What’s the Big Idea?: We Need to Focus on the Big Picture

global warming
Oh, the irony…
Photo credit: Flickr/Vineus

The Big Picture?

This week, the House of Representatives’ Science, Space and Technology Committee unveiled the Frontiers in Innovation, Research, Science and Technology (FIRST) Act. This legislation wants to prioritize the way the National Science Foundation funds projects in life and chemical sciences, computer science, and mathematics based upon how the projects specifically address national needs. To increase the muddling between science and politics, the NSF would be required to justify the projects funded to Congress and how each benefits the national interests. The measure comes as the Republican-controlled House is pressured to cut federal spending and this would filter out projects with no tangible or timely returns. The bill would also limit the NSF from funding projects that already have funding from other federal agencies in an effort to prevent mission creep and double dipping. The bill fails to address how some projects are complex and have components that have benefits at multiple levels.

This legislation is the latest in a long line of efforts the GOP has used to hinder the scientific community from using its internal peer-review process to advance research and development which in turn would lead to the next generations of innovation desperately needed to sustain the United States’ leadership in science and technology. GOP efforts to appease the extremists within their party by slashing spending no matter who is affected are naive and short-sighted to say the least.

Beginning with the powers of the oil and gas industries masquerading as a conservative, grassroots Tea Party movement, conservatives have fought tirelessly to create an absurd climate debate instead of working on a bipartisan effort to ensure the sustainability of our planet. Congressional leaders have used ‘data’ gathered by conservative think tanks and biased institutes to assert the ‘science is still out’ about the man-made cause of climate change. Ultimately, what are their interests, protecting those who fund their elections or protecting…well, the rest of us? Who stands to lose by enacting cap-and-trade, emissions limits, or biofuel standards? The public as a whole? However, who wins if these and other efforts are in place to fortify our environment for future generations?

Also this week, the U.S. Global Change Research Program released the latest National Climate Assessment stating climage change is no longer a future threat. It’s here. Climatologists have sounded the alarm about global warming for over 30 years. Now the science is as solid as diamond and the consensus is strong. It is very apparent Congress will not actively take measures to grant future generations the awesome pleasure of enjoying our national parks as we have or enjoy time on local lakes or rivers. 

If there is something I’ve learned in the past couple weeks, it is the precious time we have with those we love can end at any moment. I cannot help but think what happens when I am gone? What do I leave behind? How can I show my children how much I loved them and wanted the best for them? It certainly is not doing everything possible to ensure I am victorious every election cycle by bowing to fundraisers.

What can we do to help?

 

It is past time to take back the power by electing members of Congress who can see the big picture by looking past this term in office to the selfless good they can do to help us all. The big picture is increasingly heating up as is our atmosphere.

Images

Images. The page has finally been updated to include my most valued pieces. Hope you all enjoy!

Bacteria; They’re not only for biofuel anymore. Unsung heroes for bioplastics

illustrated bacteria, microbiology, bioplastic, bioenergy, environment
Illustration of PHB within bacterial cells

I spend a lot of time on this blog illustrating and promoting the benefits of the things we can’t see, however, we can’t live without and finding new ways they can help us out. To focus on bacteria along for now, they are beneficial overwhelmingly more than they are hazardous. Lots of research is going into utilizing them in new arenas from ethanol to diesel and jet fuels.

Helping solve the forthcoming energy/climate crisis is not the only area these guys can help. Lots of bacteria, under certain environmental conditions, can and will produce huge internal polymers as carbon stores, especially when nitrogen supplies are limited. Think of this polymer like starch in plants and glycogen in mammals. Research is still ongoing into the mechanisms that regulate polymer synthesis and degradation.

The bacterial polymer is special, unlike the molecular make-up of starch or glycogen, this polymer is a class of polyhydroxyalkanoate (PHA).

Structure of poly-(R)-3-hydroxybutyrate (P3HB)
Structure of poly-(R)-3-hydroxybutyrate (P3HB) (Photo credit: Wikipedia)

One of the most prevalent forms of PHA is polyhydroxybutyrate, or PHB. Speaking from experience, PHB is an interesting macromolecule to study and observe under the microscope with cells treated with a fluorescent dye that stains PHB. PHB can account for up to 75%  of the total cell weight. PHB, and PHAs in general, can be used to make plastic thus replacing the need for petroleum based plastics.

Illustration: Synthetic Biology; Turning bacteria poop into a hot commodity

bacteria art, E. coli art, bioenergy, biomass, biodiesel
Illustration showing the concept of E. coli engineered to digest plant cell wall material (green) and produce fatty acids (white) that can be used as diesel as a waste product. The fatty acids shown are actual 3D structures of linoleic acid.

Breaking down the wall: Illustration of the cellulosome as an impressive bacterial machine to degrade plants…think Legos

cellulosome, bacteria, bioenergy
Components of a major cellulosome of Clostridium thermocellum

I have heard of the cellulosome for quite some time. It discribes a extracellular ‘factory’ of enzymes some bacteria (or fungi) are equipped with to degrade the components of the plant cell wall. These enzymes are held by a scaffold structure projecting out of the cell. Several bacterial species to date are known to encode some sort of cellulosome. Here, I will focus on a model species, Clostridium thermocellum.  I never really thought twice about cellulosomes until recently when researching for an upcoming project. Now, however, I have a great appreciation and respect for this massive, impressive apparatus.

The backbone of sorts for the cellulosome is the scaffoldin CipA. CipA is a monstrous protein with many domains, most of which necessary to attach the enzymes needed to break down plant cell walls. CipA contains 9 cohesins, domains used to securely allow different proteins to interact. The enzymes ( I will describe soon) contain dockerin domains that interact with cohesins. CipA also contains a carbohydrate binding module (CBM) which allows it to directly interact with cell walls.

Many of the cohesins are used to attach carbohydrate degrading enzymes, usually of two classes: endoglucanases and exoglucanases.  These work in concert to breakdown cellulose and other carbohydrate polymers. Apart from the catalytic portions of these proteins are dockerin, needed to bind to CipA, and other domains like the Ig domain or X domain.

These enzymes ‘fit’ onto the scaffold protein like Legos. This makes them very modular. Now consider other scaffold proteins have a different type of cohesin (cohesin II) that can be used to attach other scaffold proteins thus making polycellulosomes. For example, Cthe_0736 is a scaffold protein with 7 type II cohesins. This means Cthe_0736 can have 6 other scaffold proteins attached to it meaning this polycellulosome could contain up to 63 individual enzymes which is potentially common considering isolated cellulosomes vary in molecular weight considerably.

illustrated bacteria, cellulosome, microbiology
Illustration of a polycellulosome attached to cell (blue) on substrate (brown)
animated bacteria, cellulosome, microbiology, bioenergy
Closer look at the polycellulosome

In a later post, I will go into a little detail on how these cellulosomal enzymes actually are able to degrade anhydrous polymers of carbohydrate.

Living at the Boiling Point: What we can learn from extreme heat-loving microbes

Thanks to the decreasing costs of sequencing genomic DNA, finding novel microorganisms that add to our understanding of metabolism in myriad environments is becoming common place. Not only are we learning about the diversity of life in extreme environments, like heat, cold, pressure, and altitude, but we are also learning what life on other planets may be like. With each additional genome added into ‘the cloud’, our synthetic biology toolbox gets a little bit bigger and our ability to manipulate tiny organisms to produce novel compounds is possible. Enter the “rushing fireball”.

Pyrococcus furiosus is an archeal species that thrives near deep-sea thermal vents where temperatures are between 90 and 100 degrees Celsius (or 194 to 212 degrees F). P. furiosus can grow at temperatures as low as 70 degrees C (158 deg F). To live in such conditions, this organism’s proteins must be tolerant to what we would consider harsh conditions. This organism’s ambient conditions makes wild-type proteins well-suited for industrial processes where temperatures are near boiling.

So far, P. furiosus has been utilized to produce 3-hydroxypropionic acid, a common industrial chemical used to make various products including acrylics. The kicker is that these cells were wired to make this chemical from atmospheric carbon dioxide. It is not crazy to think of what other useful products can be produced by P. furiosus with small modifications within the genome; products like ethanol or butanol as biofuels.

Pyrococcus furiosus, bacteria, archea, illustration, microbiology
My illustration of Pyrococcus furiosus

Reference

Keller, M., Schut, G. J., Lipscomb, G. L., Menon, A., Iwuchukwu, I., Leuko, T., Thorgersen, M. P., Nixon, W. J., Hawkins, A., Kelly, R. M. and Adams, M. W. W. (2013) “Exploiting microbial hyperthermophilicity to produce an industrial chemical using hydrogen and carbon dioxide”Proc. Natl. Acad. Sci. U.S.A. (in press).