Author Archives: Clay Clark

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About Clay Clark

I'm a professor of biochemistry at NC State University, where I research allosteric control of caspase activation. My lab routinely uses biophysical and structural techniques as well as molecular techniques to exam protein structure and function. I spend as much time as possible in the dojo practicing Sanshinkai karate.

RecA: A glimpse into the cosmos

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Joe Maciag

Joe MaciagI'm on ScienceSeeker-Microscope

Waking up thousands of miles from home was a normal occurrence in the summer months as a child. I was never the first awake, there was always one who was waiting for me. To say my grandfather was an early riser is an understatement, and I have since lost my love for meeting the sun. He did, however, instill something else in his youngest male grandchild – a love for the cosmos. Each morning I would slip out of bed, head down stairs and meet my grandpa as he prepared his coffee (black). We  would make our way to the yard in the crisp New York summer air and watch the sun rise as he listed the planets and their relative diameters. He was the first to explain to me the mechanics of the solar system and cultivate a love of science in a young boy. I have been intrigued ever since even though my science pallet has changed somewhat. I don’t want Biochemistry to think I am cheating on her because I love her, but the cosmos is always my first love.

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Introducing WolfPub – A publication management system for webpage development

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WolfPubWe are pleased to announce the launch of WolfPub, an easy and secure way to manage your publications. WolfPub is a web-based system that allows you to maintain and store your publications, then WolfPub uses the database to format and post your publications to your webpage. As a faculty member, you can create an account and then start adding your new publications in a simple and secure way. You will no longer be required to open your webpages and edit them manually whenever you have a new publication in press. Just add the manuscript to the list of publications in your WolfPub account, and the WolfPub widget will take care of the rest.

WolfPub works with PubMed and it’s own database to manage your publications. On your webpage, it formats and displays your manuscripts that are “published” as well as manuscripts that are “in press,” if any. Users are only required to add publications that are in press in their WolfPub account. WolfPub automatically retrieves your “published” manuscripts from PubMed. WolfPub also updates the database when the in press manuscript lists on PubMed. During this process, if a publication added into the WolfPub database as “in press” has been listed on PubMed, your publication will be marked as “published.” The information displayed on your webpage will then be changed accordingly to reflect the journal volume and page numbers. Because of this feature, you are no longer required to keep watching your publications for a change in status.

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NCSU Biochemistry graduates stellar students

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May Graduation 2013

May Graduation 2013

In the May 2013 graduation ceremony, the department conferred BS Biochemistry degrees to 56 students and PhD Biochemistry to 5 students.

Previous graduating classes were approximately 40:60 men:women; the current class is just about even at 52:48 [same as the ratio for December 2012 graduation!]. There was good diversity of the students who specified their ethnicity: 43% – non Caucasian with 20% Asian, 2% Hispanic, 11% Afro-American, 4% American Indian and 5% mixed.

The undergraduate students were quite accomplished, with an average GPA of 3.35.

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The traveling biochemist: Science in the far east

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Clay Clark

Clay Clark – @biochemprof I'm on ScienceSeeker-Microscope

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

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Joe Magliocca

Joe MaglioccaI'm on ScienceSeeker-Microscope

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

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Robert Lefkowitz

 

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

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Bob Grinshpon

Graduate Student Bob GrinshponI'm on ScienceSeeker-Microscope

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

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Flora Meilleur

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

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Annette Bodenheimer

Graduate student Annette BodenheimerI'm on ScienceSeeker-Microscope

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

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Cindy Hemenway

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.