MyTH: A new weekly series about one bacterial species. First Post: Escherichia coli « Taking Science to the People

MyTH: A new weekly series about one bacterial species. First Post: Escherichia coli « Taking Science to the People

This thought came to my head as I couldn’t sleep last night. My Tiny Highlight (MyTH) will be weekly and will showcase interesting or useful bacteria. For the first installment, I will focus on the gold standard of biology; Escherichia coli or E. coli. E. coli was discovered in 1885 by a German doctor in feces of healthy people. He called it Bacterium coli commune because it was found in the colon. The classification system of bacteria was much different before the ability to sequence DNA as novel bacteria were initially classified and named by their shape and motility. The name later changed to Bacillus coli before finally being reclassified and named Escherichia coli after the original discoverer. How would you like it if someone named a bacteria from feces after you?
E. coli receives a bad reputation thanks to pathogenic strains that force recalls of all kinds of food products. However, those strains are very uncommon as E. coli is one of the most abundant species found in the GI tract of mammals. Also, without this bacterium, many of the scientific discoveries of the past 50 years would not be possible including solving protein 3D structures, mass production of insulin, and understandingsignal transduction; the process of a cell sensing surrounding signals or cues and responding to them in a way that is favorable for the cell. One reason E. coli was such a well suited model organism is the doubling time or time to divide one cell into two daughter cells. A doubling time of only 20 minutes means in less than 48 hours, the mass of E. coli cells would roughly be equal the the mass of Earth and have the combined volume equalling a 1 meter thick layer of bacteria covering the entire surface of Earth (including oceans). This is incredible and gives E. coli a major advantage over slower growing bacteria.
I want to discuss, briefly, a major influence of mine. Julius Adler was born in Germany and became a lover of Nature as a child. He was fascinated with butterflies. adler
His lifelong passion has been behavior of living things. Luckily, he spent most of his professional career studying chemotaxis in E. coli although he now studies fruit flies. Adler is known as the father of chemotaxis, or the movement of a cell in response to sensing chemical signals. His landmark early papers in the journal Nature about chemotaxis in E. coli in 1966 and his later paper on the chemoreceptors, the proteins that interact with the surrounding chemicals, in E. coli laid the foundation that maid the chemotaxis system of E. coli the best characterized signaling pathway in Biology. In regards to chemotaxis, however, E. coli is on the simplistic side of the scale. For example, E. coli has 5 chemoreceptors and 1 chemotaxis operon, or a stretch of genes that are transcribed into RNA together but lead to distinctly different proteins that usually interact with each other. Through the explosion of genome sequencing, scientists can scan newly sequenced bacteria genomes for chemotaxis genes. The average number of chemoreceptor genes is roughly 5 times more than E. coli (~25) and it is more common for bacteria to harbor multiple chemotaxis operons suggesting most bacteria have evolved to use chemotaxis for regulate more than the motility behavior in these cells.
Let’s think a minute about why E. coli is ‘stupid’ compared to other bacteria. By ‘stupid’ I mean, they have less capacity to integrate signals from their surroundings into a cell response. Why doesn’t E. coli have 25 chemoreceptors, for example? For the answer, we just need look at where this microbe is found. The GI tract of mammals is fairly constant meaning there is less need to scavenge for a new home or adjust to changes in temperature or nutrients. We as mammals have no problems eating meaning E. coli has no problem eating as well. How about the other sequenced bacteria? They predominantly live in more variable environments like soil or oceans where is would be to their advantage to be able to sense a lot of chemicals or nutrients in their surroundings. Therefore, through evolution, they have acquired new abilities to sense through duplicating genes and mutating DNA favorably. Changing only a few nucleotide bases (A,C,G,T) could mean acquiring the ability to physically interact with different environmental chemicals that could serve as an energy source. Nature is awesome and she knows how to keep us, as observers, guessing.
You may feel I am biased about chemotaxis ( I am). This was my dissertation work in another bacterium. Check back next week when I will highlight a little known (publicly) soil bacterium, Azospirillum brasilense. If you have any comments, questions, or suggestions PLEASE LET ME KNOW!

What is in a genome? « Taking Science to the People

What is in a genome? « Taking Science to the People

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. Unlikehumans, and other animals, bacteria have only one truechromosome which is circular. Many bacteria, however, have extra DNAnot 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 functionalproteins. 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)
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I will leave it at this. I hope you enjoyed my little ramble about genomes. Let me know what you think…please…

Neanderthal cloning chatter highlights scientific illiteracy | Reuters #science #scichat #STEM #scied « Taking Science to the People

Neanderthal cloning chatter highlights scientific illiteracy | Reuters #science #scichat #STEM #scied « Taking Science to the People

Deutsch: Rekonstruierter Neandertaler im Neand...

Deutsch: Rekonstruierter Neandertaler im Neanderthal-Museum (Photo credit: Wikipedia)
I would like to bring some attention to this very important issue. This is a perfect example of things that can happen when outlandish stories start circulating on the internet regarding anything scientific in nature. Renowned scientist George Church said:
“The public should be able to detect cases where things seem implausible. Everybody’s fib detector should have been going off. They should have said, ‘What? Who would believe this?’ … This really indicates that we should have scientific literacy.” 
George is spot on. The internet, right or wrong, fuels the fodder on 24 hour news channels. The montra “if it’s on the internet, it must be true” is scary and not going away. He also states: “We really should get the public of the entire world to be able to detect the difference between a fact and a complete fantasy that has been created by the Internet.”
 “I do want to connect the public to science because there are so many decisions to be made if the way they learn it, if they learn it faster by talking aboutNeanderthals than they did by getting rote learning in high school, that’s great.” 
There is a great need to  improve science literacy in the general public. In my opinion, logic should be a requirement in the standards taught as part of science in primary and secondary education. It is so troubling. I can see it now…next there will be a claim that a scientist in South Korea has successfully cloned wooly mammoth DNA into a stem cell that replicates itself opening up the possibility of bringing back the long extinct species.
BTW, did you hear the news? They have cloned a wooly mammoth!
One day, I will write a post about using the word “they” for any statement about experiment results or innovation.
I digress…
The Woolly Mammoth at the Royal BC Museum, Vic...

The Woolly Mammoth at the Royal BC Museum, Victoria, British Columbia. (Photo credit: Wikipedia)

Climate Change Series: The Governance Challenge | Cognoscenti « Taking Science to the People

Climate Change Series: The Governance Challenge | Cognoscenti « Taking Science to the People

This is the third article in the weekly series. Great read.

When hairstyle trumps policy « Taking Science to the People

When hairstyle trumps policy « Taking Science to the People

I decided to go into the office while the Inauguration was taking place. I will catch the speech on the internet this week. I’ve heard good things about President Obama’s speech and the wording he used (finally) on climate change. However, the most (in quantity) buzz was about the First Lady’s new hairstyle sporting bangs. I adore the First Couple. I think they have taken the spotlight in stride and I expect big things in the second term. It is just troubling to think a considerable amount of press is coming from a change in hairstyle by Mrs. Obama. I must admit, it did make The Daily Show andColbert Report fun to watch. I dream of the day when substance will garner more ratings than discussing the change in appearance of a public official (or their spouse). My only hope the new twitter account and bangs are just the first step in promoting more grand ideas to make the country better. You have to love a good bait and switch.