Week 3

Hello again! I hope you guys have been enjoying your internships and your Rodeo Break.

On Monday, Feb. 17th, I started to run gels with my mentor Naomi. We ran a small gel with a primer called up2 which was a primer that is a little before the target segment of DNA that we're looking at. Later, we scored some older gels that the AGI team made and took pictures of and decided to re-run some of them. So we ran large gels with PCR plates that were made before. I got to insert the DNA using a 12 channel multi-channel pipette. At first, it got a little tricky trying to make sure I got all the PCR products inside each pipette and that I put all of the product inside each well and the pipette kind of gets unbalanced as you pipette out the PCR products. So I also did some practice pipetting with water and a plate.

12 Channel Multi-Channel pipette

After seeing the results of the gels we ran, we decided that the primers that were used before may not be working such as the down1 primer (which is further down the DNA from the target segment). The bands seen in the gel represent whether the DNA have the O. glaberrima or O. barthii allele or both. Also, the ends of each gel are the base pair ladders (I believe for this gel we used the 100 bp ladder). You could also see how there were some gaps in the gel...there might not have been DNA in there.

Large gel with down1 primer (it might be kind of hard to see)

Therefore, I got to prepare new primer solutions. Mostly, it consisted of making tons of dilutions and dealing not only with molarity but also nano-moles and micro-molar solutions. I felt like it was chemistry math (mainly the dilution equation: M1V1 = M2V2) on a whole different (smaller) level. These new primers were called qSh1-1, qSh1-2, sh4-b1, sh4-b2, sh4-b3-R. So instead of just handing out the primers already made for us like in our Capstone Bio class with the mitochondrial DNA primers, I got to actually prepare the forward and reverse primer solutions. Although it was just simply diluting and pipetting, I'm glad I got to know how things were made from the beginning.

On Wednesday, I observed my mentor preparing the PCR with the new primer solutions I made. After loading the PCR mixes into the PCR machine, I went into my second lab meeting. The more I see these lab meetings, the more I think, "Good thing we got lots of practice presenting during our capstone classes." Although these lab meetings are more of discussions and informal presentations, I could notice things that went well and things that didn't. But anyway, the main topic for this lab meeting was on new data relating to SNPs and imputations. I'm not sure what those terms mean and I think the other members of the AGI team didn't quite understand either, so a lot of time was spent trying to understand how the data was computed. At the end of the meeting, there was a discussion about rice and arsenic (which thankfully I had some background info in). It seemed as though there was more arsenic in the food supply in general than what everybody thought. Although there were jokes about how this fact might negatively affect the rice project the AGI team was doing (since they said rice was the answer to the 9-billion people question and could feed the world). However, it also seemed like the arsenic was coming into the food supply not only from natural causes such as volcano eruptions but also from human activities such as using pesticides/herbicides, mining, and burning coal and oil. So there were also discussions of how this issue of rice and arsenic can also provide a new path for research since the team was already interested in starting a new study on the roots of rice plants, they could study the arsenic levels and how the arsenic gets into the rice plants/roots (so we possibly may have a new research study underway in the next few months).

After the lab meeting, another member of the AGI team, Dario (who has been helping me a lot) and I ran a medium gel with the PCR products. I got to make the medium gel from scratch with about 1 g of agarose and 70 mL of TAE buffer (which is a common buffer used in gel electrophoresis and for those who are curious what TAE stands for -- it is Tris-acetate-EDTA). The results of the gel showed that one of the rice species (O. glaberrima) was highly concentrated so it did not clearly show the results of the other two rice species (O. barthii and the man-made heterozygous mix of the two species). So, I prepared another PCR but diluted the DNA. (I also accidentally diluted the O. barthii when I wasn't supposed to -- this just shows how important proper communication is in a lab -- but it was fine). I then continued to prepare a new PCR mix and loaded it into the PCR machine.

That was the end of my week! Hope you guys have another great week! I look forward to your next posts! See ya'll then!

Week 2

Hi guys. I hope you guys have had a great week at your internships.

This week I have finally started my internship and figured out a schedule. I still need to work on my training which officially won't be over until the 25th where I have to take a course. However, I can work in the lab! (under supervision, of course) 

On Wednesday, I was able to go to my first lab meeting. Unfortunately, the guy who was supposed to lead the meeting couldn't make it that day, so I didn't get to hear a whole bunch of science-y terms or hear about the new data for the rice genome project. On the other hand, I was able to listen in on a program called "R" (yes, it is only one letter). I'm still trying to wrap my head around it, but what I got was that it is a language programming system that can be used for bioinformatics and statistics and so on. What I got from the demonstrations of using R so far was that it was almost like a huge computer-version of a graphing calculator. I believe I'll get to see more demonstrations and hear more about it at the next lab meeting. I think I'll ask if it can make 3D graphs (but we really don't need any of that in biology). But it involves like vectors and components of vectors, assigning characters to values, and all that stuff. Oh, and the good thing is...it's FREE! 

I also got a pipetting 101 lesson. I had to test the accuracy of 3 different pipetts by pipetting back and forth water. Although it was super tedious, not only did I see that the pipettes I used were accurate, but I was also complemented for being a good pipett-er. I think the purpose of the exercise was to pay attention to accuracy and practice my pipetting to make sure I get it right every time. 

On Friday, I was able to see another demonstration of PCR and making a gel. I am also getting myself more familiarized with the lab, where things are, and which doors to get in and out of (it gets confusing sometimes). I was also able to help prepare the PCR and it seems like I still need to practice my pipetting. But the process is basically the same as what we did in our capstone biology class.

I have also continued to do my research and my supervisor gave me a side note to look up arsenic poisoning in rice. Apparently the FDA found traces of inorganic arsenic (which is known as a human carcinogen) in rice since around 2012. They are in what the FDA considers very small amounts ranging from about 11 to about 160 parts per billion per serving in rice and rice products. The public might disagree with these being small amounts because on average, single servings of some rice products exceed the arsenic limit of drinking water which is 10 parts per billion (as determined by the EPA). Brown rice seems to have the most arsenic because it is not as refined or polished since the arsenic is usually clustered around the seed hull (which is the outer portion). Also, instant rice and rice wine tend to have the least arsenic. Although the FDA has analyzed arsenic levels in over 1300 types of rice and rice products, they are continuing their research since the levels tend to very greatly sample to sample, even within the same product. However, thus far, the FDA has concluded that the arsenic levels in rice will not have any immediate or short term adverse health effects, and they do not advise changing the people's consumption of rice. Ironically, they also advise to have a more balanced diet and also consume other grains and not daily eat rice.

With the rest of my research, I have been looking more at the history of rice and its domestication. The history of rice gets pretty complicated as it seems like it has been twice domesticated and twice de-domesticated. There are also many species of rice, the most common being Oryza sativa and Oryza glaberrima, and there are many subspecies such as under O. sativa are known as japonica and indica. The first is typically found in Asia and the second in West Africa. These two are 2 domesticated species of rice and are believed to have come from wild species called O. rufipogon and O. barthii, respectively. After some species of rice were domesticated, it seems that there was a weed that resembled an Asian rice variety and another strain that resembled rice grown in the tropics. This made and continues to make scientists question, did the domesticated rice revert back to their wild forms or were there mutations?

Wild type v. domesticated rice phenotypes: (A) Immature panicle from O. rufipogon; (B) Mature panicle from O. rufipogon with dark hulls and long awns; (C, F) Dehulled seed from O.rufipogon (C) and O. sativa (F); (D, E) Grain bearing O.sativa ssp. japonica (D) and ssp. indica (E) panicles w/ straw-colored hulls w/ closed structure.
(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759204/figure/MCM128F1/)

I have also been researching phenotypic traits besides shattering that differs between wild type and domesticated rice and also began researching the genotypic relationships. For example, wild types have very long awns while domesticated rice has short awns if any. Also, wild rice has higher dormancy levels while domesticated rice has reduced dormancy for uniform germination (making it easier to harvest all the rice grains at one time). Also, the pericarp and seed coat of wild type is typically red while domesticated rice is white, and grain size are also small in wild type and domesticated rice has varied sized grains. The panicle structure in wild rice is an open panicle with few secondary branches that carry only a few grains while in domesticated rice is a densely packed panicle that carries a large number of seeds. I am still trying to wrap my head around the parts of a rice plant and trying to understand all the data related to the genotypic information.

I will be looking more closely at the shattering genes and researching the certain genes and hoping to understand all the science language in these journals. Until then, hope you guys have a great week.

Week 1

Hey guys. 

I should probably first talk about what I am going to be doing with this Senior Research Project. I am going to be interning at the University of Arizona Genomics Lab under my supervisor Dave Kudrna and my mentor Naomi Rhodes, who is an undergraduate at the U of A, and I will working on plant genomes, specifically, on rice from the genus Oryza. I will be focusing on the shattering trait of these genomes. 

Unfortunately, I haven't been able to do much at the laboratory because there have been issues with my lab safety training. I finished half of it, which was the Laboratory Chemical Safety Training, but there have been problems with the other half which is the biosafety training. I hope to resolve the issue by early next week (Monday or Tuesday) and start working in the laboratory. After resolving the issue and finishing my training, I can have a set schedule for my internship. 

On the other hand, I got my own little office space. I will be doing some of my research, reading, and writing there (and at home ^-^). I also did some reading on my topic, and as I was reading, some of the papers and articles answer questions like "Why are we studying this?" and "Why should we care?"

This project with the Oryza rice genomes hopes to answer part of the "9 billion-people" question. According to the article "The 9 billion-people question" in The Economist, it is estimated that by 2050, our world population will have increased from almost 7 billion to 9 billion people. Sooo...how will we feed all these people? When we look at our food supply compared to even today's population, we can barely feed everybody (and the food prices are not helping). This crisis brings up Malthusian fears and if we keep this up then how are we going to feed 9 billion people in 40 years? Well, rice, especially Asian rice (known as Oryza sativa), feeds more than any other crop in the world, and the rice-dependent population is expected to at least double in the next 25 years. Therefore, scientists must find a way to produce/grow twice as much rice as efficiently as possible. So, how is shattering related to this? Well, first, you might ask, "what is shattering?" (I mean, I kept using the word, I should at least define it or give some background, right?) "Seed shattering is an adaptive trait for seed dispersal in wild plants...[and it] causes yield loss for domesticated crop plants during harvest." Our ancestors began domesticating rice when they started selecting rice with less shattering (Zhou et al. 1). Reducing shattering in wild rice species may be a way to help domesticate rice making it easier to harvest. So we also get into some evolution and history of Oryza rice plants. 

Although I haven't been able to do all the fun lab stuff yet, I am really looking forward to doing experiments and learning about the thing that I eat most at home (RICE!). 

I hope you all have a great weekend and for my fellow seniors, another fantastic week at your internships. I will look forward to your postings. Until then, ta-ta for now.