Monday, August 6, 2012

Master's Defense: Passed!

My Master's defense went really well. I mean really, really well.

Not only did I pass, but...
  1. It was the longest presentation I've ever given
  2. It was the biggest audience I've presented to (other than my 10 minute presentation at the conference this past April)
  3. It was the most important presentation I've ever given
  4. And it was the BEST performance I've ever given
Needless to say, I am really proud of myself. I put a lot of hard work into my thesis, my powerpoint, and my presentation. Hard work does pay off sometimes.

Following my presentation, there was a reception in the "social lounge" where we usually meet following departmental seminars. We celebrated my defense and the defense of my friend Darcy, who defended the day earlier. Because the semester had ended some two to three weeks earlier in the start of May, it was really cool that Darcy and I defended on consecutive days. This is particularly cool because Darcy and I "came in together" to Clark, as we were part of the same first year seminar. Our first year seminar was a small, tightly knit group of biology-minded first years. Not only was the seminar great, but it was taught by one of my all time favorite people, Dr. Hibbett (he served as my undergraduate adviser and was a member of my thesis committee this spring.)

Defending our Master's theses in the same week and celebrating them at the same reception was a great way for me to end my student career at Clark. In a sense, I came in and left alongside a fellow student who I both identified with and really respected. Now that I'm finally finishing this post in early August, I can look back and feel fondly about the end of my stressful fifth year.

After my defense, I made some final touches to my thesis and started the process of getting it printed. It was a pretty big hassle and I didn't enjoy. Beyond that, I'll spare you the details.

But I did get it printed and professionally BOUND. A few weeks ago, I got my copies in the mail. I'm really pleased with the final product and it's great to have my thesis physically come to a close.

My professor is wrapping up my project and we'll use my thesis as a starting template for a manuscript to submit for publication.

Wednesday, May 16, 2012


Earlier today I submitted my thesis to my committee. I'm so stressed and nervous–a lot more than I thought I would be.

I thought once I got into graduate school things would be so much more relaxing. Well, things have come up and ended up a lot differently that I had planned out in my head. In my defense, I did not have unrealistic expectations. I sort of feel like unrealistic things have come up. It's been the culmination of many ups and downs, but mostly downs. This problems and issues that have arisen have of course taught me a lot, but I need to move past all of this and put an end to this anxiety.

Now, I need to finish my powerpoint and prepare a defense presentation.

I hope once I have a finished powerpoint product, I can write out my talk and prepare enough to feel confident going into my defense. I'm frustrated though, because I know I've put more than enough work into my project to warrant a Master's, but I'm not as confident that my thesis and presentation will demonstrate that. I suppose these are things I need to stress in my powerpoint.

I have a rough draft of my powerpoint, but I need to improve some areas and make sure certain things are emphasized and other things are not glossed over too quickly.

Here's hoping I kick this defense's butt!

Thursday, May 10, 2012

Things are starting to wind down

The past few days have been kinda slow–but that really awesome kind of slow. The kind of slow where I can take things at an enjoyable pace.

I submitted a second draft of my Master's thesis to my adviser this morning. Once she looks over that, I'll make the necessary changes before I send my thesis to my committee. After I submit my thesis to my committee, I'll be working on my defense presentation. I hope to have my powerpoint almost done before I get back my thesis from my adviser. This would allow me to make minor changes and practice my defense heaps and heaps between submitting my thesis to my committee and giving my defense.

Between there and now, I'll also be doing some bench work trying to get my diatoms in working order for future experiments.

In other news, my supervisor Wendy, who has been advising my work study projects for Clark from blogging to video blogging to Clark videos to photography gave me this sweet travel mug as a parting gift! Such a sweet idea, I know.
Even though I won't be moving out until the end of May, I've been eager to start packing a little bit. As a result, my room has been a complete mess of late. It goes through cycles of being very tidy and very messy, at a high rate of turnover. One of my Australian mates had this to say on the Facebook:
Facebook lolz. My room has been a mess because I've been doing some early packing.
While a little breezy, we had some really nice weather today. As such, I decided to take some pictures:

A second mural was painted on Downing St., which is going to be turned into a walking mall. You should check out that link–it talks about the major improvements the Clark campus will experience in the next few months/years. I'm really excited about them all!

Here's another (new) shoot of the first mural, on the corner of Downing and Woodland streets. Atwood is in the background.

This is a shot I've been wanting to take for a while. Below is Estrabrook Hall, on the corner of Woodland and Charlotte streets.

Sunday, May 6, 2012

Bowties and science

While we've had a few nice days recently, it's been pretty rainy over the last few weeks.
Finals are almost over and the students are moving back home. It's kind of a bittersweet time of the semester. The weather and feel of campus brings back memories of just a year ago when I was finishing up my undergraduate career. After being at Clark for 5 year (9 semesters and 2 summers), I'm really going to miss it. I know I'm not looking forward to packing up and moving home myself, but I have plenty to do before then.

I'm defending my Master's thesis on May 22nd, and I hope to be completely done a few days before the end of the month. I have a first draft of my thesis completed, which will probably head over to my thesis committee once my adviser okays it. I've already made corrections from a working (almost complete) draft, which was nearly sufficient for submission anyway. I'm pretty excited about this. Once I submit the draft to the other two members of my committee, I'll focus on finishing my powerpoint presentation.

My powerpoint presentation for my defense will probably be about 45 minutes long. Just thinking about it right now is making me nervous. However, I hope to have a final draft of my presentation completed more than a week before I defend, giving me ample time to practice. This will be the third presentation I've given this semester, and by far the longest, most difficult, and most important. While I'm nervous now and I'll be nervous on my defense day, I just know I'll knock my presentation dead. The closed question period may prove to be much more difficult, but I know I've done more than enough work to complete my Master's.

Between now and the time I move out, I'm almost working on some diatom cultures. I hope to have a large array of diatoms lined up for my professor to work with this summer. Below I discuss part of this process:

And, as a bonus, I made this video in my spare time–how to tie a bowtie!

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.

Sunday, March 25, 2012

untitled post but there are pictures!

Nearly four years ago, my friends Emily (center) and Nikki (right) and I would meet on the green and have takeout lunches from the Bistro. I would always get a grilled cheese with fries (which I'd eat with a combination of ketchup and mayo) and a Dr. Pepper. After admittedly an up and down freshman year at Clark, the warm spring weather was met with open arms and made us all feel whole again after a long, cold winter. While this past winter was not nearly as cold, last week's warm weather was still appreciated. While we didn't have lunch on the green in the picture above, it still reminded me very much of those times four years ago, which I think of very fondly.

A summery kind of picture taken in March. The sight of green grass and budding flowers is a sight for sore eyes!
A sort of random place for me to take a picture, but this isn't the first time I've taken a shot of the sunset from this spot. Going back up the hill from Shrewsbury to Worcester, this shot usually is quite pretty by the time I've finished my weekly Friday grocery shopping at Trader Joe's.
From the bridge going back into Worcester from Shrewsbury. Crew clubs often practice on this river which is pretty cool to see.
Fig. 1 - I am such a nerd.
This is what my desk has looked like as of late. Papers, notebooks, and lab manuals everywhere. I can't get away from it! Gahhhhh!

Wednesday, March 21, 2012

A sneak peak of spring

Below are a few photos I've taken this week from our early (but beautiful) spring weather. It's warming up and the student population has responded really well. Take a look!
L to R: The Jonas Clark building, Bullock Hall, and the Goddard Library.

The green with the JC on the left and Atwood, Jefferson, and the Geography Building
on the right, in that order.

A different view of the green, with the UC in the distance on the far left, the JC
in the middle left, the library set back in the middle right, and Atwood on the far right.
This picture should be viewed at full zoom!

A view of Main St. from behind where Freud likes to hang out.

Thursday, March 15, 2012

Taking 1-step intsead of two.

As of late, there have only been a few things on my mind: the glorious weather, Physiological Ecology of Marine Algae, and 1-step Quantitative PCR.

Spring break ended with spring hitting Worcester with extreme velocity. All of the snow that fell before break has been replaced with highs well into the 60s. There are rumors of temperatures hitting the 70s or 80s next week.

Why yes, I'd love some sunshine while I read.

Aside from the end of this week, with temperatures dropping today and rain expected tomorrow, we've been blessed with sunshine and more warm weather. On Monday I got to spend some time outside while doing some reading during class. While we were given more time than needed to do the reading, I certainly will not complain about the amount of sunrays I was able to soak up while hanging outside. I've beginning to worry about the amount of work I have to do between helping to run two projects in PEMA and finishing up my own research, in addition to preparing presentations, writing my thesis, and giving a defense... all while the weather is getting really nice.

I could try shifting my sleep cycle so that I work a lot at night, sleep in, and enjoy the weather during the afternoon before going back into lab. I highly doubt this is something I'll try. Instead, I'll probably start packing killer lunches and having them on the green in the sunshine.

I have so much to do but I'm still waiting for cultures to grow up and things to be mailed in to retry some of my real-time experiments. I tried running some 1-step QPCR reactions recently since we had the kit on hand. 1-step QPCR makes the cDNA and amplifies it all in one reaction, rather than making the cDNA separately and adding it to the QPCR reaction. While this is definitely easier, saves time, and limits contamination, 1-step QPCR is not as accurate when it comes to estimating the amount of starting template in a sample. As determining the amount of relative template among samples of different test conditions is of the utmost importance to me, it looks like 1-step QPCR won't really fit into my plans any more. However, some initial results suggested my experimental lines of diatoms are behaving as expected (and see previously with normal QPCR), so that's really promising. Once I get a new QPCR kit in and some cells to analyze, my work should be all downhill from here (aside from heaps of lab work).

Watch the video below for a bit more on our beautiful weather and 1-step QPCR.

Sunday, March 11, 2012

Oh hai Spring

We've been seeing weather
like this in Worcester for
the past two weeks.
We're starting to see spring weather and it's such a nice feeling. Granted since our first snowstorm, it's been a really mild winter for the most part. Nonetheless, we've been enjoying some warm temperatures over the past few weeks.

Right now it's 44°F with a forecast of highs in the 60's all week. Aside from one day of rain, it looks like sunshine all week.

Clark has a tradition of getting serious snow just before spring break--the first week of March--only for the snow to melt by the time the students return. We got 4 or 5 inches of snow in the days leading up to spring break. Below you can see what campus looked like after some of the snow started to melt.

March 5th.
With some rain and warmer weather, the snow has since left campus.
March 7th. Within a day the rest of the snow had melted.
For the most part, Spring Semester at Clark can hardly compare to Fall Semester in terms of good weather. If we're lucky, Clark can usually have great weather from the start of the semester until mid October or later. In the Spring, we're lucky to have a good April.  This is one of the reasons why I decided to go abroad my junior spring rather than in the fall. By going to Australia, I traded a northern hemisphere winter for a southern hemisphere summer. Not a bad trade in my book.

I'm glad tradition has continued this year. While Worcester could certainly get another big snowstorm before the end of April, I really hope spring has decided to come and stay early. Unfortunately, we've had a pretty dry winter which means we will be in a drought once the trees try to break their winter fast. I guess this means if we have a rainy spring I can't complain, since we need the rain.

Monday, February 27, 2012

Positive Preliminary Results

My post today doesn't get more clearer than the post title.

In re-examining my preliminary data on Wednesday, I realized I had collected some positive results! I had run a set of samples through a QRT-PCR reaction on Tuesday with the new primers that I received on Monday. These samples were from my experimental assays and represented different time points and test conditions. When I looked at the results on Tuesday, I didn't think much of them, other than the fact that my no template controls (the reactions that are supposed to be blanks) gave me some product, indicating the reactions are still not 100% clean.

But when I went back to the numbers the computer gave me for my test samples, I realized I overlooked the initial data. This is because the data that the program gives me is sort of backwards and not entirely intuitive in the way that I'm using it. The program gives me cycle threshold (Ct) values (marked by the dotted red line in the graph), or the number of cycles that it took a sample to reach a certain threshold in terms of amplified product. This allows us to directly compare the amount of starting product (cDNA) between two samples. For instance, if sample A has a Ct value of 25.88 and B has a Ct of 27.34, sample A had more starting template since it crossed the threshold at an earlier cycle. This is where it gets confusing. In my mindset, the higher value would have more product, but really, it's the other way around. When comparing these values between different samples and time points, it gets even more confusing in determining whether there are changes in starting template.

If sample A was the time 0 value and sample B was the time 60 value, we'd essentially get a graph like this on the right. Sample A's Ct of 25.88 is greater in cDNA abundance than sample B's 27.34 Ct. My QPCR comparisons will look a lot like these two cartoons, where I compare Ct values and determine what that data looks like on a graph.

So here I am going back through the data, comparing starting Ct values (0 minutes) with end Ct values (60 minutes) between two different treatments and DNA constructs from my transformed diatoms. Of these eight Ct values (four combinations, two time points each), I realized I had something. My three "controls" all showed the appropriate increase or decrease in mRNA transcript levels, mirroring previously established results by our lab. But when I looked at the experimental line of diatoms, the line I'm most interested, this pattern completely changed from its control. OHHHH YEAHHHH.

Positive preliminary results: victory!
The cool part was that my real hardline controls were basically the same between both conditions (the orange and red here below), show how accurate my techniques were in collecting that data. But really, my favorite part was the dramatic shift in the results for my experimental line (the blue line). This is really, really exciting. Essentially, if my hypothesis was wrong, the blue line should have looked just like the green line. The green line here is the down-regulated transcript levels previously established by my lab. However, there is a stark difference in the transcript levels (cDNA abundance) between the normally down-regulated line (green) and the experimental line (blue). This strongly suggests I'm on the right track. *phew*
A cartoon representing my results.

However, I'm not out of the woods yet. I'm still having trouble with my primers and I may need to order the primers a third time. My no template controls are still giving me product, but that may be due to primer dimers. I'm going to run a gel in an attempt to see what is going on, but I may have to eventually sequence the bands to see whether I have some plasmid DNA contamination that I don't know about. All of this will be sorted out, hopefully, sooner or later. But I have some other projects going on that I really should take care of as well. Juggling so many different things is really time consuming, but that's a topic for another time.