Writing in Biology

The researchers will take a personalized adoptive cell transfer and cancer vaccination immunotherapy approach to eradicating pancreatic cancer. Identification of expressed and immunologically active tumor-specific neoantigens in each patient will be performed in vitro and resulting neoantigens will be engineered into a gene incorporated into isolated peripheral blood mononuclear cells (PBMCs) and dendritic cells. Expression of endogenous antigens will be displayed via MHC class I, while a different cellular model will express an identical engineered gene with an additional signal sequence that will excrete the neoantigens subsequently displayed on the dendritic cells via MHC class II. CD4+ and CD8+ T cells will then be activated and incorporated into a vaccine delivered to the patient.

Using the Primer3 software, primers were created to amplify the region of the NaN1793 mutation. These primers were chosen with respect to the fact that Sanger sequencing can only sequence about 1000 b.p maximum, and the mutation should not be too close to either primer since the beginning and end of sequencing data is usually less accurate than the middle. The expected size of the amplicon is 874 b.p. In order to confirm that DNA was extracted from the plants and to decide which samples to take for sequencing, gel electrophoresis was run. Two gels were run. One gel contains PCR products in a ¼ dilution in T10E1 (TE) buffer while the other contains PCR products in a ¼ dilution with H2O as a control. T10E1 buffer protects nucleic acids from degradation.

It was determined that unknown #6 is 2-hexanone. The reaction with 2,4-Dinitrophenylhydrazine was a positive test confirming that the compound was either a ketone or and aldehyde and not an alcohol. The Schiff’s test showed a light pink color meaning it was a negative test determining that the compound was a ketone and not an aldehyde. The iodoform test showed that the compound was water soluble and formed a yellow precipitate confirming the compound to be a methyl ketone. The melting point of the compound was found to be at 111-112°C which is comparable to the melting point of 2-hexanone (110°C). 5-phenoxy-2-pentanone also has a comparable melting point of 110°C, but after observing the H-NMR spectrum of the two compounds it showed that unknown #6 was 2-hexanone. This is due to the peaks visible at 2.5-2.0 ppm and the peaks at 0.5-1.5 ppm. 5-phenoxy-2-pentanone shows peaks further downfield due to the presence of a double bonded oxygen and an oxygen bonded to a benzene ring.

In this experiment, dog DNA was extracted and amplified through polymerase chain reaction (PCR). The DNA was then sequenced and analyzed using the Sanger Method. Excitability and size were chosen as traits to further analyze. By creating primers for dCAPS, the specific alleles for each trait were determined. The DNA was then dissolved with the digestive enzyme and ran on the gel for analysis. We had hypothesized that excitability and size are traits where heterozygous alleles exhibit codominance. Due to error in selection of the proper primer for creating our dCAPS, only the DNA marker was present on our gel. Therefore, no conclusion to our hypothesis was made. 

Raptors hunt larger prey than other types of birds, so their sharp, hooked beaks allow them to pierce prey, tug away skin, pluck out feathers, tear meat into smaller-sized chunks that are easier to swallow. Insectivores use their slender, tweezer-like beaks enable them to catch insects midair, pick insects off leaves, or probe between small crevices of tree bark, or for drilling holes into wood. Seed-eating birds have short, thick, and strong beaks equipped for cracking open hardy seeds. The size of the beak can indicate the type of seed or nut the bird is adapted to eat. The variation in beak size within the raptors, seed-eaters, and insectivores observed across grasslands, woodlands, and marsh habitats can be explained by the specialized diets in different habitat types.

Parkinson’s Disease is a disorder that affects the central nervous system. Signs and symptoms include tremors, rigidity, bradykinesia, and akinesia. There are reasons to suspect that certain signs and symptoms come from the medication that are being consumed to help with PD. Medication such as Levodopa, an antiparkinsonian medication. An experiment was conducted to see how people with PD would reacts to commands when they are on Levodopa or not. Results showed that PD volunteers, who were introduced to the drug or not had a lower false alarm rates on the high reward. The premise of the experiment was to see the reaction rate of the volunteers with or without the drug. Even if the volunteer wanted to move faster their bodies cannot and there was a difference between the volunteers taking and not taking the drug. The results of the study can be used to design new drugs that can improve motor initiations. Now we know that the current drugs are not allowing people with PD to move fast enough. 

We do not just memorize all the information that is presented to us. We have to use the information we know to evaluate the problems and solve them based on the information we have. That information could be sets of laws. For example, in physics (Physics 131) we have very few laws like F=ma, or Sum of torques = 0, that are used to solve numerous problems and likewise, in organic chemistry, the mechanisms behind reactions are the laws that determine the outcome of countless reactions. Likewise, in a biology course, like BIO152, although there a lot of information, the general patterns we observe in nature may be applied to behaviors of different species and we can therefore accurately predict the causes of certain behaviors or problems in nature.

Fatty acid synthesis is mainly carried out in liver cells and involves multple processes and is not the reverse of fatty acid oxidation. Fatty acid synthesis consists of 3 steps; acetyl-CoA transport, malonyl-CoA formation and the synthesis cycle. The product of fatty acid synthesis is palmitate. The first step being acetyl-CoA transport involves acetlyl-CoA being transported from the mitochondrial matrix directly into the cytoplasm. The second step is malonyl-CoA formation and this occurs when acetyl-CoA is carboxylated to form this compound which is direct substrate of fatty acid synthesis and is catalyzed by acetyl-CoA carboxylase. The last step to create palmitate is the synthesis cycle. This cycle involves several sequential cycles of reactions. The priming step then each cycle adds two carbons from malonyl-CoA. All fatty acid chains that are produced by the enzyme fatty acid synthase are 16 carbon chains long however, with both elongation and desaturation the ability to generate other fatty acids is possible making them each different. When fatty acids are desaturated, double bonds are added. These double bonds result in a less of an energy yield when they are broken because they are more oxidized. 

Action potentials are generated in axon hillock, opening sodium channels as they go (starts moving in all directions). The ones on the right, are depolarized and have not seen action potentials yet. The ones on the left (retrograde) have closed inactivation gates which are essentially on a timer. Things that are retrograde are in absolute refractory, the things that are anterograde are depolarized.