jnduggan's blog

The Labrador is the one the most intelligent breeds of dogs on the planet. Their relaxed temperament and ability to learn quickly has proved them to be extremely versatile, yet widely competent dogs. They have an incredible sense of smell, and throughout history have been used for hunting and tracking. Labradors are also known to have the largest litters among any other breed, lending the vaccinated pregnant mother the highest chance to produce the most puppies. Maximizing the output of puppies from a mother is the most logical decision because in order to increase the density of dogs on the planet, the growth rate must be large. In order to maximize the growth rate, we must pick an animal that will grow exponentially while also producing the highest output of puppies in their lifetime.

Imagine a world without man’s best friend by your side, without the warm welcome wag and a sloppy kiss every time you walk through the door.  The happiness brought to this world by our canine friends will vanish if we sit back and allow this devastating retrovirus to diminish the world’s dog population.  With our meager supply of vaccine, we are able to save one mother and her litter of puppies. It would be nearly impossible for me to choose just one breed, but with a limited amount of vaccine, I would choose the Labrador Retriever.

The Labrador is the one the most intelligent breeds on dogs on the planet. Their good temperament and ability to learn quickly has proved them to be extremely versatile dogs. They have an incredible sense of smell, and throughout history have been used for hunting and tracking. Labradors are also known to have the largest litters among any other breed, lending the vaccinated pregnant mother the highest chance to produce the most puppies.

A world without the presence of dogs is a scary thought. Having spent the last twelve years of my life with a black lab, their sweet and loving temperament is evident to me. While I have spent time with many other breeds of dogs, none are quite like the Labrador. While my family has chosen the Labrador as our companion and best friend, many others have done the same for their shining qualities and lovable spirit. Chosen by the disabled for their utility as a service dog, and chosen by hunters for their adept sense of smell, and chosen by police for their prowess in detection, I can confidently say I’m not alone in choosing the Labrador given a dire situation where only one breed could be saved.

Even though Labradors have proved their worth to the world through their ability to help mankind, their steady temperament cannot be understated. A world without dogs is one in which I never hope to imagine, but with the ability to save one breed it would have to be the kindest, sweetest, and most caring breed around. Whether I am sick, tired, or lonely, my black lab Maddie has always been by my side, looking after me. Only being able to choose one breed to save is a devastating decision, but I am certain that my life would not be the same without my Lab, and I wouldn’t want others to not have the chance to miss out on one of the most lovable and loyal breeds around due to the new retrovirus.

In this lab the number of organic compounds in two unknown analgesics and three known analgesics was measured by thin layer chromatography.  The two unknown analgesics were identified by comparing their elements to the elements in the known analgesics. During the first part of the lab, Aspirin, Acetaminophen, Caffeine, Unknown 1 and Unknown 2 were dotted onto a silica plate using capillaries.  The silica plate was then developed in about 4 mL of ethyl acetate. In order to stop the small samples of analgesics from being washed away it was important to ensure that the ethyl acetate level stayed below the dots. It was also important to keep the silica plate vertical so that the solvent did not move up the silica plate at a diagonal. Once the solvent reached about a centimeter away from the top the plates were dried and observed under UV light and in Iodine crystals.  The distance traveled by the solvent and spots was then measured and the Rfs calculated. The average Rf of Aspirin was found to be .3305, Acetaminophen to be .337, Caffeine to be .347, seemingly corresponding compounds in Unknown 1 to be .085 and .3565, and finally Unknown 2 to be .2625. After reading into research, it was discovered that caffeine should have a much lower Rf than was found. Therefore, the organic compounds that are in Unknown 1 appear to be the same organic compounds found in Caffeine and Aspirin. The organic compounds found in unknown 2 appear to be the same unknown compounds found in Acetaminophen and Aspirin. These results were found by comparing the Rfs of the known compounds to the unknown compounds.   

     For the second part of the lab, the effect of solvent polarity on Rfs was tested.  In order to accomplish this, two identical plates were prepared with Anthracene, Benzil, and Triphenylmethanol.  The difference between the two plates was their development solvent. One was developed in Ethyl acetate (the same solvent used in the first part of the experiment) and the other was developed in 95% hexane and 5% t-butyl methyl ether (a nonpolar solvent).  Since Ethyl Acetate is so polar, the Rfs of all three compounds dotted onto the silicone were close to one. This means that the distance traveled by the compounds was almost as much as the distance traveled by the solvent. This is due to the tendency of the compounds being more drawn to the polar solvent than the less polar silicone plate.  The Rfs of the compounds developed in hexane were much smaller meaning the compounds were more drawn to the polar silicone plate than the nonpolar solvent.

The “Yeast Mutation and Analysis” lab protocol served as a guideline for the first day of our Yeast Mutagenesis experiment. On day one we performed a serial dilution of ~107to ~104yeast cells using a pipette, sterile test tubes, and vortexer. From the105dilution, we pipetted 100µL onto a YED plate and repeated with a second YED plate.  We then exposed both plates to UV radiation for 5 seconds. We made a control plate that we did not expose to UV radiation and incubated all three plates for 3-5 days.  After that time, the lab professor removed them from the incubator.

The “Yeast Mutation and Analysis” lab protocol served as a guideline for the first day of our Yeast Mutagenesis experiment. During the first day, we performed a serial dilution of ~107to ~104yeast cells using a pipette, sterile test tubes, and vortexer. From the105dilution, we pipetted 100µL onto a YED plate and repeated with a second YED plate.  We then exposed both plates to UV radiation for 5 seconds. We made a control plate that we did not expose to UV radiation and incubated all three plates for 3-5 days.  After that time, the lab professor removed them from the incubator. During the next lab period on September 26th, we observed the plates. Since we had no mutants, mutated yeast cells were provided to us.  We designed an experiment to test what gene the mutants were mutated in. We decided to cross the 4 unknown types of mutants we were given with 4 known types of mutants to see which mutants complemented and which mutants had mutations in the same genes. During the same lab period, we streaked the 4 unknown mutants and the 4 known mutant parent groups onto a YED plate and left them to incubate for two days. The streaks contained 1a, 2a, aMw, and aMx on the horizontal axis and 1ɑ, 2ɑ, ɑMy, and ɑMz on the vertical axis.  On September 28th, two days after streaking and incubation, we mated the UV mutants. A small sample of each of the corresponding parent colonies was put where the two parent groups would intersect and mixed with each other. We allowed 2 days of incubation after mating before replica plating onto an MV plate. On October 2nd, the YED plate was replica plated onto an MV plate and an MV+Ade plate. We left the replica MV plates in the incubator until the following lab period.

In the Fall of 2018 at the University of Massachusetts Amherst during Biology 284- General Genetics Lab, my partner and I designed an experiment to mutate Saccharomyces cerevisiae, or baker’s yeast, and categorize the resulting mutations.  

Baker’s yeast has two almost identical mating types, MATa and MATɑ, which can sexually reproduce with each other and asexually reproduce themselves.  If the environment they are in is nutrient poor, the yeast cells can exist in a haploid form of MATa or MATɑ. A colony of haploid cells can be maintained by asexual budding.  If the environment they are in is nutrient-rich, the different mating types will become shmoos, a nodule of the original cell that the cells use to join together. Once they become an a/ɑ diploid, they can bud to asexually reproduce two yeast cells, the new cell being exactly identical to the first. If a diploid cell is starved of nitrogen and also on a carbon-poor source, it will sporulate to form four ascospores within an ascus.  Those spores can be released from the ascus membrane and become 4 haploid yeast cells, two a and two ɑ cells.

Mutations come about by mutagenesis, which is a relatively rare event in nature.   DNA replication is a highly regulated event that rarely lets imperfections slip by. Even when a mutation occurs in DNA, it does not always lead to a change in phenotype. Mutagens such as UV light, as used in this experiment, X-Rays, and chemicals are often used to increase the frequency of mutations for scientific study. In order to successfully study mutations, the cells must live and be able to reproduce through the mutagen exposure and contain a non-lethal mutation.  

The appearance of the actual photos in the multipanel scientific figure was due to the different conditions on those days.  On the day that the pictures from the original figure were taken, it had not rained in several days and was very sunny outside resulting in the bright complexion and dry stones.  On the day that the replica photos were taken, it had rained earlier and the sky was still dark.

The difference in the appearance of the photos was also due to the two photographers holding the camera in a different way.  The angle of the two close up pictures is different; it appears that the replica picture was taken straight on, while the original picture was taken from an angle to the left of the spider web.

The markings on the pictures of each figure are also different from the other figure.  In the original, the letters labeling the picture are in the bottom left corner, whereas they are in the top left corner in the replica.  The arrows pointing to the location of the spider web are on different pictures in each figure. The original has the arrows on the environment picture and the replica has them placed on the close-up picture.

The two map pictures varied.  The two maps show different areas of campus.  The replica map also has labels on the map already that the original map does not.  There are labels added to the original map, while all labels on the replica map are a part of the picture itself.  There is no circle showing the area of the map in which the spider web was found in the replica map, but there is on the original map.

The pictures themselves also differ from original to replicate.  Due to the quality of the pictures and lack of arrows on the environment picture of the replica, it is difficult to tell if the two spider webs are the same. The appearance of the stones relative to the spider web is different between the original and replicate in the close up picture.  In the environmental picture of the original figure, the curb and a blue building are visible in the background, but in the replica picture an orange building is visible and the curb is not. There is also a different number of posts on the fence visible in the replica vs. the original.

ABSTRACT

As a part of my Writing in Biology class in the Fall semester of 2018 at the University of Massachusetts Amherst, I conducted an experiment to test the reproducibility of a multipanel scientific figure based solely on the methods I wrote while conducting the experiment. In order to increase reproducibility, I sought to control as many variables as possible while creating my multipanel figure. While writing the METHODS section, I recorded my steps with detail to allow for simpler replication.  The results exhibited variation in areas such as the format of the figure itself, markings on the pictures within the figure, and the content of the pictures. The factors that caused the disparities include differing programs used to create the figure, differing conditions on the two days, and the original spider web no longer being available for photography. The original multipanel scientific figure was not reproduced exactly causing disparities between the replicate and original figure.

TITLE- 

Reproduced Multipanel Scientific Figure of Spider Web Contains Disparities from Original Figure

ABSTRACT

As a part of my Writing in Biology class in the Fall semester of 2018 at the University of Massachusetts Amherst, I conducted an experiment to test the reproducibility of a multipanel scientific figure based solely on the methods I wrote while conducting the experiment. In order to increase reproducibility, I sought to control as many variables as possible while creating my multipanel figure. While writing the METHODS section, I recorded my steps with detail to allow for simpler replication.  The results exhibited variation in areas such as the format of the figure itself, markings on the pictures within the figure, and the content of the pictures. The factors that caused the disparities include differing programs used to create the figure, differing conditions on the two days, and the original spider web no longer being available for photography. The original multipanel scientific figure was not reproduced exactly causing disparities between the replicate and original figure.