Laura Edwards
“Why isn’t this working”? “Should we go get coffee”? “We have some of *this* in our sample.”
Here are a few phrases overheard in the NCSU Biochemistry department.
In the video: Laura Edwards, Annette Bodenheimer, Brian Rogers, Xun Lu.
Clay Clark - @biochemprof
Since I’m traveling to San Diego this week, I thought that I’d leave a reading list. These publications may or may not make it into a blog, but here’s a list of what I’m reading this week and why.
Congratulations to Christie Cade and Lars Cade, proud parents of Theodore Rex Cade.
Clay Clark - @biochemprof
An interesting discussion occurred on a popular social networking site following a post about evolution theory. The following represents excerpts from the discussion. Because The One-Word Professor believes that verbiage is overrated, his part of the discussion is succinct. We do, however, get to delve into the inner workings of TOWP’s mind. The content represents an actual discussion and was edited very little, because it’s funny enough on it’s own. Even though we (the editors) are at risk of a reader invoking Poe’s Law, we recreate the conversation for you here. While the conversation is humorous, the topic is quite serious since only ~40% of Americans believe in evolution.
Believer 1: All those evolutionists that “study science” are so smart. But seriously, who is more dumb, those who believe without question, or those that come up with crap answers? I guess I shouldn’t let the willing forgetfulness bother me.
TOWP: Hmmm.
Grant deadline next week. Have to edit and return paper by Friday. Hey, what the hell is this?? “Crap answers”? “Study Science”? Is he f***ing kidding? Leave it alone, TOWP. Leave it alone. (After several “likes” of the post) Aww sh*t, now I have to get involved.
Believer 1: It baffles me to see the unwillingness and laziness when it comes to actually thinking about how this incredibly complex world was made. I don’t think that scientists are dumb people, but it comes down to the point of accepting or rejecting the Truth. How can you start with goop and end up with this?
TOWP: Evolution?
Clay Clark - @biochemprof
A new paper published in PLoS Biology characterizes two bacterial death pathways
Programmed cell death (PCD) in eukaryotes is a well-studied process that is used by organisms to maintain homeostasis. The mechanisms of PCD are under intense study because altered regulation leads to excessive cell death (inflammatory diseases) or excessive cell growth (cancer). The classic pathway in eukaryotes is apoptosis. Likewise, some bacteria also contain PCD pathways, but the reactions are less well characterized. In bacterial PCD, it is also not clear how a death program in single-celled organisms provides an evolutionary advantage. It is important to note that PCD refers to any form of cell death mediated by an intracellular program, regardless of whether the program displays all of the hallmarks of eukaryotic apoptosis.
In bacteria, PCD is mediated through modules that consist of a pair of genes, called “addiction modules” or toxin-antitoxin (TA) systems. One gene of the module encodes for a toxin, and the second gene encodes for a labile antitoxin. Under normal growth conditions (that is, non-stressed), the continual production of the antitoxin inhibits the activity of the toxin.
An open letter to my graduate students and post-docs
Clay Clark - @biochemprof
Dear Students and Post-docs,
I’ve learned a few things as my career in science has progressed from graduate student to post-doc to assistant, associate and finally professor. I’d like to share some of these pearls of wisdom with you in hopes that you’ll be able to use them during your journey as a scientist. I post these suggestions here because, although I see you working diligently in the lab, we haven’t had enough time recently to drink beer together and have this discussion.
Great Belgian Beers
A few years ago, when I was in graduate school at Texas A&M University, I was involved in a protein folding project. This was a new project started by my advisor, so there was a sense of urgency to spend the time required to learn new techniques in order to collect data, to attend classes and seminars, and to learn material on broader topics related to our work. This also helped me develop a passion for science. You too should develop a sense of urgency. JAYFK recently posted a blog entitled “5 Things you should know before dating a scientist”, and I repost point #4 here. Although this is a very funny and irreverent look at science, there also is good advice in this particular blog:
By Joe Maciag
Since we’re on break this week, we thought that a comparison of spring break activities for undergraduates, faculty and graduate students would be interesting.
Rapid bioorthogonal labeling of proteins
Clay Clark
By Clay Clark, @biochemprof
There are a number of current methods for labeling proteins for imaging either in vitro and/or in live cells and organisms, including fusions with fluorescent proteins, dyes, tags (such as SNAP, HALO, CLIP), ligases, spin-labels, or unnatural amino acids. Some of the methods are summarized in the figure from Chen & Ting, which shows several approaches to labeling proteins with small molecules, either through fusion proteins (A), chemical or enzymatic labeling of a protein tag (B,C) or site-specific labeling using genetically encoded amber mutations (D).
Protein labeling strategies, from Chen & Ting, DOI 10.1016/j.copbio.2004.12.003
In recent years, several chemical probes have been developed that allow the incorporation of reactive tags into proteins. The tags can then be modified within the complex mixture of the cellular milieu, providing a powerful technique to examine protein structure and function as well as interaction networks in native conditions (see review of the tags by Best).
While some of the tags allow rapid labeling and have been used in numerous cell biological studies, many of the methods result in the addition of extra amino acids to the protein, which may affect the protein structure or function. In addition, some of the chemical probes have slow reaction times, which limits their use.
Why bridging funds are critical in today’s funding environment
Clay Clark
By Clay Clark – @biochemprof
I’ve just returned from study section in Washington, D.C., where I and twenty-two other scientists met to review grants submitted to the National Institutes of Health. As a bit of background into the process, I receive the grants about six weeks before the meeting, and I spend countless hours reading and critiquing the grants. A grant proposal receives a score based on several criteria and is given an overall impact score between 1 (high impact) and 9 (low impact).
Based on the initial scores from three reviewers, the top half of the grant proposals are discussed by the study section. Following a summary of the proposal by the three reviewers, and questions by the panel, the proposal receives a score from each panel member. The proposals are then ranked against other grants in the study section and given a percentile score. Confusing? I invite you to read a thorough description of the review process here. NIH also has a series of videos that explain the process.
One conclusion that I’ve come to over the almost six years of reviewing grants for NIH is that universities should give serious consideration to bridging funds. I’ll define “bridging funds” as money supplied to a researcher when his grant did not get funded or renewed, so long as the researcher is productive and is attempting to get the grant funded or renewed.
