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.

Comm final project intro

Submitted by koganezova on Fri, 04/28/2017 - 13:06

    In the study of animal communication, many factors can influence behavioral response, even in cross-species interactions (Elgier 2009).  The domesticated dog, Canis lupis familiaris, is an animal known for its positive social interaction with humans and has even been nicknamed “man’s best friend”, as they seem to have “a flexible understanding of humans’ communicative intents (Brauer 2009).  Dogs have a variety of behaviors that occur in response to verbal prompts from humans. This is due to the fact that dogs are very good at tuning into the feelings of their owners(Morelle 2014). Previous research suggests that dogs use associative learning “to form a variety of connections between vocal signals (from humans) and other signals, actions and emotions having more immediate significance and meaning to them”, such as tonal variation of voice or visual gestures rather than actually understanding human words (Lindsay 1999: 356). Furthermore, research conducted by Attila Andics at Eotvos Lorand University in Hungary concluded that dogs have the ability to distinguish between praise and other forms of verbal communication by listening to the “meaning and intonation of words” (Greenfieldboyce 2016). But how would that affect the overall behavior of  Canis lupis familiaris when presented with different tonal stimuli?

In this study, we observed and recorded the response of two domesticated dogs when exposed to different tones of voice from familiar humans.This research was conducted in an environmental context the dog is acquainted with (the homes in which they live). The first video consists of a series of clips recording the dogs’ response to an upbeat tone of voice classified as “happy”. This tonal variation is usually used in contexts associated with positive interaction with the dog. The second video displays the dogs’ behavior when the human takes on a more “condescending” tone. This tone is associated with disappointment or punishment due to behavior considered bad (eg. getting into the trash, defecating on the floor, etc.). The stimuli were random, and did not occur in response to a previous behavior of the dog. We predicted that both dogs would have different responses when they were spoken to in a happy tone in comparison to when they were spoken to in a condescending tone. This would show that dogs understand that different tones of voices portray different meanings in communication.

 

PP: Virtual Reality to Repair Spinal Injuries

Submitted by eriklee on Fri, 04/28/2017 - 12:52

His study involves patients with 3-15 years of being paralyzed by the spinal cord with partial function. He uses a three step system to model the brain signals transmitted when walking or moving around. The first step involves the patient using a virtual reality machine to control the motions of walking with brain waves. The second step puts the patient on a treadmill with mechanical legs, controlled by brain waves. The third step places the patient in an exoskeleton, similar to the one shown in the World Cup to practice walking around. The team has noted that patients have shown signs of partial recovery for the ability to emulate walking. 

Cancer genetics project 3 excerpt 2

Submitted by jdantonio on Fri, 04/28/2017 - 12:06

One of the major problems that the immune system faces when fighting cancer is a lack of T-cells that are able to recognize the cancer as a pathogenic entity and begin an immune response to the cancer cells.(Drake et al 2014)We propose that we create adapted T-cells that are capable of recognising and binding to tumor cells via tumor specific neoantigens (Rosenberg 2014). We will accomplish this with a multi step T-cell adaptation which will include selection for T-cells with endogenous neoantigen bind receptors and an addition of a chimeric neoantigen specific receptor via gene transfer to those cells already selected for endogenous receptors. These double neoantigen  receptor possessing T-cells will then be further genetically modified to remove T-cell inactivation pathways thus preventing tumor cell inhibition of T-cell activity. Specifically we will be be down regulating the PD1 receptor which stimulates T-cell death and the CTLA-4  which inhibits T-cell activation.(Rosenburg 2014)This will lead to T-cells that have a very high binding specificity to cancer cells and that are resistant to T-cell suppression mechanisms thus allowing them to activate the cell death pathway in cancer cells and elicit a greater immune response against the cancer cells.

Drake CG, Lipson EJ, and Brahmer JR. 2014. Breathing new life into immunotherapy: review of melanoma, lung and kidney cancer. Nature Review 11: 24-37.  <http://www.nature.com/nrclinonc/journal/v11/n1/full/nrclinonc.2013.208.h....



Rosenberg SA. 2014. Decade in review—cancer immunotherapy: Entering the mainstream of cancer treatment. Nature Review 11: 630-632. <http://www.nature.com/nrclinonc/journal/v11/n11/full/nrclinonc.2014.174.....

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