Final Lab Report: Isolation of Staphylococcus saprophyticus from an atypical environment
This link will take you to my final lab report on Staphylococcus saprophyticus.
https://cloud.acrobat.com/file/a21f0c76-2efb-4c3f-b343-3d0b55e20c8b
Art Project: Colorful Cycle’s
For my project I wanted to re-create the carbon cycle in a colorful and abstract way. I layered fabric of different colors and shapes to create an outdoor scene with plants, water, sun, microbes and nutrients that are circling in the air, water, and soil. I used colorful fabric’s with different shapes to represent microbial and nutrient diversity amongst plants, soil, and water. I wanted to show that carbon cycling is a natural process that is constantly happening around all of us. 
A2: Lack of oxygen not a showstopper for life
https://phys.org/news/2017-04-lack-oxygen-showstopper-life.html
Lack of oxygen not a showstopper for life April 17, 2017.
Phys.org
Charles Q. Choi
Summary: Scientists sampled organisms from 15 different hot pools to see how many different chemosynthetic communities are thriving in the springs. The team focused on the oxidants present in communities, and worked on nailing down what type of bacteria are in those communities. They found that microaerophiles dominated mainly planktonic communities. This information helps provide a look at what kind of life may have been present in early earth, and if this life may be possibly survive on other planets.
Connections: In class we have talked about how microbes may have lived in an anoxic environment, and how they evolved with earth’s evolving environment. Eric Collin’s lecture gave an insight on how and why microbes should be able to survive on other planets.
Critical analysis: I like this article because I find it fascinating that so much science can be going on in one of the worlds most natural wonders. People visit Yellowstone all year round just to see these hot springs, and it is so interesting to think that these pools of water can offer so much insight on our environments future and past. I find this article to be accurate because we have learned a lot about how and why archaea that can survive in harsh environments, and how that can be an insight into life on other planets.
Question: This team focused on a small amount of microbial communities and were able to come up with plenty of information. Do you think it is even possible to find, analyze, and classify all of the microbes that could be living in just one hot springs?
Extra Credit: Dan Stinchcomb
Dan Stinchcomb’s seminar was about his work with vaccines and vaccine companies. He has done work with many for- and non-profit organizations to research vaccines for popular diseases, including the current company he is working for, IDRI. Stinchcomb focuses his lecture on the details of working with tropical mosquito spread viruses and working on vaccines for these popular diseases effecting thousands of people. He talks about the details of developing vaccines for Dengue fever, West Nile virus, Chikungunya Disease, and Zika virus, and discuses his research working with the diseases and their genomes, and trying to increase immunogenicity to fight the diseases. Stinchcomb talks about the work necessary to take a vaccine from research, to testing, and then to production, and goes into detail about the steps that are necessary to take in each phase of the vaccine production process.
Dan Stinchcomb starts his lecture asking about why tropical mosquito transmitted diseases could be relevant to people in Alaska, and I believe that the information he shared with us very relevant because of our large mosquito population and we should always be aware of the risks. Since our weather is changing here in the arctic being knowledgeable of any new diseases that could make there way up here is going to become more important. All of the diseases he referenced in his talk are well known, and infect so many people every year, the work being done to combat this epidemic needs to be known and supported. In class and lab we have been talking about antibiotic susceptibility and resistance, and how one may be able to attack a disease or virus to make it susceptible to antibiotics. Dan Stinchcomb gave us a real life example of how somebody can research and take steps to fighting a disease.
A2: CRISPR
https://schaechter.asmblog.org/schaechter/2017/03/on-the-discovery-of-crispr-an-interview.html
In one day I had heard a clip on the radio about a thing called CRISPR that is a hot topic in genomics, and then I saw that radiolab had done a segment on CRISPR. So I figured I needed to look more into this subject. The link above takes you to an interview with a microbiologist who played a role in discovering CRISPR and he talks about how he discovered the genetic sequences and talks about CRISPR’s role in microbes. The link below takes you to the radiolab podcast where you can listen to them explain CRISPR in a fun way, and they talk about its applications to human genetics. The rest of this post will refer to the link above: On The Discovery of CRISPR – An Interview.
https://www.radiolab.org/story/update-crispr/
Summary: in 1992 Francisco Mojica was working on trying to sequence the genome of some type of halophilic archaea when he noticed a bunch of repeated, equally spaced sequences in the genome. Since genome sequencing was not very good at that time, they repeated there project many times and every time saw that the same regularly spaced sequences. He noticed this same pattern in the genome of E. coli and continued to work with E. coli for this work. Mojica worked on other topics for 10 years before returning to study these repeated, equally spaced sequences. He talks about his difficulties publishing work, how hard it was for him to prove his hypotheses. He believes that CRISPR played an intricate role in the evolution of prokaryotes, and with the discovery of CRISPR it opens up many area’s to study in the fields of genomics and biotechnology. (Radiolab references making super humans thanks to CRISPR)
Connections: In class we have talked about genome sequencing of microbes, microbial evolution, and characteristics of archaea. In lab we have actually gone through the process of DNA sequencing, and we are very lucky that we have the technology to sequences genomes faster, easier, and read them quicker.
Critical analysis: This subject is fun and interesting, and the fact that are so many places where you can find information on this topic means that this may be a big topic in science in the near future. CRISPR research involves many biological disciplines from microbiology, genetics, to possibly engineering. It will be really interesting to see what kind of work comes from these short, repeated sequences.
Question: Do you think it is a possibility that there could be CRISPR sequences in the genomes of our project isolates?
Painting with Microbes
My artistic intent was to draw a picture using microbes whose colors would grow in contrast to the agar plates. My goal was almost accomplished except for the MAC plate. For the MAC plate my goal was for the agar to stay pink, with the a white flower drawn in the agar; but I ended up selecting microbes that increase the pH of the agar and changing the color from pink to colorless, not allowing us to see the flower very well. My EMB plate had some bubbles in the agar, which is why I drew a fish in an attempt to make it an “aquatic scene.” Neisseria flava ferment lactose which is how the outline of the fish turned out so well. My favorite piece of “art” is the tree on the TSA plate. Although it was easiest to determine how the colors would turn out on the plate, I just love the idea of pink leaves on a tree! Serratia marcescens ended up being very thick on the plate and created the nice bright pink color!
Eric Collins Extra Credit
In Eric Collins seminar he talks about past and current trends of the Arctic Ocean, and possible future trends of its movement, geography, and microbial environment. The water that enters and exits the arctic ocean happens by multiple currents coming through the Bering straight, Greenland and various locations, all carrying fresh & salty water of varying temperatures and nutrients. He talks about the layers of the water that is created by ice, movement of the water at different depths, and location of the water. Each layer also holds slightly different environments and microbial worlds based on from where the water came from and how long it has been circulating in the ocean, and how much ice it may have been exposed to. He talks about the age of ice and how quickly it has been melting. The sudden change in the water and ice causes numerous negative effects in biology when it comes to spring, polar bear environments, and the lifespan of certain microbes that may only be found in the old sea ice. Eric Collins mentions that he is interested in finding out if there are any microbes that may be specific to the sea ice in the arctic, and how high the possibility of them becoming extinct may be due to the ice melting.
The information that Eric Collins shares with us in his seminar is very interesting. He gives some “fun facts” about the ocean, like how it used to be all fresh water and that it eventually sank and became oil; which is a little historical biology lesson about Alaska. The evidence of climate change due to melting sea ice is constantly talked about, and Collins’s evidence, graphs, and animations are great tools to help visually show people the evidence. We have talked about extremophiles in class and how important it is for each kind of organism to live in its proper environment to survive. Question: Eric says that the ice is melting at a quicker rate than people are able to observe and analyze, he says that because of this melting there is a possibility of losing some of microbes; is the ice melting too fast for any type of evolutionary change to happen with these microbes?
A2: The 48 uses of dragon’s blood
The Economist: The 48 uses of dragon’s blood. March 2, 2017
https://www.economist.com/news/science-and-technology/21717808-komodo-dragons-could-be-source-new-generation-antibiotics-48-uses?fsrc=scn/tw/te/rfd/pe
Summary: Two scientists from George Mason University have just recently discovered 48 new types of potential AMPs (antimicrobial peptides) that have never been seen before in Komodo dragon blood. The goal is to be able to do more testing on these newly discovered peptides and hopefully use these peptides as a base for new antibiotics for infections.
Connections: In class we have talked a lot about antimicrobial resistance and how much of a problem it is. The scientists conducting this study used spectrometers, they must have done DNA testing, and also have done some type of physiology testing to discover these peptides.
Analysis: One reason I enjoy The Economist is because it is a source that reports on EVERYTHING, and sometimes articles are very short and get straight to the point so they are easy to read fast. But for this article and articles about science short is not always good. This article needs more information. It leaves you on a cliffhanger! The idea of gaining new medicines possibly from Komodo dragon’s is incredibly interesting, I can not wait for a more scientific article to be published about this study. But thanks to The Economist we now know that this research is being conducted.
Question: The article says that the Komodo dragon’s blood may be useful because the animal is so poisonous. What are other poisonous animals do you think could potentially be studied for this same type of experiment?
Microbial Worlds
Microbial Worlds
- De:composition: Stephanie Rae Dixon and Mary Beth Leigh
“Decomposition” is both aesthetically and auditorily pleasing by combining many medium’s to show how decomposition can come full circle in science and the beautiful, natural world we are meant to live in. The artists successfully embodied their decomposition study done at the Kevo Subarctic Research Station. The videography and photo’s done of the scientist’s in the decomposed dresses to me is how the art tied the connection between science and life. This was especially emphasized by playing the video onto the sculpture, the decomposition site. Our natural world is constantly working to create life and decompose life; whether that be plant material or people. We all have to work together to keep the circle of creation, living, and decomposition flowing smoothly in the environment we live. This collaboration piece is beautiful. Very hard to accurately describe everything it makes you think about. - Mycorrhizae: Gail Priday
While visiting the exhibit I found myself drawn to many pieces done by Gail Priday. I love how she uses many natural colors, and creates a simple, beautiful, realistic setting in her art. In this piece she takes the very complex mycorrhizal system, and simplifies it. I believe that she did successfully embody the symbiotic relationships between fungi and plants she was wanting to portray based on her write up in this piece. In her write up she says, “This system of interdependence is a beautiful example of nature modeling for us the value and necessity of working together.” I find the piece to possibly be a little too simple when compared to the underground web that mycorrhizae creates, but that is also what makes the piece beautiful and relatable. - Veiled Unveiled: Mariah Henderson
This piece is a great example of how difficult seeing and discovering organisms can be without the aid of stains and the many technological improvements that have made discoveries in science a little easier. “Veiled Unveiled” shows that seeing an organism under a microscope can be aided by using a crystal violet stain, just like the one we used in lab. We also learned that a stain can show up differently depending on the organism based off of its cellular structure, which can also help scientists understand the organism. I love the title of this piece, gives a spooky/suspenseful spin on the staining process and using the microscope. - If I were an artist I would want to attempt to portray some aspect of prokaryotic cell structure and function, specifically phototaxis. I would combine painting and fabrics and create a piece with different textures, natural colors, with many shapes to make it fun. There would be bright sun/light, and then underneath the light have different shapes being lifted up or moving towards the light (organisms), and also showing some moving away and hiding from the bright light. As the organisms gets closer to the light they become bigger, and their flagella become more motile.
Assignment 1: Introduction
Hello! My name is Kimberly Fitzgerald, but you can call me Kim. I am a super senior Biology major here at UAF with a concentration in Physiology. I enjoy learning about how everything works together, and how we can be our best/healthiest selves. I have lived in Fairbanks my whole life and I love it! This is a picture of me from a few years ago backpacking in Glacier National Park. This is a common look on my face, but I am actually always in a pretty good mood (:
