Blogs

Once DNA is isolated, it must be quantified.  There are two common methods for quantifying the amount of DNA present in a solution.  A spectrophotometer measures the amount of 260 nm light that shines through the solution.  The absorbance is based on the ratio of transmitted light to incident light. Based on this, a concentration of DNA is calculated.  Unfortunately, a spectrophotometer cannot distinguish between DNA and RNA, so the reported concentration includes all nucleic acids.  Gel electrophoresis is quite accurate in telling size of DNA chains, but concentration of DNA of particular sizes in solution may also be inferred.  A ladder is loaded in the first lane of the gel in order to compare the samples to. The darkness of the samples is compared to the ladder to estimate concentration.  Gel electrophoresis utilizes the fact that the phosphate groups of DNA nucleotides give the molecule an overall negative charge. An applied electric field causes DNA to move down the gel towards the positively charged electrode.  Smaller DNA molecules will migrate faster than bigger ones, and will appear lower on the gel. Results from these two methods can be analyzed to draw conclusions about the true concentration of DNA in solution.

Although it is true that whales have flukes instead of hindlimbs this does not mean that whales do not belong in a monophyletic group of mammals that have hindlimbs. The reason being that early whales did in fact have legs. Even though they no longer possess these hindlimbs it does not take away from the fact that whales once did have them. Occasionally there are whales born with vestiges of these limbs. Whales losing their limbs is just one example of a dramatic evolutionary change, something that has happened countless of times to different species.

I've been holding onto the larva since the last class that was held and there has been a dramatic change in the appearence of the larva. When I brought the larva back into my room I put it on top of my desk and to the side I did not want to keep disturbing it, I wanted to see how it would be reacting without any type of interference. As the day progressed I noticed that it no longer moved around the perimter of the container as a matter of fact it did not move at all. The larva remained off to the side of the container without any movements. This was a huge difference when compared to how it acted before, during class the larva moved rather quickly around the perimeter. Now it was staying still. Even when picking up the container the larva did not make any type of movement. This changed the day after, this is when I started seeing some action from the larva once again it kept busy and moved around the container. This monday the larva no longer moved at all, instead it decided to pupate. It's a dark brown color and when I move it around the container I can tell it is surrounded by a hard shell. It took about four days of having it in order to have this transformation occur. 

PanNETs are often associated with somatic mutations in the MEN1, DAXX, ATRX, PTEN, TSC2, and PIK3CA genes, with the MEN1 gene most frequently mutated (Jiao et al., 2011). MEN1 is a tumor suppressor gene that codes menin, a protein found in the nucleus that regulates chromatin remodeling and plays a role in cell cycle regulation (Jiao et al., 2011). A study by Schnepp et al. found that excision of the MEN1 gene in embryonic mouse tissue led to misregulation of the G0/G1 checkpoint and accelerated entry into S-phase, as well as downregulation of CDK inhibitors in the pancreas (Schnepp et al., 2006). Therefore, MEN1 is a crucial gene to prioritize in treatment as its mutated form can lead to proliferation of cells and eventually, PanNETs. The five other genes mentioned previously will also be studied to understand their interaction with MEN1, but as MEN1 is most frequently mutated, it will be the main focus of treatment. More specifically, the researchers would like to prevent MEN1 excision from occurring and explore targeted treatments involving molecules possibly related to this excision, although more research must be performed in order to find these. Further exploration of this may lead to additional signaling pathways the researchers can utilize in targeted treatment.

    At the University of Massachusetts, Amherst, there lies an interspecific interaction that while in principle is dangerous, it seems to be a regular occurrence for the majority of dormitories. At the university, access to the dormitories require a specific ID in order to unlock the doors. These ID’s are only acquired if a person is given permission and is approved by the university. This includes paying expensive housing fees, attending the university itself, and paying the tuition.
    In principle, there lies a very high requirement in order to gain access into any of these buildings. Yet on the contrary, if you happen to catch a resident leaving the building at the same time you’re trying to enter it, more likely than not the resident will leave the building, and hold the door open for you to go inside. This occurs so frequently, that it’s very likely that if you were to wait outside one of these dormitories, eventually someone will notice you’re standing outside and invite you in.
    The buildings are so incredibly easy to get into, that it almost doesn’t make sense to have the ID card authorization a requirement to enter the building. It’s functionality serves as more of a formality, rather than security like it was originally intended.

I don’t know how many of you kept the larvae from last week but I did. When I took the larvae back to my dorm room I found out that the larvae feed off of decaying vegetation. I put an orange peeling into the cup to see what would happen. A day later the larvae started to move slower around the perimeter of the cup and eventually stayed in one spot. I thought that I had killed the larvae due to the acidity in the orange peel, but the larvae was just moving in a slower rate. Two days after the larvae turned into a cocoon. The cocoon is a dark brown color similar to that of a coffee bean. The cocoon is smaller in size from the initial larvae stage, around 5 segments in length. It has been four days since the larvae turned into a cocoon. 

DNA extraction is an essential technique used in many scientific research endeavours. In my gene and genome analysis lab, BIO383H, we extracted DNA from a young Brachypodium distachyon leaf. DNA is found in the nucleus of cells. As such, we had to disrupt cells and tissues to obtain the DNA. First, we did that by mechanically grinding the leaves. Then we had to use detergent, found in the DNA extraction buffer, to dissolve the solubilize the plasma membrane and other membranes within the cell. Within the extraction buffer is also a metal chelating compund which locks away calcium and magnesium ions, allowing the denaturation of proteins. High temperature was also used to augment the efficiency of extraction buffer and hasten cellular disintegration. After breaking up cells and tissues, we had to prevent the degradation of DNA by DNAse enzymes. The metal chelating compound already helped us with this by locking away calcium and magnesium ions, which are essential co-factors for enzyme activity. Next, we had to remove undesirable products. We did this by rounds of centrifugation and then precipitating out the DNA  by using high levels of sodium and isopropanol. To truly purify the DNA, 70% ethanol was used to wash it. Then it was dissolved in T₁₀E₁ before being stored in a freezer.

The article from Neuroscience News (https://neurosciencenews.com/sleep-pain-10648/) explained the consequences of not having enough sleep and how that affects pain sensitivity. Researches were attempting to find out if sleep was necessary for a full recovery. Their main focus was on how to make the hospital a better place for people to recover better. The study that was conducted was a behavioral intervention. The researches put heating pads on the participants lower legs and measured their brain activity with an fMRI. The somatosensory cortex, which is the part of the brain where pain signals were received showed a 126% increase when the participant did not get a full nights rest. My question is that the knowledge is used to discharge patients back to their homes to allow for fuller nights rest due to the fact that the hospitals are too loud to induce sleep. If that is the case would it still take just as long for the patient to get well enough to be discharged from the hospital?

Identifying the differences between somatic cells and germline cells can be complicated but crucial for proper bodily functions. Somatic cells are found in body cells and cannot be passed to offspring. Internal organs, skins, bones, blood, and tissues are all made up of somatic cells. Most importantly, these cells are crucial for replacing old cells in the body and creating new cells through cell growth and development. Somatic cells also function to repair damage of cells that are neither dead or old but contain have a mutation affecting its performance for that specific cell. The cells complete the process of mitosis through DNA replication and cytokinesis to produce two new identical cells. On the other hand, germline cells occur in gametes, both egg and sperm, and can be inherited by offspring because they contain genetic material. An important aspect of these cells is the level of differentiation they obtain as they cannot be any other cell in the body other than a gamete. Lastly, they reproduce through the process meiosis in order to produce viable egg and sperm to pass genetic material to progeny.

Epithelial ovarian cancer accounts for approximately 90 percent of all cases of ovarian cancer. Common mutations found in epithelial ovarian cancer include BRCA1, BRCA2, and TP53. Common over expressions include cyclin E1, Rsf-1, and fatty acid synthases. High grade serous ovarian cancer (HGSC) accounts for approximately 70% of epithelial ovarian cancers, and BRCA1 mutations are more uncommon than TP53 mutations and are found in about 13% of HGSC cases. HGSC has the highest incident rates as well as the lowest survival rates among subtypes of ovarian cancer. BRCA1 mutations present in the ovarian cancer phenotype are sometimes heritable. According to new research many of HGSC cancer cells are thought to originate in the fallopian tubes and are thought to migrate to the ovaries and implant there. The function of the protein encoded by the BRCA1 gene is well characterized as a tumor suppressor.  On the contrary, although TP53 mutations are very common in ovarian cancers and TP53 is known to be a tumor suppressor as well, the role of its mutants in leading to a cancerous phenotype is not well understood. A study showed no phenotypic differences between a mutant TP53 and a TP53 knockout, so the BRCA1 mutation is of immediate interest.