Drafts

    Although DNA sequencing is a great way to extract information based on genotype of a specific organism, it is not the only way.  In this experiment, genotypic information about the dogs was gathered using a combination of polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP) and derived cleaved amplified polymorphic sequences (dCAPs). PCR is a method of DNA amplification that can produce an exponential number of copies of a specific sequence. PCR is run in a thermocycler in a tube containing taq polymerase, dNTPs and a primer specific to the section of DNA to be amplified. The end product of PCR is millions of copies of the desired DNA sequence. The amplified signal is useful for reliable repeated assays of that target sequence. For this lab, the product of PCR was used in dCAPs to figure out the genotype of the dogs at a gene. dCAPs is a derived version of RFLP that can be used for SNPs without a natural restriction site. Both RFLP and dCAPs use a restriction site containing a desired SNP to determine the genotype at a gene, by cutting the sequence with a restriction enzyme and running the product(s) of the digestion on a gel

The purpose of this lab is to determine how single nucleotide polymorphisms in the Canis Lupus Familiaris genome can be linked to specific traits. Dogs are perfect candidates to study how changes in ones genotype relates to phenotypic variation. This was accomplished by isolating canine DNA, designing primers to amplify desired single nucleotide polymorphisms, running PCR and digesting the DNA sequences with a restriction enzyme.The products of the digestion were then run on a gel to determine the alleles of each trait. Gel electrophoresis yielded no discernable result or conclusions due to possible errors with load dye or restriction enzymes.

Control Factors: Photos taken mid-day, around 11am. Cloudy.

My destination was the Durfee Conservatory and Garden on the UMass Amherst campus. I began by walking towards the side of the conservatory facing the library. This side contained an entrance with the “Durfee Conservatory” “Visitors Welcome” brown sign and a small garden with benches and trees in front. The door was labeled “Durfee Conservatory”. I walked through this door and closed the door behind me, as to not allow cold air to enter the building.

As I entered, I was in a room filled with many plants, primarily various tree species. Looking directly forward, there was a small stone path leading forward towards a green door. There were clusters of trees and vines on either side, about four trees in a row to my left. I walked forward on the stone path until I was in line with the last tree on my left. The base of this tree contained the largest amount of vines. There was also a label on the tree that said “Sweet Olive”.

I turned left to face this tree. For the first picture (P1) I focused on the vines. There were several species of vines wound around the base of the tree trunk, but my photo focused on the upper vines closest to the center of the tree. More specifically, focused on the strand of ivy vines with a slightly lighter green color than the ones around it (about two feet below the label). I walked closer towards the tree and held my phone about a foot away from the base of the tree, facing the camera slightly downwards towards these vines and took a picture.

The second picture (P2) focused on the tree. I stood about four feet away from the tree. This time I stood closer to the green door so I was at an angle looking at the tree. I held my camera so that the entire tree was in the frame, with only a small fragment of the vines included in the shot. I took the picture.

The third picture (P3) was of the two species together. For this I took two more steps back from the second photo so that my back almost touched the wall. When I held my camera I made sure to include the entire tree and as much of the vines as I could. I took the picture, and left the conservatory.

When you think about the replication of DNA, it is actually quite complex. There are many components necessary to duplicate the genome, including proteins and the correct environment. Considering the number of base pairs in the genome, the duplication of it is quite astounding, especially while trying to duplicate it with minimal errors. This is why there are checkpoints during which the cell checks for DNA damage, the preparation of the correct proteins, and whatever else is necessary to continue with the replication process. There is also a proofreading function built into the DNA polymerase that is extending new strands of DNA, and this helps minimize the number of mutations. Still, mutations are not uncommon when DNA is being synthesized. Point mutations are when a base pair is entered wrongly. This can be harmless and result in a silent mutation, meaning the resulting amino acid is still the same as the original sequence would have coded for. Still, there are worse effects that can result. A nonsense mutation is when the change causes a stop codon to be coded for too early. There are also other missense mutations where a different amino acid than was meant to be is entered due to the mutation. This can alter the entire protein that is being coded for in the DNA. Of course, all of these mutations are assuming that the mutation occured in the coding region of the DNA. Other mutations can go unnoticed because it is within an intron region. 

I have been involved in extensive research at my university in which we are focused on elucidating molecular mechanisms to improve basic understanding of muscle function and develop more effective treatments for diseases related to fatigue. The force generating capacity of muscle is ultimately derived from changes of muscles molecular motor, myosin. In that case, the lab that I am involved in closely investigates myosin and the mechanics and kinetics of myosin function. We hope these lines of investigation will both improve our basic understanding of muscle function and reveal the root molecular causes of related diseases, ultimately leading to improved treatments.Different techniques that are used include both in vitro motility assay and single molecular laser trap assays. The single molecular trap assay consists of an actin filament attached to two glass beads held in optical traps which are brought in to contact with a third bead sparsely coated with myosin. 

I took my pictures in the middle room of the Worcester Dining Commons, at a long table on the left side (if facing the sandwich bar) about halfway down the room. I selected an apple from the basket in the Asian room (Oak Room). The apple I selected was small enough to comfortably in the palm of my hand, and was irregularly shaped despite my efforts to pick an apple that was as uniform as possible. I took pictures of the apple with a ruler placed in front of it for scale, then took pictures of the subject who would be eating the apple holding the same ruler. The subject was a friend of mine who agreed to help. I asked the subject to sit facing the windows, so that when taking the pictures my back would be to the light. This was intended to reduce the amount of glare in the pictures and increase visibility of the subject. To document the interspecies interaction, I asked the subject to take a bite out of the apple. I had him facing away from me and towards the tv so that I could take the picture in profile, ensuring that he, the apple, and the interaction between them would be clearly visible. I documented the aftermath of the interaction (the apple with a bite taken out of it) in the same manner as previously, with the ruler placed in front of it for scale, making sure that the bite was clearly visible in the photo.

    The theory of splitters and connectors goes like this, there are essentially two types of people, and it’s possible to be inside the spectrum between these two kinds. One type of these people are known as splitters, and they are people who tend to have more difficulty connecting ideas on their own accord. For example, if you were to teach a child how to subtract two large numbers using the traditional method, one child may ask “why do we have to carry the one?” when it makes sense to another child without them having to ask. This second child is an example of a connector. A person who naturally is able to connect ideas without them being explicitly told. This concept connects with academics, but it can also relay into our daily lives as well. For example, you can dine at a restaurant, and if you notice that you aren't getting water--some people may complain about the service explicitly to a busser or a server. Others may notice that there is only two waiters in a restaurant seated for 40 people, and may think to themselves “oh, they must be understaffed” so you are able to sympathize and not complain all together. Then there are those who before even walking in, notice there are only two waiters in a busy restaurant and decide not to dine there at all. These three examples represent one person who is a splitter, another who is in the middle, and finally one who is a connector.

In the Luo 2007 article “Transformation and diversification in early mammal evolution”, Figure 1 shows that modern carnivores did not descend from Repenomamus. Node 3 in the figure shows that modern carnivores share a common ancestor with Repenomamus, however the Figure also shows that after this common ancestor a diversification event occurred. One of the resulting branches of this diversification was the order eutriconodonta, and Repenomamus was a genus in one of the subgroups of the eutriconodont order. Further separate diversification events lead to groups such as the multituberculates, the spalacotheroids, the stem cladotherians, and the stem boreosphenidans. Modern carnivores share a more common recent ancestor with the stem boreosphenidans than with the eutriconodonts, and the fact that the genus Repenomamus had branched off long before this common ancestor shows that modern carnivores did not descent from Repenomamus.

As a result of the more strenuous birth process humans often require assistance from others during childbirth to avoid complications, while most non-human primates give birth alone with relatively little difficulty. The assistance is necessary because the physically painful and exhausting process of overcoming the passing of a relatively large infant through the narrow birth canal can result in medical issues for both the mother and child. In addition, the fact that babies rotate to pass through the canal means they exit face down, thus making it difficult for the mother alone to remove the child without risking spine injury. Because the task of childbirth can be so physically intense or even dangerous, it can also be emotionally daunting, which also gives rise to the desire for support from others. In addition, because childbirth is often viewed as an momentous event, many cultures view the presence of close relatives or other community members as necessary to help guide the mother and properly welcome the new child.