Dr. Thimme Reflection

During our Skype conversation with Dr. Thimme, he gave us a clearer understanding of Hepatitis C and its treatment. Hepatitis C is a cytolytic virus transmitted through contact with blood. Therefore, it can be common amongst heroin addicts and people given a tainted blood transfusion before the introduction of blood screenings. Four million people in the US have Hepatitis C, yet many do not realize it. It was discovered in 1989 by Michael Halten. This discovery led to the use of blood screening in order to identify potentially harmful discrepancies. In some third world countries, blood screenings are inaccessible due to their relatively high cost. In Egypt, specifically, ten percent of the population is infected with virus. In some regions of Egypt, entire villages are infected due to previous use of a single syringe to vaccinate the whole village. 

The symptoms of Hepatitis C are inflammation of the liver and the formation of scar tissue on the liver (liver cytosis). Unfortunately, liver cytosis can lead to liver cancer. In the world, the average age of diagnosis is 20 years old. However, in Germany, the average age of diagnosis is 40-50 years old with the discovery of liver cytosis. Eighty percent of all Hepatitis C patients do not have complications. The other twenty percent develop liver cytosis. Research has shown that young, pregnant women with Hepatitis C are at a lower risk for developing liver cytosis. 

The virus has been treated using HCV therapy. Primarily, interferon has been prescribed as a remedy. The downside to interferon therapy is that it has flu-like symptoms among other equally undesirable side effects. There are some problems with the current treatment. First, only thirty percent of patients are able to clear the virus. Second, failure of the killer cells is widespread. Three current goals for scientists are: to identify and prevent the cause of killer cell dysfunction, to develop IPN free therapy and to keep symptoms from returning.

Ludovic Orlando and Revising the Recent Evolutionary History of Equids using Ancient DNA

Ludovic Orlando

For my letter to a biologist, I have chosen to write to Ludovic Antoine Alexandre Orlando. He is a research lecturer at the Natural History Museum of Denmark's Centre for GeoGenetics, located in Copenhagen. He also supervises a team that is developing bioinformatic tools to study biogeographical ancestry. The research paper that I chose is titled "Revising the Recent Evolutionary History of Equids using Ancient DNA". It has about twenty authors, so I chose the first listed since that is usually the team leader.

The research paper describes the process of using phylogenetic analysis to gain insight to the reasoning behind unexpected evolutionary patterns that have been discovered in ancient equids. The team studied 35 ancient specimens from South America, Southwest Asia, South Africa and Europe. Their discoveries revealed the need for major revisions to many taxonomic levels surrounding the evolution of Equus. Not only that, but the researchers also discovered two new species of equids and revised the extinction times for others.

I have a couple of questions for Mr. Orlando. For one, it would be interesting to learn more about the process of discovering a new species. Also, I'd like to ask what countries and fields the other researchers worked and lived in. I'm curious to know what it is like to work with people from all over the world and would also like to know what language that they communicated in. They used mitochondrial sequences to come to a lot of these conclusions and I'd be interested in knowing a little bit more about how that is conducted. Finally, I will ask him a little bit more about himself. I'd like to know how he became interested in this field of study and what colleges/universities he attended.

Stay tuned for more on Ludovic and his adventures!

A Day in the Life of Tom the Carbon Atom

Honors Biology Times

Friday, December 07, 2012

By Stu D’ent

In the dawn of time, there was nothing. Then there was a single carbon atom, alone in the Universe. His name was Tom.

Tom was part of a carbon dioxide molecule floating alone in the atmosphere. But, billions of years later, you’ll find that Tom’s life has become much more exciting. Now he is an integral part of the carbon cycle and the palm of my hand.

We here at Honors Biology Times had the opportunity to meet Tom over coffee.

Honors Biology Times (HBT): Hello, Tom. Do you have a last name?

Tom…something (T): Hi there. And the name is Tom. Just Tom.

HBT: I apologize. Well, can you describe to me just how the Carbon Cycle works?

Tom, just Tom (TJT): I am quite sorry, but I don’t actually know how it works.

HBT: What do you do every day?

TJT: Oh, you know the usual. I wake up in the morn-

HBT: Tell me about what happens once you get to work.

TJT: Oh, okay! It’s actually kind of hard to explain. Would you mind if I just show you an educational documentary on it instead? It was narrated by Morgan Freeman.

HBT: That’s not actually how an interview works. It’s more of a Q&A sort of thing…Maybe another time?

HBT: Why don’t you tell me about the first step of the Carbon Cycle?

TJT: The Carbon Cycle is actually a really difficult and complicated process. That’s why they pay me the big bucks.

HBT: I didn’t realize it was a paid gig. But let’s get back to the topic.

             

TJT: I can tell you about my simplest transfer, how about that?

HBT: Yes, please. That’s why we’re here. Just…you’re wasting my valuable time. Please enlighten me with a description of your simplest transfer.

TJT: It all starts with the sun.

HBT: Doesn’t it always?

TJT: Why, yes, I suppose that is true. There was this one time when-

HBT: The transfer, Tom.

TJT: Right. So the sun shines on a plant and fuels photosynthesis. Then the plant uses the sun’s energy to convert CO₂ into organic material. That’s where I come in.

HBT: Great start. Now, who do you bond with to become carbon dioxide?

TJT: I like to form a carbon dioxide molecule with two of my oxygen buddies. They’re twins, Larry and Gary.

HBT: They sound like fun guys. Tell me about the conversion into an organic material. What’s that like?

TJT: The entire purpose of photosynthesis is to produce glucose, which I happen to be a part of as well. Basically, after Larry, Gary and I get together, we enter the Calvin Cycle. In the Calvin Cycle, we meet up with two other groups of folks we hang out with a lot: ATP and NADPH! They’re so great. Anyways, we all get together and from glucose (C₆H₁₂O₆). It’s pretty much a huge family reunion with the Carbon, Hydrogen and Oxygen clans all together. Got everything so far? You haven’t written anything.

HBT: Yes. It’s an interview, I’m recording it.

TJT: Recording it without paper? What are you, a magician?

HBT: Just keep telling the story.

TJT: The glucose enters glycolysis. Glycolysis is a part of cellular respiration, so we’re in a completely different process now. I hate glycolysis. Do you want to know why?

HBT: I have a feeling that you’ll tell me either way.

TJT: How do you know me so well? We just met?

HBT: They say I can read people.

TJT: I hate glycolysis because that’s when we get eaten. Have you ever seen the episode of The Magic School Bus when Arnold eats the school bus? It’s like that, but gooier.

HBT: Lovely.

TJT: Finally, I move throughout the biotic world as I move up the food chain. Remember how I started out in a plant? Imagine that plant was a blade of grass eaten by a cute, fluffy bunny. Next, I enter the bunny’s body. Bunnies aren’t as soft on the inside as they are on the outside, by the way. Eventually, I’ll reenter the atmosphere either through respiration or decomposition if the bunny dies without being eaten. And that’s a day in my life.

HBT: Wow, it sounds like you’re a pretty busy guy.

TJT: I can handle it.

HBT: I’m so glad you told me about all of this. I learned in Biology class a long time ago, so I’m glad you refreshed my memory.

TJT: I’m glad to have been invited here. I don’t often get invited places, people don’t really like me. And then there’s all of those environmentalists who think I’m killing the ozone and-

HBT: The interview’s over now, Tom.

TJT: Oh, okay.

HBT: Thank you.

TJT: No problem!

As you can see, the conversations I have with myself are quite interesting.

Into the Woods-November Plot Reflection

Yesterday was our November plot visit. Seeing as winter is nearly upon us, the weather was less than pleasant. It was gray and overcast with a steady, albeit light, rain. By the end of our visit, around noon, it was only 41 degrees (Fahrenheit).

Like the October visit, we could hear cars going by. Notably many more cars than the last visit. Also, since we are well into fall, nearly all of the trees are bare. Only a couple of stragglers and the evergreens still had their leaves. Another difference between November and October was the presence of animal sounds. Back in October, you could hear lots of birds chirping and leaves rustling. But yesterday, we heard nothing but the road. The plot was completely devoid of animal activity except for one spider and a squirrel Alexandre claims to have spotted. No one else saw or heard any evidence of a squirrel, so we can't be certain of even that.

Now, since the majority of the leaves are gone, visibility in the woods has grown to be much better. Our group can observe the surrounding land much better now. For instance, I noticed that there is a house about 40ft away from the plot. Also, there are more fallen logs and branches than there were before. They were all covered in various species of moss and lichen.

In addition to that, there were also two different species of shelf mushrooms present. However, they were the only type of mushroom present. Unlike in October there were no stereotypical "cap and stalk"mushrooms to be found beneath the ground cover in our plot. I wonder why that is. Like last time, we visited after a day of rain. It still rained while we were at the plot. Perhaps it is the change in temperature that determines the types of mushrooms we see?

Overall, I think that our group works really well together and we get along. This is shaping up to be a great project.

 

Cells R Us

In class on Tuesday, we constructed a life size model of a cell. Everyone in class created an organelle to make up part of the cell. I created the Golgi apparatus. The Golgi apparatus is where proteins are processed, sorted and delivered. It contains enzymes that make changes to the proteins. Some proteins are stored within the apparatus while others are sent to other organelles or outside of the cell entirely. The approximate real size of the Golgi apparatus is 10 um (micrometer). The magnified size of my model was 40 cm. I'm not sure what type of cell it was, considering that there were some organelles present that  were only found in animals, some only found in plants and some found in both. If I had to make a final guess, however, I'd guess that we built a plant cell, considering that one of the organelle's made was chloroplast. Since chloroplast only helps with photosynthesis, I'll guess that it was a plant cell. The largest organelles were the nucleus and Golgi apparatus, the smallest were the ribosomes and mitochondria. If I looked at a cell under a microscope, I'm certain that I'd be able to see the nucleus and possibly the Golgi apparatus. In order to see the really miniscule organelles, I'd have to use an electron microscope. I was surprised by exactly how small the ribosomes were, and the fact that the average amount of ribosomes in a cell is 15,000. I guess that, considering how small a cell is, I didn't think there would be something so tiny inside of it.

How pH affects Enzyme Activity Lab

We recently finished a lab observing Changes in Enzyme Activity. My group tested the effects of pH levels on enzyme activity. To do so, we cut three 1g slices of potatoes and put them in a test tube filled with 15mm of hydrogen peroxide. Then we poured in acid into one test tube, a base into another and water into yet another test tube. We then watched and measured the enzyme activity which could be observed by bubbles being produced on the potato. 

In the Changes in Enzyme Activity Lab, my lab group tested to see if pH affected enzyme activity. pH is the level of acidity in an object or its environment. We hypothesized that the pH would affect enzyme activity. I believed that a higher pH would increase enzyme activity. However, in our experiment, the test tube containing hydrochloric acid produced no bubbles at all. 

Some errors that our experiment had were that the amounts of water weren’t exactly the same and that the hydrogen peroxide levels weren’t the same on each potato. We sort of did a visual estimate when pouring the acid, base and water into each test tube. In the future, we could measure out each liquid before pouring it in. We could also use pieces of the same potato and make sure they all had the same amount of skin. Besides those somewhat conscious errors, I think everything else was under control.

Our investigation on enzymes could be applied to real life in a situation like acid reflux. Perhaps eating foods with a lower acidity could keep the condition in check. WE can manipulate enzymes in the environmental industry to benefit an ecosystem by creating/finding enzymes that would cancel out pollutant. Or find an enzyme that would make plants grow faster or produce more food when photosynthesizing.

Plot Reflection

In my honors biology class, we have begun a new project. We have been split into groups and have each chosen a plot in the forest to observe over the course of the next year. The groups consist of four or five members and each has a specific job to do. There are four possible roles: leader, photographer, naturalist and arborist. The leader is in charge of the group’s wiki-space page and delegating tasks to the group. The photographer takes a visual documentation of the environmental growth and changes in the plot over the course of the school year. They will photograph and take videos of both the creatures that live in the plot and the group hard at work. Eventually, the video clips and photographs will all be compiled into one film in the spring. It’s the naturalist’s job to record, collect and identify various organisms found in the surrounding area of the plot site. The arborist identifies the trees within the plot and measures the growth of the young trees. I am the leader of group number 4. Our group’s name is set, which means ‘3’ in Korean. The other group members are: Madeleine, the photographer; JB, the naturalist and Alexandre, the arborist.

We have plenty of trees for Alexandre to study. All the orange flags mark the baby trees.

Our plot site is the closest to the road out of all of the groups in our class. However, the road cannot be seen from our plot. What you can see is the gate separating the forest from the road. You can also clearly hear cars and trucks passing by. In our plot, there is a large, rotting, fallen tree. It is covered in moss and shelf mushrooms. A colony of ants lives within the log and eats the mushrooms. The ground is thick with dead leaves and acorns from the surrounding oak trees. The creatures hiding beneath the leaves mostly consist of large spiders and the occasional ant. Within in the center of the plot is a gathering of over 40 baby trees. All of the trees, both young and old, have leaves that have either fallen off or are living their last days. The day we visited the forest and staked out our plot was just after a plentiful rainfall. As we all know, that’s prime condition for mushrooms. We found some fascinating fungi, including a purple mushroom.  

One thing I really appreciate about this project is its longevity. I think that being able to actually watch the plot’s changes from autumn until spring will be incredible to observe. I love that we’ll be making a video at the end of the project that will serve as somewhat of a digital time capsule. Looking forward, I see my group’s biggest obstacles being organization, time and focus. However, if we continue on the path that we started on a couple days ago, this is going to be a great year.