An article in the New Scientist caught my eye this morning, “Bacteria churn out first ever petrol-like biofuel,” which is a popular press summary of an article recently published in the Proceedings of the National Academy of Sciences. I’ve written about the challenges of using microorganisms as sources of biofuel previously, but the problems with using microorganisms are two-fold; first, the process is most useful if the organism can utilize a carbon source which is available in large amounts and is poorly degradable on its own such as cellulose, and second, the process should generate the most useful potential fuel product possible, and the organism should stop any further metabolism at that point. Ethanol is a common endpoint for many fermentation processes, and is something that is readily generated in large scale industrial processes. Unfortunately, biological production of ethanol as a fuel requires the further purification of the ethanol before it can be used, and the purification process uses energy as well limiting the net energy obtained in the procedure. Current production of other fuel additives by bacteria generate products that can be used in internal combustion engines, but not effectively, and they tend to degrade the engine over time. It would therefore be highly desirable to enable bacteria to biochemically synthesize hydrocarbon molecules which are identical to the ones used in petroleum-based fuels.
Researchers at the University of Exeter developed an artificial biochemical pathway in E. coli by introducing a number of genes from other microorganisms related to the synthesis of long chain hydrocarbons. E. coli on its own will produce long chain fatty acids, but these are not useful end products for use as a biofuel. Introducing genes related to fatty acid biosynthesis from two other bacteria, Photorhabdus luminescens (see this article for my story of this organism in a completely different context) and Nostoc punctiforme, which allowed E. coli to use its existing fatty acids to produce branched chain alkanes. Genes introduced from Cinnamomum camphor (a plant), and Bacillus subtilis (another bacterium) were used to enable E. coli to produce the fatty acids which were best able to enter the new pathway for forming fuel molecules.
The authors demonstrated by several analytic methods that production of industrially relevant long chain alkanes was accomplished by the introduction of these genes into E. coli. Future directions for the research are several fold. First, the process must be scaled up in order for it to be useful. Second, this process started with glucose as the initial carbon source, which is energetically costly to produce in itself. Third, the process laid out in the flow chart to the left is not terribly efficient; altering the expression of various components may force the pathway to be more efficient, but this leads to another problem. Long chain alkanes are extremely hydrophobic and will actively disrupt membranes they come into contact with. Organisms that produce these compounds would additionally need to be able to resist the effects of the toxic compounds they produce.
One of the challenges of cancer therapy is to obtain a high accuracy map of the tumor distribution. This is further complicated by by the movement of tumor cells from their initial site to distal sites, via the process of metastasis. Whole body imaging techniques are excellent, however they may miss cancers that very closely resemble the tissues that surround them. A new study summarized at Science Daily, from the open access journal PLoS One, describes a novel way for trying to obtain images of tumors using non-invasive means.
Previous research has demonstrated that bacteria that are injected will with high efficiency begin to associate with tumors. Indeed, a posting here on the BIO230 blog last summer, found that the association of strictly anaerobic bacteria within the hypoxic environment found in a solid mass tumor could potentially be used as a novel form of anti-cancer therapy. This newer research is utilizing harmless bacteria normally found as part of the human gut flora, and are frequently taken as part of “probiotic” therapy to treat gastrointestinal disease. These bacteria do not normally cause human disease, and when they are injected into the circulatory system in mice, they appear to hone in on solid mass tumors. Read the rest of this entry
Our discussion on microbial nutrition and growth ended with a hypothetical experiment: a flask of rich culture media broth at optimal temperature was inoculated with Escherichia coli, and samples were removed at various time intervals post-inoculation for cell number determination. This experiment, once it was plotted on semi-log graph paper, allowed us to demonstrate the characteristic phases of microbial growth.
During lag phase, the E. coli cells are adjusting to the new environmental conditions (extremely abundant nutrients, no waste products to inhibit growth) by producing the enzymes that they will need to carry out metabolic pathways. In exponential phase, microbial growth is occurring at the highest possible rate possible for the given culture conditions. The maximal growth rate is determined by the richness of the culture media (a rich, complex medium will produce a faster growth rate than a simple, defined medium), and whether the temperature, pH, and osmotic pressure are all at optimal values. As the nutrients in the culture begin to be limited by the increasing cell number, cellular division is offset by cell death, and stationary phase ensues. It is important to note that cell growth is still occurring, just not at the rate observed previously. As conditions in the culture continue to diminish in death phase, cellular growth is completely offset by cellular death. Read the rest of this entry
This was a really cool news update, via my favorite gadget blog Gizmodo, who link to it from the New Scientist popular science site. Researchers at Tufts University have described a novel way to exchange secret messages using bacteria. The process has been dubbed SPAM, or Steganography by Printed Arrays of Microorganisms, and utilizes a panel of recombinant E. coli strains that glow under under black light. The bacterial cells have all been transformed with plasmids that encode variants of a jellyfish protein called green fluorescent protein, or GFP, which has been further engineered to create many more colors than green. The panel of glowing E. coli strains are organized in pairs, creating 49 possible characters. This allows more than enough permutations to code for all the letters of the English alphabet, the numerals 0 to 9, plus some additional characters for punctuation. I know that I am a big fan of the semicolon; I do not know how I could encode any important message if I could not use a semicolon.
The glowing E. coli colonies are laid out in a specific order that codes for an intended message on media in the lab on agar plates. The colonies can then be transferred to a thin film, which can then be mailed. The recipient must then put the film back onto a specific type of bacterial media, visualize the pattern of colored dots, then decode the message. Several layers of manipulations make this a relatively secure cypher mechanism, and it can be further strengthened by the addition of specific antibiotic requirements before the dot patterns can be seen. Furthermore, transient glowing patterns of dots can potentially be used, to make a message that can only be read for a finite amount of time, much like the self-destructing messages received in the Mission Impossible movies.
The feasibility of this process is very real, and the arrays of organisms are incredibly easy to create. The security of the method is dependent, as with any coding mechanism, on only the sender and recipient knowing the cypher that was used. One might be worried from a biosecurity standpoint whether is is prudent to ship E. coli, particularly isolates that are antibiotic resistant, through the mail. Fortunately, laboratory strains of E. coli are non-pathogenic, and grow poorly outside of the laboratory setting. The most significant danger from this scenario is that pathogens of humans might acquire the antibiotic resistance gene segments from the recombinant E. coli isolates, and therefore acquire antibiotic resistance themselves. The biggest drawback of the scenario is that it is not robust enough for large messages, and currently is only useful for small, text-based messages which presently might be sent more effectively via email. Still, I think it might be prudent to examine everything with a black light in hand for secret messages.
A current headline on CNN.com reports that the death toll from the ongoing E. coli outbreak has risen to 35, with over 3200 people having fallen ill to this foodborne illness since it began in early May 2011. Identifying the source of the infection was the job of epidemiologists, who examined common connections between the infected individuals. Despite some early red herrings, the current culprit appears to be vegetable sprouts from Germany, although the method of how those sprouts became contaminated remains unclear.
The infection is transmitted from consuming contaminated food, and after a brief period of incubation leads to moderate to severe gastroenteritis as the pathogenic form of the bacterium begins to cause disease. Many forms of gastroenteritis are treated by basically doing nothing; the infectious agent causes the signs and symptoms of the disease, but eventually it is out-competed by the normal intestinal microorganisms, which causes a decline in the symptoms as the numbers of pathogen decrease. Read the rest of this entry
I found an interesting news article, via the National Geographic website. Scientists at the Japan Agency for Marine-Earth Science and Technology wondered what would happen to bacteria when exposed many thousands of times the force of gravity. Human beings can tolerate up to 5 times the force of gravity before blacking out, and fighter pilots can tolerate up to 9 times gravity through training, acclimatization, and with the aid of special suits to prevent blood pooling in the extremities. Most animals will have similar tolerances, due to the constraints of the skeletal and circulatory systems. Eukaryotic cells can be centrifuged at several hundred times the force of gravity, but do begin to lose viability if the force becomes too great.
When several species of bacteria were put into an apparatus called an ultracentrifuge, they continued to grow and divide with little ill effect. One common soil bacterium, Paracoccus denitrificans, along with the intestinal bacterium Escherichia coli, were able to survive and thrive when exposed to 400,000 times the force of gravity. The cells would clump together under these conditions, but continued to grow. Read the rest of this entry