Friday, August 29, 2014

Floating Forests

Floating Forests is one the newest Zooniverse projects. You are required to set up a username/password, but if you have already tried Seafloor Explorer or Snapshot Serengeti (previous citizen science features on the blog: here, here) then you already have a username!

Floating Forest entry screen
 In this citizen science project, they are utilizing satellite imagery to measure the density of giant kelp (Macrocystis proifera). Giant kelp is an incredible algae, it can grow up to a foot a day, hosts a wealth of biodiversity in and under its fronds, and most importantly (for this project) it can be seen from space. I learned to SCUBA dive in the kelp forests of California so this project hits close to home for me. I love spending my clicks on something that is actually helping a habitat I adore.

See the green in the ocean, that's the kelp!

According to their about page, the images provided are from the Landsat satellite's and were captured every 16 days since 1984. Needless to say, they have a lot of images! Since computer processing has proven to be tricky, human eyes and time are required to process all of these images. That's where you come in!

I have been playing around with Floating Forests for a few weeks, since they launched actually. The interface is very simple, just click and drag your mouse around any kelp you see, then hit the cloud button if there are clouds, and when finished click next image. One of the only annoyances I have is the amount of non-ocean images. Due to the way they get the photos, they have to be sliced up into squares and some of the squares will end up being nothing but landmass. There are also some where the cloud cover is too thick to see the surface of the Earth (and some of those photos are really neat) or where the satellite image was corrupted. This is to be expected with satellite imagery. Some days I get on and I hit a run of photos where I see kelp in almost every one for an hour, others I spend an hour and never see any kelp.

This is a nice way to pass the time and add to the scientific knowledge at the same time. It can get a little boring, so I do not recommend it for younger kids. But I do recommend showing them Blue Planet's Shallow Seas episode which features kelp forests. It is full of amazing videography, exposing the beauty and importance of these habitats.

I'd love to hear your thoughts on this and other citizen science sites. Have you ever used one? Do you think they are good ideas?

Wednesday, August 27, 2014

Why Plants?

The combination of the first class topic of Why Study Plants in Plant Molecular Biology and two hashtags (#IAmAScientistBecause and #IAmABotanist) on Twitter yesterday has made me reflective and contemplative. This post is longer than usual, so I hid it behind the cut.

Monday, August 25, 2014

So it begins...

Today was the first day of classes at my Uni. My classes are on T/Th, both the student and instructor one. At noon I have to be on the other side of campus from the lab to take my course. I am very excited about this course, Plant Molecular Biology! Woo plants!!! Three exams and 12 quizzes, so there will be a little stress but overall I am very excited. This course ends at 1:15.

Then at 1:30 I have to be back in the lab building to teach my lab. It's about a 10 minute walk... The weeks where I have practicals are going to be very hard. I cannot set up the practical early because there is another lab section in there until 12:50pm. The easiest fix is to simply delay class, and for the full practicals I can do this as it only takes about 2 hours out of the 3.5hr set aside. But the mini practical also includes lab activities afterwards. I might be able to delay class by 15, maybe 30, minutes but that would be all. I've never gotten a practical set up in less than 45 minutes.

Tonight, I made up both of my binders for class. Syllabi, handouts, readings are all printed, three-hole punched and nestled nicely in the binders. I printed out my color photo roster so that I have a jump start on learning names. Slides have been prepped and practiced. Now I can relax for one last night before jumping into full-blown semester mode.  

Wednesday, August 20, 2014

DFPM: Plotted Course

Dear Future Professor Me,

This might be hard for you to hear, but a lot of the students that traipse through your office will have NO idea what they want in life. Not everyone plots their lives out to minute detail. You, who plan every moment of your life down to exact details, are a wierdo. Be sure to remember that there will be those who start in your lab simply to avoid the workplace. There might be those in your lab that start with the greatest of intentions and then priorities change. And there will probably be the handful of weirdos exactly like you. Regardless, be mindful of where each student is at, where they are coming from, what pressures might come into play in their lives when you are interacting with them.

Right now, you've kept your eyes open. You've watched how faculty have treated the various grad students, both you and the others. Remember the understanding you've seen, remember the frustration. The trick, to these lowly grad student eyes, seems to lie in finding the balance between understanding their situation and pushing them forward. And that line appears to be different for each student.

You were a pretty smart grad student, if I do say so myself, who had a plan. You knew why you were here, what you wanted to accomplish, where you were going. That has always been your M.O. and you have never done well with plans being interrupted. Plotted courses are great, but when the storms come course corrections might have to be made. Be ready to navigate different plots for different students! Meet them where they are at, not where you are or have been.

Sincerely,
Lowly Grad Student Me

Monday, August 18, 2014

What to do while everything is broken..

One of the large summer projects the university is undergoing is the full replacement of the roof of our building. This will be great when it is done as they are moving the fume hood exhaust unit from the space directly over our lab. However, at the moment it's been quite the thorn in our side. Last week, they cut a big section out of the roof and ended up dropping concrete slurry on the lab. This week, they are cutting out the big exhaust unit so the lab is full of squeals, bangs, bumps and thumps! Because they are cutting out the exhaust system, the fume hoods, the cold rooms, the warm rooms and all our growth chambers are deactivated for the rest of the week. Which means I cannot do protoplasts, plasmid preps, Western blots, or plant anything for future use. The only things I can do are qPCR and GUS assay's.

qPCR is the newest technique I am learning. It requires incredibly precise pipette skills.. which apparently I do not have! Pipetting one microliter is very hard. I get it right 90% of the time, but with qPCR it has to be 100%. You can see the wells you messed up right on the screen. The department has 1 qPCR machine.. and it was signed out before I got in today. Soooo that took qPCR off the table.

I had been planning on doing GUS while the qPCR was running so just move on right? Wrong. PI came to tell me that my soybean in the greenhouse were attacked over the weekend. Some sort of stinkbug got in there and was chomping them down. So the soybeans had to be treated with some nasty chemicals which means touching them to harvest leaves for GUS Assay was out.

That left me with plan C. Thankfully, I had brought the laptop for just such an occasion. I managed to get some journal articles read and wrote one experimental section for my PhD Proposal. This is how grad school can go, you have great plans and ideas laid out and then something happens so that you have to go to plan B or C or even D. This is why it is important to have lots of plans!

Friday, August 15, 2014

Balancing Act

My life is a balancing act. Between PhD life and Motherhood, there is never a lack of things to do. I did A Week in the Life post last year which still rings mostly true, although the days that things occur have shifted around. My life, as does that of pretty much all working mothers, revolves around 3 main things: work, kid, personal.


Balancing them all so that one does not fall off the sanity tight rope into the abyss of despair is a real feat. I have great days, moderate days and why-the-hell-did-I-even-get-up-and-try days.

Monday, August 11, 2014

Fall is Coming..

While it might only be August, Fall term is rapidly approaching. Teaching schedules have come out. I am teaching the same course as I taught last year. This is a good news/bad news sort of thing. Since I have already taught this course, I have the lectures written and I know what to expect. Bad news is that I will have 2 lab sections. At least at the beginning, the sections will have about 30 students. If last year is any judge, that will drop down to around 25 by the semester end. That means 50-60 assignments to grade. This is, by no means, the most students I have ever had. When I was teaching at the for-profit college I had almost 100 students one quarter. The difference here is, that was my ONLY job. But now, I have lab work, proposal writing, and studying for my own classes on top of grading.

I was going to throw a bit of a pity party, then I realized this is Academia. This is what Profs do all the time. They have lab work, committee meetings, grant/paper writing, teaching, and I'm sure things I'm not even aware exist every semester! Graduate school is training grounds and this is training! Learning how to manage and balance all of the different things going on every semester. So here we go, bring it on Fall 2014!

Friday, August 8, 2014

First Week of School

Boo's district starts, what I consider to be, ridiculously early. The first day of school was July 31. JULY! Last day of school (scheduled not delayed because of our harsh winter) was June 4. That's less than 2 months of summer vacation. Whatever happened to the 104 days of summer promised by Phineus and Ferb?

So far, the first week + bit has gone very well. He was assigned the 2nd grade teacher that we liked. His new teacher is using both a positive and a negative scaled chart to track the kids progress through the day. I really appreciate this as last year was simply a negative scale, you got in trouble you got strikes. You did well you got nothing. This year everyone starts on the green star and can move up through blue --> purple --> pink or down yellow --> orange --> red. First full week and he has been on green or better EVERY day! Hopefully this is how the rest of the year will go ;)

Monday, August 4, 2014

GUS Assay

A lot of scientists use reporter genes to quickly analyze/visualize various different cellular features or functions. A reporter gene will make a protein that is easily measured, a lot of them glow like GFP (green fluorescent protein). One can attach any promoter to the gene, letting scientists control when and/or where the protein is produced allowing reporter systems to be highly specialized.

We use a GUS-GFP reporter in our lab. GFP comes from jellyfish and glows green under special light. Simply look under the fluorescent microscope and if you see glowing green, then your gene is active. Since finding an available fluorescent scope can be hard, I prefer to use the GUS portion of our reporter gene.

GUS is one of the reporter genes that we utilize in some of our transformed plant lines. GUS encodes the protein β-glucuronidase, which breaks down complex carbohydrates. Basically it takes great big "sugars" and breaks them into smaller ones. There are two main "food" sources for GUS, X-Gluc and MUG. X-Gluc will result in a visual blue color. MUG results in a small glowing particle.
My cartoon version of GUS "eating" MUG, he'll spit out MU which will glow!

Friday, August 1, 2014

One Year!

It's been one year since I started my graduate program. One year ago today I walked into lab as a PhD candidate for the first day. I was (still am) incredibly scared and nervous to be taking such a big step. Boo and I had been living with my parents, now we are living 2 hours away on our own. I was teaching part time and was home before Boo's school got out. Now he goes to after school care and we don't get as much time to play. I had not been in a research lab since Boo was born. Now I get to "play" in one every day. A lot of things have changed for both of us.

Now some Year 1 comments: 
  • What pleasantly surprised me the most this year, has been how easily I slipped back into research and study habits considering I had not been a student for 7 years. 
  • What unpleasantly surprised me the most this year, the costs of grad school, utilities, and how much these costs can vary month to month.
  • My big accomplishment was to complete Quals
  • Just this week, I obtained a homozygote line for my soybeans, which means I can do experiments with these soybeans soon. 
  • I still worry about balance of being a great mom and a good grad student. Thankfully I have a very understanding adviser that lets me run off when I need to do important mommy stuff.

Year 1 Complete!
Bring on year 2! Hopefully, it will also bring with it some data ;)

Edit: Update - I got my  awesome grad school contest jewelry from Vexed Muddler in the mail!! How beautiful is this soybean with DNA seeds necklace!