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...

Example of how ciliates look (Source: http://www.woodrow.org) This week, DW Radio covered an interesting topic in their science news radio show. In light of the recent EHEC outbreak in Germany, experts have been trying to trace the source of this deadly outbreak. For those who do not know what EHEC is, it stands for Enterohaemorrhagic Escherichia coli. In other words, these special strains of E. coli are very tough bugs that can cause intestinal bleeding - obviously not desirable and potentially dangerous. The search for possible sources has lead back to water treatment plants because the majority of water treatment plants treat water according to ecological aspects only, that is to say, they ensure that nutrients and waste in the water do not exceed certain levels. Many German water-treatment plants do not specifically try to reduce the number of bacteria in the water. That part is left to water companies that produce drinking water. The result is that high concentrations of...

This is a brief post while I am still mostly writing my thesis. I found another TED video with an interesting way to combine fashion with bio-based products - very interesting indeed.

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.

I have previously talked about the similarities and differences between the sustainable economy and the bio-based economy . As I am working on completing my PhD in 2011, I have started to look towards the next step. My goal for 2011 is to start a career in the sustainable biotechnology field, and so I have surveyed my options in California. In my survey on this topic, I have found that the sustainable biotechnology companies can be divided into three areas of activity: biofuels, industrial enzymes, and bio-based biochemicals. Perhaps the most visible field area of sustainable biotechnology is the biofuels field given the increased need to develop alternatives to fossil fuels. Because of the large potential market in this area, it may not be too surprising to learn that nearly every company in this field is involved in one form or another. This part will focus on companies that mainly are associated with biofuels development. They are characterized by mostly not having any products on...

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 came across an interesting article posted at Discover which talked about a company by the name of Micropidas . It seeks to convert human effluent into a polyesterbelonging to polyhydroxyalkanoates or PHA family. Why is this important? Plastics often times are derived from oil. Using this bio-based approach cuts that out. In this case, there is an added benefit: they produce plastics while cleaning up the water. And lastly, Micropidas claims that the plastic produced is actually bio-degradable! I haven't had time to research this in more detail, but thought I would share this here.   To read the full, article please go here: http://news.discovery.com/tech/poop-plastic-puts-waste-to-work.html

Recently, “Forschung Aktuell” , a science news radio show on Deutschland Radio, highlighted some interesting research by the German scientist Hauke Harms on his approach to affordable solutions to detect arsenic in drinking water which is a common problem in some parts of the world. I was interested to learn how arsenic is sometimes found in drinking water. According to the show, arsen naturally exists in the environment as arsenopyrite. Natural processes can erode these layers and transport them down the river. There, arsen can react with organic matter that is commonly dumped into the river in heavily populated areas without proper waste water treatment to form arsenic. These arsenite containing waters can sink all the way into the ground water. Arsenite is a big problem because it is a non-biodegradable toxin which can cause cancer and other serious diseases as it accumulates in our bodies. To address this problem, one needs to have means to measure the presence of arsenite. Usi...

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...

There is one more talk I want to summarize because I thought it was really good: Susan Golden's talk about cyanobacteria was very educational because she reminds us all that when talking about algae not every algae is eukaryotic. According to her, cyanobacteria belong to the prokaryotic kingdom. There is a large variety of them out there with very unique metabolic processes and physiologies that can be exploited. Some fix nitrogen, others produce hydrogen, or other secondary products. Many are individualistic, while some form filaments that can be beneficial for harvesting. From a technological perspective, some cyanobacteria are very easily transformable – that foreign pieces of DNA can easily be absorbed into these organisms. From a research perspective, there are 10 genetic model systems providing a wealth of tools and information for further research questions. There are, however, challenges when it comes to working with cyanobacteria to extract oils for biofuels productio...

Paint-By-Numbers Statue of Liberty In the latest Science Issue, the Venter Lab (Gibson et al. 2010) report that they have successfully created an "artificial genome" Mycoplasma mycoides which they transplanted into Mycoplasma capricolum cell to create a new Mycoplasma mycoides cell. In other words, they put the DNA of "A" into an organism of type "B". Just by doing so, they "converted" B into A. This begs the question.... So what? The dream of creating artificial life - that is to say recreate life from scratch with inanimate starting components - has been the dream of some researchers that want to get at the question of:"What is life?" Of these researchers, Craig Venter probably has been the most recognized figure. Craig Venter claims that understanding how one can create life from scratch will also give us the ability to create purpose-driven life-forms. With the current oil spill an example comes to mind where one could cr...

I found these news rather intriguing: According to "Forschung Aktuel" [1],  a German-based science radio news show, there is a research group in Germany that is trying to develop an integrated 2-step biogas reactor. Normally, this would not be really that big of a news but what they use as a source for biogas generation and how they do it is very intriguing. In the quest for renewable non-fossil-based resources, cellulose, the sturdy sugar based plant material, is often considered the holy grail for energy generation as it is in this case. The question is how to generate energy efficiently from cellulosic containing material because as mentioned in a previous post , it is difficult to break down cellulose into usable sugar molecules using traditional mechanical and chemical processes. For this reason, research scientists have looked to nature like the gut of termites and other wood-eating insects, and in this case the stomach of the cow for inspiration on how to break down ...

Introduction I was recently asked why this site is called "Bio-Based Ideas". So I thought I would give a brief answer before leading into today's post. There are several reasons for naming this site the way it is. For one, having been trained as a biologist, I write what I know and am interested in. Naturally, many of the posts discussing ideas come with a biological slant. I wanted to make that clear in the title of the blog. But "bio" also comes from Greek meaning "life". And just as life organically grows and evolves, the posts here are meant to capture the richness of diversity of ideas. Lastly, it is my personal belief that the richness of biological ideas will have an increasing impact on our societies especially in this century. And so today with the last post on directed evolution in mind , I want to discuss: What is the bio-based economy? There are two basic ideas the bio-based economy relies on. 1.) Transition to biobased, renewable r...

After spending the last few blog posts on different aspects of dissimilatory bacteria , I want to switch the focus to a different class of organisms I have been interested in for a long time now. These are the algae. Algae comprise a large diversity of "sea weeds" and an even larger variety of single-celled organisms that mostly are capable of doing photosynthesis. They include the ordinary sea-weed, and make up a portion of the green slime found around the edges and the bottom of a pond. More exotic types of algae can live symbiotically - that is together with another organism in a mutually beneficial way. Lichens are an example of symbiotic relationship between algae and fungi. More information about the evolution and lineage of algae can be found in this wiki article . Image via Wikipedia Typically, these organisms are either not mentioned at all or only in conjunction with toxic algal blooms. But lately, algae, of course, have been in the news recently because of the p...

Though many talks are interesting, once in a while there comes a talk in a graduate student's life that is so inspiring in both content and presentation. Today was one of these days. I attended the the "Intersectional Seminar Series" here at USC which is a seminar series meant to bring the different separate biology programs - Molecular and Computational Biology, Marine and Environmental Biology, Integrative and Evolutionary Biology and Neurobiology -together. Today's speaker was Bonnie Bassler from Princeton, and her talk title was "Eavesdropping on Bacterial Conversations". Today's blog entry is dedicated to the rich history of ideas she discussed in her talk. I apologize in advance to the longer than usual post and the higher than usual complexity as I try to accurately report back the ideas discussed in her talk. To most lay people, the idea that simple, single-celled bacteria could use sophisticated means of communication may seem rather strange. ...