I wonder what wavelength the blossoms reflect?

Some days I feel that my factual understanding of the biological world drains some of the pleasure that a more ignorant interaction with it would yield. For example, a tree in the fall, while its beauty is not lost on me, inevitably reminds me of the various chloroplast pigments (the most common one being green – i.e. reflecting a wavelength of between 520 and 540 nm) and a train of thought about what is known about light absorption for photosynthesis follows. Does this detract from the simple fact of the natural beauty of the scene? Yeah, maybe a little. But other times the magnitude of the complexity underlying the beautiful natural world we live in actually contributes to the awe I feel when beholding a particularly lovely tree. To synchronize all the various biochemical, cellular, tissue and organismal events necessary to produce a flowering cherry tree for example, is so massively complicated it is impossible to comprehend. And the circulatory system? Don’t even get me started.

The green ones reflect between 520nm and 540nm wavelengths of light

Hello internet!

I was honored when I was approached by my friend and colleague, Ms. Jeannome to become an author on this exciting blog.  All of my previous attempts at maintaining a bio blog have been a disaster, ending up as mostly pictures of kittens in miniature shopping carts.

Let me introduce myself.  I’m a second year graduate student in cell biology who has just completed her dreaded thesis proposal.  Science-wise, my interests lie mostly in membrane trafficking and ER structure.  My undergraduate experience was in microbial ecology, molecular genetics and space biology (that’s right).  I’m interested in science writing and the popularization of science.  I’ve also recently become involved in graduate student recruitment, which has been quite the adventure.  When I’m not in lab, I’m looking for a new apartment, watching Lost or visiting my boyfriend.

Stay tuned for unsolicited ramblings, complaints, and  exclamations as I perform experiments that look revolutionary until I run the proper controls! 

-kD

Our lab, like many labs, do not synthesize our own DNA in-house. However, we do use a lot of synthetic DNA – mostly in the form of primers or oligos for cloning, making siRNA, and sequencing. For our purposes, we have set up an account with Integrated DNA Technologies, or, IDT. It has been my experience that this website is incredibly slow. At first I thought that it was simply this computer, from which I order oligos 86% of the time (14% of the time I order them from home).  Another possibility is that the internet connection at work and at home is slow.  But I have tested these hypotheses carefully and the data suggests that it is in fact the IDT website. Here’s what I have for data:

1. All other websites on this computer and the one at home are not noticeably slow.

2. This website regularly crashes or is unbearably slow on the two computers I’ve tested in a neighboring lab. This also holds true for all 3 of the computers in the library, mine at home, and the one at the house of a friend (yes, I have a friend).

3. Even as I type this, that website is still loading so I can copy the url here for the link I am going to put above.

So today I had a new adventure. There is an adorable little box in the top right corner of the order page that has been tempting me since I started ordering oligos when I was two. It looks like this:

Well, I finally gave in.  I must admit that I was ambivalent about it.  On the one hand, I have a rough history with this website, so I knew my expectations should be hovering around zero, but on the other hand, look at that face!  I was hoping, I suppose, for high-definition video chat with real-time expert help for any of the oligo-ordering concerns I could come up with.

So, folks, here we go.  After a pop-up window indicated that I was in the first position in line for help, I was hopeful.  4 minutes later, with my undergrad sitting next to me, both of us with bated breath, ‘Ross’ opens a chat window and asks us what our problem is.  Our problem was complex, interesting, and I was hoping that after spending a total of about 15 minutes getting in touch with ‘Ross’ and explaining what was going on that he would do some fancy manipulations on the back end of the website and recover what was apparently saved yesterday but inaccesible today.  Alas, we were disappointed.  Instructions to clear our browser history and re-enter our order was a let-down I was expecting, but my undergrad was let down as well.

“Poor Lissy” has become a mantra in the lab that I hope will not persist.  “Lissy” is not her actual name, but we’ll call her that for now.  Fortunately it’s kind of a joke, but it’s also kind of not.  However, she has a good sense of humor so far, and I hope we won’t break her too soon.  But, more on that later.

Among the extracurricular activities that I’m quietly involved in (research is A. #1 priority!), is tutoring high school kids in the local high schools. You know, get them excited about learning! I know, your gag reflex is working overtime right now. Nevertheless, a couple of my classmates and I decided to host some highschoolers here in the teaching labs and conduct a “murder mystery” complete with DNA samples and mugshots. The idea was that they’d have to collect their own hard evidence, analyze it, and determine the murderer (sometimes science is so fun I can hardly contain my excitement).

So, there’s a kit from BioRad that comes complete with everything you need to execute some DNA fingerprinting on the DNA that was found at the ‘crime scene’ and unequivocally prove who killed whom. All you have to do is come up with the story to go with the the DNA provided in the kit, and teach a bunch of kids how to use hundreds of thousands of dollars worth of equipment without having a heart attack. With the sensibilities of our nation’s youth in mind we designed the following heinous murder:

At an award ceremony for C-list commercial actors, the Geico Caveman is clubbed over the head and killed.  Several other actors with various possible motives were at the scene.  Unfortunately, their accounts of the incident are varied and unreliable (after all, people are fallible – especially graduate students – and that’s why we turn to science!)  So, here are the mugshots:

A sinister bunch, if you ask me.

I suppose I better get back to work before my PI finds me.  Fortunately, I’ve rigged her computer so she can only read parentheticals in blog posts.

Petri Eyes!

I’m changing my project. It has been said that a poem is never finished, only abandoned. This is also true in biology. A project is never finished, only abandoned. So, perhaps to be most precise (my favorite thing) I am abandoning my project. And since this here blog has suffered the same screeching, halting death, I’m changing my approach to it as well.

As a budding scientist, I read and write a lot about the experiments, data, conclusions and other vocabulary words having to do with science literature. Well, ok, let’s be honest, I think a lot about reading and writing science literature, then I procrastinate about it, then I get anxiety about my upcoming proposal or outline or what have you, then I do a token amount of reading and writing. However, the proportion of time spent in my day considering, recording, designing, and executing experiments is huge. So then, when I have a free moment to sit down at my blog, the idea of considering, recording, designing or executing anything with real scientific merit kind of makes me want to shove a pipet into an important artery or arteriole.

The conclusion then, should be self-evident. Aside from an occasional post about some shiny new science that overwhelms my violent pipet fantasies, this blog is hereby dedicated to the less scientific side of cell biology. The trials, tribulations, triumphs (and alliteration) of having an undergraduate to “mentor”, for example.

Canonical Nucleoside Diphosphate Kinase B Isoform Functions to Regenerate Nucleotide Pools.

A daunting title, perhaps, but an interesting theory. This is the precedent to the work and hopefully the publication we have on NDKB that will be coming out soon.

Nucleoside diphosphate kinase B (NDKB) is a hexameric nucleoside diphosphokinase. Here’s a ribbon model for this hexamer:

It has been suggested that NDKB may play a role in maintaining cytoplasmic GTP pools. This hypothesis is based on the fact that it can catalyze the hydrolysis of the tertiary phosphate on a nucleoside triphosphate and subsequently regenerate another nucleoside triphosphate from a nucleoside diphosphate. Thus, it would be easy for this protein to make GTP from ATP and GDP. In this way, the homeostasis of the nucleotide pools could be maintained by simple stoichiometry. That is to say that nucleotide pools could be maintained, at least in part, by a mechanism wherein a protein such as NDKB has binding affinities that correspond to the general ideal relative concentrations of each nucleotide.

This is a very exciting idea and there has been some work to support this hypothesis, but it remains a hypothesis because the concentration of each nucleotide in vivo is extremely hard to measure. Furthermore, nucleotide pool homeostasis is a very important metabolic factor and so the mechanisms in place to maintain it are likely to be redundant. So, even if there was a reliable way to measure nucleotide pools, they are unlikely to be changed much as a result of NDKB knockdown even if it is functioning in this pathway. Also importantly, NDKB has been shown to be able to function in pathways where its diphosphokinase activity are disposable, such as in COP II assembly and ER export.

There you have it, a peek into NDKB (which, notably, may be called Nm23H2 in mammalian cells). Complete references to the research I’ve alluded to here will be forthcoming.

The purpose of this here blog is three-fold. First and foremost it is a way for me to share useful experiences, protocols, general knowledge, and my recent trials and tribulations conducting cell biology research. My hope in this respect is that my investigations and mistakes can be made public so that in the search for the perfect stable cell line protocol, I can help other people avoid causing massive apoptosis in COS cells, for example.

The second purpose of this space is to serve as a personal website of sorts where people can find out basic information about yours truly: contact information, CV/resume, and favorite Ph.D. comics.

Finally, the third purpose of this space, in true scientist fashion, has yet to be elucidated. The literature has some tantalizing hints, but the exact mechanism is far from unraveled. Stay tuned, I guess.