Monday, June 30, 2014

Coral bleaching

Coral bleaching is a crappy situation facing worldwide coral reefs due to increasing sea surface temperatures. Most people are familiar with coral the animal, they see it's massive structures and oo and ahh in awe as Sir David Attenborough narrates the splendors of the reef. And if you've never listed to Attenborough, watch this video immediately and then continue reading.

While even astronauts can see the structures made by the coral animals from space, not everyone is aware of the real marvel of the reef, algae. Inside the gut of many coral polyps are microscopic algae commonly called zooxanthellae (Symbiodinium spp.). These algae are photosynthetic, making food from sunlight which is also used to feed the coral. In fact, for some species of coral up to 95% of the corals daily requirement can come from the algae. Coral bleaching occurs when the algae is expelled from the coral host, which leaves it with a ghostly white color as if someone had poured Clorox all over it, hence the term bleached.
Bleached coral on a wreck, 2011. Photo credit: Me

Friday, June 27, 2014

Firefly Watch

It's officially summer! Do you know how I can tell? The fireflies are out! I love fireflies, chasing after them in the dark is a cherished childhood memory. I don't feel like it's summer until I catch one, peek in my hands to watch it flash, and then watch it fly away. Boo and I have hunted for fireflies since he was little and I hope someday it will be one of his cherished childhood memories too.

Imagine my excitement when I discovered Firefly Watch, a citizen science project from the Museum of Science, Boston. It takes a little bit of energy to get registered because they have you pinpoint close to your area on a map and then describe the habitat in a small amount of detail. But once you get it set up, then all of that information is there and you just report on the fireflies.
Firefly Watch Home page:

The scientists are hoping to track firefly behavior across the U.S. and investigate the potential effects of man-made lights and pesticide applications. You can observe the fireflies throughout the summer, 10 minutes one night a week. Their observation sheet is a little long and will need to be completed by the adult. But kids can easily be involved!

First, sit down with the family and have everyone look at the virtual habitat which explains the 3 main observations: color, pattern and location. For color, there are 3: green, yellow-green and orange/red. Pattern is the number of flashes, single, double, triple, quadruple, more than 4, flicker. Location describes where was the firefly when you saw it, was it flying or sitting on something (bush/grass/etc.). Fairly simple stuff! I think even young kids could have fun keeping count of their fireflies and it would be a good sit in the backyard and practice observation skills activity.

The adult can be responsible for most of the environmental conditions (and I recommend you write all of that down before you start your observations!). But if you can get the kids involved even better! My suggestion would be to have the whole family evaluate and write down the conditions before everyone uses their own simple firefly counter I'll post below. If you have a thermometer around, let the kids measure the temperature in the backyard. You can discuss/observe the other conditions, cloud cover, precipitation, wind, and moonlight with the kids. If you're doing this over time, it can even lead to having the kids hypothesize about what conditions might be changing the firefly observations from one night to the next.

Once you have collected all your data, pool it into a single report. Then you log in and submit your observation. I have had some trouble doing this in Firefox but it always seems to work in Internet Explorer and I have not yet tried Chrome. So if you are having problems, try changing the browser.

Have you ever done a citizen science project? Do you like catching fireflies? I hope you'll give Firefly Watch a try and if you do please post your experience in the comments!

Wednesday, June 25, 2014

PhD Proposal: Mapping Your Journey

Remember when I first introduced qualifying exams, I mentioned that this was only the first flaming hoop of death in the path to a PhD? Hoop #2 is rapidly approaching... the PhD Proposal: Mapping Your Journey. Or more accurately, the PhD Proposal: Write down everything you can think of and hope you stumble upon Treasure Project along the way.
Disney's Treasure Planet
The PhD proposal is basically a combination of a literature review paper and a hopeful, idealistic outline of how your experiments will go for the next 4-7 years. Everyone knows that it is incredibly optimistic and the final PhD dissertation you write will have deviated massively from your proposed outline. That's ok, this outline is not about getting it perfect/right. It's about forcing you to sit down and really take a look at where am I going and how can I get there. It also is a chance for your committee (the people in charge of judging every aspect of you for the duration of your PhD) to evaluate your knowledge about the literature and writing ability. And to every science major I knew in undergrad who complained about the gen-ed English requirements, guess what... great writing is important!

The introduction is the easy part, all that information exists somewhere out there, all I have to do is collect and explain it. I've done a lot of web searches for literature and have a healthy collection already started so that bit is done. I need to read a lot of the various articles and there will always be the, "hey what about this, I should see if there's a paper on this" event that comes up during this process that will send me back to literature searches. Then once I've collected all my information, I can sit down and write it all up so that it flows logically. It takes a lot of time, but it is relatively simple.

The second piece is more complicated. What experiments will I be doing for the next 4+ years of my life? Well.. it sort of depends on what I find out in the course of those 4 years! I know my short-term goals (next year) and I have some ideas for if this works, then try that. But, honestly, I do not feel like I know enough information to describe sufficient experiments to justify the bestowing of a PhD!

I had planned on working on the introduction, aka review paper, portion of the proposal this summer anyway. But PI would like me to have a draft of both the introduction AND the experimental layout by August. That means I need to carve out more writing time during my week! 

Monday, June 23, 2014

PCR the molecular biologists best friend!

PCR (polymerase chain reaction) is an incredibly common method used in molecular biology. I'm not sure you can find a molecular biology lab that does not posses a thermocycler (the machine that runs PCR). PCR was invented in 1983 (which makes me older than PCR.........) and enhances small segments of DNA into millions and millions of copies. It is a powerful method because you can take a very small sample and end up with a great deal of DNA.

The first step to a PCR is to identify what segment of DNA you wish to amplify. For research, one is often amplifying a single gene of interest in the study. For my current work, I use primers that are designed to identify the GUS gene of my transformed plants. This lets me identify which plants have been successfully transformed as they will have the gene while non-transformed plants will not. Picking your primers is one of the most crucial steps in PCR. Primers are small segments of DNA that will pair with the genome DNA and direct the amplification of your gene. They must be designed so that they can only base pair in your gene of interest and not to other random segments of DNA, otherwise your PCR will give you meaningless information.

Once you have your primers and your DNA sample, then comes the master mix. The master mix will contain the primers, buffer, magnesium ions, dNTPS (extra nucleotides), and a polymerase. The one we use is hot start Taq. DNA Polymerase is the enzyme that builds new DNA. Taq stands for the species from which this polymerase comes from the bacteria Thermus aquaticus. T. aquaticus lives in hot springs and thus its enzymes do not degrade under increased temperature, like those in the cycling steps of PCR. 

Friday, June 20, 2014

Dragon sequel did not disappoint

We went to see How to Train Your Dragon 2 last week on opening day. The theater was giving out free posters so we actually have copies of this poster now :) Boo gave it two thumbs up and a hearty "loved it!" I had been cautioned by so many people not to get too excited, we all know sequels don't hold up to the originals. Well, they were all wrong! This sequel felt like a natural and perfect follow-up to the first one. It stands as it's own story, no need to have seen the first one and no need to see the 3rd to feel satisfied. Though I am really excited about the 3rd one now!

Like it's predecessor, the flight sequences alone justify the cost of the 3D ticket and would probably be worth the IMAX price (but we did not go to that one so I cannot say for certain). All our favorite characters returned, all grown up, as 5 years have passed. There was, obviously, a lot of character development in Hiccup and Astrid, but Stoic, Gobber, Snotlout, Fishlegs and the twins had their own moments, as well. We also meet some very interesting new characters (though the man bad guy, Drago, is pretty one dimensional). Dragons are everywhere on Berk and Boo was quick to point out various species from the Dreamwork's Dragons TV show, as well as tell me which ones he did not know. The imagination and details put into the various dragon species was mind blowing.

The one thing I was not prepared for, my need for tissues. I cried... to the point that Boo complained I got his Toothless stuffed animal's head wet. The little boy next to me (little older than Boo) was sobbing. I was tearing up at the death of a beloved character but then a Viking funeral is performed and the eulogy given sent tears flowing over. In addition to the death, there is lot of dragon on dragon combat which might be to much for younger viewers, so bear that in mind when deciding to take the little ones.

That being said, load up your Dragons enthusiast, grab some popcorn and Icee and sit back for an hour and 42 minutes of incredible animation! 

Wednesday, June 18, 2014

My Writing Process Blog Tour

I love this idea!  A prompt going around Twitter has bloggers stop and think about what and how do they write called #MyWritingProcess.

Here are the My Writing Process Blog Tour Instructions:
Step 1: Acknowledge the person (& site) who involved you in the blog tour.
Step 2: Answer these 4 questions about your writing process.
Step 3: Tag another writer or 2 to answer the questions the week after you. Give a one-sentence bio of each, and link to their websites.

I came across this from Kristy over at Sexy Grammar.  Kristy is one of the very talented writers I follow from NaNoWriMo.


 Right now I have 3 projects: A) this blog, B) PhD proposal, C) outlining NaNo '14!


 A) I feel like my blog is a crazy hodge podge, just like my life. It's got some science and some parenting... sometimes I use it to try out different writing styles. The one thing it does is keep me on a schedule. I know I have to write something because I have deadlines!

B) My PhD proposal is different... uh... well the work is different... but the format is similar to everyone else, as it needs to be.

C) This, and the past few, years NaNo is science fiction.. my science fiction is different because I try to go heavy on the current science in an educational type fashion and be sparing with the fiction. Though this years will dive deeper into fiction than previous attempts! Though I'm still planning on a big dose of education to go along with it!


A) Connection.. I'm blogging my journey with the hopes of connecting with people. It's a crazy collection because I write about what I want to write about. Sometimes it's cutting edge journal articles, sometimes it's motherhood, sometimes it's a look at what I'm doing in lab, or even just favorite websites!

B) Organization.. PhD proposals, in addition to being required, are really helpful for getting your thoughts and experiments organized into a realistic set of goals.

C) Freedom.. I love writing fiction because it feels freeing. While I have been trying to focus on more "educational" science fiction, it is 100% mine and I can create anything I want for plot points!


For the blog, I just write. I choose what I'm going to write about and start typing, start to finish without any planning. Type, type, type, type until I run out of things to say. Then I edit it into something I'm not horrified to post on the internet.

But for anything longer than a few pages, I like to outline.  My old fashion tendencies come out in the outline, I prefer to do it with paper and pen. I like having the notebooks to flip through and refer to when I'm writing. When I take the time to outline, I always finish the story. When I decide to use the jump in and go method, I usually end up with a long, bloated, incomplete manuscript. Once the story is complete, then I edit.

Now comes the fun part, I get to tag another blogger. This should be interesting because while I love following her blog I'm not sure she knows mine exists!

Johnna Roose over at New Under the Sun is one of my favorite plant bloggers. She always has the most interesting posts that range from photosynthesis to all about a flower species. I would love to know how she manages such amazing posts.

If anyone else feels inspired to participate please leave a link in the comments so I can read your writing process too!!

Monday, June 16, 2014

Glass-like Cytoplasm?!

The biology department has started a research in progress/journal club for the graduate students. Research in progress the poor sap has to present what they are doing, while journal club the student has to pick the paper and then lead the discussion. I must admit that I am skeptical about journal club because there are so few plant people that I know I will have to read a bunch of random papers that are out in left field from my beloved plants. While I do understand, and appreciate, the acquisition of knowledge outside of my corner, I have sooooo much in my corner it's just one more thing.

Then, the first week of journal club this paper showed up:  The bacterial cytoplasm has glass-like properties and is fluidized by metabolic activity,  Parry et al. 2014. you've seen the movie Sweet Home Alabama, you'll remember the iconic scene at the end where he is putting out lightening rods on the beach to make "beach glass." It was kind of an important scene ;)  In this movie's physics, lightening hits the sand and liquifies it, which then recools into beautiful sculptures. Apparently, bacteria can do a similar process but in reverse and using metabolism instead of lightening!

Friday, June 13, 2014

Family Friday

Tomorrow I take Boo to his Dad for the summer. So today we took a true Family Friday!

Boo and I borrowed my Mom's Miata and zoomed down to the theater for How to Train Your Dragon 2. On the way, we had Happy blaring from the speakers and the lady in the car next to us started clapping and dancing along it was hilarious.

We really enjoyed the movie. It was well worth the cost of the 3D and probably would have been worth IMAX. The flight sequences were amazing, Hiccup and Toothless aerobatics were heads and tails cooler than the first movie. There was a really sad part that made me cry and more dragon combat than the first movie so parents of younger kids be warned.

After the movie we went out to lunch and then he wanted to take the Miata down the freeway at top speeds. I floored it a few times for him, he loves it :) Then home for some Legos and my grandparents came in for Thai food. It was a great day :)

Boo will be gone for 5 weeks so Family Friday is going to be taken over by randomness for the next few weeks.

Wednesday, June 11, 2014

Random Updates

First: I PASSED QUALS! Wooohoo!!

7.94 on the memory written part and 9.0 on the review paper (out of 10). Sooo happy! Quals are now behind me! Any exams will be downhill from here.

Research: Plants are almost large enough for protoplast work to begin next week and I have been busily making plasmids. I laid out my hopeful experiment schedule for this summer.

Student: This summer the Bio department has added a weekly grad student meetings on Friday that flip back and forth between research in progress presented by a grad student and journal club. My research in progress is Aug 1.

Mommy: Boo finished first grade with 2 weeks of no strikes and no take home work! They had a play called the Night the Crayons Talked, he was the Blue Crayon, and it was so cute.

Random: I won a grad student jewelry give away from thevexedmuddler! Her stuff on Etsy is absolutely awesome, go have a peek! Now I have to decide which piece I want.. it will be tough, so many amazing things.

Tuesday, June 10, 2014

Electrolyte Leakage Assay

*Note - I had tried to schedule this to self post yesterday but apparently it did not... soo here it is a little late :) * 

Most people when they hear the word electrolytes they think Gatorade. Most people have seen the commercials and know that after working out you should replace the electrolytes lost from exercise. Gatorade has electrolytes, thus you should drink Gatorade, right? Well... yes and no. Yes, you do lose electrolytes when you workout via sweat. But, you have to be sweating a lot for Gatorade to actually be better than water. Gatorade has calories, and honestly we get a lot of salt (one of the electrolytes) in our diet in the U.S. anyway, so water is sufficient if you are exercises for an hour-ish. Now if you are running a marathon or playing a full game of football/volleyball/soccer etc., you should turn to Gatorade or other sports drinks to replace the electrolytes in a quick and efficient manner.

So now the question is, what do electrolytes have to do with my research topic of cold stress in plants? Glad you asked, let me explain!

I am learning a new technique in lab right now, the electrolyte leakage assay. It is a technique I see a lot in various articles that I read, not to mention one that other labmates have mentioned in their presentations. But I never knew what it involves, and honestly, I only had a vague idea of how it works. Before I volunteered to do this for my PI while on vacation, I knew that high numbers are bad and mean that the plant is not coping with the cold.  Now that I am actually doing this technique I decided that I needed to know more about it.

In the lab, my PI explained the basics of how I collect the data, and then how I plot the data. It is fairly simple. The plants were either acclimated (had been in cold temperatures) or nonacclimated (had been at normal temperatures) for a few days. Then we cut leaf discs out of them and put them in test tubes.
Acclimated plants must stay cold, so sampling must occur in the
walk in fridge! So, so cold!

Friday, June 6, 2014

Toothless and the Axolotl

We love the How to Train Your Dragon movie. Love, love, love! When Build-A-Bear had their limited edition Toothless, we made one the first day. We watched the show Riders/Defenders of Berk on Cartoon Network every week. I'm really sad that they are moving it to Netflix, I like having things on the DVR more than streaming with the buffering issues... but I digress. The sequel comes out next week..

needless to say, we will be first in line to see it! But first, I want to make a quick observation about Toothless. By now everyone probably knows that Toothless looks a lot like Stitch from Disney Lilo and Stitch because it's the same animator/directors. But has anyone ever noticed how much Toothless looks like an axolotl? In case you've never seen an axolotl (aka Mexican Salamander, though axolotl means water monster which, I think, is a much more impressive name) I refer you to this comparison of Toothless and Mr. Axolotl.

They could be cousins!  Both have projections from their flattened melon shaped heads, mouths that appear toothless, and distinctive eyes. Toothless has ears and who knows what the other things are supposed to be coming off of his head. But, in the axolotl's case these projections are actually gills that allow the salamander to live in the water. Axolotl's are aquatic salamanders, they become adults without undergoing metamorphosis which would lead to the abandoning the larval tadpole-like stage. This is why they retain their tail and caudal fin. They have teeth but they are very small and not fully developed, due to the lack of complete metamorphosis. Toothless on the other hand has retractable teeth.

Obviously, there are couple of glaring differences.. Toothless has wings, can fly and shoot fire. He looks super strong, where Mr. Axolotl looks weak and puny. But I would like to share with you how incredibly awesome these water-dwelling salamanders are! Like starfish, they can regenerate limbs. Unlike starfish, they have bones that must be involved in this regeneration process. But not only that, axolotls can also regenerate their spinal cord should it be nicked or severed. There are scientists right now trying to identify the physiological process by which they do this to see if we can apply that ability to humans. With this level of regeneration I think we need to rename these guys from Mexican Salamander to The Wolverine.

Wednesday, June 4, 2014

To cat or not to cat

That is the question. I go back and forth about getting a cat. I told Boo a while ago that if we moved out of grandma's house we could get a cat. And we have moved out, but we still have no cat. I love animals. I miss having a cat. My childhood kitty was a snuggler, he always slept right next to me, and would crawl up on my chest and give me kisses in the morning. He was fluffy and huge and lived to be 16. I'm sitting here tearing up a little bit even thinking about him and he has been gone for almost 7 years.

As a kid, I told my Mom all the classic lines. I'll take care of it! I'll clean the litter every day! I'll brush it! And I so totally did..... for maybe a week. Then it was hit or miss and my mom did get stuck with a lot of it. I now hear those same things from Boo. "I'll feed it! I'll take care of it! I'll brush it!" except he is smarter than I was and straight up admits that I will have to clean the litter cause he is not touching that. And you might think that is what gives me pause, but it's not (though it does factor in!).

We like to go see my parents, which means travel. And I know a cat can be left for a few days and be fine, unlike a dog, but I still feel bad. I want a cat that is a cuddly cat, one that likes to be around us and not run and hide. So then I'd feel really guilty to leave it for a few days.

Then there is the cost. The apt requires a $400 nonrefundable pet fee. And it will want food.. and potentially vet visits and all that. I'm honestly not sure we could afford it right now.

But then I have nights were Boo is gone, like over spring break and soon for the summer, and it would be nice to have a cat waiting for me to come home and give me a purring snuggle. It will be interesting to see if I make it through the lonely summer without him. Bets on if I make it?

Tuesday, June 3, 2014


I, personally, call melatonin magic sleepy pills because without them Boo has a really hard time sleeping. His pediatrician recommended it and BOY what a difference! Take the dose, hour later he is calm and yawning and ready to sleep. Then I get my night to do whatever I want! Which with quals had meant studying. But now that quals are over it means..... more studying. Just instead of textbooks, I am reading journal articles.

I was doing a Google Scholar search for articles in 2014 on cold stress and I came across this gem:
Role of melatonin in alleviating cold stress in Arabidopsis thaliana by Bajwa, et al. in Journal of Pineal Research. Needless to say I was intrigued. 

The abstract claims that melatonin up-regulated several genes involved in abiotic stresses: CBF, a cold-induced transcription factor which activates cold responsive genes, COR15a, a cold regulated gene, CAMATA1, a calcium responsive abiotic stress gene, and ZAT10/ZAT12, antioxidant genes. The abstract did its job, made me read the rest of the paper. Of course, I am thinking oo if this is true I wonder if adding some melatonin to my soybeans would increase cold response.

They grew Arabidopsis thaliana on Petri plates or liquid media with different concentrations of melatonin. The seedlings were then put in the cold for 3 or 5 days and then allowed to recover for 2 days. Those treated with melatonin grew better after cold, based on the longer roots, shoots and more mass, which is why they said that melatonin alleviates cold stress. They did measure the genes listed above via RT-PCR and at some point, under at least one of the melatonin concentrations, the gene production was increased versus the control.

The most interesting part, in my opinion, is that melatonin, the stuff that helps us sleep, could help plants regulate their stress response. I find that idea fascinating and I want to do a bit more research on it!