Marshall Nirenberg (April 10, 1927 – January 15, 2010)

Marshall Nirenberg passed away recently from cancer. Nirenberg is famous for "deciphering" the genetic code. I wrote a piece about him earlier in this blog. In the classic experiment with Heinrich Matthei, the duo showed that nucleic acid codon poly-uracil (UUU) coded for the amino acid phenylalanine.

According to a New York Times Obituary, Nirenberg was “enthusiastic and magnetic. He had an idea every two or three minutes."

NIH has an excellent exhibit on the genetic code discovery.

Nirenberg shared the 1968 Nobel Prize with Robert Holley and Gobind Khorana.

Nirenberg's collected papers can be found at the National Library of Medicine.

Parasite of the Day

My colleague at the American Museum of Natural History, Susan Perkins, has started an ambitious new blog. She will be introducing a new parasite to the world each day in Parasite of the Day. Unfortunately, perhaps, for the hosts of the world, Susan has plenty of subject matter and should be busy for quite some time. A recent paper in PNAS (Dobson et al. 2008) states that although they "estimate that there are between 75,000 and 300,000 helminth species parasitizing the vertebrates. [They] have no credible way of estimating how many parasitic protozoa, fungi, bacteria, and viruses exist. At least the helminths parasites of vertebrates will keep Susan busy for the next 821 years or so.

The photo above is of Neoechinorhynchus emyditoides a species of acanthocephalan, or thorny-headed worm, by Mike Barger.

Ava at the Reef Tank interviewed me on my thoughts on evolution and fish husbandry. I confess that while I absolutely love aquariums, I don't have much by way of aquacultures at present. We've got a few really-easy-to-care-for Bettas and Telescope goldfish, but that is about it. I'm fairly lazy when it comes to maintaining animals in my lab and house, and try to chose animals that require minimal care (Leopard slugs anyone?). I did buy a female Betta with some breeding in mind, but it turned out to be a wild-type male. I was really disappointed since Bettas have such interesting breeding behaviors. Males make large bubble nests with their own saliva.


After female Betta has spawned, the eggs float up into the nest from below or the male Betta carries them there in its mouth. The male fertilizes the eggs and initiates embryo development. The male Betta will guard the nest for the next 24-48 hours until the eggs hatch. He also keeps a close watch on the eggs and will retrieve any eggs or fry that fall from the nest. He will also repair the nest by adding bubbles where needed. After the fry hatch (in 24-48 hours) the male will tend the fish for the next couple of weeks. How cool is that?

You and Your Research

Richard Hamming is not a household name. As a long-time Bell Labs scientist, Hamming made lasting impacts on mathematics, computer science, and engineering. He also gave one of the best talks I have come across for anyone pursuing/interested in pursuing a career in science. This talk, titled "You and Your Research" was presented to the Bell Communications Research Colloquium Seminar on 7 March 1986. It could be titled "How to do Great Research".

Hamming first discusses his motivation:

At Los Alamos I was brought in to run the computing machines which other people had got going, so those scientists and physicists could get back to business. I saw I was a stooge. I saw that although physically I was the same, they were different. And to put the thing bluntly, I was envious. I wanted to know why they were so different from me. I saw Feynman up close. I saw Fermi and Teller. I saw Oppenheimer. I saw Hans Bethe: he was my boss. I saw quite a few very capable people. I became very interested in the difference between those who do and those who might have done.

Hamming found that the major difference between good and great is largely one of attiHe summarizes his findings:

In summary, I claim that some of the reasons why so many people who have greatness within their grasp don't succeed are: they don't work on important problems, they don't become emotionally involved, they don't try and change what is difficult to some other situation which is easily done but is still important, and they keep giving themselves alibis why they don't.

In other words, ask yourself three questions:

1. What are the most important problems in your field?

2. Are you working on one of them?

3. Why not?

Virus Evolution

Here is a short video on virus evolution from the Instituto de Biologia Molecular y Celular de Plantas and the Santa Fe Institute Professor Santiago Elena.

Synopsis

Viruses can evolve fast and sometimes adapt quickly to a new host species. For example, an influenza virus that normally infects birds can become adapted to humans. The tobacco etch virus normally infects tobacco plants. Professor Santiago Elena from Valencia wants to find out what it takes to make the tobacco virus capable of infecting another plant: Arabidopsis. The movie shows how Santiago Elena does the evolutionary experiment and we see that after 30 rounds of experimental evolution the virus is indeed adapted to the new host plant! After the experiment, Elena looks at the genetic code of the adapted virus and finds that there are just three differences between the genetic code of the normal (tobacco loving) virus and the virus that is now adapted to Arabidopsis.

Lawrence Basil Slobodkin (1928-2009)

Larry Slobodkin, eminent ecologist, founding chairman of the Stony Brook University Ecology and Evolution Department, and Fellow of the American Academy of Arts and Sciences passed away last Saturday.

Larry's impact on the science of ecology is immeasurable, particularly with regards to linking population dynamics with ecosystem ecology. A concrete example of this is his famous HSS paper. With coauthors Nelson Hairston Sr. and Jerry Smith, Slobodkin use a simple observation (the world is green) to deduce that predators limit herbivore abundance, thus allow plants to flourish.

Beyond his scientific contributions, Slobodkin is reknown for creating the world's first graduate program in ecology and evolutionary biology (at Stony Brook University). Many of the best and brightest in the field have either taught or schooled in this program.

Larry's (academic) nephew, ecologist Mike Rosenzweig, wrote a great piece about him for Evolutionary Ecology Research. Larry contributed this autobiographical article. More articles in the EER special issue in his honor are available here.

NY Times Obituary

Update: Carol Reid wrote a nice tribute to Larry here.

Update: An obituary was published in PLoS Biology.

Phage Hunters

18 freshmen students have enrolled in my Genomics Research Experience course aka Phage Hunters. This course is supported by the Howard Hughes Medical Institute's Science Education Alliance. My students have begun the process of isolating novel Mycobacteriophages by collecting soil samples from the wild and plating them on lawns of Mycobacterium smegmatis, a M. tuberculosis relative. Unlike M. tuberculosis, M. smegmatis is non-pathogenic and is easier to grow and manipulate under experimental conditions. Nonetheless, by virtue of their close phylogenetic relationship, the two bacteria are quite similar in many respects. Thus, M. smegmatis may be an excellent model for deriving treatments against tuberculosis.

Collecting Mycophage is already paying handsome dividends. Albert Einstein College of Medicine Professor William Jacobs isolated a phage he named the Bronx Bomber from soil from his own backyard in the Bronx. With University of Pittsburgh Professor Graham Hatfull, Jacobs characterized this phage in the laboratory. They found that this phage is able to insert itself into the genome of M. smegmatis at a very specific location in the groEL1 gene, thus disabling the gene. One of groEL1's functions is to facilitate the production of biofilms.

Biofilms are extracellular polymeric substances that aid and protect microbes. They allow bacteria to persist in the face of antibiotics. It's estimated that 80% of infections involve biofilm formation. While biofilm formation in tuberculosis has not yet been uneqivocally confirmed, M. tuberculosis does have a groEL1 gene with 90% similarity to that of M. smegmatis.

If the phage is able to infect M. tuberculosis or is mutated to infect M. tuberculosis, it is possible that some day the phage could be used as therapy against tuberculosis. As one of the three primary diseases of poverty, tuberculosis has a devastating impact in the developing world.

Top Photo: Bxb1 is a mycobacteriophage that was originally isolated from Dr. Jacobs' backyard in the Bronx. It is affectionately called "The Bronx Bomber" as it forms large plaques on a plate with lawn of Mycobacterium smegmatis cells (left panel). The Bxb1 phage plaques are characterized with their clear centers surrounded by turbid rings. The turbid rings represent lysogens (i.e. M. smegmatis bacterial cells into which Bxb1 has integrated) of M. smegmatis that are resistant to superinfection with Bxb1 phage. These lysogens are defective in biofilm formation. A transmission electron micrograph of Bxb1 is shown in the right panel. Courtesy of Jordan Kriakov, William R. Jacobs, Jr.

Middle photo: Image shows Mycobacterium smegmatis growing as a biofilm on a liquid surface, with its characteristically textured folds. Courtesy of Anil Ojha, Tom Harper, Graham Hatfull.