Genetics Lab Paper Abstract

Submitted by kcapri on Sun, 04/30/2017 - 16:49

Investigation of Breed-Defining Traits of Canines Through DNA Isolation, Sequencing, and Analysis

 

ABSTRACT

Through several different procedures involving DNA samples taken from 15 dogs, we were able to analyze the unique morphological variances in dog breeds that define them. This included analyzing polymorphisms or SNPs in the genome that lead to traits such as low snouth ratio, high weight and tall height, short coat, and even trait behaviors like pointing or herding. These procedures included DNA collection, isolation, primer design, polymerization chain reaction (PCR) runs, and DNA sequencing and analysis. The results allowed us to create hypotheses of which DNA samples matched which dog breeds.

 

Urushiol Paper 6

Submitted by kcapri on Sun, 04/30/2017 - 16:48

Research and experiments involving urushiol are still continuing today. In 2012, researchers at Duke University engineered a molecule that reacts with urushiol and creates a fluorescent glow under ultraviolet light (Braslau et al., 2013). This can help campers, hikers, and other outdoor recreationists identify plants containing urushiol and prevent urushiol dermatitis. Studying urushiol and trying to understand its synthesis, storage, release, and impacts of humans and the environments can lead to other conclusions and discoveries in other fields. Duke University conducted another study of urushiol over a six-year period and discovered an increase in poison ivy growth when carbon dioxide was increased in their environment (Mohan et al., 2006). Additionally, the poison ivy plant used more of its energy on urushiol production in increased carbon dioxide environments than in lesser ones (Mohan et al., 2006). Knowing information like this can help researchers understand and infer what might happen as carbon dioxide levels increase globally. Not only this, but researching poison ivy, oak, and other plants with urushiol can aid in better the understanding of the human immune system and possibly help treat tumor cells. Recent studies suggest that urushiol induces cell growth inhibition as well as cell apoptosis by a specific pathway called p53-dependent pathway, which could be important in future cancer research (Kim et al., 2013). Examples like these studies demonstrate the importance of urushiol research and understanding for the future. Furthermore, experiments like these illustrate the importance of plants in general and understanding their physiology because they impact not only the earth, where we call home, and the animals around us, but humans as a whole.

 

Urushiol Discussion 5

Submitted by kcapri on Sun, 04/30/2017 - 16:47

A dermatitis reaction due to urushiol can happen through direct contact (touching the bruised/damaged plant directly), indirect contact (touching a glove or piece of clothing with urushiol on it), or inhalation due to the burning of a urushiol-containing plant (Ewing, 2015). When urushiol touches the human skin, tiny chemicals called haptens are secreted into your body and skin-proteins called antigens are activated and adhere to the urushiol chemical (Ewing, 2015). Next, Langerhans cells then adheres to the antigen with the haptens. It will then recognize that the molecule is foreign and send signals to helper T- cells in the body. If it is the first contact of urushiol, the helper T-cell will remember the urushiol for the next contact and not react until the second exposure. The first sensitization of urushiol causes the Langerhans cells with the antigen to migrate to the lymph nodes to present it to the T-lymphocytes for recognition and reaction during the second exposure (Rietschel and Fowler, 2008).  If one is exposed again and is allergic, the helper T-cells will release cytokines and chemokines that cause the dermatitis reaction of the skin. Then, they signal macrophages, T-lymphocytes, and more t-helper cells to that all can eliminate the Langerhans cell with the foreign hapten urushiol chemical (Ewing, 2015). Yet, these fighters also kill healthy cells as well. The dermatitis reaction is dependent on the amount of urushiol that has secreted into the bloodstream, how susceptible one is to urushiol, and any past contact with urushiol. It could take up to 24 hours to a week for people who have never been exposed for dermatitis to show up on human skin (Ewing, 2015).

The rash caused by urushiol is non-lethal and only in rare cases has caused death. It can also be caused year-round since urushiol is stored all year, as previously stated. Therefore, it is wise for humans not to touch dead or dried poison ivy plants during the winter months as well. Symptoms caused by urushiol can be alleviated by creams such as calamine lotion, hormones, and steroids now. In the past, different cultures have tried applying anything from crab meat, banana juices, shoe polish, and marshmallows onto the rash (Dickinson et al., 2013). Additionally, acupuncture has also been an option to relieve dermatitis pain.

Besides causing a painfully itchy dermatitis reaction, Urushiol can also serve beneficial purposes. It can serve as a sealant for the plants’ wounds, and thus increases water retention in plants when damaged, and retardation of growth of infectious fungal and bacterial spores (Mullins, 2015). Urushiol was used by Native American tribes and traditional Chinese culture for medical purposes because of its antioxidant, antimicrobial, and antigenic properties (Dickinson et al., 2013). Some also believe in the treatment of osteoarthritis by urushiol to alleviate pain. Though now, the sensitive nature of urushiol to oxidation and polymerization restricts its therapeutic use. Other uses of urushiol include components in face paint, certain types of honey such as poison oak honey, and even erosion-barriers.

In order to prevent dermatitis and remove urushiol-contact from human reach, several methods have been implemented. Different chemicals sprays can be added to lawns and areas to kill poison ivy. Another method of urushiol removal that may be more environmental-friendly are goats. There are several companies that can be hired to bring goats that eat poison ivy and urushiol-containing plants (Dickinson et al., 2013).

 

Plant Physiology - Urushiol 4

Submitted by kcapri on Sun, 04/30/2017 - 16:46

Plants are impeccable chemists and it is critical to understand the chemical traits of urushiol before discussing synthesis. This toxin is a mixture of alkyl catechols that is comprised of a 1,2 dihydroxybenzene ring (Flank, 1986). It is a phenolic compound, which means it consists of a benzene ring with a long hydrophobic side chain consisting of a large number of carbons on the carbon-3 position of the benzene ring, as shown in Figure 2. Depending of the specific plant containing urushiol, the amount of carbons in the side chain differs. While poison ivy and sumac have 15 carbons on its chain, poison oak has 17 carbons.

Urushiol is synthesized in the secretory cells of the resin ducts by the shikimic acid pathway. Resin components are derived from carbohydrates that are produced from photosynthesis.  As shown from Figure 3, Protocatechuic acid is a product of the shikimic acid pathway and then used to produce urushiol (Caspi et al., 2013).

When discussing the amount or concentration of urushiol in plants, it does depend on the growth conditions and the particular season. A study performed by Japanese researchers indicated the percentage compositions of urushiol depending on its unsaturated bonds in Japanese, Korean, and Chinese Rhus vernicifera (lacquer trees). Researchers found that the most abundant urushiol was the triene urushiol at 71%, while the next most abundant was mono-urushiol at 14-16%, and diene urushiol at 5-8% concentration (Tetsuo et al., 2002).

Urushiol is vital to research and understand for a number of reasons. It is believed that urushiol’s purpose may be a defense mechanism for plants. When humans touch plants such as poison ivy are damaged, a skin dermatitis reaction due to urushiol results. Yet, it is interesting that while humans are allergic to urushiol, most other animals are not. Besides humans, only guinea pigs, rabbits, mice, and sheep have slight sensitivities to this toxin  (Dickinson et al., 2013). Furthermore, it is also interesting to note that humans came late to North America, after poison ivy and urushiol were already present and prospering on the land, which also conflicts with this defense mechanism theory (Senchina, 2006).

There are several impacts urushiol has on humans and the environment -- both positive and negative. To start with harmful impacts on humans, there is the dermatitis reaction caused by urushiol when poison ivy tissue is damaged and it is released and in contact with humans. Some people are so sensitive to urushiol that only 2 micrograms on human skin can cause a reaction (Epstein et al., 1974).  Around 80-90% of adult American individuals were reported to have a dermatitis rash when exposed to  50 micrograms of urushiol (Epstein et al, 1974). Additionally, urushiol can be difficult to wash off clothing and skin, so it can be spread by touching an urushiol-contaminated item. It is important to wash all skin and articles of clothing that may have come into contact right away to prevent the spread.

 

Journal #34 - Bastian Mimicry

Submitted by robynfarrell on Sun, 04/30/2017 - 15:33

In one of my classes we had talked how some organisms use mimicry to help them escape predation. One form of mimicry that was discussed was Bastian mimicry. This is when one species tries to mimic a species that is distasteful and toxic. There are different results that can happen with this occurs. If a population consists of many toxic species, the species that is going to be mimicked, and few non toxic species, the species that will do the mimicking, the predator is more apt to run into a toxic organism. This is due to the chance of probability. When the predator goes to attack the toxic organism it learns that it is something that they should try to avoid and lessens the predation. So now both the toxic species and the species that is not toxic but looks like the toxic species get ignored, a stable strategy. This would go into fixation, and evolution would allow it to continue down this path.  If there is a population that consists of many mimics, an only a few toxic species the predator is more apt to run into the mimic first, eat it, and not learn that this species is something to avoid. This is an unstable strategy which is going to make the toxic species evolve into something different and get a new morphology. If a different morphology evolves in the toxic species it will be selected for. 

T4 bacteriophage

Submitted by amprovost on Sun, 04/30/2017 - 13:39

I recently experimented with T4 bacteriophage in a microbiology lab. My findings were as follows: 

This lab involved two experiments, the titration and isolation of a lytic phage and a phage typing experiment.

            In the experiment with the titration and isolation of a lytic phage, it was predicted that as the lytic phage became more diluted, it would produce less plaques on the Escherichia coli lawns, and that at least one plate would produce a countable number of plaques. This experiment was performed by creating a serial dilution of the T4 phage. This phage was diluted to 10^-8 dilution by initially combining 0.1 mL of T4 phage with 0.9 mL of TM buffer, then taking .1 mL of this solution and transferring it into another tube with0 .9 mL of TM buffer. This process was repeated until the 10^-8 dilution was achieved. Each of these solutions then had 0.1 mL transferred onto its own individual Luria agar bottom plate. Each of these plates also had 0.1 mL of E. coli B/r poured onto them. These solutions were swirled around the plate to make sure all of the surface area was covered. After these bacteria and phages were allowed some time to grow on the plates, the plates were inspected for plaques, which are small holes in the bacteria lawn caused by phage lysing. Plates with over 300 plaques were considered too numerous to count, and plates with less than 30 plaques were considered too few to count.

Dilution levels 10^-1 through 10^-5 were too numerous to count, and dilution level 10^-8 was too few to count. Dilution level 10^-6 had 205 plaques, and dilution level 10^-7 had 73 plaques. The plaque forming units/milliliter were then calculated using the equation average of PFU/ amount of phage added to the plate * dilution factor. The plate at dilution factor -6 was found to have 2050000000 PFU/mL, and the plate at dilution factor -7 was found to have 7300000000 PFU/mL.

The expected results of this experiment were confirmed, two plates with a countable number of plaques were cultivated.

            In the phage typing experiment, it was expected that the two E. coli strains would be infected by T4 phage, as E. coli have binding sites on their cell surface that T4 bacteriophage can bind to and infect the cell from. A LB plate was divided into four quadrants, and each was swabbed with its own individual bacteria (E. coli B/r, E. coli K12, Salmonella arizonae, and P. vulgaris). Each of these tiny lawns was then inoculated with T4 phage from the original plate, using a toothpick to stab the burst zone on the original plate and transfer it to the new plate. A new toothpick was used for each lawn in an effort to prevent cross contamination. E. coli K12 and E. coli B/r  both developed burst zones around the area of inoculation, and Salmonella arizonae, and P. vulgaris did not, showing that the T4 phage only affected E. coli K12 and E. coli B/r. The expected results were confirmed, as both strains of E. coli were infected with T4 bacteriophage.

Myopia

Submitted by amprovost on Fri, 04/28/2017 - 17:53

Myopia, also known as nearsightedness, is a visual impairment that causes one's vision to blur when looking at an object that is more than an armslength away. This condition has been around for a very long time, but has recently seen a very large increase in the percentages of populations that it affects. For some time scientists thought that this phenomenon may be caused by "near work", or work that requires visual focus on something at a close range, such as reading or writing. However, there has never been a firm scientific link made between near work and nearsightedness, so scientists are looking for other explanations. Another popular theory is the genetic theory, but this theory also has some holes in it. For example, one study showed that a community that only had a 2% rate of nearsightedness saw an increase to 50% in just two generations. This rapid increase is simply too much to be explained by genetics, so now popular convention believes that only a fraction of what controls myopia is genetically coded.

     After a series of different studies that ended up with no distinct results, researchers have decided that perhaps the possible link to levels of myopia are related to childhood exposure to sunlight. It is well known that children now spend less time outside than previous generations did, but this phenomenon may now be linked to nearsightedness. One study took chinese children living in Australia and compared them to Chinese children living in China. Asia is known to have some of the highest rates of nearsightedness in the world, so if it was a genetic factor it should show up in the Asian children who live elsewhere. However, despite the fact that the children in Australia did more near work than the children in Asia, the amount of myopia in the Asia group was still much much higher. The only major difference in the studies that researchers found was that on average, the children in the Australian group spent more than four times as much time outdoors than the chilldren in the Asian group. While the direct link to nearsightedness, if there is any, is unknown at this time, many scientists theorize that it may have to do with conditions such as vitamin D levels. Further research must be done on this topic before concluding whether or not natural light can help prevent myopia.

Nitrogen PP II

Submitted by amprovost on Fri, 04/28/2017 - 17:01

            In the denitrifying experiment, four different tubes of nitrate broth were used, one contained P. vulgaris, one contained P. aeruginosa, one contained rich soil, and one contained poor soil. The expected result was that it one would be able to determine the presence or lack of nitrite and nitrate in the broths using nitrate reagent A, nitrate reagent B, and zinc. After applying nitrate reagents A and B, a red color change indicated that nitrite was present. If there was no color change, zinc was added, if there was still no color change, this indicated that nitrate was broken down into a compound other than nitrite. If a red color change occurred after being exposed to zinc, this meant that nitrate was still present and never denitrified. The NB rich soil had nitrate break down into compounds other than nitrite. Both the NB poor soil and the P. vulgaris had the presence of nitrite. The sample with P. aeruginosa had nitrate broken down into compounds other than nitrite. The expected result was confirmed, as it was possible to determine the presence of nitrite or nitrate using these tests.

 

Abstract comm final PP

Submitted by koganezova on Fri, 04/28/2017 - 13:20

    The purpose of this study is to examine the behavioral response of domesticated dogs, Canis familiaris, to different tonal variations of human voice.  A series of video clips were recorded of two dogs in their own separate and familiar homes. Stimuli in the form of tonal variation by the dogs’ masters was presented to the dogs to observe their response. The clips were sorted into two videos according to the tone of voice: a “happy”, more upbeat tone associated with positive interaction between human and dog, and a “condescending” tone, usually reserved for response to “bad” behaviors eliciting human disappointment or punishment. Stimuli were random and did not occur in response to a previous behavior of the dogs. A key of behaviors associated with each tone was created, and a time budget analysis was performed using the Jwatcher program to examine the proportion of time the dog spent in each behavior according to tonal context. Results showed that “happy” tone stimuli resulted most often in  jumping, followed by licking and tail wagging, which are behaviors commonly associated with positive social intention. In the video with clips presenting the “condescending” tone stimuli, submissive behaviors such as lying down and looking up were more common.

cancer genetics project 3 PP

Submitted by jdantonio on Fri, 04/28/2017 - 13:12

The first step in our treatment process is the identification of our cancer’s neoantigens. These would vary from patient to patient and would have to be Identified experimentally. Identification of neoantigens begins by first sequencing the genome of the patient's tumors using massive parallel sequencing(MPS). MPS is a system which readily identifies tumor cell mutations by comparison of the genome of the cancer cells to the genome of a somatic cell (Gubin et al 2015).  This method of genome analysis has been shown to be an effective means to identify cancer cell gene mutations (Shiraishi et al 2011).We will use a hybrid exome sequencing technique which allows for the analysis of only genes which encode proteins and allow sequencing on a time scale that is relevant to clinical treatment (Hodges et al 2009). Once the tumor genome has been sequenced and analyzed to identify mutations we will then determine which of the tumors mutations are in oncogenes capable of binding to the MHC protein within the cell (Gubin et al 2015). This will be accomplished by utilizing bioinformatic databases and softwares, specifically the  NetMHCpan algorithm system which identifies a wide range probable MHC binding sequences in Human and nonhuman primates (Nielsen et al 2007).We will then harvest lymphocytes from the patient and test them for neoantigen binding specificity in vitro and select T-cells with tumor suppressing ability that possess the receptor for one of the neoantigens we derive from or cancer cell genome analysis. Following this we would grow these cells in culture to create a large amount of tumor infiltrating lymphocytes (TIL) (Perica et al 2012). These TIL’s will be further modified to improving their binding specificity and resistance to T-cell suppression.

 

Gubin MM, Artyomov MN, Mardis ER,and Schreiber RD. 2015. Tumor neoantigens: building a framework for personalized cancer immunotherapy. The Journal of Clinical Investigation 125(9): 3413–3421. National Center for Biotechnology Information[NCBI]. <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4588307/>. Accessed 2017 April 24.

 

Hodges E, Rooks M, Xuan Z, Bhattacharjee A, Gordon DB, Brizuela L, McCombie WR, and Hannon GJ. 2009. Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nature Protocol 4(6): 960-974. National Center for Biotechnology Information [NCBI]. <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990409/>. Accessed 2017 April 24.

 

Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Røder G, Peters B, Sette A, Lund O, Buus S. 2007. NetMHCpan, a Method for Quantitative Predictions of Peptide Binding to Any HLA-A and -B Locus Protein of Known Sequence. PLOS one 2(8): e796. National Center for Biotechnology Information [NCBI]. <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1949492/>. Accessed 2017 April 24.   

Shiraishi T,Terada N,  Zeng Y, Suyama T, Luo J, Trock B,  Kulkarni P, and Getzenberg RH. 2011. Cancer/Testis antigens as potential predictors of biochemical recurrence of prostate cancer following radical prostatectomy. Journal of Translational Medicine 9: 153. National Center for Biotechnology Information [NCBI]. <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184272/>. Accessed 2017 April 24.

Pages

Subscribe to Writing in Biology RSS