Lab Report: An Exploration of Bacteria Found on a Personal Keyboard
Hi guys, here is my project about what bacteria I found on a laptop keyboard!
Grand Prismatic
“Microbes of Grand Prismatic”
Courtney Hill
In this drawing I set out to capture the Grand Prismatic Spring located in Yellowstone National Park. Notable for its vibrant colors and layered features the spring is a popular attraction. The attractive color scheme is actually a result of the various microbes that constitute the different environments in each layer. Temperatures in the spring rage from 145 to 188 °F so it is evident that only the most thermophilic microbes will be sustainable. Further microbial selection is a result of the temperature differences in each layer. Essentially, each band of the spring represents a mini-ecosystem. The colors that each layer produces is a result of what pigments the microbes possess.
Outside of the circular depiction of the spring I drew some of the microbes that represent the microbiomes found in the park. There are thermophilic Bacteria and Archaea that have developed amazing techniques to survive extreme conditions. One such example is the genus Sulfolobus (yellow-brown microbe near bottom of drawing) which uses mechanisms involving DNA exchange and homologous recombination to aid in DNA repair that is necessary for living in high temperature.
EXTRA CREDIT: Microbial Worlds art exhibit
1. “Impermafrost’ by Gail Priday, is a beautiful piece of work that I found particularly visually appealing. I liked the color choices and the circular parameter that it was created in. Gail’s description talks about what permafrost is and how the melting of permafrost can lead to accelerated climate change conducted by microbes. After reading the artist statement I really appreciated the art because I recognized how the rising greenhouse gases were illustrated. I think that the microbes were illustrated in an appealing way as well. For these reasons, I think this work of art successfully captured the concepts it set out to portray.
2. “Veiled Unveiled’ by Mariah Henderson & Eric Henderson is an interesting piece that describes the laboratory issue that comes about when a microbe cannot clearly be seen even when it is under a microscope. This has to do with the transparent nature of many microbes. Scientists’ remedy is to use a variety of stains that are available in the lab. This art piece illustrated this concept by illustrating what microbes look like before and after a stain. I thought this was an interesting piece of work and explained the concept in a fun way.
3.’Inoculation The 1%’ by Mariah Henderson & Eric Henderson describes a concept we discussed in class. About only 1% of bacteria can be cultured in a petri dish in a laboratory setting. Obviously this limits the extent of microbiology that can be conducted by physical methods like plate streaking. This art piece plays into that idea by creating illustration of the “1%’ that can actually be cultured- (the bacteria the lab had actually grown on petri dishes) Putting the number it in that context makes it a bit unbelievable just how small our scope of microbes is without molecular biology techniques.
4. If I created artwork for this show I would consider capturing the concept of microbial ubiquity and diversity. Since microbes are so different and can be found in so many opposing places and exist with different lifestyles. I think the variety of environments could provide some interesting work. I would like to create a visual representation of some of these environments.
Dan Stinchcomb XC Seminar
Summary
Dr. Stinchcomb started with an overview of Dengue Fever. This virus can escalate into hemorrhagic fever and is found in sub-tropical regions. Significantly, exposure to one type of Dengue can increase risk to the other kinds. This poses a challenge in creating an effective vaccine for the disease. Vaccine candidates for this disease were discussed. One example was CYD which neutralized all 4 Dengue types but did not protect equally among all which could cause long term problems. TDV, another vaccine candidate, is significant for evoking cellular responses. Throughout the lecture, there were descriptions of trial methodologies and how vaccine efficacy was tested with safety in mind. Dr. Stinchcomb mentioned an overview of what work IDRI is focusing on and what is expected in the future. One such project is vaccines for West Nile Virus. Birds act as a reservoir for this disease and humans can be infected from mosquitos. One vaccine suggestion for this virus is to target the viral envelope. Next, there was discussion about Chikungunya Disease. This disease is concerning as there has been rapid spread since 2005 due to a mutation causing greater transmission ability. The lead vaccine here is a mimicry of the entire quaternary structure of the virus. Lastly, Zika virus was discussed. It was interesting to hear some of the background of this disease and how it became a public health issue. Dr. S. presented IDRI’s work with creating a vaccine for Zika that has a platform that could be replicated for other purposes.
Thoughts
I enjoyed this lecture. I think that public health, especially pertaining to infection disease is a critical global issue. It was also interesting to get a look at vaccines from not only an academic perspective but also an industry perspective. This lecture was closely associated with the virology unit in class. The discussion of vaccines was just an extension and more detailed version of what was talked about in class. Specifically, the way in which vaccines are developed and how the structure of viral targets play a role. It was very eye-opening and saddening when Dr. S. mentioned all of the defects that have been identified with Zika. It makes sense that the threat has caused such an explosion of candidate vaccines for the disease. Dr. S. also introduced the idea of RNA vaccines. I was interested in this idea and I would like to know how the challenge of RNA instability could be overcome to make this style of vaccines more feasible?
Eric Collins XC Seminar
Summary
In this seminar, Dr. Collins introduced results from the recent Arctic expedition by discussing different properties of Oceans. Mainly focusing on the movement of Arctic waters, sea ice and chemical properties. He entertained the idea that sea ice is very diverse and that water samples (including what microbes can found in water samples) are heavily dependent on the chemical properties of ice. There was also a description of the different layers of water and how the layers originated. Comparisons of how the flow of water looked like in the past and what it looks like now was mentioned. One example is how oceans used to be freshwater and why that impacts the modern Arctic. There was also an exploration of how density, temperature, salinity and nutrient density are related in seawater.
The discussion of microbes in seawater began with a query about how distinct layers of microbes in the ocean came to be and how they are correlated with water movements. Dr. Collins also brought up the idea that melting ice could cause microbial extinctions. Microbes are also essential for nutrient cycling in the Arctic. Primarily, the most conducive location for microbial growth is the boundary between the warm waters and cold winter waters since it is the area that allows for the simplest nutrient access. Results showed there are significant differences in what microbes were found in different regions of seawater. Dr. Collins finished his seminar with another project he has been working on-mapping how microbes differ by only 10 miles in seawater. He said that there have been issues with this project since sequencing produces mass amounts of data but he created a cool globe-like map for representation.
Thoughts
The seminar was concentrated on ideas about oceanography and I thought it was interesting to learn about this topic as it is not something I have spent much time considering before. I liked that Dr. Collins tied in a lot of the chemical basis of why ocean water moves the way it does. I also enjoyed that he made an effort to include interesting facts and why his seminar is relevant. In class we have talked extensively about ubiquity of microbes. The diversity of microbes in sea ice is an example of that ubiquity. There is also the idea that conditions more conducive to certain microbes selects for those microbes, which is something that we have talked about in class. For example, temperature and salinity surely impact what kinds of microbes can inhabit a region.
This seminar has piqued my interest in the microbes of sea ice. The idea was not discussed in depth and I would like to know more details about it. For example, what specific biochemistry allows microbes to exist in the conditions? Also, how relevant is the microbial extinction that Dr. Collins mentioned?
Lab 8
My artistic intent was to depict the Eiffel Tower, the iconic Parisian symbol. I painted the same picture on two different media (EMB and MAC) because I thought it would be interesting to see the contrasting colors. I liked the EMB piece the best as the dyes caused the bacteria to change to a pink-purple tone while the MAC agar left the bacteria as red.
Candida auris Outbreak in the U.S.
Title: “Deadly Drug Resistant Fungal Infection Outbreak Causing Concern In U.S.”
Source: ReliaWire
Date: March 12, 2017
Link: https://reliawire.com/candida-auris/
Summary: Candida auris has led to almost 30 infections in the United States. The outbreak is troubling because the fungal strain happens to be multi-drug resistant and is linked to a high death rate. Even though that the outbreak is fairly new, researchers are confident that there may be a way to work against it.
Connections: We’ve talked about antimicrobial resistance in class and this is an example of a drug resistant fungus. This also incorporates with the overarching theme that public health and science are intertwined.
Critical Analysis: I find it interesting that this fungus has been able to cause an outbreak despite how many downfalls it has. For example, C. auris cannot produce spores. This is surprising considering that it has been able to spread and infect patients so easily in hospitals. Also, not every strain even has the enzymes that allow for infections in body tissues. It is strange that the fungus has been able to be so successful considering these things. This article seems to be factually correct. It quotes both the CDC and a professor at the Center for Medical Mycology at Case Western Reserve School of Medicine. The article may have had some scientific terms that could be tough to understand for someone that is unfamiliar with medicine or biology. Despite that, it was not written to be misleading and does not describe the infection in a way that would cause panic in the public. Instead, it describes what has happened to cause the outbreak and what researchers and healthcare workers are doing to prevent spread.
Question: The article mentioned that combatting this fungus is an issue because it can be especially hard to identify in labs. What could be a method to properly identify the pathogen?
Sinks as a Reservoir for Bacteria
Title: Turning the water on in a sink can launch pipe-climbing superbugs
Source: Ars Technica
https://arstechnica.com/science/2017/03/superbugs-fester-in-sink-p-traps-and-can-crawl-back-up-to-cause-infection/
More Information: Applied and Environmental Microbiology, 2017. DOI: 10.1128/AEM.03327-16
Date: 3/2/2017, 3:10 PM
Photo: Pseudomonas aeruginosa taken from CDC website
Summary: Around 2004 and 2006 there were issues in a Canadian hospital when patients began to die from outbreaks of Pseudomonas aeruginosa. Now, researchers have described how this outbreak occurred. Bacteria can reside in the P-trap of sink piping and slowly climb up with the use of biofilms. When running water hits the bacteria it scatters on surfaces around the sink. This article also describes how researchers ran their experiments and articulates some of the findings.
Connections: During the cell structure and function unit in class we discussed biofilms. This article describes an instance of when bacteria are using biofilms. Bacteria attach to the surface of pipes and then happily climb the pipes (at rate of 2.5 cm/day) while having nutrients poured down the sink to them. More specifically, the lethal incident in the Canadian hospital was a result of a biofilm-forming bacteria we talked about in class- (Pseudomonas aeruginosa) – which is involved with cystic fibrosis.
Critical analysis: I had never considered that you could find bacteria thriving in sinks and piping underneath sinks . It makes sense though, especially when you consider that people don’t just wash water down sinks but also dump drinks and other fluids that may act as bacterial nutrients. Also, it was a bit alarming that the study this article was based off of found that bacteria could splatter up to .75 meters away from the sink and onto touchable surfaces. (And that is in addition to the bacteria moving down the piping to head to other sinks if design allowed for it) I found it a bit ironic since the purpose behind P-traps are to trap debris and to prevent water in the pipes from becoming gaseous and smelling badly. However, while solving those issues, P-traps have created a whole other problem.
I think the article was concise and easy to read for a public audience. The author of this article actually has a Ph.D. in microbiology and so I trust her interpretation of the science. She also writes in a way that conveyed experimental methods and results easily and understandably. There was no jargon or any writing that would confuse the reader.
Question:
What could be done to prevent microbial growth in piping and from sinks becoming a public health issue?
Extra Credit Simon Lax Seminar Response
1. The talk began with Lax presenting the idea that microorganisms shape our lives through the environment that we live in. Now that we spend much of our lives in fabricated environments (our houses, schools, workplaces) our relationship with microbes has changed. Simon Lax described two projects that set out to describe the interactions between the microbes in our built environments and the microbes on our skin. First, Lax introduced the Home Microbiome Study, undertaken to understand the relationship of microbes found on an individuals skin and the microbes found in their house. There were some interesting conclusions from this project – including the suggestion of a microbial “fingerprint’. The results provided evidence of being able to identify an individual’s environment from their skin (or an environment from an individual). Lax then talked about colonization and persistence of microbial communities in new hospitals. The succinct results showed that there was an entirely different microbial community in the hospital pre-opening and post-opening. Also, the most notable interactions of environment and individuals were between what you would suspect to be highly correlated- for example, a nurse and her phone. The talk finished with a brief look into the clinical results of the hospital study such as the concerns around antibiotics and other factors that influences skin microbiomes.
2. I enjoyed this lecture and though that the presentation was both informative and captivating. Additionally, the topics Lax is researching are very relevant. I found myself wanting to know more about the results of both studies that Lax described. Specifically, I began to question- as someone in the audience queried- what kind of surfaces are most accommodating to, bacterial growth? For example, will hardwood floor or carpet be more conducive to a diverse micro biome? And how would a different floor material impact the exchange of bacteria from us to our built environments. I was also curious about some of the factors in the hospital study that influenced how similar surfaces in one area would be. Lax said that larger surface similarities are found when the temperature is colder and humidity is higher. I thought those results were interesting and I would like to know more about these factors and why they impact the similarities in the way they do.
When we discussed the history of microbiology in class we talked about the scientific developments that were made as reactions towards the isolation and discovery of microorganisms. A lot of those, such as microscopes or Koch’s postulates, were made to understand and explore what microorganisms are and what they do. The research that Simon Lax is involved in is also reactionary in this way. Humans have transitioned to a lifestyle that is spent primarily inside our built environments and this has influenced our relationship with microorganisms. The quest to understand what that change is and how it will affect humans mirrors the way that history was propelled by the fundamental question about what a microorganism is.
Antibiotic Pollution
January 31, 2017
Source: https://phys.org/biology-news/microbiology/
Journal reference: Nature Microbiology
Summary:
Researchers have identified a diverse amount of antibiotic resistance genes within bacteria found in Chinese estuaries. These resistance genes come into the natural bacterial populations from antibiotic pollution and could dangerously propagate through the human population eating fish from these waterways.
Connections:
While we haven’t explicitly discussed antibiotics in lecture yet I think this ties into the idea that microbes are important- not only because they’re super cool to us scientists- but because they can influence human health. Also, this explores the topic of how misuse/mishandling of antibiotics can accelerate the path to the creation of the, “superbug”.
Critical Analysis:
I find the history and development of antibiotics to be very interesting and I think it is important that the medical community (and society as a whole) is wary about what can happen if they are misused. I was also surprised to learn about this type of antibiotic pollution as I had not even thought about the effect of rare antibiotic resistance genes being introduced into ecosystems (bacteria—> fish —> humans) . This article was concise and appeared factually correct. I think that it was written in a way that presents the information in a way that the general population could comprehend it.
Question:
After reading this article I want to know just how prevalent this type of pollution is and by how much is it propelling the development of antimicrobial resistant genes