The Past and Future of Genome Sequencing

This week in Class we had the opprotunity to sequence a whole genome from a Vibrio bacterium and see how complicated it is to piece a genome together. This was using modern technology, and the “difficulties” we had where nothing in comparison to those that first sequenced a whole genome. By reading both the highly technical scientific research paper by Fleischmann, and then a commentary that put things in to more general terms by Nowak on the initial sequencing of the Haemophilus influenzas genome, I was able to get a glismpe into the historical moment of sequencing full genomes.

It was incredible to see paper with a genome mapped out and possible functions of each gene mapped with it, but while the Fleischmann’s article was impressive, I didn’t fully understand until I read the Nowak’s review. In his review he states the incredible discovery of there being no citric acid cycle and the idea that influenzas can pick up genes from the environment from other influenzas. It also sates how incredible it is that this project took six months rather then three years. I read that and thought, six months? We just sequenced an entire genome in one class period. That was when it hit me that todays technological advancements are incredible, and something the past would have look at in awe.

This whole experience makes me certainly consider what I have to look forward too in my future as a scientist, what new technology will come out? And how will people in the future be looking at the scientific articles of today?

Five Important Questions To Ensure Scrutiny of Researches Findings

In W. P. Hanage’s article he uses human microbiome research as an example to discusses five questions we need to consider when reading scientific literature before we make any conclusions. The first question, “can experiments detect differences that matter?” is important because so many inaccurate conclusions are shown to the public before experimental findings are confirmed. Hanage describes this problem discussing how markets are manipulating published microbiome research from a single to a few studies to try to get products out to help control everything from mental health to diabetes. The reality is the gut biome is so complex that experiments have done little more than scratch the surface on the microbial diversity. 

Considering what research has actually shown leads us into the second question,“does the study show causation or correlation?”. It is difficult to know if the microbial composition can cause differences in human functioning or if the two (human health and microbiome diversity) fluctuate together because as the environment changes both will change but separately. Hanage’s makes a good point though, that correlation usually indicates a sort of casual relationship, and that is why the third question must be asked, “what is the mechanism?”. In order to determine how much one is related to another we need to lay out an exact mechanism that the interaction occurs through. 

The fourth question, “how much do experiments reflect reality?” is especially important in microbiology because so much of the work is done in a lab, in a controlled environment where the effects of the experiment are easily visible. For example, according to Hanage, gut microbiome changes have observable effects in diebetic lab mice, but in order to do these experiments the lab mice are germ-free and designed for lab work, not natural. Natures ever changing environment and hard to control factor, especially when examining the human microbiome that fluxuates per day per person, leads us to our fifth, and final question; “could anything else explain the results?”. This is extremely important to consider because we never want to draw permanent conclusions from data after an experiment that has all sorts of varying factors. I will discuss this more below, as I consider which questions to consider during scientific controversy. 

I would argue that “Can experiments detect differences that matter?” and “Could anything else explain the results?”, are the two questions that are helpful when discussing controversy. The former is important because it allows scientists to state whether there is even any point in examining an individual experiment, or if you can’t make a decision until multiple experiments have been done and recorded and duplicated. The latter is important because there are always many factors in science, no matter how much we try to control, that affect the result. This is particularly true when doing microbiology research, when even the tiniest contaminate can skew the results. Therefore when discussing controversial topics, we again need to identify if our results are valid and if there are other options, so no inaccurate conclusions lead to misinformed actions. 

Hanage WP. 2014. Microbiome science needs a healthy dose of scepticism. Nature 512:248. DOI: 10.1038/512247a.

Precis of Adele Mennerat’s PCR Contamination Article

(1) Microbiologist, Adele Mennerat, in her research article entitled “How to Deal with PCR Contamination in Molecular Microbial Ecology” (2014) asserts that enzyme Sau3AI when used to decontaminate PCR reagents can cause higher accuracy in PCR reads when compared to using enzyme DNase 1. (2) Mennerat provides evidence that Sau3AI is the more effective enzyme by comparing similarity in community composition, and finding that Sau3AI was more similar to the original structure. (3) The purpose of this research is to demonstrate that an enzyme is needed to clean up PCR reagents in order for the results to have less decomtanition. (4) Mennerat establishes an instructive and scholarly relationship with microbiologist and any professional that wants to use PCR.  

Mennerat A, Sheldon BC. How to deal with PCR contamination in molecular microbial ecology. Microb Ecol. 2014 Nov;68(4):834-41. doi: 10.1007/s00248-014-0453-y. Epub 2014 Jul 9. PMID: 25004997.

Analysis of Experience with Genome Computer Analysis

This was my first time using my own terminal to analyze output from high through put sequencing of the 16s rRNA. It was an experience that was both frustrating but also very awarding. Being able to manipulate so much data using just your lab top that quickly is a valuable skill I am sure I will have to use in future research. It was a process that required problem solving skills, for example when the code wasn’t given and you had to look it up, and also team work skills, as I learned how helpful it was to have peers (and especially professors) to bounce ideas off of and help me solve problems. This year has been hard as we haven’t been able to work in person, on a lab bench, to visually learn, so I appreciated having a challenge that brought me closer to a lab bench like experience. I am not saying I am going to switch majors and go into computer science or that I would rather be coding than doing wet lab research but I do have a greater respect for data analysis now.

If I had something to say to the next class it would be; you can get through this, it’s going to be frustrating, you are going to get errors, but when you make the errors you learn because you are forced to confront the mistakes you made. Also that genome analysis is extremely important for microbiology and it is amazing the amount of conclusion you can draw with a few key strokes on your own laptop.

Post Panel Review Reflection

The panel review process of a paper, as I have discussed before, is not only time to improve the authors writing and proposal skills but for the panel to consider their own. In molecular microbiology lab we were able to review in small groups three papers (the larger groups experienced technical difficulties so we were unable to participate) and therefore were able to explore more ideas quicker and contrast experiments easier. Through the process of discussing I discovered concise writing with a plausible but interesting research design drew the groups vote. It made me realized that while I found my own project design interesting I was not writing enough for an audience. It is so valuable to be both the reviewer and the paper being reviewed because feed back comes from both other people and your own experience.

A Precis of Carl Woese’s Three Domain Proposal

(1)University of Illinois microbiologist Carl Woese in his proposal “Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya” (1990) argues for that phylogenetic system at the time should be updated by expanding from kingdom to a new taxon “domain”. (2) Carl Woese provides background on how the phylogenetic tree was first created, and different branches formed, then cites his own work with microbes to explain how the three newly proposed domains are evolutionarily separate due to molecular level differences. (3) The purpose of this proposal is to present eukarya, bacteria and archaea as the overarching categories for the evolution of life now, demonstrating that on a molecular level archaea is separate from bacteria and actually closer related to eukarya. (4) Woese establishes a solid argument and therefore respect from the other scientists he is proposing this new system too.

Peer Review:

Me and roommate were discussing peer reviews and how the process is definitely necessary, but also contributes to the elitist nature of some science. In a similar manner to how it was brought up during lecture, we both expressed annoyance that scientific papers that are written to glorify the head researches ego rather than to just discuss the findings and the facts. At one point my roommate laughed out loud at the peer viewed paper she was reading for her class. The author, who was a friend of her professor, had cited an “incredible piece of research” to support the researches claim, and it turned out the “incredible research” was the authors own old project. The fact of the matter is that people have implicit bias towards a friend rather than a stranger and towards themselves, especially if there ego can be given a boost. I am not saying that papers should not be peer reviewed, it is an extremely important process that allows ones work to be viewed by another. I am rather suggesting that neither the author nor the reviewer should know who the other is. And that when ever we read anything we need to consider our own bias along with the authors, take everything with a grain of salt.

Peer Review

The peer review process is a huge and important part of the scientific community. It allows outside perspectives to contribute to someones writing and question the authors findings to make the paper more credible. I have had a few opportunities to act as a peer reviewer so far in my scientific career and each time I have found ways to not only improve others writing but also my own. And when reading others research you are going to learn new things and new ways to view things. This is what truly makes peer review amazing, it allows you to see into someone else’s thought process and contribute to their work while also bettering your own.

Microbial Populations and The Communities They Make Up

When you find a microbe and study their internal workings you are not just studying one, you are studying a population. Microbes do not grow alone as they grow and reproduce at an exponential rate as long as they’re in a supportive environment. When it is the same strain reproducing colonies form, and therefore a population, and these populations have specific characteristics.

There will be certain textures, shapes, sizes, they have specific metabolites and byproducts. Some populations occur in your home while others occur in extreme environments, and when there are multiple populations in the same area they make up a community.

When there is a community you are examining the differences in the population characteristics, and also observing how each population interacts. Are the different microbes going to be beneficial for each other? Parasitic? Maybe one population creates a byproduct that the others need to survive. Or maybe they are competitive, fighting for resources and space. It is this interaction, between the species, that make microbes all the more interesting and enable us to see where the behaviors of complex animals in their communities stem from.