Week 6

In molecular biology on Monday and Wednesday, Dr. Peng discussed DNA replication.  We reviewed the full process of replication as well as how it is regulated.  In bacterial physiology on Tuesday and Thursday, we covered membrane bioenergetics, starting with a section on transport mechanisms (diffusion, solute transport, and group translocations).  A section on protein transport followed, which covered the Tat and Sec secretion systems in E. coli. The final sections were bacterial respiration, proton potential, and the electron transport chain.

Biochemistry class on Tuesday was an introduction to enzymes.  One thing that I did not remember well was the catalytic mechanisms of enzymes, which include acid-base, covalent, metal ion, and electrostatic catalysis mechanisms.  Another topic I have previously struggled with is enzyme kinetics, so I will make sure to study that in detail before the next test.  On Thursday Dr. Popescu discussed nucleotides and nucleic acids.  None of the information in that lecture was particularly new or challenging since we have already discussed nucleic acids in molecular biology and bacterial physiology.

On Friday I was traveling to a wedding in Colorado, so I was unable to go to bacterial genetics lab or communications.  My lab partner conducted PCR product cloning on two of our PCR products from last week (the two that showed strongest bands on the gel electrophoresis).  She started with ligation of the PCR product, then transformed the plasmid into E. coli.


Week 5

This week began with a review in molecular biology in preparation for the first test on Wednesday.  The test included DNA and RNA structure, the genome structure and organization, and techniques used in molecular biology labs.  On Tuesday morning, I had another review in biochemistry I for the first test on Thursday.  Needless to say, I spent a lot of this week studying for both of these tests.

On Tuesday afternoon, two of my bacterial physiology classmates and I presented a PowerPoint summarizing a research paper.  We were the first group to present, and I am relieved that I don’t have to worry about doing that later in the semester when there is more going on in other classes.  Our paper was titled “Inhibition of Bacterial Cell Division Protein FtsZ by Cinnamaldehyde.”  On Thursday, Dr. Roberts started a lecture on membrane bioenergetics, though we only got part way through the lecture on transport through bacterial cell membranes.

I took the two tests on Wednesday and Thursday, and finished up the week in bacterial genetics lab and communications on Friday.  In the lab, we ran a gel electrophoresis to visualize the DNA we amplified last week.  We also prepared our samples to run in a nested PCR, which will amplify only parts of the genes that were amplified last week.  This is sometimes necessary because, while the 18S RNA genes are highly conserved between species, there can still be some differences that interfere with amplification of the gene.

Article Review 2

FtsZ protein determines the point of cell division in bacteria by polymerizing into fibers that form the Z-ring, or the site of cell division.  Cinnamaldehyde has previously been shown to have bactericidal effects while being non-toxic to humans.  The authors studied the effect of cinnamaldehyde on FtsZ protein binding.  To show that cinnamaldehyde inhibited the GTPase activity of FtsZ, a light-scattering assay and GTP hydrolysis assay were used.  Electron microscopy of FtsZ showed that cinnamaldehyde inhibited the formation of protofibrils, which inhibited the formation of Z rings, and resulted in longer cells, as was shown in E. coli cell.  Additionally, the binding of cinnamaldehyde to FtsZ was shown through favorable enzyme kinetics, epitope mapping of cinnamaldehyde, and in silico molecular modeling of binding.

As explained in the paper, compounds targeting FtsZ have the potential to be very useful as antibiotic agents with a new mode of action.  Cinnamaldehyde can also inhibit methicillin-resistant Staphylococcus aureus (MRSA) and other antibiotic resistant bacteria, so it could be used as a last resort against infections.  Therefore, this research is very relevant to today’s scientific research.  The experimental approach is also sound, in my opinion, because they use multiple assays/approaches for measuring each aspect of the FtsZ/cinnamaldehyde interaction the paper was focused on.

Future research in this area should include compounds that are stable in air, since cinnamaldehyde can be oxidized to cinnamic acid, which does not have the same bactericidal properties; this would be prohibitive to developing cinnamaldehyde as a useful antibacterial agent.  However, since the authors of this study explored the binding site structure of cinnamaldehyde, similar drugs could be designed that would bind to FtsZ to block polymerization.  Cinnamaldehyde could be a good starting point for future research.

Works Cited

Domadia, Prerna, et al. “Inhibition of Bacterial Cell Division Protein FtsZ by Cinnamaldehyde.” Biochemical Pharmacology 74. (2007): 831-340. ScienceDirect. Web. 16 Sept. 2016.

Week 4

This week I continued working in the Department of Plant and Soil Sciences in Dr. Paul Tseng’s lab.  I am currently performing plate assays on annual bluegrass (Poa annua) seedlings to determine the effects of different rates of herbicide (foramsulfuron).  I am using four different biotypes of annual bluegrass collected from golf courses in Alabama and Mississippi.  On Monday, I sterilized seeds of each of the four biotypes and transferred them to a plate with Murashige and Skoog medium to germinate.  Next Wednesday, I will be transferring the seedlings to new plates of MS media before innoculating with herbicide.

On Monday and Wednesday afternoon I continued learning about genome structure in molecular biology.  On Tuesday and Thursday, we finished the information for test 1 in biochemistry, which covered the function of globular proteins such as myoglobin, hemoglobin, antibodies, and the mechanism of muscles.  Later in bacterial physiology, we reviewed questions that were commonly missed on the test last Thursday, and had a quiz this Thursday.

In bacterial genetics lab on Friday morning, the instructor lectured on primer design in detail for our test next week.  We then prepared a polymerase chain reaction mix with various primers and our two DNA samples isolated from the amoebas.