Genomic and Physiological Identification of Bacterial Isolate from Canine Ear
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For my art project, I decided to take up cross-stitching. I heard that knitting and sewing are great ways to improve hand dexterity (which is very useful if you want to be a surgeon) and I thought the tiny embroidery that resulted looked really cool. Choosing the subjects was easy – I took some ideas from the Virology class I am taking this semester and put some happy spring colors into it, and the cytomegalovirus and T4-bacteriopage are the result of that. I think viruses are really interesting microbes, since nobody knows if they are alive or not, and have really different morphologies and abilities. However, I did not want to leave bacteria out; the P. putida was initally supposed to be Helicobacter pylori, but the two look very similar and I felt more affinity with Pseudomonas putida, since it can live on pure caffeine. I had also already pictured “bad bugs”, and wanted to give a broader idea of microbial life. P. putida is used for bioremediation, and is non-pathogenic, thus representing the “good” bacteria.
Overall, the project took longer than expected, because it turns out I am not very good at sewing at all. Each microbe took a few hours to make, and I was never able to understand the instructions that came with the kits, so they don’t look like they were supposed to, but I think they came out okay.
Summary: Since the Zika virus is relatively new and is spreading to various areas of the world, it is essential to stop its advance before the number of cases gets too high. One way of doing this is designing a vaccine, or finding an effective cure, but another way that is now being developed is an accurate way to diagnose the infection. The Zika virus presents with fever, fatigue, exanthema and headache. These symptoms are not specific and could be linked to many other illnesses. Also, viremia (virus in the blood) is short-lived and low and the presence of antigens can no longer be detected after a few days. Saliva and urine samples, however, present with a much higher load and make the diagnosis faster and more accurate. At the moment they are testing for antigens with ELISA and for viral RNA with RT-PCR (polymerase chain reaction, using reverse transcriptase since the genome of Flavivirus is RNA and has to be converted back to DNA to be detected).
Connections: This connects to the ELISA testing we did in lab and talked about in class as well, and also to the Dan Stinchcomb lecture, which focused on the Zika virus and vaccine specifically.
Analysis: Research on Zika virus has progressed at a fast pace, considering that Zika emerged in 2016 and that we are already developing a vaccine and a way to diagnose the virus efficiently. This article is just a preliminary study on some patients that had no viral load in their blood but resulted positive for infection when their saliva, urine and serum were analyzed. Overall it seems promising and it might help preventing the spread of the virus by informing people of their infection, and shining some light on whether or not the virus can be spread with sexual contact.
Questions: Why is viremia so short-lived and low? If the virus is present in bodily fluids, can it also be spread through them? What are the preventive measures taken to avoid the spread of the virus?
Summary: The scientist proposed that natural selection acting on microbes caused them to be more successful when they manipulate the host by changing its behavior, for example by making it more social in order to have a chance to spread to other hosts. That also explains why a person that has received an act of kindness is more likely to reciprocate it, starting what is called a “snowballing effect” of favors, and probably microbial spread.
Connections: This article connects to the lecture about the human microbiome, and how the kind of microbes living in and on us can affect not only our health, aging, and energy levels, but also our behavior.
Analysis: This research is extremely important in more than just the field of human medicine; it has the ability to influence what we think we know about ecology and relationships among animals, such as ants/bees and other social insects and animals caring for offspring that is not related to them. It could be considered one of the main theories about the evolution of altruism, and the first to consider factors other than genetics.
Questions: What happens if the microbe and the host have conflicting interests? How can the host avoid being controlled by its microbes? What is the effect of antibiotics or probiotics on the behavior of the host? Which microbes are able to manipulate their hosts?
Dr. Stinchcomb talked about various diseases and the development of effective vaccines for them. Dengue’s was developed from a pre-existent vaccine for Yellow fever, but it caused many problems since it caused secondary infections and it only protected against some strains. Trial methods were also discussed (safety, durability, etc). He discussed IDRI, the laboratory he works in, that creates and tests vaccines for many major diseases. West Nile disease was also mentioned – together with Chikungunya and Zika. For each virus, the symptoms, the distribution, the general structure and genome were examined, in connection to the vaccine development and human trial methods.
Reflection, Connections, Questions:
Diseases such as Dengue and Zika are not very well known in developed countries, but they are becoming more common because of global travel and climate change. The availability of vaccines for exotic diseases is a critical tool for the prevention of worldwide outbreaks. This lecture was very detailed and technical; even though I am taking a Virology course, I did not understand everything that was mentioned during the lecture.
This lecture connects to the Virology portion of the class, but it definitely goes much more in depth than we did. It was still very interesting to see how vaccines are created and tested before being commercially distributed. I wonder how they make the jump from computer models and laboratory animals to human trials, and what other methods other than RNA could be used to create vaccines for these diseases.
For the TSA plate, I thought that the red color available would be fun to use to depict a fox. The end result is not great, but the shape turned out to be the best one out of the three. The MAC also worked out pretty well, the subject I wanted to draw initially was a snake. Even though the gel changed color from pink to yellow because of lack of fermentation, the picture is still visible. The EMB plate had Charles Darwin’s face on it, but sadly it did not grow.
The first half of the seminar was an explanation of the geography and history of the Arctic, including an overview of how the water cycles between the Pacific and the Atlantic ocean, and how this in turn affects the temperature, salinity etc. of the Arctic. Dr. Collins’ study was based on seawater samples collected all around it, including the Bering Sea, Northern Alaska, Svalbard, and many more. The second half was a presentation of the preliminary results from the sequencing of the samples. The goal is to create a map to locate the various microbial strains and their distribution within the Arctic waters.
I don’t have much of an interest in geography usually, but I thought this seminar was very interesting and actual, because it touched on the topic of climate change and how it’s affected the ice and the sea in the far North in the past forty years or so. The microbial communities are undoubtedly changing along with their habitat, and this period of transition is a very interesting one to study in my opinion. Some connections with our class are the fact that even in the Arctic, cold and inhospitable as it seems, hosts an incredible quantity of microorganisms, including protists, bacteria, diatoms, and many others. Also the fact that all the data collected through the analysis of seawater comes from genome sequencing, which we have done in lab. I would like to know which microorganism is most abundant overall in the Arctic, and how the diversity and distribution of microorganisms is changing with the climate, along with what microbiologists predict at the moment.
The seminar was an overview of the various research projects done by Simon Lax and colleagues in the field of metagenomics. His first study consisted of sampling several households and the people living in them for an extended period of time to analyze how the microbiome varied between location on the body, individuals, and households. He looked into the correlation between the microbes on the surfaces of the house and the people’s and animals’ coming into contact with them. Another study he mentioned followed him and one of his fellows, with samples collected from their shoes, cell phones and various surfaces they touched. The last project was centered around a hospital, starting before it opened and following the microbial diversity in two of its floor after patients and nurses started occupying them.
It seems to me like the applications of microbial fingerprinting are not very useful in the forensic and medical field; the microbial community on surfaces disappears just a few days after an individual stops touching them, and in crowded places there’s just too many microbes to be able to isolate a specific track.
The connections to our class include the use of bioinformatics and DNA sequencing, and the idea of microbiome, which we have discussed before, both in relation to the lab project and to human health, especially the gut microbiome.
I thought it was very interesting to see that use of antibiotics does not affect the skin’s microbes, but I would like to know if it affects the gut’s. Also, as one of the people present at the lecture mentioned, how does genetic relatedness impact the microbiome? I wish we had spent more time talking about people moving in together. How do their microbes change, and how quickly? Is there selection for the most successful microbes between individuals?
“Scientists Have Found a Way to Reverse Antibiotic Resistance” Health and Medicine News January 23, 2017 Reference: Futurism.com (https://futurism.com/healthmedicine/) Full article available at: Journal of Antimicrobial Chemotherapy Link: https://futurism.com/scientists-have-found-a-way-to-reverse-antibiotic-resistance/ Summary: A group of Oregon State scientists found a molecule that fights against one of the enzymes responsible for antibiotic resistant mutations. This molecule (PPMO) is …