July 24, 2013
Jason at the beamline.
After many days of image analysis, I have gotten some comprehensive and presentable data. Reconstructing the images took some manual work, but most of the time it was a lot of computer algorithms that I did not have to do. After reconstructing the images and editing the images, I could then stack the reconstructed images into a 3-D object that I can visualize. I had to learn some new computer science terminology and Avizo software skills to analyze the images to get a more accurate representation of the actual biomass. There were several data sets as we ran several tests on the beamline. All the data sets have their own problems. Some were incomplete or stopped early, one of the experiments led to the biomass curling up in a weird orientation so the images were no good as well, and some are too fuzzy to see the actual biomass pores. At first, I worked on one of the unclear data sets and tried to edit them constantly in order to get improvements in discerning what is the biomass and what is not. I did some calculations as well and the graphs seemed pretty nice; however, my method of analyzing that data set is quite biased based on what I expect the numbers should be and some images I could not reliably state that I analyzed only the eucalyptus or analyzed enough of the eucalyptus.
Yesterday I gave a presentation on the image analysis I have done in the past 2 weeks; my supervisor and another person who worked on the same material gave me some great feedback on interpreting my data and showing me where I could improve. Recently, I started to work on another data set which shows the biomass much clearer but was ended early. It is easier to work with due to its clarity and so far the numbers look even better; moreover, I am more confident in my method of how I calculated and interpreted the data. Next week, I will have a few hours of beamtime and plan to collect more images but this time with a slightly different set-up. Hopefully it works out okay and the images look good!
July 3, 2013
The experimental set-up.
After several beatime sessions, I have made some progress! The parameters of my project were difficult and required some creative thinking, but I really appreciated the need for creative thinking to design the optimal experimental set-up. It makes me feel like a real engineer. There were several parameters in particular that were in need of much thinking and modification. The heater system was heavily re-designed in order to optimize it for microtomography imaging. Previously we had used two glass slides with a small slit in between where the biomass and ionic liquid could be put; however, that created a limited view of the biomass and was very hard to set-up to ensure it was perfectly level in order to take good images. Then we tried to have no top slide and just take images that way, but the large surface area in comparison to the biomass caused problems again. What eventually worked was putting the biomass on top of a nail head. In this set-up, the x-rays could hit the biomass at various angles and the surface area was reduced significantly.
Adding the biomass and ionic liquid also presented a challenge. The biomass could not move at all when adding the ionic liquid, and since the biomass is so small, it often floated up when bubbles were forming in the reaction. Adding a small amount of ionic liquid right on top of the biomass was also hard as the there was very little room for error. Another predicament was that the bubbles formed during the heating of the biomass and ionic liquid. We tried to stop this by putting a glass slide with a small metal ball as our weight but the glass slide could not be positioned perfectly flat. However, with some creative design modifications, like using x-ray see-through washers to support the glass slide and reducing ionic liquid needed for imaging, we produced several good images. Soon I will reconstruct and analyze the data!
June 18, 2013
The roof in the Advanced Light Source (ALS) building.
I just finished creating a 3-D movie showing biomass degrading when ionic liquid is added and heated over a period of time. Through various modifications and drafts, I finally created a presentable movie. I am very proud of the movie I made as it shows various time points of how the 3-D structure breaks down as you perform this ionic liquid pretreatment. Though there could still be many more modifications to this movie, I think I am satisfied with what I have now.
Recently, I have gone through more rigorous training as I will be starting to collect data. Doing actual lab work really excites me. However, the lab work I will soon be conducting in the Advanced Light Source (ALS) seems very daunting. I have never done something as complicated as X-Ray Microtomography.
For the last few weeks I have been going to the Joint Bioenergy Institute (JBEI) to see parts of the actual biofuel process and analysis and this really excites me. I do not understand computers and physics as well as I understand biology and chemistry so it was like the researchers at JBEI were speaking my language. Although I have a lot to learn of course, I find it very interesting how they collect, analyze, and interpret data. I was talking to an engineer at the ALS a few days ago who imaged the exact same processes as me, but with different imaging techniques, so I learned a lot from his experience and hopefully he can guide me in the right direction with this exciting project.
May 31, 2013
The view from the Berkeley Lab.
Right after finishing school and I am here to be placed in another work environment; I am very grateful and satisfied with my internship here at LBNL where I will be investigating the delignification of switchgrass. LBNL, which has had 13 Nobel Laureates to its name, always has this aura and mystique; everyone is really smart, the leading scientists are all pursuing their research endeavors and it is quite intimidating. But after a few days working in LBNL I find some comfort and pride in working in this great lab.
I am assigned with a beamline scientist, Dula Parkinson, who has various projects being conducted with various people working for him. My project deals with the depolymerization of high-lignocellulosic plants, specifically the detachment of lignin from the lignin-cellulose/hemicellulose network. Lignocellulose contains cellulose and hemicellulose polymers, which are comprised of simple sugar monomers, and can be converted into ethanol through enzymes. Ethanol is the final biofuel that is hopefully attained through this whole process. There have been many important contributions and problems tackled in creating ethanol from biomass; the Joint Genome Institute have sequenced various genes of enzymes that come from various sources such as cows and fungi, the Joint BioEnergy Institute, which is where I will do some sample preparation later this summer, discovered that ionic liquids can delignify most of the lignin from high-lignocellulosic plants, and the Energy Biosciences Institute bioengineered microbes that can more efficiently react with the lignocellulose and produce ethanol. All three of these institutes have contributed greatly in making biofuels a more viable fuel for the future; however, biofuels are still not as economically competitive as existing oil markets, meaning much more research on biofuels is still needed. This quest for biofuels greatly is what excites me about working in this field of bioenergy, especially since Berkeley is in the center of all three of these science labs.
3-D rendering of switchgrass bubbles that Jason has been working on.
For my first week, I did not conduct many per-say “wet lab” experiments which I am used to; I was out of my comfort zone by working in a cubicle, doing computer analysis and animations. I learned this new software called “Avizo” which can render 3-D objects by stacking 2-D images on top of each other. For my first real assignment, I had to make a 3-D movie of switchgrass, a plant that is high in lignocellulose, degrading due to ionic solvents. The movie records the bubbles formed in the process as the microtomography experiment recorded the bubbles at a better resolution than the actual switchgrass structure. Programming the movie has been a challenge but the results have been great so far. My supervisor tells me that a congressman might come up to LBNL and take a look at the 3-D animation. I hope they do come because I spent a lot of time on this.