The traveling biochemist: Science in the far east

Posted on May 17, 2013 by Clay Clark

Clay Clark – @biochemprof

When I’m lucky enough to be invited to a conference outside the United States, I jump at the chance to visit faculty and students at other institutes. Recently, I was invited by the Biochemical Journal to attend the yearly editorial meeting in Beijing, China. I’ve been a member of the editorial board for several years, and the editors usually meet in London each spring to discuss issues pertaining to the journal. Two years ago BJ opened an office in Beijing in anticipation of the tremendous growth in scientific research occurring in Asian countries. In order to highlight research of the editorial board members, BJ held a one-day research symposium (Cellular Processes: the Life and Death Decisions of a Cell) at Tsinghua University prior to the board meeting. The talks focused on new imaging techniques, nanotubes and intercellular communications, membrane dynamics and tumor suppression, and molecular switches between apoptosis, autophagy, and programmed necrosis.

I traveled to Beijing several days before the meeting in order to visit tourist sites around Beijing as well as to visit Dr. Yigong Shi and his students at Tsinghua University. I’ve crossed paths with Yigong on several occasions since we are both interested in cell death mechanisms and we both served on NIH study section, so he invited me to give a seminar on my research. The room was packed with faculty and students who were quite engaging. Yigong then treated me to a lunch of Peking Duck and other delicious dishes before he returned to his duties as a delegate to the National People’s Congress, which was in session at the time.

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Cadmium: toxic to mammals, harmless to a bacterium, helpful to an alga

Posted on May 15, 2013 by Clay Clark

Joe Magliocca

Heavy metal poisoning is a major health concern across the world. Heavy metal ions frequently leak into the environment from industrial waste causing multiple health problems in humans, animals, and other organisms. While there is no universally accepted definition of what elements are heavy metals, the definition I find most useful includes the metal rubidium and all metals heavier than it. These metals have large atomic masses, and aside from molybdenum (and possibly tungsten), have no essential biological function; they only interfere with other biological functions.

One heavy metal of significant concern is element 48, cadmium. This element is mostly found in nature as an impurity in zinc ore, but small amounts are scattered throughout soil, seawater, coal, and other mineral deposits. It first became known as an environmental and medical hazard when a disease known as “itai-itai” (literally “it hurts-it hurts”) appeared around the city of Toyama, Japan between the Russo-Japanese war and World War II (roughly 1905-1945). This city was a major center for zinc mining, and the cadmium waste from this process was found to be the cause of the disease.

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Matrone lecture by Dr. Robert Lefkowitz

Posted on April 29, 2013 by Clay Clark

Dr. Robert Lefkowitz presented the 2013 Matrone Lecture in Biochemistry at NC State University on April 18.

The Department of Molecular and Structural Biochemistry, Biochem Blogs and NC State University present the Matrone Lecture by Dr. Robert Lefkowitz: click here to watch the 2013 Matrone Lecture.

The department held a reception prior to the presentation, and a slideshow of the reception is shown below.

Novel industrial applications from salt loving extremophiles

Posted on April 25, 2013 by Clay Clark

Graduate Student Bob Grinshpon

This blog will review two recent publications that explore environmentally friendly advances in biotechnology by exploiting halophilic organisms from the family Halobacteriaceae. Halophiles are found in all kingdoms of life. They employ two different survival mechanisms to cope with their typically inhospitable environment. The first strategy, ‘organic solutes in,’ excludes external salt from the cytoplasm, and synthesizes osmolytes to balance the turgor pressure with the
environment. The second survival mechanism, ‘high salt in,’ is less common, and requires that the entire proteome adapt to high salt conditions. Halobacteriaceae consist of members that strictly
use the second strategy. The similarity between the two papers ends there, but each approach is
interesting in its own right.

In the first paper (1), they characterize β-galactosidase (bga gene) from the recently discovered polyextremophile, Halorubrum lacusprofundi, and assess it for potential use as an extremozyme. β-galactosidase is involved in the breakdown of β-galactosides into monosaccharides. It is noted for its use in production of lactose free milk. However, it is assumed that lactose is not typically available in H. lacusprofundi’s environment, and the bga gene is found clustered with other genes that suggest their role is in the breakdown of plant polymers.

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National Science Foundation IGERT training program sends young scientists to learn neutron scattering at ORNL

Posted on April 11, 2013 by Clay Clark

Flora Meilleur, Course Organizer

Graduate student Annette Bodenheimer and Dr. Meilleur participated in an Integrative Graduate Education and Research Traineeship (IGERT) workshop in neutron scattering conducted at the Oak Ridge National Laboratory Spallation Neutron Source, February 25 through March 1. The workshop educated graduate students in the benefits of neutron scattering in (1) biological macromolecules and biomaterials, (2) the structure and dynamics of strongly correlated electronic materials, and (3) the design of artificial nanoscale materials.

IGERT is the NSF’s flagship interdisciplinary training program for PhD scientists and engineers from the United States. Since 1998, the program has made 215 awards to more than 100 universities in 41 states, the District of Columbia, and Puerto Rico and has provided funding for nearly 5,000 graduate students. Dr. Meilleur is a co-PI on an IGERT project led by Professor Haskell Taub, a Professor of Physics at the University of Missouri, Columbia, entitled “Neutron Scattering for the Science and Engineering of the 21st Century.”

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Rubredoxin the Indestructible

Posted on April 8, 2013 by Clay Clark

Graduate student Annette Bodenheimer

Most biochemists have had the “pleasure” of working with proteins that require cool atmospheres and a comfy solvent to keep them temporarily happy (until they randomly decide to aggregate into protein snot). Rubredoxin from the organism Pyrococcus furiosus, on the other hand, is like an old Jeep that keeps on working despite repeated abuse and temperature fluctuations.

P. furiosus was initially discovered near a deep sea volcanic vent. This hyperthermophilic archae is an anaerobe that grows optimally around 370K (or 100 °C). Rubredoxin, as seen in Figure 1, is a small 53 amino acid protein and has a high spin state iron that is coordinated between four cysteine residues. It is responsible for electron transfer reactions, although the specific reactions it participates in is still unknown. Early research found that rubredoxin maintains its globular or tertiary structure up to 473K.

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Central Dogma: The Movie

Posted on April 1, 2013 by Clay Clark

Cindy Hemenway

It all started in 2004 when I was trying to explain the trombone model for DNA replication to students in BCH453/553 (Biochemistry of Gene Expression). The conversation went like this…

Student X: Dr. Hemenway, it is really hard to visualize how that looping process works.

Dr. Hemenway: Yes, it would be nice if we could build a working model to understand it better.

Student Y: Can we do that for extra credit?

Dr. Hemenway: Great idea!

The rest is history. After years of students asking if I had examples for them to see, I finally gave in and filmed them in action. Although I was hesitant to do this because it might hinder the creative process, the reality was that I was finding it hard to get enough notes taken down on my grading sheet during their presentations. And, there were so many memorable projects!

So, please enjoy the links below of the spring, 2012 BCH453/553 students modeling prokaryotic DNA replication forks, eukaryotic transcription and prokaryotic translation.

The ever important role of thermophiles in biofuel production

Posted on March 26, 2013 by Clay Clark

Laura Edwards

Well, it’s no secret that there are some major issues with our current dependency on fossil fuels. First of all, they don’t last forever, so at some point we’re going to run out (don’t worry, not any time soon). Second of all, when they are burned they emit greenhouse gases that are bad for the environment… not to mention the environmental damage done trying to get fossil fuels out of the ground. Lastly, the cost of gas for the American consumer has dramatically increased in the past years (it’s definitely hurting my wallet). These and other factors have prompted the research and development of alternative, renewable fuel sources such as biofuel (using organic matter for energy). Plants are a great source of energy, and the concept of using that energy for biofuel production has been around for decades. So why can’t we just stuff a stalk of corn in our gas tanks and call it day? Well, several reasons… plants are really good at converting solar energy and storing it as cell wall polymers, but the challenge comes from extracting out that energy and converting it into usable fuel, such as ethanol.

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Computer security is important

Posted on March 25, 2013 by Clay Clark

Earlier this week the X-ray generator control computer was hacked into from an IP address assigned by an internet provider in Shanghai China. The attack started with repeated root login attempts starting sometime before 3:00 Sunday morning and continued until success Monday morning at about 8:00 AM.

The intruders did no damage to the files on the computer but did install some software of their own which was designed to attempt to break into other computers. CALS (College of Agriculture and Life Sciences) IT discovered the break-in through monitoring suspicious network traffic outgoing from the computer and disconnected it from the network at about 9:00 AM Monday.

In recent times, there have been numerous news reports of high profile computer break-ins against large companies and other organizations. It is not uncommon for those break-ins to be achieved using university computer facilities that are first hacked. The strategy makes it easier for hacking since activity sourced to American computers is less suspicious and it provides the hacker some insulation from discovery.

In summation, our computers are targets and we must do what we can to minimize risk. Make sure that your fire-walls are up to date and turned on. Make sure that all of your accounts are pass-worded and that the passwords are at least 8 characters long with numbers, capitals and special characters. If you are running a computer with Linux OS make sure that remote root login is prohibited and that local root login is prohibited.

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New Course Offered: ‘Physical Chemistry for Life Scientists’

Posted on March 14, 2013 by Clay Clark

Chuck Hardin

Have you seen the bumper sticker “Honk if you passed P-Chem”? I recently finished teaching the first semester of a new course offering designed to make P-Chem “come alive” for our students.

It seems obvious to me that every dry, hyper-theoretical lesson one encounters in the standard P-Chem course deserves to be refocused to highlight how it bears on biochemistry. Not only does it reveal how the biochemistry works, it also provides a much more interesting and example-driven way to actually hook into the concepts. For example, we learned about diffusion theory by covering the limitations placed on the use of pheromones by the size of an organism and the rates of diffusion of both the pheromone and the organism. In another, we used the Boltzmann distribution to understand how voltage-gated ion-channels work. In a third, we looked at the use of lattice models and the canonical ensemble to understand how the search process that leads to protein folding works.

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