal cells produce filaments that take up manganese, which after heat treatment forms structures that have electrochemical properties that are suitable for use in supercapacitors or lithium-ion batteries. The carbonized fungal biomass-mineral composite has excellent cycling stability and retains more than 90% capacity after 200 cycles, according to Gadd and his collaborators.
Right click to download MMP014 (32.5 MB .mp3, 43 minutes).
This story was featured in the June 2016 issue of Microbe Magazine.
Tweet me your questions about this episode or just say hi!
Host: Jeff Fox with special guests, Ron Milo and Shai Fuchs.
Ron Milo of Weizmann Institute of Science in Rehovot, Israel, and Shai Fuchs at the Hospital for Sick Children in Toronto, Canada, talk with Jeff Fox about their efforts, with Ron Sender at Weizmann, to redetermine the ratio of microbial to human cells. This ratio, widely cited as being 10 to 1, is closer to even, they find, while arguing that it may prove helpful in the long run to have a better and more rigorous grasp of how many cells there are in both the host and the microbiome.
Right click to download MMP013 (30.5 MB .mp3, 42 minutes).
Milo, Fuchs, and Sender update the widely-cited 10:1 ratio, “showing that the number of bacteria in our bodies” is instead “of the same order as the number of human cells. Indeed, the numbers are similar enough that each defecation event may flip the ratio to favor human cells over bacteria.”
Thus, the total number of bacteria in the ″reference man″ is about 3.9 x 1013 with an uncertainty of 25%, and a variation over the population of 52%. For human cells, they find that the hematopoietic lineage of cells plays a “dominant role, accounting for about 90% of all body cells. They also revise estimates to the a new total of 3.0 x 1013 human cells in a 70-kg ″reference man″ with a 2% uncertainty.
This story was featured in the May 2016 issue of Microbe Magazine.
Tweet me your questions or just let me know you heard this episode!
Host: Jeff Fox with special guest, Jon Telling.
Jon Telling of Bristol University in Bristol, United Kingdom talks with Jeff Fox about his findings suggesting that the grinding of glaciers over rocks can liberate hydrogen, which, in turn, drives the growth of methanogens within microbial ecosystems.
Right click to download MMP012 (32 MB .mp3, 44 minutes).
Telling and his collaborators provide evidence that the grinding of rocks beneath glaciers can free hydrogen gas from minerals in those rocks. In turn, that hydrogen provides energy to furnish the metabolic needs of particular microorganisms, called methanogens, that produce methane and other organic molecules from carbon dioxide through a non-photosynthetic process.
“This is an important new mechanism for hydrogen production,” says Christopher McKay, senior planetary scientist at the NASA Ames Research Center at Moffett Field, Calif., who was not involved in conducting this research. “Water-water reactions producing hydrogen are usually associated with high temperature systems, and it has been thought that they could not operate at low temperatures. This shows how hydrogen can be produced in an ice-covered system and has huge implications for ice-sealed Antarctic ecosystems such as Lake Vida and for the ice-covered ocean moons of the outer Solar System, Europa and Enceladus.” The research also has important implications for subglacial environments that acted as refuges during the early history of our planet, enabling microorganisms to survive during the Neoproterozoic glaciations, also called Snowball Earth.
This story was featured in the April 2016 issue of Microbe Magazine.
Tweet me your questions or just let me know you heard this episode!
Host: Jeff Fox with special guests, Øjvind Moestrup, Peter Ulvskov, and Jesper Harholt.
Øjvind Moestrup and Peter Ulvskov, both at the University of Copenhagen and Jesper Harholt at Carlsberg Laboratory, also in Copenhagen, Denmark, talk with Jeff Fox about their hypothesis about terrestrial plants, based on analyses of the cell walls of charophycean green algae.
Moestrup, Peter Ulvskov, and Jesper Harholt thought that something was amiss with our current understanding of the evolutionary development of terrestrial plants after they carefully examined features of the cell walls of charophycean green algae. “Our hypothesis is simple,” they note. “Charophycean green algae ancestors were already living on land and had been doing so for some time before the emergence of land plants.” This new hypothesis takes issue with the widely accepted view that land plants originated from a charophycean green alga. "You have to be patient and sometimes pursue your crazy ideas, even when they differ from the dogmatic thinking in the field," Harholt says. "If you pile up enough evidence, at some point you may realize that you might be correct."
This story was featured in the March 2016 issue of Microbe Magazine.
Right click to download MMP011 (33 MB .mp3, 45 minutes).
Lewis and Krithivasan Sankaranarayanan—“Krithi”-- both from the University of Oklahoma in Norman talk with Jeff Fox about their analyses of the gut microbiomes of American Indians of Cheyenne and Arapaho ancestry.
Lewis, Krithi, and their collaborators learned that the gut microbial taxonomic profiles of these Native Americans are characterized by a reduced abundance of anti-inflammatory bacteria and also that their fecal metabolite profiles are similar to those found in individuals with metabolic disorders. Although this was a random sampling from a generally healthy group of individuals, their gut microbiota suggests that some of them might have health problems brewing below the surface—not a surprise among a population prone to metabolic disorders such as obesity and type 2 diabetes. “For three years, we collaborated with the Cheyenne and Arapaho to discuss these topics and identify common ground for the research process, including our microbiome data," Lewis says. I don't believe the microbiome pattern resulted from the genetics of the American Indian. It is likely related to the socioeconomic challenges and resource availability in rural areas of Oklahoma."
This story was featured in the February 2016 issue of Microbe Magazine.
Details appeared December 6, 2015 in Current Biology (DOI: http://dx.doi.org/10.1016/j.cub.2015.10.060).
Right click to download MMP010 (32 MB .mp3, 44 minutes).
Host: Jeff Fox with special guest, Timothy Lu.
Lu, an Associate Professor of Biological Engineering and Electrical Engineering and Computer Science at Massachusetts Institute of Technology in Cambridge, Massachusetts, talks with Jeff Fox about efforts to develop new phage varieties, swapping in phage tail genes that enable them to target specific bacterial pathogens, including those carrying virulence or antibiotic resistance factors.
Lu and other members of the MIT team worked with T7 phages that ordinarily act only against Escherichia coli. However, by substituting genes from other phages for the T7 gp17 gene, engineering them to target other bacteria, including pathogens such as Yersinia and Klebsiella. “We used this technology to redirect E. coli phage scaffolds to target pathogenic Yersinia and Klebsiella bacteria, and conversely, Klebsiella phage scaffolds to target E. coli by modular swapping of phage tail components,” Lu says. Phages also can be used to speed diagnostic testing of clinical as well as environmental and food pathogens, and such diagnostic tools might be needed to optimize the use of narrow-range antimicrobial products that target very specific bacterial pathogens , he points out.
This story was featured in the January 2016 issue of Microbe Magazine.
Right click to download MMP009 (30 MB .mp3, 42 minutes).
Host: Jeff Fox with special guest, Stijn Mertens.
Mertens, a graduate student working with Kevin Verstrepen at the University of Leuven in Belgium, talks with Jeff Fox about their efforts to develop new yeast strains for making lager beers—imparting novel flavor and aroma notes without detracting from the freshness and drinkability of lagers.
Unlike other beers, lagers are brewed at low temperatures and with two special hybrid versions of yeast that date back about 600 years. Those hybrids aren’t so easy to produce, but Verstrepen and Mertens first made about 30 new varieties and, by now, about tenfold more, looking to find varieties that yield unusual flavors but still produce enough alcohol at cold temperatures to make lagers of acceptable uniformity and familiarity to brewers and to consumers. Underlying these practical challenges to make better beer are some important fundamental questions about what happens when two different species of yeast are forced to mate and produce stable hybrids. During that process, a good deal of genetic change takes place, but little is known about the details or what leads to genetic stability, according to Mertens. Part of his dissertation research entails investigating some of those processes at the molecular level.
This story was featured in the December 2015 issue of Microbe Magazine.
Right click to download MMP008 (34 MB .mp3, 47 minutes).