More on repair

Submitted by sjurgilewicz on Thu, 04/27/2017 - 21:12

All repair occurs post-replication. Errors and fixes always occur in the newly replicated strand. Mismatch repair must occur soon after replication or else errors will be passed along and turned into mutations. How does the cell recognized which is the template and which is the newly replicated? In E. coli, detection occurs through methylation or lack of. The adenine gets methylated on the template strand, replication occurs. An enzyme is used to recognized the methylated adenine. Therefore, it is known which is the newly synthesized. There is also a nick present. Mismatch creates a bump, the mistake is cut out and then some extra, approximately 2000 nucleotides long. Helicase, DNA pol, exonuclease, DNA ligase, ssDNA binding protein, endonuclease and clamp/clamp loader are all some of the things needed for mismatch repair to occur.

  1. Initial MMR bind proteins
  2. Endonuclease, creates nick
  3. Helicase, unwind strands
  4. Exonuclease, remove piece of strand greater than the error
  5. SSB, bind to ssDNA
  6. Clamp/clamp loader/ DNA pol synthesize across gap
  7. DNA ligase

If cells had no way to distinguish between newly synthesized DNA, how often would yo expect to see mutations from mismatch base pairing? 50% of the time.

DNA damage is caused by UV, x-ray, tobacco, reactive oxygen. Depurination occurs when entire base comes off. Deamination occurs when cytosine converts to uracil. 

Cancer genetics project 3 excerpt

Submitted by jdantonio on Thu, 04/27/2017 - 20:00

The first step in our treatment process is the identification of our cancer’s neoantigens, this would vary from patient to patient would have to be experimentally Identified. This is done by first sequencing the genome of the cancer tumors using massive parallel sequencing a system which readily identifies tumor cell mutations by comparison of the genome of the cancer cells to the genome of a somatic cell (Gubin et al 2015).  This method of genome analysis has been shown to be an effective means to identify cancer cell gene mutations (Shiraishi et al 2011).We will use a hybrid exome sequencing technique which allows for the analysis of only genes included in the cells exomes and allows for faster sequencing in a time scale that is relevant to treatment (Hodges et al 2009). Once the tumor genome has been sequenced and analyzed to identify mutations we will then determine which of the tumors mutations would be indicative of an oncogene capable of binding to the MHC protein within the cell (Gubin et al 2015). This will be accomplished by utilizing bioinformatic databases and softwares, specifically the  NetMHCpan algorithm system which identifies a wide range probable MHC binding sequences in Human and nonhuman primates (Nielsen et al 2007). We will then harvest lymphocytes from the patient and test them for neoantigen binding specificity in vitro and select from among those harvest T-cells with tumor suppressing ability that posses the receptor for one of the neoantigens we derive from or cancer cell genome analysis. Following this we would grow these cells in culture to create a large amount of tumor infiltrating lymphocytes (TIL) (Perica et al 2012). These TIL’s will be further modified by the introduction of  chimeric receptor that binds one of the other  neoantigens which we identified.

 

Gubin MM, Artyomov MN, Mardis ER,and Schreiber RD. 2015. Tumor neoantigens: building a framework for personalized cancer immunotherapy. The Journal of Clinical Investigation 125(9): 3413–3421. National Center for Biotechnology Information[NCBI]. <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4588307/>. Accessed 2017 April 24.

 

Hodges E, Rooks M, Xuan Z, Bhattacharjee A, Gordon DB, Brizuela L, McCombie WR, and Hannon GJ. 2009. Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nature Protocol 4(6): 960-974. National Center for Biotechnology Information [NCBI]. <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990409/>. Accessed 2017 April 24.

 

Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Røder G, Peters B, Sette A, Lund O, Buus S. 2007. NetMHCpan, a Method for Quantitative Predictions of Peptide Binding to Any HLA-A and -B Locus Protein of Known Sequence. PLOS one 2(8): e796. National Center for Biotechnology Information [NCBI]. <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1949492/>. Accessed 2017 April 24.   

Shiraishi T,Terada N,  Zeng Y, Suyama T, Luo J, Trock B,  Kulkarni P, and Getzenberg RH. 2011. Cancer/Testis antigens as potential predictors of biochemical recurrence of prostate cancer following radical prostatectomy. Journal of Translational Medicine 9: 153. National Center for Biotechnology Information [NCBI]. <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3184272/>. Accessed 2017 April 24.

Louis Pasteur and Germ Theory

Submitted by eriklee on Thu, 04/27/2017 - 18:34

In 1877, a French biologist named Louis Pasteur discovered a method of vaccination. Pasteur was able to create this vaccination due to Jenner’s works, “he mediated incessantly on the work of Jenner…” (Louis Pasteur). Pasteur was able to recognize that if Jenner could create a vaccination for an incredibly infectious disease, then a vaccine could be found for other diseases. This French biologist is an important scientist because he was able to further investigate and present the germ theory. He learned of this theory after his experiments with chicken and the poultry disease, chicken cholera. Discovering germs, what they were and how they played a role in vaccines and immunization, was crucial to get science to where it was today. With the study of germs, Pasteur was [able to better understand the infectious agent of] rabies and proceed to develop the next immunization for it. And many other vaccinations would have taken longer to come across. [Germ theory: helped scientists understand the “infectious agents of disease” and use the body’s immune system to prepare for the infection.] 

journal

Submitted by jiadam on Thu, 04/27/2017 - 18:29

Methods:

The Morrill conservatory is the first location and the Durfee conservatory is the second to be observed indoors. Sylvan pond and Campus pond were observed outdoors. For each observation area, 2 sites of different measurements were examined. Humidity and temperature averages were gathered from online sources for the week. Moss with different physical features and morphology was observed for 15 minutes and pictures were taken of these. Inside, moss was found on the surface of the soil in plant pots and the plant stalks; whereas, moss outside was found among the outer edges of the water and at the bottoms of trees. The area in which the moss was found, the number of moss species found, the area (in meters), humidity averages, and temperature averages were all recorded in a data table.

Journal 34

Submitted by kngallant on Thu, 04/27/2017 - 16:52

    Animals often live in numbers to avoid predation. One species that lives in groups are the Northern Bobwhites, a type of quails. These quails live in groups called coveys that may contain 2-22 individuals.  The larger the group, the easier they can detect a predator. However this benefit is outweighed by increased competition for food in larger groups, supported by evidence that larger groups travel more each day. Smaller groups also move more, probably to search for other groups to join. The mix of costs & benefits suggest that groups of intermediate sizes get the bests of both worlds. And in fact, groups of this size have the best survival rates.

 

Fixing DNA replication errors: PP

Submitted by sjurgilewicz on Thu, 04/27/2017 - 15:30

The error rate of DNA polymerase is 1 error in every 10^5 nucleotides added. There is a proofreading function to look for errors such as the wrong base. DNA polymerase has a 3’ to 5’ exonuclease to remove the wrong bases. An exonuclease is an enzyme that destroys polymers from the ends of the polymers as compared to an endonuclease that cuts in the middle of the polymer. Nucleases are RNA specific (RNase) and DNA specific (DNase). They can work in either 3’ to 5’ direction or vice versa. During replication the error rate is 1 in 10^7 bases. Mismatch repair occurs after replication has occurred and the error rate is 1 in 10^9. When an error is sensed, the base is flipped out and an enzyme comes and cuts it off. DNA pol 3 is the main DNA polymerase. DNA pol 1 removes primer and fills in the gap from lagging strand synthesis. DNA pol 1 must have polymerase catalytic activity and both direction exonuclease activity. 

Why does replication only go in one direction? It could be due to proofreading. Energy is still able to come in properly from a new nucleotide.

If synthesis occurred the other way, then the energy would be cut off.  Our genome is 3 billion base pairs in length, how many mistakes are being made during DNA replication each time our cells divide? 1 in a billion mistakes, 6 billon nucleotides, 6 errors on average. 

If someone has a functional proofreading but a nonfunctional mismatch repair, how many more mutations will be present compared to someone with functional mismatch repair machinery? (assuming genome is 3 billion base pairs long): 6 billion nucleotides added/ 1 in 10^7 error rate = 600 more mutations.

There is an end replication problem: when the primer is removed, there is no 3’ end to synthesize and add to that end. The cell will chew back on itself on the 5’ end and the telomere region will shorten each time. The telomere has repeating nucleotides without coding for anything. If the cell doesn’t have telomeres and is naked, DNA damage repair will be activated. To prevent this, DNA bends back on itself and binds proteins. Most cells get shorter each time they divide. There is a way to fix using telomeres: DNA protein structures, prevent cell from generating DNA damage response. Once telomere is too short, apoptosis occurs. This is associated with aging. Cancer cells over express telomerase (who to keep telomeres longer).

Fixing DNA replication errors

Submitted by sjurgilewicz on Thu, 04/27/2017 - 14:57

The error rate of DNA polymerase is 1 error in every 10^5 nucleotides added. There is a proofreading function to look for errors such as the wrong base. DNA polymerase has a 3’ to 5’ exonuclease to remove the wrong bases. An exonuclease is an enzyme that destroys polymers from the ends of the polymers as compared to an endonuclease that cuts in the middle of the polymer. Nucleases are RNA specific (RNase) and DNA specific (DNase). They can work in either 3’ to 5’ or vice versa. During replication the error rate is 1 in 10^7. Mismatch repair occurs after replication has occurred and the error rate is 1 in 10^9. When an error is sensed, the base is flipped out and an enzyme comes and cuts it off. DNA pol 3 is the main DNA polymerase. DNA pol 1 removes primer and fills in the gap from lagging strand synthesis. DNA pol 1must have polymerase catalytic activity and both direction exonuclease activity. 

Why does replication only go in one direction? Could be due to proofreading. Energy is still able to come in properly from new nucleotide. If synthesis occurred the other way, then the energy would be cut off.  Our genome is 3 billion base pairs in length, how many mistakes are being made during DNA replication each time our cells divide? 1 in a billion mistakes, 6 billon nucleotide, 6 errors on average. If someone has a functional proofreading but a nonfunctional mismatch repair, how many more mutations will be present compared to someone with functional mismatch repair machinery? (assume genome is 3 billion base pairs long): 6 billion nucleotides added/ 1 in 10^7 error rate = 600 more mutations. End replication problem: primer is removed, no 3’ end to synthesize and add at the end. Cell will chew back on itself on the 5’ end and the telomere will shorten each time. The telomere has repeating nucleotides without coding nucleotides. If the cell doesn’t have telomere and is naked, DNA damage repair will be activated. To prevent, DNA bends back on itself and binds proteins. Most cells get shorter each time they divide. There is a way to fix. Telomeres: DNA protein structures, prevent cell from generating DNA damage response. Once telomere is too short, apoptosis, associated with aging. Cancer cells over express telomerase (who to keep telomeres longer) 

Research projects methods

Submitted by koganezova on Thu, 04/27/2017 - 14:47
  • 2x2 inch samples of moss were collected from the North, South, East, and West sides of a tree in front of French Hall at UMass Amherst.
  • Each sample was put on 60 mm filter paper and left to dry for 72 hours in a 20 °C growth chamber.
  • After the 72 hours, 10 mL of water was added to each sample for rehydration.
  • Photos were taken of each sample at minutes 0, 10, 20, 40, 60, and 24 hours.
  • These photos of the rebounded samples were then analyzed using ImageJ to find the relative area of moss that was rebounded.

Discussion research project

Submitted by koganezova on Thu, 04/27/2017 - 14:34
  • The samples taken from the South, East, and West sides of the tree showed very similar results to rehydration.

  • The sample taken from the North side did not rehydrate as well as the others because, we assume, that moss sample is a different species that does not respond to rehydration as well.

  • Another assumption we made about the North sample is that the lack of rehydration could have also been because of the soil that the sample was collected with.

Research Project Discussion Final Draft

Submitted by amprovost on Thu, 04/27/2017 - 12:51

The results of this experiment show that dried Sphagnum was able to absorb a relative large amount of water, absorbing 6.125 grams of water for every one gram of moss before becoming saturated. This experiment also showed that dried Sphagnum absorbs liquids relatively quickly, as it only took 30 minutes for this moss to become saturated. This is useful knowledge as the rate of absorbency of a material has some practical applications, as certain conditions such as oil spills require a material that will absorb liquids as quickly as possible. Thus, this data may be useful for future production of liquid absorbing materials.

 

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