Daily Newsletter February 21, 2012
Today, I wanted to review a little of what we discussed yesterday.
Genomics tells us the genetic possibility of an organism. Remember, we do not express all of our genes at the same time. That would be a waste of energy and resources. We have constitutive genes that are always expressed (why?), and regulated genes that are only expressed in the right environment. Genomics helps us to understand what the organism is capable of doing metabolically, but unless we know the regulatory mechanisms, we don't know which of the regulated genes is being expressed at a given time.
Proteomics gives us a snap shot of a cell's proteins. We can find out exactly which proteins have been expressed. We can take cells from a control and variable condition, and compare the proteomes. This comparison can tell us if there are specific proteins either made or missing when in the variable condition. This can help us understand regulatory mechanisms. But we may not be able to tell if all of these proteins seen in the proteome are active. Remember, we can inhibit proteins. We can also regulate their activity with allosteric regulators.
The Metabolome shows us all of the biochemical intermediates currently in a cell at given time point. In other words, it is a snap shot of the metabolic processes currently being carried out. This reveals which pathways are active, and how active they are. If we know our pathways and intermediates (and there are computer programs you can use for this), then you can determine the metabolic activity of individual enzymes (does the enzyme have a fast or slow rate). The metabolome can point us to where there are metabolic slow points or problems.
Metabolic Engineering combines genomics, proteomics, metabolomics and genetic engineering. We can optimize a specific pathway. We can remove regulation, provide strong promoters, and even a coding region for an enzyme with a fast reaction rate. We can duplicate genes, allowing for more of the gene product to be produced. In turn this will raise the Vmax of the reaction.
Having said all of that, this is not rapid work. It could take years to fully optimize a pathway. The resulting organism will most likely be a laboratory strain. In optimizing a specific pathway, you may be (and most likely are) increasing the energy and resource needs of the cell. This may result in the cell being a poor competitor in natural environments. Still, as a genetically engineered organisms, it must be approved by the government.
Readings:
Plant Genetic Engineering and Regulation in the United States
This is a short article. Though the focus is on plant genetics, the regulations go further.
NIH Guidelines for Research Involving Recombinant DNA Molecules
This page has links to various regulations overseen by the National Institutes of Health.
International Centre for Genetic Engineering and Biotechnology - General Introduction to Biosafety.
This website has a brief overview of biosafety, and concerns regarding genetically modified organisms (GMO).
Daily Challenge: As was mentioned yesterday, your challenges this week are in general about moving from genomics toward metabolomics. So there is not a required topic each day. Instead, look at things that are of interest to you in this over arching topic.
One option you have for your challenge is to talk about the regulations and ethics of making and using GEO/GMO. Feel free to give opposing view points, but make sure you have valid references to support your view. A person saying that it is bad on a website with no reference to current research or methodologies is not appropriate. There are well considered, well researched, and informative articles both for and against GMO. So be diligent in your search for references. NOTE: you can also write this as an opinion piece, but make sure that your opinion is justified and backed up with references to legitimate investigations and research.
EFSA statement on the fate of recombinant DNA or proteins in meat, milk and eggs from animals fed with GM feed
This article from the European Food Safety Authority deals with Recombinant DNA remaining after ingestion of GMO feed. A look at tracking recombinant DNA in the environment.
APHIS - Biotechnology
The animal and plant health inspection service, a unit of the USDA, is tasked with monitoring the release of genetically modified organisms (or genetically engineered organisms -GEO) into the environment. The link goes to one of their Biotechnology pages involving gaining approval for the release of a GEO/GMO.
