Submitted by jiadam on Sun, 04/30/2017 - 21:43

Meselson-Stahl Experiment
This experiment utilized 2 different nitrogens isotopes because nitrogen is a huge component of nucleotides. They were 14N and 15N. 14N is the light nitrogen and is the most abundant on earth. This makes DNA less dense. 15N is the heavy nitrogen which is not as abundant and denser. They used two different nitrogens so that they can be separated by density where the lighter would rise to the top. 15N was placed in E.coli and E.coli replicated the DNA. Using density centrifugation, they were able to see the amount of each nitrogen and which nitrogen it was because of the differences in density. After the first round of replication, the DNA was in the middle of the test tube which can indicate semi-conservative or dispersive because each DNA molecule is half 14N and a half 15N. After the second round of replication, one set of daughter cells were intermediate (half 14N/15N) and the other was lighter which answer the question between semiconservative and dispersive. DNA is replicated semi-conservatively. After numerous rounds, the amount of 14N was significantly more than 15N.


Submitted by jiadam on Sun, 04/30/2017 - 21:22

Nucleotide addition during DNA replication

It is known that DNA is always synthesized from 5’ to 3’ direction and not 3’ to 5’. The incoming nucleotides are added from the 3’ end of the nucleotide that was added previously. DNA polymerase is the actual enzyme that is used in replicating the DNA strand, but it needs a nucleotides already there that has a free 3’ hydroxyl group. Primase solves this problem because it can add an RNA primer without an existing 3’ OH group. The nucleotide that is being added is a deoxyribonucleoside triphosphate. The triphosphate gives the reaction energy to proceed. To make sure the nucleotides being added are the correct ones, there is complementary base pairing between the nucleotides. Cytosine and Guanine have three hydrogen bonds as opposed to two between thymine and adenine. When the deoxyribonucleoside triphosphate is brought in, a phosphate is let go and a hydrogen from the hydroxyl group on the 3’ end of the previous nucleotide is cleaved and a bond is formed. This interaction creates a phosphodiester bond.


Submitted by robynfarrell on Sun, 04/30/2017 - 20:59

All extinctions are generally due to a change in atmosphere, that leads to a closing niches, which in turn leads to species dying. Volcanoes dump large amounts of carbon dioxide into the air, and that gets incorporated into oceans as carbonic acid. This changes the acidity and pH of the ocean messing with the thermal regime and amount of oxygen in the ocean. Rising acidity levels in the ocean precipitates a lot of marine invertebrates to slowly dying out. When a meteorite strikes it causes for an increase amount of iridium, which at an instant cause a radical change of a decrease in the number of species in that location.

Journal #36 - The Five Extinctions

Submitted by robynfarrell on Sun, 04/30/2017 - 18:30

Since the Earth has come to be there have been five mass extinction: Ordovician, Devonian, Permian, Triassic, and Cretaceous. The Ordovician extinction was an omega event, and occurred due to interglacial episodes and changing in marine heights. The Devonian extinction is technically not an extinction rate, it was more of a case where there were not enough new species being produced, and that was due to global cooling followed by global warming. The Permian extinction was an omega event that was caused due to volcanism. The Triassic extinction was another omega event, that was also due to volcanism and increased levels of carbon dioxide. The Cretaceous extinction was due an impact of a meteorite, and global warming followed by global cooling.

All extinctions are basically due to a change in atmosphere, that leads to a closing niches, which in turn leads to species dying. Volcanoes dump large amounts of carbon dioxide into the air, and that gets incorporated into oceans as carbonic acid. This changes the acidity and pH of the ocean which changes the thermal regime and amount of oxygen. Rising acidity levels in the ocean caused a lot of marine invertebrates to slowly die out. When a meteorite strikes it causes for an increase amount of iridium which at an instant decreases the number of species, such a radical change. 

Journal #35 - Environment Changes and Animals

Submitted by robynfarrell on Sun, 04/30/2017 - 17:02

When the environment changes it leads to rapid diversification of animals. Things such as the warming and retreating of glaciers, oxygenating of the ocean, changes of the acidity in water, and decreasing levels of carbon dioxide in the atmosphere can all have major effects on species. For example, the Cambrian radiation of animals was brought about due to an increase in oxygen availability. Species started developing genetic toolkits, body segments, and even skeletal structures. The Devonian radiation of plants happened due to the colonization of terrestrial environment. Plants started developing seeds, and vascular tissue during this time period. These are all examples of adaptive radiation, which means that a group or organisms diversify in order to fill out different ecological niches. 

Urushiol Perfect Paragraph 2

Submitted by kcapri on Sun, 04/30/2017 - 16:52

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 percent compositions of urushiol depend 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 percent, while the next most abundant was mono-urushiol at 14-16 percent, and diene urushiol at 5-8 percent concentration (Tetsuo et al., 2002).

Genetics Lab Paper Introduction

Submitted by kcapri on Sun, 04/30/2017 - 16:50


Genetics is an important subject in biology to understand and learn for a number of reasons. It can help us learn not only more about ourselves as humans, but more about our favorite furry friends -- the canine. Dogs and humans have been friends for a while now. There are over 350 domestic dog breeds that have been selected artificially thanks to humans in the last 200 to 300 years (Rimbault and Ostrander, 2012). This artificial selection has caused breeds with varied traits such as body size, leg length, and skull shape. These small variances are a result of hundreds of genes. An example of a gene that codes for a phenotypic dog trait is the melanocortin receptor type 1 (MC1R) gene that codes for coat color. While many genes do control coat color, MC1R is one we observed.

The experiment aided in learning about the genetic mechanisms that control morphological traits that define certain breeds. In order to do this, we performed several different laboratory experiments over several different weeks. First, we isolated the canine DNA samples that were collected from the dogs’ of the classmates.  We then decided on certain primers to observe different SNP markers, or mutations in the genome, that result in specific traits of dog breeds such as anything from their trainability, excitability, to their snout ratio. Once we designed these primers and purchased them, we performed a number of Polymerase Chain Reaction (PCR) runs on the dog DNA samples in order to analyze the traits of the different dogs and try to classify them. PCR was developed in the 1980’s by Kary Mullis and uses the ability of DNA polymerases to synthesize a new strand and uses a primer to make it possible to delineate a specific region of a template strand and amplify it (“Polymerase Chain Reactions,” 2014). By doing this amplification, we can sequencing DNA and learn more about certain traits, as done in this laboratory report.


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



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).



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