Bio-Based Ideas

Cover of Science Issue 335. It has been a while since we have done a journal club , and so today I thought I would write about an article I recently read. Adam J. Wargacki, who works in Yasuo Yoshikuni's group, recently published the above titled paper. In light of problems associated with the use of fossil energy sources (cost, scarcity, environmental impact, and geopolitical considerations), the search for new energy sources is starting to become more important. The paper in discussion today proposes that a coupled system consisting of brown macroalgae and engineered bacteria could be used. Of course there are more traditional biofuel feedstock sources such as corn and sugarcane. There a couple of hurdles such as the debate about “food versus fuel” and technical hurdles such as the degradation of lignocellulosic matter that need to be solved. We have previously discussed how microalgaecould get around the difficulties of corn and sugarcane in the production of bioefu...

You may remember that a while ago I blogged about a research group that found a way to produce biogas reactor using the content of a stomachs cow . One of the questions, I had back then was what kinds of bacteria were in the cow's stomach fluids? Today, we'll look at a  massive Science article from January 28 with the title "Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen" from the Rubin Lab with Matthias Hess and Alexander Sczyrba as the primary authors recently hit the science world, and gives us that answer.

Another curious observation made the science rounds the past week: wired, electric bacteria. Reading this article reminded me of a review article on dissimilatory bacteria I read before, and one of the most interesting talks I ever attended in my life titled "Eavesdropping on Bacterial Conversations" . What did they do? Figure 1. Conceptual diagram showing electric symbiotic relationship between G. metallieducens and G. sulfurreducens. (Source: http://www.geobacter.org/) Summers, who is Microbiologist working in the Lovley lab at the University of Massachusetts, was studying Fe(III) reducing bacteria in the soil. They wondered what would happen when Fe(III) reducing bacteria would deplete Fe(III) available in the soil. In order to study this question, the research group co-cultured two strains of geobacter bacteria: Geobacter metallireducens and Geobacter sulfurreducens . The research team thought that combining the former bacteria that can oxidize ethanol in ...

Since the previous journal club where we covered an article that looked at the microbial synthesis of alkanes , another a curious observation made the rounds in the science world. In the latest Science Journal, Felisa Wolfe-Simon et. al. report their successful isolation of a bacteria that can use arsenic instead of phosphorous. The group isolated the bacterial strain called, GFAJ-1, by inoculating synthetic media containing glucose, vitamins and trace metals and varying concentrations of AsO 4 3- with sediments from Mono Lake which naturally contains high concentrations of dissolved arsenic (200  M) and performing many serial dilutions. GFAJ-1 was identified to belong to Halomonadaceae family of Gammaproteobacteria . Various tests were performed to verify that these organisms could not only live but procreate in this environment. Among the remarkable features of this organism is the observation that arsenic can get incorporated into macromolecules most notably DNA where it r...

I recently read an article titled  “Microbial Biosynthesis of Alkanes” that appeared Science (Vol. 329, 559, 2010) was published by Andreas Schirmer et. al. By comparing nine cyanobacteria known to produce hydrocarbons (alkanes, and alkenes) to one species known not to produce any hydrocarbons, genes that exist only exist in the 9 other species. The genes that were identified this way became likely candidates for the alkane biosynthesis pathway. Two classes of proteins were identified: short-chain dehydrogenases or reductases, and the ferritin-like or ribonucleotide reductase-like proteins. Previously, it was predicted that alkane biosynthesis happens by decarbonylation of fatty aldehydes. The authors speculated that the dehydrogenase-like gene could encode a protein that initiates the reduction of a fatty acid intermediate while the ribonucleotide reductase-like protein could complete the decarbonylation reaction.  The authors noted that the gene pair classes describe...