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.

#biowithdylan

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.

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!

...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.

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.

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!

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.

A picture, a video, and another picture

I need to come back to this spot and give this shot another, wider try. But I liked it enough to post.

This is one of the stairwells in the biology building, a spot I particularly like. (More content below)

I did go back a little later and took this wider shot, which I like a lot more:

I put together the video below, which has a long intro (:-p) and a hidden something or other, which is kind of embarrassing, as the end.



And I'll leave you with this Facebook gem. My friend Dan apparently had a bit of trouble with his lab lizards today:

An untitled post about my advisory meeting and a busy semester

Recently, several different groups of people have been asking for permission to use my photos which always is very flattering. Currently, the Clark homepage is using my picture of the Jonas Clark building. Just below that picture on the front page is a video I made, which is a part of a series asking Clarkies what their favorite things are from area restaurants to classes. The Graduate School at Clark has also asked me for my permission to use my photos, but they haven't picked them out yet. Additionally, I've been asked to share my pictures and videos from our October snow storm to be used as part of a new class at Clark that is chronicling the changing landscape of the campus on a historical timescale.

Preparing for my advisory meeting.

At the end of last week (just over a week now), I had my first thesis committee meeting for my master's project. My committee is comprised of my adviser Dr. Robertson, the genetics professor Dr. Thackeray and my undergraduate adviser Dr. Hibbett. The role of my committee is to make sure my project is on the right track, give me advice, and determine whether my work is worthy of a master's degree. This meeting was the first time I've presented my work outside of my lab, so it was a real test of my knowledge and presentation skills. This is something I will be practicing a lot this semester however, since I may be presenting at least thrice more (more about that below). My advisory meeting, save for a few slip ups, went surprisingly well. However, I do have my work cut out for me and it's pretty daunting.

I have the opportunity to present my work at 51st Annual Northeast Algal Society meeting in April, either in a poster or oral format. Additionally, I may also present my work here on campus alongside a collection of research projects representing the Clark Graduate School. These presentations are of course in addition to my thesis defense, which I hope will happen in May.

From my thesis committee meeting and my potentially busy presentation schedule, I have a long list of things I need to accomplish:

• First I need to fix my quantitative PCR reactions, so I can collect data for my project. More on this topic later...
• Second, after I fix my quantitative PCR reactions, I need to complete a lot of bench work that includes growing discrete lines of diatoms, processing them through experimental assays, extracting their RNA, and preparing the RNA for quantification through QPCR.
• This brings me to collecting all of the data I can to support my thesis through many rounds of quantitative PCR.
• In and around here there are multiple experiments and procedures I need to complete to double check on certain things, like sequence my plasmid DNA used to transform the diatoms and check for the number of construct copies each of my diatom lines received in the genetic transformation.
• I also will need to prepare for each presentation and make sure everything is pulled together.

With so many things going on in my research project, I don't think I'll have much time to do anything else. This is of course without considering the work I need to get done in the class I'm helping out with--Physiological Ecology of Marine Algae. It's very likely I will be leading a group research project with 2-4 undergraduate students. This work will be crammed into about 6 short weeks. While I know this will be a great learning experience for me, I know those weeks are going to be very stressful.

Unflagging speed

The start of the semester is beginning with unflagging speed, and I find myself dazed from the extreme acceleration. I’m desperately trying to prevent further acceleration and maintain a steady pace so I can catch up and organize my plan of attack on these beastly final few months.

I have tons to be worried about this semester too, which is just fantastic:

• I should hear back from grad schools within the next few weeks
• I need to correct and tweak my lab experiments as soon as possible so I can collect data worthy of a Master’s thesis
• I need to then find time to conduct those experiments and collect that data
• Following that, I need to write my thesis and prepare a lengthy presentation
• I should probably also defend my thesis in front of a treacherous jury (complete with torches and spears)
• Aside from my Master’s work, I’m going to be helping out with a research seminar in my lab, which has the potential to eat up a lot of my time, especially in the second semester
• And it would also be great if I could make some money

Slaving away at the bookstore.

All of this to me seems incredibly daunting, especially since I haven’t had much spare time after I got back from my trip to Florida thanks to a lot of time at the bookstore. But there is a glimmer of hope at the end of this dark, damp tunnel that is the beginning of the semester.

Things are the bookstore have looked like this recently: were does the work start and where does it end?

I hope to essentially eliminate all of my commitment to the bookstore after next week, freeing up a lot of my time, which I can devote to lab work. I also hope to get my project on track really soon, and have a set of goals by the end of the month. If I can get my project on track by then, I can grind out a lot of lab work over the month on February (thankfully we have that extra leap year day).

Then I could have the month of March (which includes a week of spring break) to collect my thoughts and write my paper and put together a presentation.

I can’t decide whether I’m tricking myself into thinking this is feasible, but I guess that’s the only option I have right now. The only option I have is to tear this semester apart and make it mine.

The remainder of this week is already completely full of plans to start my project back up again and working at the bookstore. While I’ll miss the extra income from working at the bookstore, I can’t wait to devote all of my spare time into my project so I can get comfortable with it’s progress and outcome once again. Once things slow down with the beginning of the semester at the end of next week, I’ll be taken off the schedule and I can devote entire days to lab and do a lot more with my blog and do more blog projects, which is something else I’m looking forward to. More science with my next post, which I'll post soon!

From GRE to RT-PCR

The view of Lasry the other day on my way into lab.

A few weeks ago I took the GRE as part of my quest to continue graduate school in a Ph.D. program. Standardized testing is such a money scam given all of the fees involved from taking the exam to getting your scores and sending them to your schools. Furthermore, I don't think standardized exams are particularly informative, which is funny because Clark was just in the news because they are no longer requiring SAT scores for undergraduate admissions.

But I digress: I'm not here to complain how ridiculous the whole process of taking the GRE is. I'm just super glad the GRE is behind me and I can focus on things that actually matter. Yet ever since, I've been taking it slow with my workload because I needed a bit of a break. Thanksgiving marked the end of that break though, and now it's time to jump right back into things to finish up a productive semester.

I have a very hopeful list of things I'd like to accomplish by the end of the semester in mid December. But because I'll need to be working a lot more hours at the bookstore to help with the end of semester rush, it's going to be a big squeeze.

We're starting to get books for the spring semester at bookstore, & they're piling up.

This  picture is enhanced with the iPhone app Cat Effects.

Meanwhile in the lab, I have heaps to do. I want to finish up my experimental assays, screen and grow out more diatom cultures for future experiments, prepare a presentation and do some writing, and finally start with some RT-PCR experiments.

Now previously I extracted RNA from my frozen cell samples and used the mRNA present from the cell samples to generate cDNA.

RT-PCR, or real time PCR, will allow me to quantify the cDNA that I have made from my RNA. This is because RT-PCR can measure the number of DNA copies at each copy cycle by measuring the fluorescence of a special dye that hybridizes with the DNA. This is pretty snazzy, but it looks like I'm getting myself into a lot of grunt work.

You see, in order to get precise data from RT-PCR, one usually runs three replicates from one DNA sample and compares the output. But it's not like I only have one DNA sample. I have tons.

This is because I have 8 DNA samples at the minimum per experimental assay that I run in the beginning: I have two different cell lines that I test per assay, which get divided between two different test conditions, from which I take cell samples at multiple timepoints.

For the time being, I'm going to start with time zero and my end time of 60 minutes. This will hopefully give us start and end data that will display the overall trend of my experiments.

But because of positional effects, I need to run more than one experimental assay. I'll probably run three sets of samples through RT-PCR, but I hope to have up to 5 samples completed and ready for RT-PCR by the end of next week.

This is from today while I waited for my next sampling time.

Wait, what's that positional effects you just mentioned a second ago? Oh, yeah, positional effect. Because we transformed our diatoms with ballistics, our DNA was randomly inserted into the diatom's genome. By chance, the DNA we're trying to measure in our experiments might be inserted into a region that is either expressed more or less often, which would skew our data. By gathering data from multiple replicates, we'll get more accurate data regarding gene expression. Cool how science works, huh? We think of the neatest little caveats. Well, I mean, my professor does.

But sometimes I do too!

Like last month or so I came up with a solution as to why our cultures weren't growing so well. And then more recently I figured out how to screen my diatoms for our reporter gene more effectively.

So yes, sometimes I come up with cool things too.

The Jonas Clark building. I can't stop taking pictures from this vantage point! Gah! I love it! 11/18/2011

Marine Biology Research

I made a new video discussing what it's like to do research at Clark. This video pairs really well with the video I made called Bio @ Clark.


Marine biology research at Clark University.

October Snow Storm Carnage

Last night on October 29th, central Massachusetts got a fair amount of wet snow. Estimates and measurements vary, but the campus got about 5-6" of snow. The problem with wet snow is that it weighs down trees, especially if the trees still haven't lost all of their leaves yet. The problem is amplified with longer branches as it creates more downward force on the branch (basic physics thank you), causing the branches to snap off.

I've taken a bunch of photographs and have posted two videos, here and here. I'll also embed the main video at the bottom of this post.

A somewhat complete photo album is here.

My tumblr post is here.

A slideshow on the New York Times of some of the damage to the northeast.

Before the storm: Saturday October 28th, 2:30 PM.

After the storm: Sunday October 29th, 12:00 PM.

My favorite post-apocalypse photo.

A sample of the carnage:

A video of the tree carnage on the Clark campus.