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


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:

10:30-11:30am TA meeting

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

Do ALL the research!

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

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!