A summary of our student bloggers for the Protein Journal Club and their blogs for spring semester 2012
Christie Cade: PhD student who studies caspase activation and cancer drug development
How hats, baby toys, and amber help us learn more about the nature vs. nurture debate
And: Scientist gives birth to T. Rex
Chunxiao Ma
Recently I posted a blog on using miRNA profiling as biomarkers for cancer. Protein profiling is another potential tool for hunting biomarkers. Traditional microarray data are 
based on the assumption that each individual protein contributes independently to clinical outcomes. As the data are inconsistent across different data sets, we start to think that not all proteins should be weighted equally. The first step is to identify the significant protein sets or pathways involved in disease, that is, the so called protein biomarkers.
Fan Liu
What is referred to as “MudPit” here is not “a pit of mud” but a technique in the mass spectrometry field which stands for “multi-dimensional protein identification technology”, a very powerful approach that has been widely used since the year of its inception in 2001.
Many efficient technologies have been developed to reveal global behaviors of DNA (genome) and RNA (transcriptome), such as DNA-DNA interactions (through chromatin conformation capture on chip) and global gene expression (through transcriptome sequencing). However, the systematic study of proteins (proteome) lags behind the analytical DNA and RNA analysis.
Dr. Greg Buhrman
This is the second blog piece I’ve written, although it may be the first one you’ll read. Dr. Clay Clark asked me to blog about my experiences teaching BIO 414 (Cell Biology) for the first time. I wrote one piece half-way through the semester about one particularly interesting teaching experience. Then Clay asked me for the backstory but I never felt introspective enough to get into it. Now it’s the day before graduation and I’m feeling introspective, so here goes…
Laura Greeley
Traditional light microscopes are not able to resolve images small enough to explore the details of cells. One of the techniques used to investigate nanoscale samples is atomic force microscopy (AFM). AFM uses a very fine tip (atoms in diameter) attached to a cantilever to “feel” the surface of a sample. This method is ideal for measuring microfabrication, like silicon chips, but traditionally was too harsh on living organisms. Yet, advancements in the technology and new techniques have opened new possibilities for exploring the fine details of microbes.
Clay Clark - @biochemprof
Fifteen years ago Dr. Dennis Brown became the sixth head of the NC State Department of Biochemistry. He had served previously as the Director of the Cell Research Institute and Chair of the Division of Biological Sciences at UT Austin and came to NCSU with a mandate to build a strong structural biochemistry program. Prior to Dennis’ start at NCSU, the department had spent many years under the leadership of Dr. Paul Agris building a program in molecular biochemistry, particularly in the area of RNA structure and function.
The biochemistry department has thrived in the past 15 years, with a strong vision from the head as well as strong support from the administration. Dennis will step down as department head in June, and as I step into the headship on an interim basis, I want to take a moment to look back at some of the highlights of his tenure.
John Cavanagh
I recently took my crack squad to the 53rd Experimental NMR Conference (ENC), held at the lovely Intercontinental Hotel in Miami. The crack squad consisted of myself, our currently injured lab manager Richele Thompson, Research Assistant Professor Ben Bobay, post-doc Andrew Olson and graduate students Sean Stow and Ashley (AT) Tucker. We flew coach, walked from the airport to the hotel and our rooms were extremely cheap, of course.
The ENC is the largest conference of its kind and is an annual rite of passage for the hardcore NMR crowd. Everyone who is anyone is there. I had breakfast with Richard Ernst – Nobel Laureate. When I say I had breakfast with him, he was on the other side of the room at a completely different table, looking out of the window. But I could see him from where I was sitting, somewhere below the Cholula sauce.
Joe Maciag
What if I told you there may be a new way of determining whether non-cancerous cells have the potential to form malignancies. If this were possible, it may lead to earlier diagnosis and treatment. The method may sound like a way to see into the future, but it is not fictitious.
Over the last decade scientists have uncovered new evidence in the field of DNA methylation due to advances in technology. DNA methylation is the covalent addition of a methyl group (CH3) at position 5 of the nucleotide base cytosine (see picture below).
Clay Clark - @biochemprof
Earlier this year I was asked to serve on the executive committee for the NCSU Molecular Biotechnology Training Program. This program is directed by Dr. Bob Kelly and is designed to augment graduate training by exposing students to biotechnology through laboratory-based courses and seminars.
Students also are encouraged to participate in the Professoriate Training Program (PTP), which gives them the opportunity to work with a professor one-on-one to enhance classroom teaching skills.
Chunxiao Ma
“A thing serving as a standard” —-This is the definition of a marker. As a graduate student, the concept of a
“marker” permeates every corner of my research life. When I
made our zebrafish video, I was very surprised to learn that we can make a green tumor and use it as a tool to monitor the shrinkage of tumor tissue. A related question then came to mind. Do we have similar tools to monitor tumor shrinkage in human cancer? This got me interested in searching for a biomarker of human cancer.
The cancer biomarker is a headache for scientists interested in cancer drug research. Years ago, when high-throughput techniques were only a dream, scientists wanted to find a molecule that can distinguish cancer cells from healthy cells. However, all the efforts seemed futile because cancer cells developed from healthy cells and thus were difficult to target.