Saturday, April 28, 2012

A Ph.D. in Biology, here I come!

I am really excited to announce that I got into graduate school for the fall!

I have been accepted into the Doctoral Program in Biology for the Fall 2012 semester at City University of New York, which is coincidentally my first choice for grad school.

Accepted! #winning
I really couldn't be happier and more excited. For more, check out my statement regarding being accepted that has since been immortalized on the YouTubes:

What I don't talk about in the video is why I wanted to do CUNY's bio Ph.D. program so badly.

Well, for starters, I found this really awesome lab, and they have room for me. The professor leading the lab has a Masters in environmental engineering, a Masters of science in journalism, a Ph.D. in biological oceanography, and did his post-doc in molecular biology. That's a really awesome, well-rounded background.

The lab he runs is interested in coral reef ecology (with an empasis on the mesophotic coral reefes and fluorescent proteins), marine microbial ecology in relation to biogeochemical cycling, and identifying and developing novel compounds from marine and reef organisms. I don't know which sounds the coolest. I could go on and on about this lab, but I'll spare you.

Secondly, the classes I'd have to take are classes I'd want to take. Students are required to take one course from each of the following four areas
  • Behavior
    BIOL 72407 Animal Behavior II
    BIOL 72406 Behavior and Evolution

  • Ecology
    BIOL 76005 Population Ecology
    BIOL 76001 Ecology
    BIOL 76003 Community Ecology

  • Evolution
    BIOL 70901 Population Genetics
    BIOL 70503 Evolution
    BIOL 70803 Molecular Evolution

  • Systematics
    BIOL 70603 Principles of Systematics
In addition, students are required to take:
  • One graduate statistics course consisting of both lecture and lab. This can be fulfilled with either Biostatistics I (BIOL 78201 - lecture and lab) or Mathematical Biology I and II (BIOL 78001 lecture and BIOL 78002 lab). 
  • One 3-credit graduate seminar course (For example: Seminar in Evolution BIOL U79001, Seminar in Ecology BIOL 79006, Seminar in Biomathematics BIOL 79008, Seminar in Systematics BIOL 79011, Seminar in Zoogeography BIOL 79012, Seminar in Animal Behavior BIOL 79022). 
The above list is a balance of I-can't-decide-what-I-want-to-take and courses I know I need to take in order to make myself a better rounded student. While I expect my path to change my study focus, I hope to pursue an molecular ecology approach to coral reef ecology with an emphasis on microbial ecology and identifying novel compounds from reef organisms.



Tuesday, April 24, 2012

Small lab techniques (or nerdy, depending on how you look at it)

Last week I needed to run a gel for approximately 19 lanes, but our small gel boxes only fit up to 14 lanes. Our large gel box fits plenty of lanes, but I only needed half of the length it provided and I didn't want to waste any agarose. I came up with a solution: the usage of lab tape to cut the length of the functioning casting tray into half. Check it out:
The frugal gel--using lab tape to prevent to use of excess agarose.
The plates have dense diatom populations at the initial streaking point.
In other creative news, I'm using lab tape to slow the growth of my diatom plates. Why might I be doing this? Well, I'm growing these diatom cultures on plates to select for single clones for use in my experiments. But as you can see in the plate to the right, I have really dense diatom streaks from the initial plating. You could just yell at me to plate fewer cells, but because of the slow growth rate of diatoms (in comparison to bacteria), I usually plate a lot more cells to ensure the diatoms inoculate the plates. Additionally, the growth of my diatoms appears to be sensitive to the initial density. That is, there appears to be a starting threshold density required for successful culture growth. Therefore I plate more cells that normal in order to ensure good culture growth.

Tape on the lid blocks light above the densely populated agar.
Working form these dense cultures, I streaked out a small portion of the dense cells in order to get some single colonies. In the meantime however, I don't want the dense portion of the plate to overgrow, use up all of the nutrients, and bleach while the single colonies proliferate. So, by using tape on the top of the petri dish, I can slow down the growth of the dense population while allowing full light exposure to the single colonies. (Continued below)

Color coding of discrete diatom genetic lines!
(Red refers to my diatoms transformed with my NR-EGFP-NR DNA contructs; orange, NR-EGFP-Actin; green, NiR-EGFP-Actin)

These plates are exposed to lights at 3 points.
Here we can see that my plates are exposed to 3 different light sources. Source #1 provides a majority of the light as it is perpendicular to the plate surface. Sources #2 & #3 run parallel to the plate surface, with most of the light passing over the top of the plate (and not the sides). The way I see it, by taping the tops of the plates, I'm preventing a majority of the light from hitting the densely populated plate regions. This densely populated plate region is still getting some light however, and they should persist on the plates just fine. This was inspired by a really cool discovery for my thesis work, but I won't spoil that surprise right now. 

A single layer of porch screen is added to the taped plates.

Saturday, April 21, 2012

NEAS 2012

I woke up this morning at 6:00, which is really early for me.

But of course I hit the snooze multiple times. But it is now 6:47, I am dressed, and I am looking gooood.

I'm here at the 51st annual NEAS conference. Well, it's the Northeast Algal Symposium, so I guess it's a symposium and not a conference if symposium is in the acronym.

I'm presenting on 11:15-11:30, or 9th in line. That gives someone ample time to screw up before I do. (I'm kidding. I think.)

Today's weather will not compare to anything we had yesterday; it is overcast and it wants to be drizzly. Hopefully it will stay relatively dry until we start our main activities for the day in the main building.

We're staying in the "old" dormitories of what used to be housing for the Navy cadets here on site.

I'm going to go over my presentation a little bit before going to the commons to get breakfast. So... I'll.. be back later. For science!

Sunday, April 15, 2012

...and spring is back! YES!

I've been taking some pictures over the last few days since the nice weather has finally come back. Since it looks like we'll be having nice weather all week, I hope to get a lot more pictures taken. Here are a few so far.

The Geography Building from Main St.

Red Square from just inside the gate.

The main part of campus from just outside the gate.

Yeah, I've done this shot to death over the past year, I know.

This one too.
Here's another take on the artwork on Downing Street.
The corner of Jefferson along the corner of Downing and Main St.

Sunday, April 1, 2012

Clark Spring (where have you gone?)

Awesome weather.
March 30th, 2012 – Jonas Clark, Red Square, Jefferson.
So we were super lucky to get about 10 days of awesome early spring weather.

Our normal spring weather.

I mean, some of the weather we got felt like early summer. But, living in New England we should have known it wasn't going to stick around forever.

Unfortunately, our glorious spring weather has disappeared and no traces of its existence have been seen since. Aside from the early budding and flower blooming (which has been slowed down considerably during this "cold snap"), one wouldn't have known about our nice early spring.

This week the weather should return to sunny weather with highs around the 50s which is much more tolerable. The sun has returned as seen in the above picture of Red Square, and that is always appreciated. But now that things are going to be getting really crazy work-wise on the Clark campus, I'm not so sure I'm going to be able to welcome the spring weather once it returns for good.

I've now tacked on a draft of a post I was supposed to post about two weeks after this original post:

In practicing for my upcoming presentations this month, I have simultaneous powerpoint presentations running to mimic an actual presentation where I have Presenter Tools running on my laptop and the "presentation screen" running on my desktop computer. I'm pretty silly/nerdy.
A panning shot of the first floor to the third floor of Lasry (the bio building) late at night.

Planning out some science (with my undergraduate students).
Downing Street will be soon turned into walking plaza (and is now closed to traffic), so a Clark student spray painted a sweet mural.
(The view from Wright Hall; Atwood Hall is in the background.)

While the weather has been kinda crappy recently in Worcester, we have had a few nice sunsets.