Animated GIF: Extracellular electron transfer to soluble iron. Example of Geobacter respiration

extracellular electron transfer, geobacter
Electrons: yellow
iron: black
MacA protein: dark green
PpcA: blue
OmcB: black
other outer membrane cytochromes: orange and light green

When Geobacter are in an environment where soluble iron is present, this can serve as the terminal electron acceptor in metabolism through an elaborate electron highway.

Another animated GIF: growing iron oxide on Geobacter pili: bacterial nanowires

bacterial nanowire, bacteria, chemotaxis, microbiology, geobacter
A bacterial nanowire. Electrons (yellow) are passed through pili (purple) to OmcS (cyan) for reduction of iron (black).

Micro! Polo!: Discovering the beneficial bacteria needed to clean our messes

Micro polo

Bacteria do not have taste buds or eyes. However, they have very fine-tuned senses that relay information about the status inside as well as in their environment. To compete and survive in virtually all environments on the planet, bacteria have evolved to sense and utilize many chemical compounds (most of which are still unknown) for energy and existence no matter how we as humans feel about these compounds. Even toxic compounds are easily metabolized by some bacteria. Whether it is hydrocarbons like petroleum or groundwater contaminated with dry cleaning chemicals, bacteria have evolved pathways to utilize these compounds.

Imagine restoring highly contaminated land for public use without expensive machinery or excessive human exposure. Current research within DOE is working towards this goal through bioremediation, utilizing bacteria with ability to render radioactive or otherwise hazardous material harmless. Even though most microbes presently performing this task are unknown, meta-sequencing projects are turning up a common set of genes (and proteins) necessary for this process.

Let’s briefly take a look at some of these toxic compounds.


Here we have (from left to right) perchloroethene, trichloroethene, and dichloroethene. PCE is a common chemical used in dry cleaning and easily contaminates groundwater. It’s removal is expensive and time-consuming, not to mention dangerous given its toxicity. However, a small number (so far) of bacteria can actually use these chemicals during metabolism when oxygen is absent from the environment (deep underground, for example). DCE is still considered a contaminant, so, how do we get rid of it? A group of bacteria discovered not long ago actually have the complete set of genes to breakdown perchloroethene to ethylene, Dehalococcoides. These bacteria have small genomes relative to the average bacterium but contain a set of genes that will render these contaminants essentially harmless.

vinyl chloride and ethylene

Vinyl chloride, the next step in PCE degradation can be further reduced to ethylene by an enzyme called vinyl chloride reductase (Vcr). To date, only Dehalococcoides are found to contain Vcr genes.

Next, I will talk about other common contaminants and the wonderful bacteria that can clean them up.

‘Zoomable’ map of poplar proteins offers new view of bioenergy crop

‘Zoomable’ map of poplar proteins offers new view of bioenergy crop.

What is in a genome?

English language svg version of Image:Plasmid ...
English language svg version of Image:Plasmid (numbers).svg Description : This image shows a line drawing of a bacterium with its chromosomal DNA and several plasmids within it. The bacterium is drawn as a large oval. Within the bacterium, small to medium size circles illustrate the plasmids, and one long thin closed line that intersects itself repeatedly illustrates the chromosomal DNA. (Photo credit: Wikipedia)

I first have to apologize. The mission of this blog is to inform those who are curious about science and nature. My ADD gets the best of me sometimes and I digress towards more policy and advocation.

So…what is in a genome? A broad question with lots of answers. Let’s start with the ‘simple’ example of a genome; bacteria. Unlike humans, and other animals, bacteria have only one true chromosome which is circular. Many bacteria, however, have extra DNA not on the chromosome. This extra DNA is also circular and usually called a plasmid. Many bacteria have several plasmids, and some even have very large plasmids called cosmids.

There is not a lot of room within a bacterial cell, so there is not a lot of ‘junk’ DNA in its chromosome. If an average gene is 1000 base pairs (bp), then a 7 Mbp (7,000,000 bp) genome usually has about 6500 genes. This means bacteria pack a big punch in a small size cellular blueprint. Other than genes, bacteria contain DNA elements that help regulate what and when genes are actively transcribed into RNA to produce functional proteins. Promoters are areas of DNA upstream of genes that are attractive places for some proteins to interact with. Some proteins activate gene transcription while other repress transcription. This ensures only the proteins needed by the cell are being produced since making and degrading unneeded proteins costs energy.

What about plants and animals?

I’ll leave plants out since I’m not knowledgeable enough to write about them. Animals have very elaborate genomes. The number of chromosomes vary for each organism and are not circular. For simplicity, I will discuss humans. Humans have pairs of each chromosome that are identical except for the pair that determine a persons sex. Even identical chromosomes are essentially different in the characteristics of individual genes (see dominant and recessive alleles). Strands of DNA are wrapped around proteins known as histones which interact to compact the size of the chromosome.

The major chromatin structures.
The major chromatin structures. (Photo credit: Wikipedia)

Human genes have MANY ways of being regulated. The histones themselves can undergo modification by enzymes that affects how compact they are and how attractive they are to proteins regulating gene transcription. Like bacteria, human gene transcription can be regulated by promoters. However, unlike bacteria, these genes will not totally be used to make a protein. Human genes are composed of introns, regions not translated into a protein, and exons, regions that are translated into protein. Human messenger RNA is processed after transcription which removes intron sequences leaving only exons that will be shuttled out of the nucleus for protein synthesis. To make this more complicated, during processing, many genes can undergo something called alternative splicing. This means as mRNA is being processed, even some exons can be removed resulting in different versions of a protein! 

Other elements can regulate gene transcription besides promoters. Animals have DNA elements called enhancers and insulators that may or may not be located close to actual genes. Enhancers and insulators can intricately interact to regulate gene expression.

Français : Organisation de l'ADN en chromosome...
Français : Organisation de l’ADN en chromosome National Human Genome Research (USA) (Photo credit: Wikipedia)


I will leave it at this. I hope you enjoyed my little ramble about genomes. Let me know what you think…please…

Online resources for STEM Education

I have spent countless hours online over the past few months looking for current resources available for educators or curious members of the public in bioinformatics and genomics. The offerings across the web are not overwhelming. One important need, I think, is a resource allowing teachers to show their class ways scientists use online biology resources everyday in their research.

First, here are the most important sites for discovery.

The Universal Protein Resource

NCBI’s BLAST service

The Protein DataBank

Unfortunately, these sites are virtually not usable by K-12 educators who don’t have a scientific background. My search began by looking at guidelines for teaching STEM in American schools and what resources are in place to help educators get children involved in the scientific process.

One great tool is the Gene Gateway which has activities and introduces web-based resources to research genes, proteins, and genetic disorders in humans. It is based on the DOE work in the Human Genome Project. DISCLAIMER: This resource was created by my predecessor and I am not affiliated with its work. However, my goal is to expand the Gateway. My background in microbiology and plant biology gives me a wealth of resources that I have used and want others to know and understand, including the websites listed above.