Wolbachia Lab

This week our AP Biology class finished out the year strong with our last lab, theWolbachia lab. Wolbachia is a type of bacteria that is being found more and more often within the reproductive tracts of arthropods (insects). It is currently estimated that about 20% of all insect species are infected with Wolbachia. Scientists are very interested in collecting data about Wolbachia because it has some extremely stange effects on insects. Since Wolbachia is most often transmitted through insect populations vertically (only through a female’s eggs), and since Wolbachia cannot live outside of a host, it is advantageous for Wolbachia to infect mostly females. This ensures that Wolbachia is transferred through the generations with great efficiency, and prevents the “dead end” transmission that would occur by infecting a male insect. In keeping with the “infect-only-females” goal, Wolbachia has evolved a number of adaptions that increase the number of females in a population. Here are a few…

• Wolbachia can cause “cytoplasmic incompatibility,” meaning that infected females can only reproduce with infected males.
• Wolbachia can cause females to reproduce “parthenogenetically,” meaning that eggs develop without fertilization, producing only diploid females.
• Wolbachia can suppress masculinizing hormones, causing male embryos to develop as female.
• Wolbachia causes abortion of male embryos, which means that females have less competition and a better survival rate.

Wolbachia’s feminizing affects on insects can be considered negative for the well-being of insect species. Wolbachia can decrease insect population size over time because a high female to male ratio within the population means that few females will find mating partners. Wolbachia can also reduce the diversity in a population when the parthenogenesis method is used, since all females reduced will be genetically identical to their mothers. This makes the population much more vulnerable to disease or pathogens. Since Wolbachia gains a lot from insects, while insects are affected negatively, Wolbachia and insects are considered to be in a type of symbiotic relationship called parasitism. Wolbachia may also be a pretty negative bacteria for humans; besides harming important insect populations, there is evidence that it increases West Nile susceptibility in insects. Interestingly, Wolbachia can also live inside filarial nematodes, but it has a mutualistic relationship with the nematodes, where both organisms benefit.

Our purpose in this lab was to determine whether a given insect was infected with theWolbachia bacteria by analyzing the insect’s DNA. We began by combining the insect’s abdomen (where Wolbachia resides) with different substances that would break down cell membranes, un-fold DNA, etc. Watch my DNA Extraction video to get an idea of this initial extraction process. After a lot of substance-adding, tube-transferring, and centrifuge-ing, we had our pellet of DNA! We then used PCR to amplify a sequence of this DNA, which would make it easier to see and analyze later on.

PCR involved adding a restriction enzyme to cut the segment of DNA that we wanted to look at. This segment of DNA is larger (in number of base pairs) in insects than inWolbachia. Therefore, when added to a gel electrophoresis chamber, Wolbachia DNA will travel further down the gel than insect DNA. If both Wolbachia and insect DNA are present, two distinct bands will be visible. If only insect DNA is present, one band will be visible, and it will be closer to the wells of the gel chamber than the Wolbachia DNA. Here is the data we obtained…

I ran the experiment using our Wolbachia-positive control insect, so I was very relieved to see that the data came out as I expected! My well of the gel showed two distinct bands, one with Wolbachia DNA, and one with insect DNA. Nicole, Bharathi, and Marissa also got results from the lab, and their insects tested negatively for Wolbachia, as there was no band of Wolbachia DNA on the gel. Davis’ well seems to show the presence of WolbachiaDNA, but there is no band for insect DNA. This result is inconclusive, as something must have gone wrong in the process for no insect DNA to be present. A variety of errors could have contributed to the lack of DNA in other wells, from not mixing the DNA and additives well enough, to the DNA and gel chamber simply not cooperating!

As you can see, this lab combined a lot of the techniques we have been learning about and practicing throughout the year, including micropipetting, gel electrophoresis, and PCR. I actually had a lot of fun going through the procedure with all of these techniques because I felt very confident in each step and it was cool to be so familiar with such high-tech tools. I think it was a great lab to end the year with, since it reminded us all of how much we have done this year and what we have accomplished as a class. For me personally, I loved ending the year with this lab because my insect’s gel came out as well as I could have hoped! Labs can be frustrating because there is so much opportunity for error, but this lab reminded me of how satisfying it is to run one successfully.

Thanks for reading!

–Allie

Wolbachia Lab

This week our AP Biology class finished out the year strong with our last lab, the Wolbachia lab. Wolbachia is a type of bacteria that is being found more and more often within the reproductive tracts of arthropods (insects). It is currently estimated that about 20% of all insect species are infected with Wolbachia. Scientists are very interested in collecting data about Wolbachia because it has some extremely stange effects on insects. Since Wolbachia is most often transmitted through insect populations vertically (only through a female’s eggs), and since Wolbachia cannot live outside of a host, it is advantageous for Wolbachia to infect mostly females. This ensures that Wolbachia is transferred through the generations with great efficiency, and prevents the “dead end” transmission that would occur by infecting a male insect. In keeping with the “infect-only-females” goal, Wolbachia has evolved a number of adaptions that increase the number of females in a population. Here are a few…

• Wolbachia can cause “cytoplasmic incompatibility,” meaning that infected females can only reproduce with infected males.
• Wolbachia can cause females to reproduce “parthenogenetically,” meaning that eggs develop without fertilization, producing only diploid females.
• Wolbachia can suppress masculinizing hormones, causing male embryos to develop as female.
• Wolbachia causes abortion of male embryos, which means that females have less competition and a better survival rate.

Wolbachia’s feminizing affects on insects can be considered negative for the well-being of insect species. Wolbachia can decrease insect population size over time because a high female to male ratio within the population means that few females will find mating partners. Wolbachia can also reduce the diversity in a population when the parthenogenesis method is used, since all females reduced will be genetically identical to their mothers. This makes the population much more vulnerable to disease or pathogens. Since Wolbachia gains a lot from insects, while insects are affected negatively, Wolbachia and insects are considered to be in a type of symbiotic relationship called parasitism. Wolbachia may also be a pretty negative bacteria for humans; besides harming important insect populations, there is evidence that it increases West Nile susceptibility in insects. Interestingly, Wolbachia can also live inside filarial nematodes, but it has a mutualistic relationship with the nematodes, where both organisms benefit.

Wolbachia within an insect cell (Wolbachia bacteria can be seen as some of the large circles within the cell)

Our purpose in this lab was to determine whether a given insect was infected with the Wolbachia bacteria by analyzing the insect’s DNA. We began by combining the insect’s abdomen (where Wolbachia resides) with different substances that would break down cell membranes, un-fold DNA, etc. Watch my DNA Extraction video to get an idea of this initial extraction process. After a lot of substance-adding, tube-transferring, and centrifuge-ing, we had our pellet of DNA! We then used PCR to amplify a sequence of this DNA, which would make it easier to see and analyze later on.

PCR involved adding a restriction enzyme to cut the segment of DNA that we wanted to look at. This segment of DNA is larger (in number of base pairs) in insects than in Wolbachia. Therefore, when added to a gel electrophoresis chamber, Wolbachia DNA will travel further down the gel than insect DNA. If both Wolbachia and insect DNA are present, two distinct bands will be visible. If only insect DNA is present, one band will be visible, and it will be closer to the wells of the gel chamber than the Wolbachia DNA. Here is the data we obtained…

I ran the experiment using our Wolbachia-positive control insect, so I was very relieved to see that the data came out as I expected! My well of the gel showed two distinct bands, one with Wolbachia DNA, and one with insect DNA. Nicole, Bharathi, and Marissa also got results from the lab, and their insects tested negatively for Wolbachia, as there was no band of Wolbachia DNA on the gel. Davis’ well seems to show the presence of Wolbachia DNA, but there is no band for insect DNA. This result is inconclusive, as something must have gone wrong in the process for no insect DNA to be present. A variety of errors could have contributed to the lack of DNA in other wells, from not mixing the DNA and additives well enough, to the DNA and gel chamber simply not cooperating!

As you can see, this lab combined a lot of the techniques we have been learning about and practicing throughout the year, including micropipetting, gel electrophoresis, and PCR. I actually had a lot of fun going through the procedure with all of these techniques because I felt very confident in each step and it was cool to be so familiar with such high-tech tools. I think it was a great lab to end the year with, since it reminded us all of how much we have done this year and what we have accomplished as a class. For me personally, I loved ending the year with this lab because my insect’s gel came out as well as I could have hoped! Labs can be frustrating because there is so much opportunity for error, but this lab reminded me of how satisfying it is to run one successfully.

Thanks for reading!

–Allie

CSI: What Happened to Wilbur?

Recently, after completing our fetal pig dissections, our biology class completed a project called CSI NDB. We all divided into groups and were assigned a body system (immune, endocrine, or nervous) and had to come up with a murder mystery type scenario where our fetal pig died as a result of a problem with that body system. Each group presented their evidence to the class and everyone got to work together and figure out what happened to the pigs!

My group had the endocrine system, so one of the first things that came to mind was diabetes. A problem with severe high or low blood sugar would surely cause our pig, Wilbur, some health problems. Then we discovered that cortisol, another hormone, could counteract insulin to cause insulin resistance. Cortisol is a fairly common hormone that can be prescribed for things like severe allergies and skin irritation. Throw in a mistress for Wilbur, an angry wife with allergies and a cortisol prescription, syringes with cortisol on them, and a sickle cell diagnosis just to throw everyone off, and we had our crime scene set. In the end, cortisol continually added to Wilbur’s insulin by his wife caused him to have extremely high blood pressure, which led to a stroke.

Doing CSI NDB was such a unique experience. I have never done a project like that before, and each group had so much free reign and opportunity to be creative. It was a lot of work, but every single project turned out so well. It was really interesting to see how each project differed too; everyone had unique ideas and used unique tools to present and teach the material, from a urinalysis test to a quiz game about how burns affect the skin. We definitely learned about the body systems in a very creative way!

Field Trip Time: Tide Pool Edition

This past week, our AP Bio class joined with the LiMPETS (Long-term Monitoring Program and Experiential Training for Students) program to explore marine life. Our field trip took us to the Fitzgerald Marine Reserve in the wee hours in the morning (a.k.a 8 o’clock), where we examined and collected data on organisms living in the tide pools. I had a really good time on the field trip, and I think it was a great experience for our class as a whole.

From Save the Bay, I realized how much being out in the field can really teach you; it’s more interactive and more interesting than a textbook or website. This field trip was no exception: I learned a lot! First, I learned that, just like the marshes in Save the Bay or the layers in the rainforest, there are different zones to tidal areas, and organisms can be very picky about their zone. The mussels grew very closely together, but there was a pretty definite line where they stopped growing. The High Tide Zone was just the place to be, apparently. Second, even sea creatures have springtime, when everything is just starting to grow and develop. This seems like a pretty obvious fact, but I had never really considered that hard, shelled animals like whelks or limpets would start out so small. I was surprised that the baby limpets’ shells were already structured and sturdy. Third, I learned that there is life all over tidal areas of the ocean. As part of our data collection, our class had to record areas of bare rock in a quadrat. We were surprised to find that none of the areas we looked at were free of life. Even the “bare” rock that our class slipped and slid over while exploring the area was made slippery by wet tar spot algae, which covers a lot of space.

Mussels clustered together

Since we just recently finished up our unit on invertebrates, our class also got to see what we have been learning in action. For example, we learned that cnidarians have the adaptation of sensory cells and stinging organelles called nematocysts. This allows stationary organisms like the sea anemone to feel, paralyze and capture prey as it swims by. At the tide pools, I was able to touch some of the tentacles of a giant green anemone. I could feel a sucking sensation on my finger, so I assume that it was trying to sting me or close its stomach over me. I was suddenly very grateful that I am not a fish. I made another connection because in class, our LiMPETS leader told us that sea stars are disappearing along northern California’s coastline due to sea star wasting disease, which may be linked to high water temperatures. Even though Abby warned us of this, I still didn’t expect to see just one sea star in the few hours that we spent at the tide pools. I remember going to the tide pools a few times when I was little, and I’m pretty sure we always saw a good number of sea stars.

Sea anemone having a snack.

Lonely sea star.

I would highly recommend this field trip to others, as it was my favorite field trip we did this year. I usually find marine organisms really interesting, so to see them up close and get to touch them and feel their environment was really cool. The one thing I wish is that we had a little more time to explore the tide pools before diving into data collection, since we all had so much fun rushing around and exploring. I will never forget our class working together to stay balanced on the slippery tidal rocks! I think it was a great bonding time for us. I especially liked the service-learning aspect of this field trip, as I think it is very important and makes the trip more rewarding for all involved. Overall, I thought the field trips were worthwhile because they were a fun chance to get outside and see what we have been learning about. We are very lucky to have things like the tide pools and bay marshes around us, so I think it’s important that we take advantage of the Save the Bay and LiMPETS programs.

Thanks for reading!

–Allie

The Botany of Desire

Recently, our AP Bio class began our unit on Kingdom Plantae. We had learned about molecular processes in plants earlier in the year, but now was our chance to find out about their evolution, classification, diversity, and place in the world. As part of our botany unit, we watched The Botany of Desire, a documentary that highlights our relationship with plants and investigates whether we control plants or they control us. We tend to think that, since we are the ones who grow, domesticate, move, or genetically engineer plants, we control them and can decide their fate. However, the movie brought up the point that plants take advantage of us in certain ways and get us to ensure their survival. For example, four of the most common plants today each offer us something to make them desirable: tulips offer beauty, apples offer sweetness, cannabis offers intoxication, and potatoes offer stability and control.

We grow millions of apples per year, all because they can satisfy our sweet tooth.

I read the Botany of Desire book’s section on apples in Honors Bio, but watching the movie really helped me consider our relationship with plants in another way. As humans, we tend to think that most of what goes on around us is to our credit or is our fault, but Botany of Desire reminded me just how powerful and flexible nature can be. I loved watching the section on tulips, which discussed how a “tulip-mania” in the 17^th Century Netherlands led to the growth of ridiculously large amounts of tulips and the selection of beautiful two-color tulips (which grow with two colors as a result of a virus). It’s odd to think that beauty can be a feature for natural selection just as powerful as something like fur color or spine length, and its odd to think that humans can be just as effective agents of natural selection as predators in the wild. All year, we have been discussing how different organisms fit in with each other, and I learned that humans are just as much a part of the web of life as anything else. Also, tulip farming is a very viable career option.

A tulip farm in Amsterdam, the result of the “tulip mania” from so long ago.

If you are interested in Botany of Desire, check it out here. Do you think it’s possible that plants play a part in controlling us? Let me know in the comments!

Thanks for reading,

Allie

Creation Theories: Aliens or Abiotic Molecules?

Recently, in biology, we have been learning about evolution, speciation, and how life on Earth (as well as Earth itself) got its start. We all researched different theories of creation, whether scientific, religious, mythical, etc. Here is just a taste of what we found:

P’an Ku (Chinese myth): P’an Ku was the first being, and he grew for 18,000 years in a cosmic egg. Once he hatched, the top of his shell became the sky and the bottom became the Earth. He soon fell apart, and his limbs became mountains, his blood became rivers, his hair became grass, etc. Any parasites living on him became people.

Scientology (the religious theory I researched): 75 million years ago, an intergalactic ruler named Xenu shipped some of his people to Earth and had them killed. Meanwhile, Earthly organisms were evolving into humans, and we still have latent memories about our evolution (Jaw pain? Ah, you are remembering being a clam.) Once we evolved, the souls of the dead alien people attached themselves onto us.

Endosymbiotic (scientific theory): Very simple organelles lived freely on Earth, and these organelles were engulfed by bacteria. This led to the formation of eukaryotic cells, which continued to grow in complexity.

Reading about all of these different stories made me realize how little we know about how we got here! The fact that people today find cause to believe some of these theories just goes to show how lost we really are regarding the beginnings of our world. Even the scientific theories about the beginning of time are widely varied, and a few seem to stretch what seems possible. At the same time, hearing all of these theories gave me more appreciation for all of the concrete evidence that we do have regarding evolution. Fossil records can tell us that life is likely not four quadrillion years old (as in the Scientologist theory), while things like embryology can tell us that we likely weren’t created separate from other organisms (as in the Iroquois theory). Looking at the facts helps prevent us from grasping at straws.

However, most of the stories we read still could not account for how God or matter came to exist in the first place. Do you think we will ever know the truth about how we came to be?

Thanks for reading!

–Allie

Sources

Beyer, Catherine. “Scientology’s Galactic Overlord Xenu.” About Religion. About.com, n.d. Web. 23 Feb. 2015.

“The Chinese Creation.” The Unicorn Garden. N.p., n.d. Web. 23 Feb. 2015.

“Top 10 Theories on Beginning of Life on Earth.” Smashing Lists. Top Ten Lists, n.d. Web. 23 Feb. 2015.

Designer Babies or Disease Prevention?

Early in February, the United Kingdom became the first country to pass legislation allowing the creation of embryos from three people. Now, you may be thinking “mutants!” or “monsters!” or “designer babies!” but the reasons for creating such an embryo are actually rooted in medicine and disease prevention. In addition to nuclear DNA (which contains traits for things we are all familiar with, like eye color and height), we also have mitochondrial DNA. Mitochondrial DNA makes up only 0.1% of our genome, and controls metabolism, which has effects on things like nerve cells and muscle coordination. Some women have defective or unhealthy mitochondrial DNA which, when passed on to their children, can lead to mitochondrial diseases. These diseases usually result in death before the age of 20.

The point of three parent babies is to substitute the mother’s unhealthy mitochondrial DNA with a donor’s healthy mitochondrial DNA. Doing this preserves the mother and father’s nuclear DNA, so things like appearance and intelligence aren’t affected. One method of creating a three-person embryo, egg repair, is shown below.

Regardless of the reasons behind it, creation of three-parent babies is still- predictably- controversial. Both the Church of England and the Catholic Church object to it simply because one method of three-parent baby creation (embryo repair) requires the destruction of an embryo made from DNA donors. However, even more people object to this new technology because they fear that from here, it’s a slippery slope into manipulating more characteristics of our children (such as intelligence, beauty, etc.).

Personally, I don’t find it unethical to manipulate the mitochondrial DNA of embryos. If doctors know that a person has damaged mitochondria, and they know that their child will likely die as a result, I find it more unethical to not act. Why wait and attempt to treat an issue with something like gene therapy, when we could act and prevent an issue now? I do understand the concern about “designer babies,” but this technology is very far off from that. This is not making your child prettier or more athletic; it is simply allowing them to live.

What do you think about three-parent babies? Is it ever ethical to manipulate DNA? For more information, check out my sources section below. Thanks for reading!

–Allie

Sources

California Academy of Sciences. “Should We Modify DNA in Human Embryos?” KQED Education. KQED Public Media for Northern CA, 17 Feb. 2015. Web. 19 Feb. 2015.

“Churches Oppose Three-person Babies.” BBC News UK. BBC News, 30 Jan. 2015. Web. 20 Feb. 2015.

“MPs Say Yes to Three-person Babies.” BBC News Health. BBC News, 3 Feb. 2015. Web. 20 Feb. 2015.

Medical Masks and the Common Cold

It’s that time of year again! No, not the Superbowl. It’s cold/flu season, and if you are like the average American, you will catch a cold about 2-3 times this year. The common cold is actually a name we give to about 200 different cold viruses, most of which can be spread through aerosols (tiny droplets of virus in the air) or self-inoculation (touching the virus on a surface and bringing it to your eyes/nose/mouth). More and more, people are wearing medical masks to help prevent the spread of aerosols. Maybe they themselves are sick and trying to prevent spreading the virus, or maybe they just need/want to take extra precaution in avoiding the a cold

Personally, I have been seeing an increasing number of people in medical masks, and although I still tend to do a double take whenever I see this, I definitely see the benefits of it. In Japan, for instance, people commonly wear medical masks when a family member is sick, to prevent catching or transmitting the virus. That family member, in turn, is legally required to stay home until 48 hours after their fever disappears. This ensures little spread of the virus and prevents the need for a sick person to wear a hot and uncomfortable mask when they are likely feeling miserable already. Although I’m not sure that similar legislation would go over well in the U.S., I do think we need to focus more on encouraging sick people to rest/stay home, while removing the stigma around medical masks can just be an added bonus.

What do you think about medical masks? Answer in the poll below!

Thanks for reading,

Allie

Works Cited:

“Should Cold Sufferers Wear Medical Masks?” KQED Education. KQED Public Media for Northern CA, 20 Jan. 2015. Web. 26 Jan. 2015.

Never Give Up!

For part of our biology homework this week, we watched a TED talk given by Diana Nyad, the first person to swim from Cuba to Florida. I had never heard of her story before, so it was really interesting just to find out about how such an ambitious mission was carried out. I would have liked to see some footage from her trip or her landing on the shore of Florida – the speech was cool, but some kind of documentary would have been even more impactful. To me, the most inspiring part of the video was just how Diana kept at her goal. It would have been easy for her to give up when she was young and had failed a couple of times already; I liked that she addressed this part of her story and encouraged people to go for their goals no matter their age.

One goal that I want to achieve is to learn (or re-learn) to windsurf. I used to windsurf over the summer when I was in elementary/middle school, as my dad windsurfs regularly, but once I got to high school I slowly stopped. I had a lot of fun getting out on the water as a kid, and I’ve wanted to start up again for a few years, but I always seem to feel like I am “too busy.” I’ve also doubted my ability to achieve this dream because the one time that I did windsurf in high school, things didn’t go too well; I struggled to even stand up! However, I want to stay motivated to keep trying and set a goal for myself to get out on the bay a few times this summer. As Diana said, it’s never too late!

Thanks for reading!

Allie

Ebola Lecture Experience

On November 1st, some friends and I attended a lecture on Ebola given by epidemiologist Dr. Donald Francis. The lecture was part of UC Berkeley’s Nano-High series, which brings in speakers to teach high school students about new and interesting subjects in science. Click on the link below to check out the Prezi I made about my experience!

http://prezi.com/r_ns8sw8ghzq/?utm_campaign=share&utm_medium=copy&rc=ex0share