DNA Strawberry Extraction Lab

DNA Strawberry Extraction Lab: 

Today in Bio we conducted a lab where we were instructed to extract DNA out of strawberries. It was a lot easier than I thought it would be and didn't take much time to do. I'll take you through what we did to extract it. 

1) We got our strawberry and washed it off to minimize any environmental factors that could lead to an experimental error.

2)  Then, we made a DNA extraction buffer by mixing 5 mL of liquid dish washing detergent, .75 g of salt, and 45 mL of water. This detergent will aid in breaking down the fatty membranes so the nuclear membrane can later be released. The salt makes gives the DNA the ability to stick together more easily and separate from proteins.

3) What we did next was the fun step. We put the strawberry in a zip lock bag and we put 10 mL of the extraction buffer in it. Then we sealed it off to make sure there aren't any air bubbles. Then we got to smash the strawberries with our fingers. We smashed them for 1 minute.

 4) After that, the DNA nuclei should have been floating around as crushing the strawberry would break open the cells. When we finished smashing the strawberry, we put a funnel, that had gauze on it, into a tube. When the gauze was on the funnel, we filtered the liquid into the tube. Then we threw away the gauze and the left over strawberry. This filtering lets the strawberry DNA pass through without the extra Strawberry cell debris.

5) What we did after that was put ice-cold ethanol on top of the strawberry solution in the test tube with a pipette. The ice cold ethanol aids in the extraction and the safe-keeping of the DNA since the DNA will collect between the alcohol and strawberry extract layer. This happens because DNA is not soluble in alcohol. That is why it precipitates and remains at the layer between alcohol and extract.

6) This last step took us the longest. We had to use a loop to extract the DNA, and it took us 6 minutes and an extra loop to get the DNA from the test tube into our small container. We had to use the second loop to remove the DNA from the first loop. We might have put too much salt because it was hard to get it unstuck from the first loop. It all worked out in the end though cause our results were pretty damn cool!

Beer: an Age Restriction or a Restriction of Age?

-Might as well start drinking when you're old according to current research: 

The natural process behind aging involves the shortening of our telomeres. The shortening of the telomeres leads to various issues, most dealing with established age-based diseases. Andrea Baccarelli, an M.D Ph.D and the head of the center for molecular and genetic epidemiology, proved that regular consumption of alcoholic beverages speeds up the process of aging at a cellular level. After the end of every cell cycle, these telomeres are shortened more and more because of the end replication of chromosomal DNA. When these telomeres get too short, it acts as a signal for cell death. In this sense, telomeres serve as a biolocical ticker for our human cells. The smaller/shorter a telomere is, the more limited the survival of the cell.

-Remember how its commonly thought that stress leads to grey hairs and aging? Reseach studies have shown that a more stressul environment coupled with bad choices can lead to telomere shortening more quickly because of oxidative stress and free radicals. Oxidative stress comes from an imbalance in our ROS's (reactive oxygen species, or reactive molecules containing oxygen)  and our ability to detoxify/repair the reactions and disturbances that are caused. Iny my opinion, this telomere shortening most likely comes from the disruptions that can occur with cellular signaliing in oxidative stress. Oxidative stress is most common in diseases like cancer, parkinson's disease, alzheimer's etc... A lot of the age-related diseases are involved with the development of oxidative stress. I did more research on free radicals and found that it has to do with the accumulation of free radicals (unpaired electrons, atoms, etc..) and that this accumulation leads to aging. 

One year later, It was found that low levels of alcohol increase led to an increase in the risk of breast cancer. The authors of the study show that the increase is associated more strongly to a sharp increase when there is a little to some increase of increase. The authors of the study have not been able to find the causal explanation between alcohol consumption and breast cancer. Researchers believe it has to deal with circulatory estrogen levels. 

In the same year it was found that heavy drinking led to an increased rate of pancreatic cancer. 

"Findings from the prospective study presented herein strongly support the hypothesis that alcohol consumption, in particular heavy intake, also is an independent risk factor for pancreatic cancer, the fourth most common cause of cancer mortality [death] in the United States," the authors conclude.

Researchers aren't able to completely connect alcohol consumption to increased cancer rates with a complete evidence. However, I feel that the explanation falls with cell signaling, as most people in cancer research believe today. I think study done with telomere shortening and increased alcohol consumption provides more evidence towards that. I will definetly keep doing  research on this, and keep this in mind the next time I go to a pub!

beer and telomere shortening

Photosynthesis: Exclusive to Plants?

Photosynthesis: Exclusive to plants? Over the past 4 years, there have been findings of processes similar to photosynthesis in non-plant organisms. In November of 2008, it was discovered that Elysia chlorotica (green sea slug) was able to live off of solar power.

This doesn't provide evidence for the existence of photosynthesis in non-plants; however, it is part of a trend I have started to follow dealing with photosynthesis-like processes that are occurring in organisms.

The abstract of the paper basically states that the slug aquires plastids through ingestion of Alegae. The organelles it acquires are taken into the digestive epithelium. They photosynthesize there for months even without a nucleocytoplasm which is where the confusion kicks in. These slugs, are able to steal plastids from Algae and live off its photosynthesizing for week even WITHOUT the algal cytoplasm.

--> Plastid Metabolism is dependent on the nuclear genome for the proteins. So this is where it becomes a puzzle and the paper provides 2 explanations for the ability of photosynthesis to take place in these slugs

1. The plastids are able to survive without the nucleocytoplasm and are retain their autonomy. 
2. The molluscs provide the plastids with the proteins it needs. 

The paper goes on to argue for the second point, that if it is true, then it means genes that are required for hte process of photosynthesis would have been aquired by animals with a horizontal gene transfer. It also means that the already encoded proteins are retargeted to the plastids.

I realized that this process sounded incredibly similar to Phagocytosis, a concept we learned about a few chapters back. It is basically a process where the cell devours particles with its membrane to form a phaosome. Phagocytes and protists use this process. This is a form of endocytosis which is what we studied in particular. The  main function for phagocytosis is for removing pathogens, but it seems as if these snails are using this process to acquire a photosynthesis fueled system. It marvels me how these processes can be used   interchangeably and can be connected just through a process that was used for other primary functions! The process of 'eating' is only available with single-celled organisms, but in multi-cellular animals, the process is only used for eliminating debris and pathogens. It is amazing how this snail is able to use it as fuel for cellular processes.

When they sequenced the whole plastid genome, they found that it lacked the required genes for photosynthesis but:

 In support of the second scenario, we demonstrated that a nuclear gene of oxygenic photosynthesis, psbO, is expressed in the sea slug and has integrated into the germline. The source of psbO in the sea slug is V. litorea because this sequence is identical from the predator and prey genomes. Evidence that the transferred gene has integrated into sea slug nuclear DNA comes from the finding of a highly diverged psbO 3′ flanking sequence in the algal and mollusc nuclear homologues and gene absence from the mitochondrial genome of E. chlorotica. We demonstrate that foreign organelle retention generates metabolic novelty (“green animals”) and is explained by anastomosis of distinct branches of the tree of life driven by predation and horizontal gene transfer.

 This http://www.pnas.org/content/105/46/17867 http://www.newscientist.com/article/dn16124-solarpowered-sea-slug-harnesses-stolen-plant-genes-.

Experience at STEMware

Over the summer of 2011 I worked on a fascinating project over at UC Davis with their STEMware team. A team of professors, teachers, engineers, artists, and students came together to help work towards a project dedicated in finding opportunities for education in different mediums. While I worked there, the main focus was on the world of Biology and Video Games. I knew I loved video games, and I have always been fascinated by biology, particularly because of everything that my brother tells me. I got interested in educational learning my freshman year, when I used software designed in a video game format to help me memorize the functions of particular organelles in the cell. It helped a lot with my studying and felt that something like this with more funding could make big strides in the world of education. Near the end of my sophomore year, my sister sent me a link to the STEMware program after hearing about my fascination with the role of video games in learning.

UC Davis faculty members and professors came and told us about their respective fields and their personal journey towards their respective fields.

When I saw there was an application process for this I was a bit discouraged, but I was surprised to find that my knowledge in video games was actually desired. They valued my input and used my strengths and weaknesses in biology for their own benefit. On the first day we were lectured by professors about their work and what they do in their perspective fields.

In the game, students have to identify a pathogenic microorganism which causes a deadly outbreak leading to a zombie infestation. The students have to discover a cure and implement it. The program deals with the process of diagnosis, treatment strategies, career connections, and lab instruction. These can be applicable to other viruses, bacteria or fungi. You are introduced to the real world and are taught about modern applications in biology. You are able to specialize your character as well and learn about the many different pathways one can take with modern biology. You also learn about the recent diagnostic technologies taht are found in the real world. There is also an ability for a teacher to track student progress within the game. There are a total of 7 levels available for the completion of Zombie Plague.

 The product we worked on designing is titled: STEMware: Zombie Plague You can find a video of the project at: Stemware: Zombie Plague

In STEMware: Zombie Plague, "students investigate a 3D world where they are responsible for identifying the pathogenic microorganism causing a deadly outbreak and implementing a cure. Although we have chosen to have the symptoms of our fictional disease be zombieism, the science content embedded in the software deals with diagnosis, treatment strategies, and career connections that are applicable to any disease caused by viruses, bacteria or fungi. Interactions with characters in-game, introduce students to the variety of career pathways in modern biology along with diagnostic technologies used in the real world. Embedded assessments are included in the game."

Inherit the Wind: A Personal and Technical Analysis:

 I absolutely loved Inherit the Wind and will definitely recommend this movie to my family and friends. The technical elements as well as the structure of the movie worked well towards trying to achieve the movies’ theme of man replacing his sanity with religion and the power of blissful blind ignorance. 

     
    Kramer did a fantastic job adapting this work. Drummond stands for all that I personally stand for, but that's not the only reason why I love this film. This film does everything right from a screenwriter's and a filmmaker's perspective. The structure is set around the lives of Matt Brady and Drummond. We are taken through the perspective of Drummond, but we are able to witness Matt Brady's transformation through the life and perspective of Drummond. In the end, the character we initially felt contempt for, we feel pity for. We are shown that trying to rationalize something to the irrational is not rational :D. Stanley Kramer does something sensational with this movie, and that is showing what happens to man when his whole foundation on how he should live his life is shaken. I loved the scene where Matt Brady goes crazy among all the chaos near the end of the movie. The camera breaks 180 degrees which is a characteristic of a turning point in a scene. It represents his loss of sanity and the complete switch in his character. We get a full rotation on Brady showing how his whole world has turned around and that he's now lost in it. His realization is what led to his fall. 

                
   Kramer does something interesting with the fan shot. In the scene where we are introduced to the courtroom he starts it by shooting above ceilings. Many directors use this as a way of showing a cyclical nature in whatever is going to occur in the room. The same device has been used in Bladerunner and Apocalypse Now. In this case it represents mankind’s cyclical nature towards using religion as a form of persecution and a hinderence to progress. The fan also mimics the irony in how technological progress would be hindered if it were not for the amazing scientists and engineers who the religious zealots are so intent on stopping. I feel as if Kramer's use of the fan is completely appropriate. The people in the courtroom who are expressing contempt for science and technological progress are subsequently being 'cooled off' with the epitome of technological progress. 

"Progress has never been a bargain. You have to pay for it.  Sometimes I think there's a man who sits behind a counter and says, "All right, you can have a  telephone but you lose privacy and the charm of distance.  Madam, you may vote but at a price. You lose the right to retreat behind the powder puff or your petticoat.  Mister, you may conquer the air but the birds will lose their wonder and the clouds will smell of gasoline." 

         This angle also provides another perspective. It provides the perspective of a god looking down at the people through the wall of technology that they have put up. If you look at the fan shot I posted above (I noticed this on my second watch), we see Drummond's wife praying up towards the camera through the fan. This completely supports the notion that the viewer is a god in this case and all we can do is watch the blind ignorance of mankind to derail himself. There is not much we can do to prevent the irrational, other than to watch its own inevitable, cyclical fall. 
      I absolutely loved this movie. It spoke out for all that I stand for and really hits home with me. I will be posting a more personal statement in the future with regards to me and my opinion on Biology and how it has influenced my faith. 

      Kramer also did a great job with the characters. There was a point to having Hornbeck in the movie. Originally, I thought he would act as a spectator that added a few laughs to the movie, but he developed Drummond’s character and gave us insight into the ideology that he followed. I felt like the court seemed a bit unrealistic but It was set in older times so I assume it was much more different.

      
      The dialogues and monologues were also amazing. I loved all of Drummond’s speech and how Kramer was able to make us show empathy for his character. I felt like this movie hit home with me. Kramer’s adaptation of Inherit the Wind is amazingly directed and written for the big screen. This movie is one of my favorite of all time. Thank you Mr. Wong for sharing this movie with us!!!!!

My favorite quotation: 

 Can't you understand? That if you take a law like evolution and you make it a crime to teach it in the public schools, tomorrow you can make it a crime to teach it in the private schools? And tomorrow you may make it a crime to read about it. And soon you may ban books and newspapers. And then you may turn Catholic against Protestant, and Protestant against Protestant, and try to foist your own religion upon the mind of man. If you can do one, you can do the other. Because fanaticism and ignorance is forever busy, and needs feeding. And soon, your Honor, with banners flying and with drums beating we'll be marching backward, BACKWARD, through the glorious ages of that Sixteenth Century when bigots burned the man who dared bring enlightenment and intelligence to the human mind!