ewinter's blog

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.

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.

The transition from Gap 1 phase (G₁) to the Synthesis (S) phase in the cell cycle involves two important checkpoints.  The first checkpoint assesses DNA for damage.  p53, when active, is a transcription factor for p21, which inhibits G₁ and S cyclin-dependent kinases (CDKs), leading to cell cycle arrest or apoptosis.  To pass the checkpoint, Mdm2 adds a ubiquitin tag to p53, targeting it to the lysosome for degradation.  The “Restriction Checkpoint” is perhaps the most vital checkpoint involved in the G₁ to S phase transition.  The two main proteins involved are the retinoblastoma protein (Rb) and E2F.  The null state involves Rb sequestering E2F in an inhibitory manner.  When favorable conditions for cell division are met, G₁ CDKs hyperphosphorylate Rb, inhibiting its ability to bind E2F.  E2F is a transcription factor, so when active, it is able to go into the nucleus and promote transcription of S-phase cyclins.  At this point, the cell has committed to undergoing mitosis.  Mutations in either of these checkpoint pathways are quite common in cancer.  Common mutations leading to a cancerous phenotype include a loss of function in p53, or a gain of function in E2F.

This organism is estimated to be 1.5 cm in length, and about 5 mm wide.  It has translucent tan skin that appears oily.  It is split into nine sections.  It has two red structures that resemble eyes on a flat surface of circular nature, which is believed to be the head, and a pointed dark structure that resembles a tail.  The slight dark color that is evident through the skin of the tail is hypothesized to be fecal matter.  The organism moves using both transverse and longitudinal waves, that propagate from the head to the tail.  The direction of motion is with the tail at the front, which is used for grip.  It prefers to move on the perimeter of its circular enclosure.  The organism experienced about a 1.5 in. fall when the enclosure was inverted, and it remained rigid for approximately 30 seconds, resembling a state of shock, before resuming regular movement.  At a later point, the enclosure was violently shaken, and the same shock phenomenon occurred.  Through the skin, a dark long discoloration is thought to be a spine, and lighter muscles are observed.