mglater's blog

ussion:

    The 2,4-dinitrophenylhydrazine test produced a yellow precipitate. 2,4-DNPH reacts via an imine formation mechanism, reacting with aldehydes and ketones but not with alcohols. This meant that the unknown compound was either an aldehyde or ketone. The yellow color of the precipitate also suggested that the carbonyl group of the unknown was unconjugated. The precipitate was used as a solid derivative to determine the melting point of the unknown. The Schiff test had no change in color, giving a negative result. Schiff’s reagent is very bulky, and as such will only be able to react with molecules which have enough space. Ketones are unable to react with the reagent due to its size, so only aldehydes will react and show a change in color. This meant that the unknown present was a ketone. Lastly, the iodoform test was performed to determine if the unknown was or was not a methyl ketone.

We would make a scatter plot of hours studied vs GPA. On the plot we would include a line of regression for the data of only males, one for the data of only females, and one for everybody overall. This would show the relationship between the hours studied and the GPA, as well as showing if there were any large differences in the relationship between males and females. We would also make a scatterplot of hours of sleep vs GPA, to get an idea of that relationship.

Along with the positively regulated genes, there were also genes found which were negatively regulated. An example of such a gene is the pax3 gene. It was found via microarray that the expression of pax3 was lowered in the embryos which had been injected with Shh mRNA, and expression was slightly higher in the smu(smo) mutants. pax3 is involved in many different developmental processes in the brain, including closing of the neural tube and differentiation of various cell types. The researchers examined the promoter of pax3 and discovered that it contains Gli binding sites. This suggests that Hh and Gli act to reduce the transcription of pax3 by Gli binding at the promoter, and therefore reduce the expression of pax3.

Along with discovering new genes, the experiment also identified Shh affecting transcription of other already known genes. These genes were divided into categories of positively regulated and negatively regulated. Multiple genes in each category were grouped together based off of common effects on development. One group of genes found to be positively regulated by Shh was follistatin and follistatin-like2. These genes are known to work on the Bone Morphogenic Protein (BMP) pathway. The fact that increased levels of Shh also increase the levels of these two proteins provides a link between Shh and BMP. It had been previously shown that BMP signalling had an effect on Hh signalling, but this experiment is the first evidence of Shh regulating follistatin. Other groups of genes were found which suggest Hh plays a role in development of different neural areas in the brain, modify expression in specific locations, and interact with other signalling pathways such as the iroquois (irx) genes.

Sonic Hedgehog (Shh) is an extracellular signalling protein which modulates expression of a number of genes. The hedgehog protein binds to a transmembrane protein called Patched (Ptch). The binding of Shh stops Ptch from inhibiting another transmembrane protein called Smoothen (Smo). When Smo is active, it is able to induce the Gli transcription factors to being transcribing genes. While many of the genes regulated by Hh/Gli are known, further experiments with the Hh pathway continue to identify new genes.

Shh is an extracellular signalling protein which modulates expression of a number of genes. The Hh protein binds to a transmembrane protein called Patched (Ptch). This binding stops Ptch from inhibiting another transmembrane protein called Smoothen (Smo). When Smo is active, it is able to induce the Gli transcription factors to being transcribing genes. While many of the genes regulated by Hh/Gli are known, further experiments continue to identify new genes.

    Dr. Rolf Karlstrom is a professor in the biology department at UMass Amherst. Since 1999, he has has performed research in his lab using the model species of the zebrafish. The research done in the lab covers many different subjects, with the overarching topic being the study of developmental neurobiology. The lab studies both larval and adult zebrafish brains to answer questions about how and why the brain forms in the way it does. The lab studies many different genes which influence the development of the brain. One of the main focuses of the lab is looking at the Hedgehog genes, specifically Sonic Hedgehog (Shh). The lab has published papers in the past detailing some of the ways Shh effects brain development, and is still today looking to answer further questions about the gene.

What I have done in the lab so far has been mainly learning how to do different procedures. Most of what I have done so far has been dissecting fixed larva, mounting the brains on slides, and imaging them. I have done some work with analyzing the images by counting cells. I have also recently learned the procedure for the dissection of adult fish which is being performed for the Atlas project.

                My goals for next month are to continue developing my skills at dissection of larval and adult brains, and to work on getting data out of the images. I also hope to work out what I can do experimentally to help move the projects forward.

    As part of the first assignment for Writing in Biology at University of Massachusetts Amherst, the author created a methods section for a scientific figure which he created. The author took photographs of a flowering plant found on the school campus, and created a figure of the images along with a map of the plant range. The methods of these steps were shared with a classmate, who attempted to recreate the figure. The figures had differences in the shape of the flower, the quality of the pictures, and some miniscule details of the pictures. These differences are believed to be due to the trimming of the plant in between the taking of the original and the replicate images, and the fact that different photographers had different items with them to use in taking the picture.

The use of different phones caused a difference in image quality. The creator of Fig. 1 used an android phone, while the creator of Fig. 2 used an iPhone. The two styles each have their own type of camera, and as such the image comes out looking slightly different. The difference in card used to measure the flower is also a result of differences between the two photographers. The photographer for Fig. 1 chose to use a “Dunkin Donuts” gift card to provide scale, an object which the photographer for Fig. 2 did not have. Fig. 2 contains the back of a “Ucard”, which was chosen by the second photographer due to its similar shape and size to the gift card.