Drafts

Receptor tyrosine kinases (RTKs) are a class of membrane-spanning proteins that dimerize when a dimer signaling molecule binds the extracellular receptor domain. When two RTKs dimerize, they autophosphorylation on multiple tyrosine residues. The adaptor protein GRB2 binds to a phosphorylated tyrosine via its SH2 domain. Ras is anchored to the lipid bilayer and is a kinase for many downstream growth pathways. SOS is a Ras-GEF, so upon binding Ras, changes its conformation to have less affinity for GDP and more for GTP so it can get a phosphate group and phosphorylate things such as the Map kinases. The RTK/Ras/MapK pathway has been implicated at multiple points to be overactive in cancer. Drugs such as dacomitinib work to irreversibly bind cystines in the ATP binding kinase domain of the RTK. However, secondary driver mutations often arise in downstream targets such as Ras, rendering treatment of the RTK useless in treating cancer.

Henry Molaison, commonly known as “Patient H.M.” was a man who underwent a bilateral medial temporal lobectomy to treat violent seizures. After this surgery, he had severe anterograde amnesia and some retrograde amnesia. The medial temporal lobe became known as the hippocampus, and we learned from Patient H.M. that is is important in encoding declarative memories, but not procedural memories. The hippocampus is also important for storing spatial memories, and place cells are known to fire both when rats are at a specific location, and during sleep so these spatial memories can be consolidated.

Long term potentiation is the form of learning at the synaptic level, by strengthening of a specific synapse. Induction of these changes results from repeated, high frequency stimulation of a synapse, also known as tetanus. The stimulated AMPA receptors open with glutamate binding, and allow Na2+ into the cell. When enough of these are opened, the voltage-gated NMDA receptors become unblocked by Mg2+ and allow Ca2+ in. NMDA receptors need both glutamate and depolarization to open. This elicits a positive feedback loop in which retrograde gaseous neurotransmitters like nitric oxide are produced to stimulate glutamate release in the presynaptic cell. Late phase long-term potentiation is characterized by structural changes such as fatter synapses, more dendritic spines, more terminal buttons, and a larger number of synapses.

How animals learn to communicate is a very interesting topic. For example, it has been shown that songbirds raised in isolation produce sounds that are consistent with their species. The Wernicke-Geschwind model of language says that language is a result of an interconnected network of components. Language processing is left lateralized in the brain. There are two types of aphasia: Broca’s aphasia and Wernicke’s aphasia. Broca’s aphasia is due to damage to the left frontal lobe, and is characterized by difficulty in language production but not in comprehension. Wernicke’s aphasia is caused by damage to the left superior temporal gyrus, and is characterized by difficulty with language comprehension but not production. The arcuate fasciculus is a bundle of fibers connecting Wernicke’s area and Broca’s area.

Which of the pathways is hampered by the ABSENCE of oxaloacetate in the mitochondrion of the cell?    A.) malonyl-CoA formation        B.) acyl-CoA transportation       C.) glycolysis

The correct answer is malonyl-CoA formation (A). Oxaloacetate needs to react with acetyl-CoA to form citrate, which can move out of the mitochondrion and re-form acetyl-CoA. Without extramitochondrial acetyl-CoA, malonyl-CoA cannot be formed, and the subsequent steps of fatty acid synthesis will not occur. Acyl-CoA transportation (B) is wrong because it happens even before acetyl-CoA formation and carnitine, not oxaloacetate, is required for that process. Glycolysis (C) is completely wrong because it has nothing to do with lipid metabolism.

We cut thin cross-sections of wild type and mutant stem internodes and stained them with phloroglucinol-HCl and toluidine blue (Figure 4). Phloroglucinol-HCl stains mostly lignin while toluidine blue stains polysaccharides and lignin. Comparing, the wild type and mutant internode cross-sections, we noticed that the wild type wall is thicker than the mutant wall, shown by the presence of more staining in the wild type cross-section (Figure 4a, 4c) than in the mutant cross-section (Figure 4b, 4d) for both phloroglucinol-HCl and toluidine blue stains. This indicates that there are possibly higher levels of lignin and polysaccharide in the wild type cell wall. Since the mutant shows less staining, we can predict that our gene is involved in the assembly of cell wall components.

Figure 4. Brachypodium distachyon internal stem internode anatomy. (a.)The stem internode cross-section from a wild type plant, stained with phloroglucinol-HCl. (b.)The stem internode cross-section from a mutant plant, stained with phloroglucinol-HCl. (c.)The stem internode cross-section from a wild type plant stained with toluidine blue. (d.)The stem internode cross-section from a mutant plant stained with toluidine blue. The positions of the epidermis (Ep), cortex (Co), vascular bundles (Vb) and pith (Pi) are indicated.

In an effort to extend the expression data in Phytozome, we designed an experiment to study Bradi3g27407 gene expression under 5% glucose growth conditions. To explore this, we conducted an experiment to study expression levels in root samples in the presence and absence of 5% glucose. We chose root samples because that is where our gene is most expressed, as indicated by our results from the e-FP browser. We used 8 root samples (5cm, young) from Brachypodium distachyon plants, growing 4 experimental samples in MS medium plates containing 5% glucose and another 4 control samples in MS medium plates without 5% glucose. We grew the plants at optimum temperature and light conditions: 24℃ day, 18 ℃ night. We created primers for the reverse transcription reaction, using primer3 software, so that they flanked introns but bound to exon sequences. The forward primer was 5’-tacaaggggaagatcagggc-3’ and the reverse primer was 5’-ccgcttgatctccttctcca-3’. These were so that the length of the sequence between the primers (not including the intron sequence) was 321bp (Figure S3). In Figure S3, the texts highlighted in yellow are the exon sequences, that highlighted in green is the intron sequence and the texts with red font color are the primers.

This semester, I learned how to genotype zebrafish. I had never genotyped before, so performing the steps regularly helped me to understand the process better. I learned how to analyze and interpret fragment analysis data. Importantly, I became more comfortable with running gels. Its importance lies in the fact that we run gels so often in the lab and it is an essential skill to have.  I also performed some TOPO-cloning, chemical transformation, inoculation and plasmid extraction, alone for the first time. This gave me more confidence to execute these processes in the future. Presenting before other members of the lab allowed me to get a feel of what it is like to make a scientific presentation. I learned not just from my presentation but from everyone else’s presentation. The feedback I received played an enormous role in my learning process here.

    I enjoyed the proposal project, although my group did misjudge the due dates and had to quickly text and email each other to finish it. The methods project helped because it made us go into more detail, trying to be a specific as possible in our description and directions. And us having to speed up to finish this made us start somewhat earlier and quicker on the poster project. 

    The poster project was my favorite. I had never printed a poster here at UMass so that was exciting. My groups topic was interesting and it was fun making a survey and sending it out to people in my section of the marching band, who after taking the survey asked me questions on the topic. I was confident explaining and it was good practice for presenting, and just sharing science topics I was interested in was awesome. 

    Overall, I did enjoy this class. I felt that it was actually helpful, being that it was writing geared towards my career path. I had one of the better presentation groups I have ever had in  both high school and college in this class, and I am grateful for that. I like to think I did pretty okay overall, but I do admit, this class was one of the most challenging for me in college purely because EVERYTHING I had learned about writing was changed and I just do not enjoy writing in any context.

    Having to go from creative to scientific writing was also a tough transition. Every writing class I have had up until this semester stressed figurative, descriptive language and having to throw that all out the window made me questioning what was the point of learning that.   

    The methods project was not really new in the sense of following a method. I thought that it was really straight forward at the beginning. But, the amount of information that needed to be incorporated in order to achieve the expect result was a lot more than I thought. Someone can interpret your instructions in a way that is completely different than you meant them to be, even if you think you are being so clear. It really showed that attention to detail and specificity was really important and no one is a mind reader.