lpotter's blog

This was also from the talk I recently attended. The results showed that Lanthanides more specifically Lanthanum play a significant role in methanotrophs respiration. It was found that Lanthanum is critical for methanotrophs to help oxidize methane to methanol. It was found that when Lanthanum was available for cells the XoxF gene was upregulated and the MxaF gene was down regulated. Conversely when Lanthanum wasn’t available the XoxF gene was down regulated and the MxaF gene was upregulated. It was shown that bacteria could survive for a limited time in the formaldehyde by fixing the one carbon in the compound. When methanotrophs were grown in a co-culture with non-methanotrophs present methanol was produced. If the methanotrophs were grown in pure culture without non-methanotrophs present no methanol was produced, this shows that there is a connection between the two different organisms and both are needed for methanotrophs to go complete respiration. The conclusions that can be drawn from these results are that methanotrophs do heavily rely on the availability of Lanthanides in the environment. This also shows that Lanthanides may be commonly used when metabolizing one carbon molecules in other organisms that have yet to be studied. Based off of the results it can be concluded that XoxF is a regulatory gene within methanotrophs that help to with the uptake of Lanthanides. In the talk it was suggested that MxaF may have to do with calcium regulation. Additionally both XoxF and MxaF may be used for communication between methanotrophs and non-methanotrophs. Co-cultures are also essential for methanotrophs respiration. It is hypothesized that methanotrophs produce methanol which is then used by the non-methanotrophs. The non-methanotrophs produce a compound that binds to Lanthanum which the methanotrophs then used for respiration and to produce methanol making them co-dependent. The methanotrophs being able to live in formaldehyde suggests that it employs a TCA cycle during respiration. This study may have environmental applications because methanotrophs can be used to reduce methane sinks around the world. A suggested application was using methanotrophs to oxidize methane in sewage facilities and reduce atmospheric release.

This was a talk I recently attended. I enjoyed this talk and believe that it may have many environmental applications. The talk was about methanotrophs that live in lake Washington. These methanotrophs live in the sediment of the lake right at the bottom of the zone of oxygen diffusion. One thing that was focused on was the use of rare Earth metals in the energy production of methanotrophs. Little is known about these methanotrophs and how they methane to methanol. However from the findings of this study it seems like methanotrophs may be a viable solution to reducing methane sinks around the globe. The way that these methanotrophs were tested was by first obtaining samples from lake Washington. In this lake alone over 60 isolates have been identified in the area of sediment just where there is little oxygen that has diffused down. To map the respiration of the methanotrophs a full flux map was created. Bacterial cells were exposed to formaldehyde to see if they could continue respiration. Next components of the respiration pathway of methanotrophs were upregulated and downregulated by providing the methanotrophs with different compounds. This was used to test the effect that Lanthanides have on methanotroph respiration. Additionally the importance of a co-culture was tested by keeping methanotrophs and non-methanotrophs in the same and separate environments.

The results showed that many aspects play a role in how cells maintain a uniform rod shape as they grow. One result showed that there are two main ways that new cell wall is inserted into the cell. The first being that new cell wall is inserted in an oriented manor, which means that filaments travel around the radius of the cell and are oriented by cell radius rudders. The second is that new cell wall is inserted in an unoriented manor, this means that cell wall is inserted randomly by enzymes. Another result showed that when mreBCD was upregulated the cell rod width decreased and it became skinnier, if mreBCD was downregulated then the cell rod width increased and it became fatter. The salt shock showed that cells with upregulated mreBCD were able to maintain their rod form for a longer time than cells with lower levels. An additional result showed that when the cells were provided additional nutrients they were able to grow into a rod shape quicker. A similar result showed that when the cell was essentially tricked into thinking it had adequate nutrients it grew at the same rate showing that a kinase domain was responsible for sensing environmental nutrients.

This is my project abstract. There has long been a desire for genetic enhancement in order to cure genetics diseases or alter the physical appearance of someone. With modern gene editing tools it is now possible to treat disease as well as select for cosmetic enhancements. However, with the ability to alter a person’s genetic makeup, comes the question if it’s considered ethical to be changing what was naturally chosen. Scientists have discovered that part of some bacterial immune systems have CRISPRs, which are are specialized stretches of DNA. A specific protein associated with this system is Cas9, an RNA-guided DNA endonuclease that can cut foreign DNA at specific sites. Together utilizing CRISPR and the Cas9 enzyme, genome engineering is now possible. With this new biotechnology, many scientists are delaying the use of gene editing in humans for a multitude of ethical concerns. For our project we discuss the ethics and applications behind human genomic engineering, specifically when used to treat inherited medical diseases or for cosmetic enhancements. To measure the University of Massachusetts Amherst student’s public opinion a mass survey was distributed. We found that gene editing for disease prevention was considered ethical while gene editing for cosmetics was not.

The results for scenario A were that editing genes to select for height with no benefit to health should not be allowed with 25 respondents disagreeing with the statement. Additionally, 25 respondents stated that this genetic alteration was not ethical. 23 respondents answered that altering genes for height would be more permissible in the sperm and egg, rather than an embryo. The results for scenario B were that editing genes to prevent disease should be allowed with 45 respondents agreeing to the statement. 36 respondents also said that editing genes to prevent disease is ethical. It was found that editing genes to prevent disease is more permissible in the sperm and egg, rather than an embryo with 25 respondents agreeing to the statement. The results for scenario C were that editing genes to select for sex should not be allowed 30 respondents disagreeing to the statement. It was also found that this kind of gene editing is not ethical with 30 respondents disagreeing to the statement. 25 respondents said that it was less permissible to select for sex in the sperm and egg rather than in the embryo.   

I am doing a project for my outbreak class and I chose to look at tuberculosis or more commonly known as TB. What I didn’t know is that TB is a top 10 global cause of death and it has been for quite some time. TB is also becoming more of an issue, not because more people are getting it, it is because TB is becoming resistant to the majority of the drug that treat it. This has become a huge problem around the globe. One example that I looked into was the spread of drug resistant TB in Russia. It has become a huge problem because of Russian prisons. People are kept in poor conditions and in close quarters. Then when people contract TB they aren’t treated properly or given drugs for the full amount of time. This allows the TB to build resistance to the common and most available drugs to treat it with. Now the TB once it is has become resistant to drugs takes a lot longer to treat and a lot more of a strict regimen of taking drugs. This is not followed frequently in prisons due to lack of higher level drugs and lack of coordination from within the prison system.

I just read about NASA’s twin study and it really is incredible. I never really thought about the effect that space or zero gravity would have on someone. The twin that went into space didn’t suffer too much on upon entering space. In fact he responded relatively well to being in space. In fact the shortening of his chromosomal telomeres was reduced when in space. This means that his aging process was theoretically slowed. That being said when he returned to Earth his chromosomal telomeres shortened almost immediately and his body had an autoimmune response. His body thought that something was attacking him when in actuality he was not sick at all. He was just adjusting to the full force of gravity. His legs started to swell, he developed rashes, he was in a lot of pain. It took more than eight months for him to return to normal. It did take a toll on his body. The purpose of the study was to see how zero gravity affects the body long term. NASA wanted to know this because they want to know how plausible space travel really is.   

This was also about a talk I went to at Harvard. This talk was very dense on the engineering aspect of microbiology which I found interesting because it was something that I don’t typically think about. The main point of the talk was discovering ways in which we can categorize and catalog bacteria. The proposed method was by looking at bacterial cell envelopes and inducing a dipole on them to determine how they behave. The other half of the talk was about about how we can use electric fields to help introduce new DNA and genes to cells. This is where the talk became incredibly engineering heavy and a prototype machine that could carry out multiple electroporation experiments at once was introduced. The way that bacterial cells were categorized by their cell envelope was with a technique called low frequency dielectrophoresis. With this technique a dipole is induced on the cell by creating a non-uniform gradient. The bacterial cells were then placed in tubes that had a constriction point, it is at this point that the now polarized cells feel the dielectrophoresis force and clump at the constriction point. The bacteria used in this experiment was a mutant strain of Streptococcus mitis. A mutant was used because S. mitis typically has a virulence factor that causes clumping, the mutant had this virulence factor removed so that any clumping near the constriction point would be fully attributed to the dielectrophoresis force and not the virulence factor. Two other bacterial strains were used to observe polarizability. The first, Geobacter sulfurreducens polarizability was studied by observing its extracellular electron transfer mechanics. The second, Shewanella oneidensis polarizability was studied by looking at its Mtr pathway. This gene was later inserted into Escherichia coli to see if it was also impact the polarizability of it. The engineering part was to make a machine that carried out multiple electroporation experiments at once. This was done by condensing the apparatus down to the size of a pipette tip.

This was for the same talk at harvard. This talk was incredibly interesting and focused on how cells grow in a defined rod shape. The purpose of the talk was to explain how cells maintained a uniform width while expanding from a spherical shape to a rod shape. The organism used in the study was Bacillus subtilis, it was used because it is a rod shaped cell. The average width of the rod shaped B. subtilis is 740 nm, this value only varies by 1% and makes it an ideal organism for this study. Knowing that this organism has a uniform width shared by all individuals the question was then asked, how does this organism regulate the width of its rod shape? The way that this was tested was by changing conditions of cell growth, using antibiotic to target certain cellular mechanisms, as well as up regulating and down regulating certain genes within the rod complex (this complex is known to be associated with rod shaped growth of cells). One condition which the cells were exposed to was a salt shock, the salt causes the cells to shrink. This process was used to determine shrinking rates of the cell when mreBCD was upregulated or downregulated. Another condition cells were exposed to was providing more or less nutrients to determine which complexes would be affected by nutrient availability and how that would ultimately affect rod shaped growth. For observing the orientation of cell walls polarization microscopy was used.

This was for the talk I attended at Harvard. The results showed that there were many aspects as to how cells maintain a uniform rod shape as they grow. One result showed that there are two main ways that new cell wall is added to the cell. The first being that new cell wall is inserted in an oriented manor, which means that filaments travel around the radius of the cell and are oriented by cell radius rudders. The second is that new cell wall is inserted in an unoriented manor, this means that cell wall is inserted randomly by enzymes. Another result showed that when mreBCD was upregulated the cell rod width decreased and it became skinnier, if mreBCD was downregulated then the cell rod width increased and it became fatter. The salt shock showed that cells with upregulated mreBCD were able to maintain their rod form for a longer time than cells with lower levels. An additional result showed that when the cells were provided additional nutrients they were able to grow into a rod shape quicker. A similar result showed that when the cell was essentially tricked into thinking it had adequate nutrients it grew at the same rate showing that a kinase domain was responsible for sensing environmental nutrients.