Wednesday, July 30, 2014

Building a committee

One of the tasks a PhD student must complete is assembling a committee. The committee is an amalgamation of a set of mentors to help guide you plus a jury of your superiors to judge you.
Just like the alien council in Disney's Lilo and Stitch
The committee is responsible for everything, from what courses you take, to techniques you use in research, to constantly questioning and pushing your knowledge level. This goes on until they finally decide to allow you to defend and, hopefully, bestow the title of PhD upon you. At my Uni, we are required to have at least 3 in-house committee members and 1 from main campus. For my master's, my adviser told me who would be on my committee. But now, for my PhD, my PI wants me to decide which of the faculty but he has veto power.

The first two out of three in house were easy, there is my adviser and the other plant PI we do lab meetings with every week. However, picking the last two is a more of a task! For starters, I only know a few faculty as we are only required to take a single class per semester and there is not a lot of social interaction in the department. Then there is the fact that I have never been to main campus so member 4 is the extremely hard one. While I can find out research interests on the webpages, personality complementarity is not easy to decipher via a few pixels and lines of code.

I've asked around for help on how to pick committee members. The most common piece of advice is to find people who complement and add to my project. For example, if I'm going to have a project heavy in bioinformatics I should probably find someone with that knowledge. They can then be a sounding board and assist with that part of the project. This is fantastic advice, but probably works better if you have a clear idea of what all of your chapters are going to be! Thankfully, I have until May to get my committee formed.

Anyone out there ever put together a PhD committee? Any things you wished you had looked for, or alternatively things you thought would be important that were not?

Friday, July 25, 2014

Zoey the Zooxanthellae

In my previous grad student life, I studied the photobiology of Symbiodinium, aka zooxanthellae, the symbiotic algae inside corals. Every year the university held a public outreach day and each lab would have a table to show their work. It was one of my favorite days of the year (I was the weirdo, most grad students dreaded it). I went all out one year and designed an activity booklet for the kids who came that included coloring pages, word search and crossword puzzle, in addition to educational information. The booklet's front section was written for younger kids and the back section for older kids/adults.

For the younger kids section, I created a mascot, Zoey the Zooxanthellae. I am not an artist but how hard can it be to draw a dinoflagellate? And this was who appeared

Hi! I’m Zoey the zooxanthellae.. 
that’s pronounced zo-zan-THEL-ee.
You know she's a girl cause she has bows ;) Of course, I could not stop there..

Wednesday, July 23, 2014

Wayback Wednesday: Puzzle Pirates

Back in my old grad school days, and when Boo was a toddler, I used to play an online game called YoHoHo Puzzle Pirates. I still love this game, but I just don't have the time to devote to it like I want. In 2005, there was a contest to create a story.. and being a writer, I decided to go for it. I wrote a fun little short story about my crew. And, since I'm swamped, I'm going to use it as my post this week ;) It's below the cut if you want to read it!

Monday, July 21, 2014

Boo is back!

Boo just got home for the last little bit of summer before he goes back to school in 2 weeks. So I don't really have a post for today.. just WOOT! BOO IS BACK!!! <3 <3 <3 <3

Friday, July 18, 2014

Project Squirrel

In the last of our regularly scheduled citizen science posts (but don't worry we'll have more of these randomly), I'm taking a look at Project Squirrel! Project Squirrel allows individuals to post their observation of squirrels in any region of the US. Building this large database of observation will help scientist find the patterns that might drive the distrubution of squirrels in an area and potentially predict how it will change with time.


To participate in this project does not require an account, they simply use a survey link where you answer 13 questions about where you saw the squirrels, what type and how many squirrels and some habitat questions. It's either bubbles/boxes to click or dropdown menus, very user friendly. You can enter your email address and they will send you updates and information but it is not required. For example, if you were out at the park and saw two gray squirrels you could log on and tell them that. There is even an additional observation box where you could note that the squirrels were in Candice's pants...


Yes, whenever I see a squirrel I do think of that song. I have a 7yo.. we watch a lot of Phineus and Ferb! :)

Project Squirrel also has apps for Droid and iPhone but I haven't tried them. Could be very useful though for out and about, quickly submit an observation.

So next time you are in the backyard, out for a walk, or just feel like getting into nature, pay special attention to the squirrels you see. Then log on and enter your report.. for SCIENCE!

Wednesday, July 16, 2014

Lab Mojo

The past few weeks in lab have been incredibly frustrating. I had big plans for my summer, I was going to collect ALL the data, I was going to write my proposal, I was going to have awesome graphs to show at my research in progress presentation! And so far.. I got nothing. I might have less than nothing! Everything has stopped working. I seem to touch things and they explode.

Yep.. just like poor Beaker..
Protoplast are no longer transforming. Yields on the plasmid preps have dropped precipitously. Soybean germination rate is way down. Arabidopsis is bolting prematurely. And to top it all off, this stack of journal articles refuse to read themselves!

If anyone sees my lab mojo laying around, please send it back to me. Things need to start turning around and STAT, fall schedule starts in about a month! Time is running down on the prospect for a productive summer. Maybe I will find it returns after I pick up Boo and go on vacation for a week. Hopefully splashing in the ocean waves with the kiddo will fix whatever is ailing me!

Monday, July 14, 2014

The CBF Cold Stress Pathway

I spend a lot of time talking about what I do in a rather vague way. For this week's Molecular Monday post I thought I would take some time to go into specifics about the pathway I am investigating. Because this is my blog, I will not be citing all my sources but just explaining things in my own words. If you want to be referred to some great review articles, leave me a comment or send me a note and I'd be happy to provide references :)


Plants have lots of different stress pathways. When it comes to responding to cold stress, there are two important pathways: ABA-dependent and ABA-independent. ABA is abscisic acid, a very important plant hormone involved in a plethora of pathways. But I don't care, as I am interested in the ABA-independent pathway.

The main "man" in this pathway is CBF (C-repeat Binding Factor) and, as such, this pathway is often called the CBF cold response pathway. CBF is a transcription factor. A transcription factor is a protein that binds to specific elements in the promoters of genes to turn them on/off appropriately. It's kind of like when the Wonder Twin's have to touch their rings in order to activate their powers, the transcription factor has to bind to the promoter element to cause a reaction. Promoter elements are composed of semi-precise nucleotide sequences in the DNA. I say semi-precise because there can be a little variation in the sequence. CBF3 (the protein I am most interested in), for example, binds to the CRT/DRE element which has the general consensus sequence of RCCGAC, where R can be either A or G.

Simplistic diagram of the CBF pathway
When a plant experiences a sudden decrease in temperature, the cellular membranes become more rigid and an increase in calcium levels are noted within the cells. This calcium increase is suspected to drive kinase cascades which can then activate ABA and/or CBF pathways. For CBF to be transcribed, ICE1 must first be activated. ICE1 is another transcription factor which is kept inactive in the cells by HOS1, which interacts and mediates the ubiqutination of ICE1. Once the kinase cascades are activated, SIZ1 interacts with ICE1 and causes sumoylation which then allows ICE1 to be stable enough to interact with the MYC promoter element in the CBF gene.

Confused yet? :-D Basically, the ICE1 protein is kept suppressed by HOS1 and has to be activated by SIZ1 before it can do it's job. That job is to activate the transcription of CBF by binding to a special spot in the gene. Then our awesome transcription factor can come out and do his job!

CBF will then bind to the CRT/DRE sequences in the promoters of cold regulated (COR) genes. There are a great many different types of COR genes that have been described. In soybean, my organism of interest, we know that CBF transcript levels go up as they do in Arabidopsis (the lab rat of the plant kingdom). But the downstream COR genes are not activated. My quest is to find what's up in soybean that makes these COR genes not activate.

Friday, July 11, 2014

Sanpshot Serengeti

The past few Friday's I've done citizen science where you have to leave your house.. today brings us Snapshot Serengeti, a trip to the African plains from the comfort of your sofa. This is very similar to Seafloor Explorer, which I have blogged about before, except instead of identify a few ocean animals you are looking through pictures of camera traps set up in the Serengeti. They have had 6 rounds identified and the 7th round is over 3/4 completed.

  

The set up is fairly easy. There is a list of common animals on the side, plus a "Looks like" dropdown menu, search bar, and a few sorting buttons (pattern, color, horns, tail, build) to help you narrow down and identify the organism in the image. Some of them are animals we're familiar with from nature shows and zoos, others are ones that might be new to you. 


Thankfully when you click on an animal name it brings up a picture for you to compare. Then you simple click how many and what they are doing before submitting. When you click "Identify" it will bring you back to the list of organisms in case there are several different types of animals on the screen. Once done, you click finish and get your next image. 

Like it's oceanic counterpart, there are photos that do not have any animals. I've really enjoyed some of the amazing landscape shots though, even without the animals. But make sure you REALLY check close, push the play button to flip through the images like a movie before you say nothing here. There might be a really cool find walking or lurking in the background.

This is a website you can easily feel safe letting your kids play on as well. Each organism has a write up so they can learn a little bit about them while they are learning to identify them. It's a wonderful way to learn about animals that might not be found in your backyard while contributing to their study and conservation. 

I hope you have fun exploring the Serengeti! Leave me a comment about your experience! I'd love to hear about it :)

Wednesday, July 9, 2014

Writing Matters!

Avast! Calling all up and coming science hopefuls! Listen up! Writing is important!!

In undergrad, there was always a sense of English majors are over there in humanities and we're in the sciences so we don't need to know all that stuff.  Or I hate English, I'm more of a science person. Or it doesn't matter if I know proper grammar, this is science. I want to clear this up once and for all. It's crap.

Seriously, utter crap. 

Writing is a huge part of being a successful scientist. And not just writing down your results but effectively communicating those results to large audiences that do not know as much about your project as you do. When you look at the yardsticks used to measure scientists, papers instantly spring to mind. Especially, first-author papers.. which means you are the author, AKA the writer. Another is grants received, which again must be written. And while the style is different than novel writing, for example, the grammatical rules you are taught in English courses still apply.

But, science writing is not as far from novel writing as you might think. Both tell stories. Novels, of course, are more imaginative and create their own plot points, where grants/articles deal with facts and data. The language is different, more complicated and specialized vocabulary goes into scientific writing.  However, they both have a beginning, middle, and an end, plus they have a moral, aka a take home message.

A well crafted novel will have a beginning where the characters are introduced and why they are important. In the middle, something will be discovered and how the characters will work with in the discovery. At the end, everything is tied together and the take home message of the story is realized. Good novels have engaging characters, enjoyable story lines and tell a story that is impactful on the reader in a broad context.

A well crafted article will have an introduction that summarizes the previous research that relates to the project which sets up what has been known and why it it is important. Then in the middle, the results/materials and methods sections will tell what they discovered and how they did the work. At the end will be a discussion which ties everything together and provides the take home message of this is our story and this is why it is important. Good articles have engaging figures, accurate information and place the research into a broad context.

The trick to putting together such an article is having an understanding of the story! What are you trying to convey, how does it enhance our understanding, what is the take home point?

Monday, July 7, 2014

Western Blots: Lessons from Immunology

Western blots are a very common method of evaluating changes in specific proteins. They rely on some basic concepts from immunology, the study of the immune system. One of the things your body does when you get sick is make antibodies Antibodies are globular proteins that have special arms that recognize one specific item, generally called an antigen. In our immune system, you have antibodies that recognize antigens you've been exposed to. For example, if you've had chicken pox you have antibodies that recognize chicken pox, but if you've never had them, you have no antibodies and are susceptible to catching them. 
GIANTMicrobe of antibody (Y shape) and antigen (red).
For more awesome stuffed microbes go to www.giantmicrobes.com!
The cool thing is all mammals have immune systems that will react to any foreign particles, which means that scientists can create antibodies to almost any protein they want. Rabbits, mice, rats, goats, sheep and horse are commonly used to generate antibodies for research. To do a successful western, you actually need 2 antibodies. The primary antibody is generated in one organism (for example rabbits) against your target protein/molecule. The secondary antibody is raised against a section of your primary antibody, for example if our primary antibody was made in rabbits, the secondary antibody would be anti-rabbit raised in a different animal, such as goat. Usually, secondary antibodies are also attached to a reporter that will fluoresce when the developing solution is added for easy detection.

Friday, July 4, 2014

BudBurst

I must give a hat tip to Johanna Roose over at New Under the Sun for turning me on to this citizen science project. BudBurst is a NSF sponsored plant watching citizen science project. Like many citizen science projects, you get to decide how involved you wish to be with the project. You can file a one time report, or commit to a long-term, periodic reporting on a single plant. This is another site that requires you log in to submit reports.








They do various campaigns throughout the year. Right now (June/July) they are running a summer solstice, what are the plants doing during the summer? In Sept/Oct there will be Fall into Pheneology, which should catch the change from summer --> fall.

The report forms are based on what type of plant are you observing: wildflowers, deciduous trees, evergreen trees, evergreen bushes, or grasses. The hardest parts will be
  • knowing the common name, but if you know Google you should be fine!
  • knowing your latitude and longitude, this a little tougher.. there are free apps for smartphones that will give you your exact GPS coordinates. And some cameras tag your picture so you can always shoot a snapshot and then pull the GPS off the image. This might also be helpful if you are going to make your report later so that you can keep a record of the plant.
After that it's very simple, answer a few questions about the state of the plant's, buds, flowers, leaves, color of leaves, etc. Submitting the report is a breeze, just click the bubbles and then hit submit.

One of the really neat things about BudBurst is they have an entire education section. This education section includes free classroom implementation guides and additional activities. I highly recommend you check out the grade block your kids are in for some really fun and mostly simple plant science related ideas. I plan on doing a few with Boo when he gets home! And if your kids do science fair, they might even stumble upon an idea.

I hope you'll get out into nature, take a moment to smell the flowers... and then make a BudBurst report on them! I'd love to hear about your experiences too, so please share some stories with me in the comments! Happy plant hunting :)

Wednesday, July 2, 2014

Figuring Outlines Out

I have been trying to work on my upcoming PhD proposal. PI'd like to see a rough draft by the end of the summer. Went to talk to him about ideas for experiments and he showed me a new way to outline.. PICTURES. I've always been a bullet point girl, list the topics that must be covered and then develop each one.

Went in to his office (which can be a swirling black hole of lost time, seriously we all know do not go into the PI's office if you do not have at least 30min to lose). I wanted to discuss upcoming protoplast work and my ideas for different experiments. We were talking when he whips out a blank piece of paper and tells me he learned to do this during his post-doc. Draws the graph that started this whole line of reasoning and labeled it 1. Next, he drew the graphs for the 2 experiments I was proposing.

"Not enough for a paper, so what comes next?" he asked me. A question I had not thought about.. I mean I had these experiments and was going to see what they said. He pushed me to think about it, well assume it will go the way we expect. What would be the next step. Thought about.. proposed something and we went from there. In about 10 minutes we had 5 figures drawn and a potential 6th for if X happened.

It was a light bulb moment for me. You have a piece of data that gives you an idea.. how do you flush it out to be a whole paper.. draw the rest of the figures! This could be the path to figuring out my PhD Proposal. What figures would hopefully go into each chapter of the dissertation? What questions do they answer? How do I generate them? If I can answer all of those questions, or at least get close, the experimental layout portion of my proposal is going to be a piece of cake!

Have you ever tried using pictures to outline? Any advise for proposal writing?