Friday, October 31, 2014

NaNo Eve

October 31, for a lot of people this is Halloween, for me this is NaNo Eve. This is the last day before the frenzied, caution to the wind writing pace for the next, great/horrible novel! For those unfamiliar, NaNoWriMo is National Novel Writing Month and takes place in the month of November. The goal is 50,000 words in the mere 30 day span of the month. I've been doing this since 2008 and I have no intention of stopping now.

This year I am attempting some science fiction in an oceanic setting, current working title is Fathoms. I've been plotting and planning all year and I only have it half outlined. Some of my research is unfinished, I've either not had the time to dive as far into as I wanted, or I've changed major plot points that have rendered all my previous research moot. Either way I have only half a poorly sketched out map to take me through this November.

Obviously, it probably sounds crazy for me to attempt this. After all, only recently did I say I was cutting back on my blog posting as I'm balancing two teaching courses, taking a course, doing research, and being a Mom. And for the first time in years I did consider sitting NaNo out. But honestly, I usually cut out all of my writing exercises for the rest of the year in favor of higher priority items. But November, egged on by the knowledge that thousands of other people are also neglecting their higher priorities, I give myself permission to raise my fun priority. I've not been disappointed yet!

Do I have 6 beautiful, publishable novels to show for it? Of course not! I don't even have 6 novels I'm proud of.. one of them I might never open again I'm so ashamed of how SUCKY it is. But I do have 6 adventures that pushed my creativity and gave me a sense of accomplishment. In another month, I will hopefully have 7!



Anyone else doing NaNo? My nick is SCUBAJfer, so if you are please buddy up with me and let me know who you are in the comments!!

Wednesday, October 22, 2014

Fall Break

This week was Fall break for my Uni, no classes on Mon/Tues and because of the way the lab I teach works both my sections are cancelled this week. For the undergrads this means run away and play. But for me, it means extra lab time! Several of the procedures I need to do take multiple days and this week I had 3 days with no interruptions to my work day. I was able to get 2 full rounds of plasmid preps done.

One of the beautiful thing about Fall break is that the school is usually quiet. It's like a mini taste of summer. Parking is a breeze, plenty of spots. Common equipment is usually available. Email doesn't flood the box like a tidal wave. No interruptions for classes prep or grading. And I actually got some things done, feeling a bit more like a responsible grad student! :D

Friday, October 17, 2014

Epidermal Leaf Slides

Leaves are incredible. They are the primary site of photosynthesis, as evident by their nice bright green color due to being full of chlorophyll. In general the structure of a leaf includes a cuticle (waxy protective covering), upper epidermis, mesophyll (home of the chlorophyll), lower epidermis and another cuticle.

When we were at the science outreach day the other week, my Post-Doc showed me how to make leaf epidermal slides. And it is so easy we let the kids make their own slides! Which they loved. All you need are: a leaf, clear nail polish, clear tape, a slide, and a microscope.


The first step is to paint a small area of the underside of the leaf with the clear nail polish. The reason you use the underside is 2 fold: typically cuticles (that waxy layer) are thinner on the bottom side and this is where the stomata are which are really cool to see. They kind of resemble cats eyes,more on those later. Note that the polish has to dry completely before you can move onto the next step.


Step 2 involves carefully putting the tape onto the nail polish. Be sure it seals along the nail polish but you keep a hold of the edge of the tape so you can do step 3 easier.


In step 3, you rip the tape back off, like you're waxing someones eyebrows. You should see the nail polish and a layer of leaf cells came off on the tape. Simply put this piece of tape on the slide, smooth it out so there are no air bubbles, and fini!

Then you simply pop it onto your microscope and you see this beautiful epidermal layer, complete with stomata and cell walls. Stomata are the cells that open and close to regulate water and gas exchange between the leaf and the environment.
40x objective lens (400x total magnification)
For more information on the role of stomata, I refer you to the wonderfully written Frozen Parody Stomata Open the Door by my favorite plant blogger @JLRoose.

The rules above are simply the start point. To make this more than a simple observation with your kids, have them examine leaves from different species of plants. How do the epidermal layers differ? How are they the same? To do some quantification have them count the number of stomata in one microscope field and compare it among the different leaves. Those are just a few examples, I'm sure there are dozens of other ones!

If you give this technique a try, I'd love to hear about your experiences! Leave me a comment :)

Monday, October 13, 2014

Fall Colors: An Inside Look!

The other weekend I attended a day of science outreach for the state. We put together a nice plant bio set up, showing different types of leaves and cell types with the microscopes. One of the things I created for the event was a poster entitled: Fall Colors: An Inside Look!

My son quickly informed me that people would look at this and say "That's a boring title"

....

Thanks kiddo, love you too. Well, I liked the title, after all the poster describes what occurs within the cells of leaves as they change from summer to fall to dead.


When leaves are green, they have lots of chlorophyll, which means lots of photosynthesis is occurring. Chlorophyll gives the leaves their nice green coloration. The leaves are doing photosynthesis and thus making lots and of sugars which can be sent out to the rest of the tree. The tree then sends water up to the leaves, keeping them hydrated.

As fall sets in, nights get longer and temperature decrease. This is a signal to the tree that it is time to start preparing for the approaching winter. The tree starts to close off the stem to the leaf, slowing down water flow and decreasing the amount of sugar that escapes the leaf. At this stage, chlorophyll starts to break down and anthocyanins are created. These anthocyanins are a protective substance, helping to protect the leaf from the upcoming stressors and stored in the vacuole. They are a nice bright red, color. Plants, such as maple, that have bright red leaves are rich in anthocyanins.

Colder temperatures cause water flow to cease and chlorophyll content to be negligible. Carotenoids, which are yellow/orange pigments, accumulate in the plastids (the same organelle in the cell where chlorophyll is found). Anthocyanins also continue to acculumate and the leaf gets deeper and deeper red. If you have a plant, such as an oak, that only turn yellow that's from the accumulation of carotenoids and not anthocyanins. Now we have bright, beautiful fall leaf.

Now it's time for the leaf to be shed, the stem is completely sealed. No more anthocyanins accumulate and the carotenoids break down, leaving a brown shade. The dead leaf now falls away and the tree hunkers down til spring when it can produce more sun catching, food making, green leaves.

So as you watch the leaves change colors, remember, you are watching the leaf die. This is one of my favorite comics about the fall:
Fall Colors Comic by Awkward Yeti
Fall Colors by The Awkward Yeti

Friday, October 10, 2014

Penguin Citizen Science

Boo has a stuffed Penguin, Kowalski. We've had Kowalski since he was really young. This has left us both with a soft spot for penguins. For a while, they were his favorite  animal (now it's sharks). When Zooniverse announced their newest citizen science project, Penguin Watch, we were ecstatic. It is a Zooniverse just like several other citizen science projects we've shared here, so it does require a username/password.


This is a simple click and tag site. You look at pictures, answer some questions and click on the center of the penguin. First question is are there penguins or other animals present?

Then, you mark the center of adults, chicks, eggs, or other (non penguins). If there are a lot of penguins, it will tell you after 30 marks that you've done enough and can feel free to move onto the next image. The last question is did you mark all of them or were there too many penguins.

 

Very simple and straightforward. If your kids can use a mouse, they can do this activity. Boo absolutely loves it. I highly recommend this for meaningful, yet slightly mindless, clicking! 

Friday, September 26, 2014

State of the Blog Fall of 2014

I really do not want to neglect this blog.. I have a lot of things I want to write about! But with my current schedule in lab and teaching, it gets pushed down towards the bottom of the pile. Three posts a week is not a sustainable pace with the other pressures! I will keep posting, I just need to drop back to once a week for a while :) Hopefully I can pop back up to 3 next semester!

Monday, September 22, 2014

Go Speed Rubisco, Go!

In addition to generating oxygen for us to breath, plants are also the main source of biologically useable carbon in our diets. The enzyme responsible for taking carbon dioxide and adding it to carbohydrate production is Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase). Rubisco is probably the most abundant protein on Earth, accounting for up to 50% of the protein in leaves. In this case, it is compensating for something... it has to be so prolific because Rubisco is very, very slow.

As Rubisco is the gate keeper for fixing carbon dioxide into edible carbon, researchers have long been interested in finding a way to speed it up which would ultimately increase crop yields. Scientists have been trying to find a way to engineer Speed Rubisco. Last week, a paper came out that described two lines of transgenic tobacco that had been outfitted with a faster Rubisco from a cyanobacteria (Lin et al., 2014).


First, I need to explain that the fact that they were able to switch the tobacco Rubisco genes with that of the cyanobacteria is fantastic. It might sound incredibly simple, after all we've been adding genes from one species into another for a long time, but, the gene for the active part of Rubisco is found in the chloroplast and plunking a gene into the genome of chloroplast is not easy.




Most of commonly held beliefs about genes are based upon nuclear genes. But that is not the only place where DNA is found in a plant cell. Plants have 3 locations where genetic material is located: the nucleus (purple), the mitochondria (orange) and the chloroplast (green). Targeting genes in the nucleus is easy, targeting to the chloroplast not so much.
Plant cell showing only genome containing organelles
For this study, they swapped out the native tobacco large subunit gene with a construct containing both the large and small units of Rubisco from the cyanobacteria, as well as, either the protein that helps Rubisco fold or a protein that supports Rubisco in the cyanobacteria. This resulted in functional cyanobacteria Rubisco being the only type of Rubisco. The original tobacco Rubisco was completely knocked out. And their transgenic lines had a higher rate of carbon fixation then normal tobacco!

You might be thinking BINGO! But this is far from the slam dunk to creating super crops. First, the cyanobacteria Rubisco, while faster, is much more sensitive to oxygen inhibition. To overcome this, the researchers grew their transformed tobacco under higher CO2 concentrations than are currently present in our atmosphere, in fact they grew their plants at more than 20x current atmospheric conditions. The cyanobacteria get around this problem by having special compartments, carboxysomes, where Rubisco and CO2 are concentrated together within the cell. One future solution to this problem would be to create carboxysomes within the tobacco.

Then even under the higher CO2, the transformed plants still grew slower than normal tobacco. Since the goal here is to create crops with higher yields, slowing the growth is not helpful. The cyanobacteria Rubisco was expressed at low levels compared to wild type (12-18% of leaf protein vs. ~50%) which might account for the slower growth. Increasing the amount of Rubisco might help bring the growth rate back up.

This is a really cool first step. But like everything in science, there are still a lot of things left to do!

Source: Lin, et al., 2014. A faster Rubisco with potential to increase photosynthesis in crops. Nature: Published online 17 Sept.

Monday, September 15, 2014

Scheduling

This semester is going to stretch and test my ability to multitask and schedule. With Mommyhood, during the week I drop Boo off at school and then head to lab. So I arrive around 8:20am and stay until 5:15 when I have to leave to pick him up before day care closes. That gives me a narrow window to get wet lab work completed. This semester I have one day without a regularly scheduled interruption to my lab work. My current schedule is:

Monday
10:30-11:30am TA meeting

Tuesday 
12-1:15 taking a class
1:30-4:20 teaching a class

Wednesday
Do ALL the research!

Thursday
12-1:15 taking a class
1:30-4:20 teaching a class 

Friday 
9-10:30 Lab meeting
10:45-11:45 department seminar
12  - 1 graduate student seminar 

One of the issues with this is a lot of the projects that I am doing take multiple days. For example, Western blots tend to take 3 days, plasmid preps take 3 days, and protoplasts take 2 days. Due to the timing of various things, I can only start Westerns on Monday, plasmids on Tuesday and protoplasts on Monday or Wednesday. qPCR is a half day process so I can do it almost any day of the week. In addition to worrying about the time various assays take, I also have to schedule my planting so that things are ready on a day I can actually spend the time to process them.

At my wits end, I finally sat down today and made a 6 week calendar. First, I put any single appointments (like Dr apt, days I need to leave early, etc) on the schedule. Then I laid out the order in which things had to be completed. Obviously, planting has to come before any experimentation on the plants. And different experiments require plants at differing ages. Once the order was set, I picked out the most time consuming part and decided which day it needed to happen based on my available wet lab time. Then I counted backward to when I needed to plant.

Now I have 6 weeks of work planned. 
If this plan works as I hope it will, in another 4 weeks I will do it for the rest of the semester.

Monday, September 8, 2014

Invasive Species

When a species is moved from an original location and thrives in the new location it becomes an invasive species. Invasive species can threaten and even decimate the native biodiversity. Sometimes these species are introduced on purpose, such as settlers bringing over herbs, and sometimes it is an accident, for example, mussels being transported in ships ballasts.

When an invasive species shows up in a new area, one question that quickly comes to scientists mind is where will this be able to spread? For plants, environmental conditions are often key to determining the range over which the invasive will be able to spread.  A plant that requires 15 weeks of freezing cold before the seed will germinate is probably not going to survive in Hawaii, even if a few plants get brought over.  But, what if the invasive species has the ability to adapt to new conditions? Ragweed has recently been shown to do just that.
 By: Meneerke bloem on Wikipedia Creative Commons

Most of us are familiar with ragweed because a great deal of us humans happen to be allergic to its pollen. If you live in the United States, well this guy is part of your normal flora so stock up on the allergy meds and suffer. If you live in Europe, oh so sorry this is an invasive species that has not only spread but has a tight grip that will not be released on your flora, so stock up on allergy meds and suffer while blaming America. 


Germination, when a seed sprouts to become a seedling, is an important fitness trait for plants and is controlled by environmental conditions. For the first time, as far as I am aware, a paper was published comparing germination rates between a native population and its invasive counterpart. (Leiblein‑Wild, M., et al., 2014. Germination and seedling frost tolerance differ between the native and invasive range in common ragweed. Oecologia 174(3):739-50).

They looked at germination and seedling frost tolerance from 10 different American populations and 17 Europe populations by collecting seeds and then planting them under varying temperatures in the lab. What they found was that European (the invasive) populations had a broader range of temperatures at which they could germinate and increased seedlings frost tolerance. This would allow the invasive population to spread rapidly and beyond the range originally predicted for ragweed to occupy in Europe. This also suggests that ragweed is adapting to the new habitats and could, potentially, continue to adapt and spread.

This study was the first to look at something incredibly important, comparing the native populations environmental requirements with the invasive populations environmental requirements. While they might be the same, there are many factors that could allow an invasive population to adapt and thrive in conditions that the native population could not. Ragweed is the first, of probably many, example of invasive species showing germination adaptation. Hopefully, more research will be done in this area.

Wednesday, September 3, 2014

The ever changing lab landscape

A lab is, and should, never be stagnant. I'm not talking about research, though this is constantly going and projects evolving. No, this post is about the cast of characters in a lab. There are several different types of characters that can grace the lab of a research based graduate program.
From top to bottom of the food chain we have
PI - Principal Investigator, the boss, the big Kahuna, when they want to work in the lab you get out of the way

Postdoc - Have their doctoral degree but not quite ready, or desiring, to run their own lab. Advantages of postdoc are often no teaching which means lots of research time, disadvantages potentially more admin/managerial roles in the lab.

PhD Student - Crazy people like me. We can be juggling teaching, courses, research, studying, writing, all at the same time.

Master Student - Also juggling teaching, courses, research, studying, writing but for only 2 years

Visiting Scientist - This is a short term, weeks to months, situation where a graduate student from another institution that wants to learn new techniques that your lab is particularly awesome at (or at least decent and willing to take a visitor). I only put them below the other grad students as they won't know the labs procedures and are there for training.

Interns - Undergrads doing research in the lab. Often they are juniors or seniors getting their research credits.

Freshman workers - dishwashers, tip rackers, anything everyone above does not have time or desire to accomplish.

Other than the PI, the individuals filling these roles flux on a semi-regular basis. The start of a fresh semester brings with it new schedules and, often, new people. This is particularly true of the fall semester. Fall is the most common time for new graduate students to start, and is always the time that new freshman workers start. Interns can come and go each semester. Grad students and postdocs tend to stick around for a few years.

This semester, our lab has picked up a new freshman worker, intern, and a visiting scientist. We also lost our senior PhD student to a Postdoc at a far away lab and one of our MS students will be finishing this fall. It never stays the same long.

Monday, September 1, 2014

Science Outreach

One of the faculty at my current Uni helps to put on a day of science outreach every year. This faculty member also happens to be the one whose lab's I teach. He has asked the postdoc and I in our lab to set up a plant booth in the Uni's area of the family science fun day. We have been thinking and brainstorming, but now it is a month away so rubber hits the road time!

When we were first thinking, I was thinking maybe 1000-2000 people. We were trying to come up with as many hands-on demonstrations and art projects and all sorts of things the kids could get into.  I was even considering writing a plant science handout with comic strips, games, coloring pages, etc. So I wanted to get an idea of #'s and asked Mr. Faculty who said that usual attendance is 3000 - 7000 and they are hoping for closer to 10,000 this year.

Copyright: Disney's Aladdin

That's a lot.. that's too many for brochures. I can't print out and assemble 1000+ books. Back in my Masters days we did an outreach and I would print out about 200 activity books and might have a few left over. Ok so ditch the booklets.

My current dilemma is how many of our hands-on items do we ditch. I think we need to ditch all of our make and takes because we would need a great deal of supplies. I worry about the assembly line of making slides and looking at them (we were going to let kids make protoplasts) being efficient enough to move kids through. I worry about the time it takes to do chromotography and will the kids stick around long enough to really understand it. We have been trying to come up with quicker, more examine and think about demonstrations. For example, Postdoc has some fly-traps to bring in and let them observe, grow avocado seeds, carrot tops, potatoes hydroponically to see rooting structures, cover some leaves of a potted plant with aluminum foil and leave some out so they can see how chlorophyll levels are affected, etc.

Now I have a question for my loyal readers, which would you rather see? Hands-on, though potentially time consuming (up to 10min), things for your kids to do (we will have 2 8ft banquet tables) OR Demonstrations/set-ups where they can learn about processes but not get to prepare anything?

 If you've ever been to, or presented at, a big outreach day like this what types of displays did you do? How did they work? Any feedback or comments you could leave would be very helpful!

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!

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?

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: https://legacy.mos.org/fireflywatch

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.

1) WHAT ARE YOU WORKING ON?

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

2) HOW DOES YOUR WORK DIFFER FROM OTHERS’ WORK IN THE SAME GENRE?

 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!

3) WHY DO YOU WRITE WHAT YOU DO?

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!

4) HOW DOES YOUR WRITING PROCESS WORK?

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.

http://weheartit.com/If 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.