Writing in Biology

Herbivore preference was analyzed by a t-test using the proportion of leaf consumed as the response. We analyzed the percent of each of the leaves eaten. Separate t-tests were conducted for the high and low fertilizer dishes. There was a significant difference in low fertilized dishes in preference of damage leaves (M = 0.53268571, SE = 0.06349263) versus control leaves (M = 0.65528214, SE = 0.06625825) conditions; t (27) = -2.1323, P = 0.0422, described in Figure 3. There was also a difference in high fertilized dishes in preference of damage leaves (M = 0.7668286, SE = 0.0507239) versus control leaves (M = 0.64629524, SE = 0.06687644) conditions; t (20) = -1.816, P = 0.0844.

For root biomass, shoot biomass, and number of flowers, a two-way ANOVA was performed for each variable on all fertilizer and damage treatments. There was a significant difference in the root biomass averaged across fertilizer treatments of damage (M = 25.607800, SE = 1.893977) and control (M = 34.944375, SE = 2.296133) conditions; F_{1, 94}= 9.838, P = 0.00228 described in Figure 1. Fertilizer had no significant effect on root biomass for treatment plants (F_{1, 94}= 1.238, P = 0.26877). There was a significant difference in the shoot biomass averaged across fertilizer treatments of damage (M = 145.416000, SE = 6.448853) and control (M = 187.067292, SE = 6.619286) conditions; F_{1, 94}= 20.108, P < 0.0001 described in Figure 2. Fertilizer had no significant effect on shoot biomass between treatment and control (F_{1, 94}= 0.336, P = 0.564). No significant difference was found in the amount of flowers of treatment versus control groups averaged across fertilizer treatment (F_{1, 94}= 0.026, P = 0.8712). Fertilizer had a significant effect on the amount of flowers averaged across damage treatments plants with low (M = 66.125000, SE = 5.807913) and high fertilizer (M= 46.78571, SE = 5.62293) conditions; (F_{1, 94}= 5.450, P = 0.0217). 

Through this experiment, we aim to find how a combination treatment of mechanical damage and application of jasmonic acid, along with differing amounts of fertilizer affects herbivore preferences and plant growth. We will grow 150 tomato plants and randomly assign which plant receives a treatment. Once we have determined that, we will then assign randomly the amount of fertilizer each plant receives. Half of the treatment group plants will receive twice the amount of fertilizer as their counterparts in that group, and half of the control group will be treated the same with fertilizer. Once the plants have grown with treatment for two weeks, we will test herbivore preference. After, we will measure the number of flowers, root biomass, and shoot biomass of each plant to determine growth differences between treatments and fertilizer amounts. With this experiment, we hope to determine if a combination of both mechanical damage and application of jasmonic acid could function as an insecticide for tomato plants. 

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.