Drafts

Facilitation: When there us facilitation, earlier colonizing species facilitate the growth of future species in some way. If there was a removal of earlier colonizing species, then the species that they facilitate may have a harder time existing. Inhibition: When inhibition is taking place earlier colonizing species are inhibiting the growth of future species. If the earlier successional species are removed, then the species that they were inhibiting would be more likely to grow. Tolerance: If neither inhibition or facilitation are occurring then tolerance is occuring. This means that species are tolerating condition. Their survival depends more on their life history strategies than on facilitation or inhibition of earlier species. Thus, if earlier successional species were removed, then only species that can tolerate the ecological conditions will survive there.

The thyroid hormone results in an increase in cyclin kinase inhibitors, p27 in particular. With this upregulation of p27 inhibitors, the cell cycle is arrested at the G2/S restriction point. In order for spindles to form for division to occur, the cyclin-CDK2 complex must be activated. Since thyroid hormones play a role in an increase in cyclin inhibitors, cyclin-CDK2 complex cannot become phosphorylated in order to become active.

Neurogenesis occurs 24 to 72 hours post fertilization in zebrafish. This is when neural stem cells differentiate to form neurons. The zebrafish that we are using in our experiment are 7 days post fertilization. Before conducting the first experiment, we hypothesized that we should see an increase in neural stem cell differentiation in T4 treated zebrafish due to an upregulation of her2. Since this study shows that her2 is not affected by Notch signaling after neurogenesis, it makes sense as to why not just one group, but most of the class saw a decrease in neural stem cell differentiation in T4 treated zebrafish.

The two main observations that are made in this paper are that there is a low level of thyroid hormone at the time of birth, with a sharp increase on day 6, peaking in day 15 and falling at day 25. This observation is shown in figure 1. The second observation is that in mice with induced hypothyroidism, the rate of mitosis increase compared to controls at day 2 and day 6. This observation is shown in figure 2. In figure 2, the researchers are measuring the cells that are going through DNA synthesis. This, in turn, indicates the cells that are going through mitosis. The difference between P2N and P6N indicates how many cells have been labeled with BrdU, and by extension, how cell division has increased or decreased in control mice brain on day 2 compared to day 6. The difference between P2N and P6N indicates how much cells have been labeled by BrdU and consequently, the amount of cell division has increased or decreased in PTU treated (induced hypothyroidism) mice in the brain at day 2 compared to day 6. P2N/P6N observation relates to the data in figure 1 because the thyroid level of the brain in P2N and P6N  which are normal levels are in figure 1. This indicates that at time of P2N and P6N, the level of thyroid hormone, which is not mentioned specifically, is found in figure 1. From figure 1, the conclusion that can be drawn is that because there was an increase in thyroid hormone from day 2 to day 6, the decrease in mitotic cells in P6N compared P2N indicates that thyroid hormone may be causing a decrease in cell division and DNA synthesis. The hypothesis of this paper hyperthyroidism causes decreased mitotic activity compared to control mice. In the paper, the researchers never explained the biological mechanism of how hyperthyroidism causes a decrease of mitotic activity, only that it does actually cause the decrease rather than just correlate with the decrease.

Weatherbee, S. D., Behringer, R. R., Rasweiler, J. J., & Niswander, L. A. (2006). Interdigital webbing retention in bat wings illustrates genetic changes underlying amniote limb diversification. Proceedings of the National Academy of Sciences, 103(41), 15103–15107. doi: 10.1073/pnas.0604934103

• Discusses the process of interdigital webbing in mammals, including examples of bat forelimb webbing retention and duck hindlimb webbing retention. Inhibition of apoptosis caused by Gre and FGF signaling within interdigital space results in retention of membrane.

Pajni-Underwood, S., Wilson, C. P., Elder, C., Mishina, Y., & Lewandoski, M. (2007). BMP signals control limb bud interdigital programmed cell death by regulating FGF signaling. Development, 134(12), 2359–2368. doi: 10.1242/dev.001677

• Discusses BMPs used as a regulator of programmed cell death within the interdigital membrane. Bmpr1a inactivation in mice after limb bud initiation results in upregulation of Fgf4 and Fgf8. Inactivation of Bmpr1a also results in decreased apoptosis within interdigital membrane, leading to webbed digits.

(Adapted from Developmental Biology essay)

Homo Lontra is a species of hominid located in modern day coastal Europe. Upon increased competition from the Homo Sapien invasion of Eurasia due to their emigration out of Africa, Homo Neanderthalensis was forced to the coast, outcompeted for access to many land animals and foraging areas. There, Homo Lontra evolved from Neanderthals, with visible adaptions for a diet of coastal marine foraging.  This included webbed feet for better aquatic propulsion, a hardened enamel for consuming hard-shelled marine animals, and the re-evolution of dense body hair to protect their bodies from the cold European winters and water. These traits are similar to those of other aquatic mammals-such as otters (Homo Lontra’s namesake)-but a complete molecular and developmental analysis must be performed in order to determine their true origins.

The teeth of Homo Lontra are much tougher than that of Homo Sapiens due to their increased enamel thickness. In mice and humans, the teeth are not continuously grown or renewed after development; therefore, any alteration to tooth structure would have to take place developmentally.¹ Muscle segment homeobox 2 (MSX2) encoded proteins act as repressors; specifically affecting epithelial-mesenchyme interactions as well as ameloblast differentiation, a cell that deposits enamel proteins during tooth development.²Msx2^+/– mutants display stronger expression of amelogenin (proteins related in amelogenesis; enamel development) than that of Msx2^+/+ individuals, with the heterozygote displaying a twofold increase in amelogenin expression.²

1. Li, J., Parada, C., & Chai, Y. (2017). Cellular and molecular mechanisms of tooth root development. Development, 144(3), 374–384. doi: 10.1242/dev.137216
2. Molla, M., Descroix, V., Aïoub, M., Simon, S., Castañeda, B., Hotton, D., … Berdal, A. (2010). Enamel Protein Regulation and Dental and Periodontal Physiopathology in Msx2 Mutant Mice. The American Journal of Pathology, 177(5), 2516–2526. doi: 10.2353/ajpath.2010.091224

Figure 2 shows that the her2 is regulated by the delta notch pathway. The authors came to this conclusion by measuring the expression of her2 in notch deficient embryos. This shows that the her2 is somewhere in the notch pathway because everything else is kept constant. Because neurogenesis occurs in the first 3 days after fertilization, since the drug was added at day 5, her 2 is no longer regulated by Notch signaling at the time that our study is done. However, because the study that we are doing involves not only neurogenesis, but also oligogenesis, and how those two things that are influenced by the thyroid hormones affect stem cells. In the paper, while the paper mentions that her2 is not regulated by notch signaling after oligogenesis, it does not discount that her2 is not affected by the thyroid hormone through some other pathway. Because of this, it is possible that her2 does have an effect on the neural stem cell. However, the only thing that is known is that if her2 does affect neurogenesis and gliogenesis, it will not be through the notch pathway.  I think that her2 is definitely playing a role that can be seen in the class data. The paper mentions that her2 induces glial differentiation and that inhibits the neural differentiation, which was similar to how hypothyroidism affects the neural cells in the papers we have read. However, I am not sure whether her2 directly responds to TH. There is no evidence for me to think that the two are related, especially since her2 is not connected to notch signaling in fish that are past neurogenesis.  I think that her 2 is promoting the formation of glia because the study is involved in glial differentiation, this would imply that her2 is promoting the formation of the glia. 

The efficiency of the mutated RHO allele cleavage is 70.7% whereas the efficiency of the wt RHO allele is 3.8%. In the wt there was 8% insertion and deletion using this method but in the mut, there was 93% insertion-deletion in this method. In the wt, the rho localized on the plasma membrane while the P23H mutant protein remained trapped in the cytoplasm. The two insertion-deletion mutations the antibodies were not seen in both of those mutations. In this experiment, after one month there was a higher thickness of OS was higher in the CAS9-VQR and sgRNA mut compared to cas9-vqr treatment only. There was no change in the ONL thickness did not differ depending on the treatment. At three months, there was a slight difference in ONL thickness, with cas9-VQR and sgRNAmut having thicker ONL layer and cas9-vqr having the least thickness. The effect on the thickness of OS layer remained the same. The CRISPR-VOR the uninjected eye presented better response compared to the treated eye, indicating that there is a detrimental effect that the procedure has on the function of the retina.The injection method allowed for the gene delivery. All subtypes of the retinal cell types were targeted. However, the rod photoreceptor had the highest transduction and the glial cells had the lowest transduction. GFP transduction was robust and diffusion the ONL. The RHO mut gene presented a significant level of cleavage GFP high cells exhibited a higher accumulation of indels High effect in unedited P23H allele. Every delivery system that was compared had the same amount of frameshift mutation in the allele. If the mutation resulted in the stop codon, it was more likely to disrupt the expression. The GFP plus cells had a 3.2% efficiency while te GFP high mutation had a 48% efficiency.