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.