September 23rd- Today I created and my log and am beginning to research possible topics for my final paper. I am thinking of basing it off of the research I did on my last co-op: the effects of PCSK9 inhibition of LDLR.[Good choice - a good place to start would be the PDB JCB]

October 7th- After checking the current logs and those from the 2009 course, I have decided to research 5 properties of cyclohexanone.

Cyclohexanone Properties

Melting Point:
-47 degrees C http://www.wolframalpha.com/input/?i=melting+point+cyclohexanone
-47 degrees C http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=398241|SIAL&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPECi
-47 degrees C http://www.acros.be/DesktopModules/Acros_Search_Results/Acros_Search_Results.aspx?search_type=CatalogSearch&SearchString=cyclohexanone
Melting_Point_of_cyclohexanone-Acros_Organics.png
-26 degrees C http://www.alfa.com/en/GP100w.pgm?DSSTK=A15607
-32 degrees C http://msds.chem.ox.ac.uk/CY/cyclohexanone.html

Boiling Point:
154-156 degrees C http://www.alfa.com/en/GP100w.pgm?DSSTK=A15607
156 degrees C http://msds.chem.ox.ac.uk/CY/cyclohexanone.html
155 degrees C http://www.wolframalpha.com/input/?i=cyclohexanone+boiling+point
155 degrees C http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=398241|SIAL&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPECi
155 degrees C http://www.acros.com/DesktopModules/Acros_Search_Results/Acros_Search_Results.aspx?search_type=CatalogSearch&SearchString=cyclohexanone

Flash Point:
47 degrees C http://www.alfa.com/en/GP100w.pgm?DSSTK=A15607
44 degrees C http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=398241|SIAL&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPECi
46.67 degrees C http://www.wolframalpha.com/input/?i=cyclohexanone+flash+point
46 degrees C http://www.acros.be/DesktopModules/Acros_Search_Results/Acros_Search_Results.aspx?search_type=CatalogSearch&SearchString=cyclohexanone
44 degrees C http://en.wikipedia.org/wiki/Cyclohexanone

Refractive Index:
1.45 http://www.wolframalpha.com/input/?i=cyclohexanone+refractive+index
1.4507 http://www.alfa.com/en/GP100w.pgm?DSSTK=A15607
1.450 http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=398241|SIAL&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPECi
1.445-1.456 http://www.acros.be/DesktopModules/Acros_Search_Results/Acros_Search_Results.aspx?search_type=CatalogSearch&SearchString=cyclohexanone
1.450 - Chemical Properties Handbook via The Merck Index (see below)
Picture_1.png

Density (g/cm^3)
0.95 http://msds.chem.ox.ac.uk/CY/cyclohexanone.html
0.947 http://www.wolframalpha.com/input/?i=density+cyclohexanone
0.947 http://www.acros.be/DesktopModules/Acros_Search_Results/Acros_Search_Results.aspx?search_type=CatalogSearch&SearchString=cyclohexanone
0.947 http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&N4=398241|SIAL&N5=SEARCH_CONCAT_PNO|BRAND_KEY&F=SPECi
0.9478 http://www.alfa.com/en/GP100w.pgm?DSSTK=A15607

Specific Gravity (g/cm^3)
0.947 http://www.wolframalpha.com/input/?i=specific+gravity+cyclohexanone
0.95 http://www.cdc.gov/niosh/npg/npgd0166.html
0.9452 - The Merck Index (see below)
Picture_2.png

Assignment 2: Summary of Journal Article
[Full Marks JCB]
DOI: http://dx.doi.org/10.1073/pnas.0903849106
  1. Proprotein convertase substilisin/kexin type 9 interacts with low density lipoprotein receptors to lower LDL cholesterol.
  2. Human genetic studies show that individuals exhibiting heterozygous loss of function mutations of the PCSK9 gene showed an 88% decrease in the occurrence of coronary heart disease over a 15-year period, as compared to individuals not carrying the mutation.
  3. PCSK9, which is expressed in great levels in the liver, consists of a prodomain, catalytic domain, and C-terminal V domain. The LDLR pathway begins with apolipoprotein B and E endoctyosed with LDLR being transported to the acidic portion of the endosome, where they leave the receptor to be catabolized into lysosomes.
  4. Although there are many published ways to inhibit PCSK9, the current focus of study involves a neutralizing monoclonal antibody, mAb1, which promotes LDL uptake by disturbing the interactions of PCSK9 with LDLR. To date, this antibody has been proven to lower cholesterol in mice and non-human primates.
  5. Out of the 3,000 hybrid lines tested, 85 blocked the binding of PCSK9 to LDLR. Therefore, these hybrid lines were ranked via a cell-based assay and the most promising were cloned for further testing.
  6. Via an in vitro assay that tested human, cynomolug, and mouse PCSK9, it was determined that 10 micrograms/microliter would effectively neutralize all of the secreted PCSK9 in these cells.
  7. The antibody mAb1 was combined with mevinolin and HepG2 cells were treated with this mixture to measure the effects of the statin on PCSK9 secretion.
  8. Steric hindrance, caused by mAb1, inhibits the binding of PCSK9 to LDLR, which therefore prevents the degradation of LDLR.
  9. Injecting mice with a 10mg/kg dose of mAb1showed a 20% decrease in total cholesterol levels.
  10. Increasing the dosage of mAb1 in mice and studying the effects over time proved that the length of time the decrease in total cholesterol levels is exhibited is dependent on the strength of the dosage.
  11. Injecting LDLR -/- mice with a dose of mAb1 showed no significant effects in the amount of cholesterol present, proving LDLRs are necessary for mAb1 to lower total cholesterol molecules in mice.
  12. huPCSK9 was injected with two different dosages of mAb1 and after 48 hours, only patients injected with the higher dose should a decrease in cholesterol levels.
  13. Using cynomolgus monkeys injected with mAb1, it was proved that mAb1 will significantly lower total cholesterol levels and minimally lower HDL cholesterol levels in vivo.
  14. The study furthers the thought that using an antibody to inhibit PCSK9 secretion can be used to treat hypercholesterolemia.
  15. mAb1 binds to a site adjacent to where PCSK9 binds to LDLR. Therefore, the antibody sterically hinders and blocks the binding of PCSK9 and LDLR. This claim was also proven in vitro, using cultured HepG2 cells.
  16. In mice, mAb1 lowered measurably lowered total cholesterol levels. However, the injection of mice in which LDLR were not present did not show a lowering of total cholesterol. Injecting mice exhibiting huPCSK9 with mAb1 showed a decrease in non-HDL cholesterol levels as well.
  17. LDL cholesterol levels of cynomolgus monkeys injected with mAb1 decreased as low as 80% when compared to the control group. In future studies, the group is going to focus on studying the immune complex of test subjects over extended periods of time to see if there are any toxicological effects.
  18. Triglyceride levels were not influenced by mAb1 in cynomolgus monkeys, but there was a small, but measurable decrease in HDL cholesterol levels.
  19. Combining the antibody with a statin will increase LDLR protein levels higher than treatment with just the mAb1.
  20. The research concludes that mAb1 is an effective options for treating hypercholesterolemia and further study is needed.
  21. The paragraph describes how the research group developed the antibody (mAb1) .
  22. A plate reader was used to determine potency of the antibody used in the various cell based assays.
  23. The binding affinity of the antibody to human and cynomolgus PCSK9 was tested using various concentrations of PCSK9.
  24. Using various secondary antibodies, western blots were imaged to gather data on liver and HepG2 cell lysate experiments and bands were analyzed using computer software.
  25. X-ray crystallography was utilized to determine where the antibody binds to PCSK9.
  26. The mice used in the experiments were kept under the same conditions and injected with either the control antibody or mAb1. The mice under study were killed at varying times after being injected with the antibodies to study the effects.
  27. All monkeys utilized were kept under the same conditions and were injected with either the control antibody or mAb1. Blood was drawn from the monkeys are various times following the injection of the antibodies.
  28. Various methods were used to analyze changes in cholesterol and PCSK9 levels.
  29. A statistical analysis was performed on each test group (mice exhibiting huPCSK9, and monkeys) to determine the effectiveness of mAb1 of lowering LDL cholesterol.


List and Describe 5 Databases for Biomolecule Information.
  1. Protein Data Bank : PDB is a free archive that provides users with information relating to structures of protein, nucleic acid, and other large biological molecules. The PDB also annotates all data, allowing for annotation based searches.
  2. Entrez Protein Clusters (ProtClustDB) : ProtClustDB provides users with access to publications, structures, annotation information, domains, and external links regarding related protein sequences.
  3. Peptidome : Peptidome is a free database that contains peptide and protein mass spectrometry data.
  4. PopSet : PopSet is a database containing related nucleotide sequences. It is used to study the evolutionary similarities of a population.
  5. UniProt : This is a free and comprehensive database of protein structure and function.