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Biology RSAT

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Mr. Sutcliffe

on 14 January 2013

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Transcript of Biology RSAT

Endrei, Tania and Allison Energy Effect on the Horse- Cause: More Activated Proteins- p16 Protein is small, less energy required to produce
Recommended some added sugar in diet
Add sweet feed such as molasses
Large amount of protein being produced Tania: effect of energy on horse Figure 1: Sweet Feed for Horses
http://www.stablemade.com/horsecare/horsefeeding/sweet_feed.htm Energy Effect on the Horse- Cause: More Activated Proteins- p300 Small amount placed in horse
Nearly no energy required to produce
Compared to other proteins, considered small
300 amino acids Figure 2: p300 and p1000 approximate size ratio
http://www.cellbio.duke.edu/faculty/Erickson/pdf's/Protein%20hydrodn%20EM.pdf References W1: http://www.millipore.com/catalogue/item/05-257#
W2: http://www.understanding-horse-nutrition.com/horse-feed.html
W3: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1150220/
W4: http://www.sciencedaily.com/releases/2011/07/110705104220.htm
W5: http://www.bio.davidson.edu/courses/immunology/students/spring2000/white/ifnbeta.html POPULATION DYNAMICS
Sebby, Kristen,Mariann, Eric &Taylor Sebby: Mongolia's Geography Mongolia’s Geography Landscape


Resources Kristen: Cancer in Mongolia Cancer in Mongolia How cancer affects the body

Mongolia has the worlds highest death rate of cancer mortality

Medical treatment is not advanced

Liver cancer mortality is 6 times the global average.

Doctors expect money up front to cover the cost of treatment before treatment is given Top Ten Countries Ranked by Cancer Mortality http://ubpost.mongolnews.mn/wp-content/uploads/2012/12/Picture1.jpg References Websites W1: Cancer in Mongolia; http://ubpost.mongolnews.mn/?p=2189
W2: Mongolia Life Expectancy; http://www.who.int/healthinfo/statistics/bodprojectionspaper.pdf
W3: Global Cancer Facts; http://www.cancer.org/acs/groups/content/@epidemiologysurveilance/documents/document/acspc-027766.pdf
W4: Healthcare in Mongolia: http://www.ghjournal.org/health-care-in-mongolia
W5: Healthcare in Mongolia; http://www.forbes.com/fdc/welcome_mjx.shtml Mariann: Mares Milk & Traditions Produce 1000-1200 kg of milk

Mare’s milk has 40% more lactose than cow’s milk

0.7 to 2.5%. Mare's Milk http://media-cdn.tripadvisor.com/media/photo-s/02/3c/42/21/traditional-milk-tea.jpg http://www.mongolfood.info/en/recipes/airag.html http:/api.ning.com/files/r6HZNzSOcfsb2tCHs0JOkMsIQP1-JC5ggKGRK*mseN7gbm2Xhld-g83rPJ8jyHymLluv8Qe1-BZ7h*GUhPmtnFOH706QajdW/777pxbowl_of_kumistm.jpg Mongolia Culture References W1:http://pediaview.com/openpedia/Kumis#Production_of_mare.27s_milk
W2: http://www.mongolfood.info/en/recipes/airag.html Websites Taylor: Distribution and Funding Distribution References Eric: Alcoholism & Poverty Geneticist's: Paul, Emily, Alena,
Francesca Nick Nick: What is P16 Protein http://www.dana.org/news/publications/detail.aspx?id=4276 http://jonlieffmd.com/blog/jumping-genes-versus-epigenetics-the-real-drivers-of-evolution What does P16 do? Error between G1 phase and S phase

CDK inhibitor http://journals.prous.com/journals/servlet/xmlxsl/pk_journals.xml_login_to_access_article?p_JournalID=2&p_requested_url=pk_journals.xml_article_pr?p_JournalId%3D2%26p_RefId%3D761413%26p_IsPs%3DN%26p_ispdf%3DN References W1: http://www.nextprot.org/db/entry/NX_P05814
w6http://journals.prous.com/journals/servlet/xmlxsl/pk_journals.xml_login_to_access_article?p_JournalID=2&p_requested_url=pk_journals.xml_article_pr?p_JournalId%3D2%26p_RefId%3D761413%26p_IsPs%3DN%26p_ispdf%3DN HOMEOSTASIS Jessica , Mikaela, Laura, Jen and Brittany Jessica The Lytic and Lysogenic Cycle Mikaela Immunosuppresants Laura The Horse's immune system Jen Quarantining the horse
and the p16 and p27 Brittany The p16 in humans Corticosteroids: Prednisolone impedes function of white blood cells
Given orally, by injection or applied to skin. Figure 1: demonstrates the molecular structure for Corticosteroids.
 http://www.pharmaceutical-technology.com/projects/astrazeneca/astrazeneca3.html Figure 2: demonstrates an example of a white blood cell
http://healthinfoispower.wordpress.com/warning-signs/ Figure 3: demonstrates an infection in a mares hoof
http://goodhorsekeeping.blogspot.ca/2010/12/frog-infections.html Short term Affects:
Increase in appetite,
Increase in water intake
Increase in urine output Long term affects:suppression to their immune system decreased ability to resist infection Lines of Defense
1st: Skin structures and nasal passages

2nd: T-Cells, B-Cells, White Blood Cells http://farm4.staticflickr.com/3276/2618595602_f7cd21dd21_z.jpg http://www.geteasyway.com/images/white-blood-cell-amungst-red.jpg The Horse's Immune System With Immunosuppressant Risk: More prone to disease.Factors affecting strength of a horse’s immune system; Stress, nutrition, age. http://www.big-t-shirts.com/ProdImages/big/986.jpg http://www.ecmagazine.net/vol5_4/winter06webphotos/HorseEatingHay.jpg http://2.bp.blogspot.com/_4z08nZJl6Kk/TGQ6WKEHNZI/AAAAAAAAAWg/RVJMpj4HmkI/s1600/OldHorse.jpg The immunosuppressant will temporarily shut down the immune system. To make sure the horse doesn’t contract any diseases and infections, it must be put in quarantine. http://s1.reutersmedia.net/resources/r/?m=02&d=20070825&t=2&i=1352686&w=460&fh=&fw=&ll=&pl=&r=2007-08-25T154334Z_01_SP213890_RTRUKOP_0_PICTURE0 And the quarantine area has to be cleaned out often to prevent bacteria growth http://l.b5z.net/i/u/10127869/h/flu3.jpg W1- http://genesdev.cshlp.org/content/26/9/877
W2- http://courses.washington.edu/conj/bloodcells/oxygenradicals.htm
W3- http://lungcancer.about.com/od/Respiratory-Symptoms/a/Hypoxia.htm
W4- http://www.elmhurst.edu/~chm/vchembook/596electransport.htm
W5- http://movies-macaulaywangrussell.blogspot.ca/2011/03/anaerobic-respiration-diagram.html
B1- “Biology 12: 2.2 Cellular Respiration” Maurice Di Giuseppe P.104 References Endrei - Cyclin-dependent kinase inhibitor 2A Apoptosis
Cell migration Figure 6: The activation of JNKs and their interactions with transcription factors and gene expression. (w9) Figure 3: Protein – protein interaction. (w13) Activator of p16 (w11)
Combines with Sp1 to form a complex (w11)
Sp1 is a transcriptional factor (w12) P300 Figure 5: P16 is activated after the release of E2F from pRB causing it then to rebind again. (w6) Figure 4: The retinoblastoma pathway. E2F binds to the pRB complex. (w6) Retinoblastoma protein pathway (w6)
c-Jun N-terminal kinases (JNK) regulate cell growth and apoptosis (w7)
JNK substrates are transcription factors (w8)
P16 supresses JNK activity (10)
Binds to glycine-rich loop of N-terminal domain (w10)
Causes Cellular Senescence (w14) Cyclin-dependent kinase inhibitor 2A (p16) Figure 1: Anaerobic glycolysis in which glucose is converted into 2 pyruvate. (w5) Figure 2: The electron transport chain. (w4) Oxygen radicals (w1, w2)
Becomes reduced (b1)
Highly reactive and can cause damage (w2)
Oncogenic mutations (w1)
Oncogenes induce glycolysis (w1)
High rate of glucose fermentation linked to cancer (w1)
Due to there not being enough oxygen for the cells to utilize, a condition called metabolic hypoxia arises (w3) Cancer cell Metabolism The most common contagious diseases of general concern are equine influenza, rhinopneumonitis (equine herpes virus), and strangles.
The quarantine period should last a few days to a week http://farm3.static.flickr.com/2799/4349580925_3462ca757a.jpg http://l.b5z.net/i/u/10127869/h/flu2.jpg http://thewatchers.adorraeli.com/wp-content/uploads/2011/07/site_1_rand_595154344_hendra_horse_quarantine_090902_b_aap.jpg Homeostasis References W1
http://www.umb.no/statisk/husdyrforsoksmoter/2005/088.pdfW5http://www.xpatulator.com/cost-of-living-review/Mongolia-Ulaanbaatar_137.cfm Funding •Death rate
•The need for better health care
•Save millions of lives http://www.pharmaceutical-drug-manufacturers.com/pharmaceutical-drugs/capsules.html http://www.horsetrailsmongolia.com/ Economic Change Accessibility Going to the Source 22% of men & 5% of Women are dependent on alcohol - 23% of government income Independence 1990 - 1 store for every 270 people the cell cycle of all eukaryotes is controlled by CDKs ( cyclin-dependant kinase) http://sgugenetics.pbworks.com/w/page/24725253/Group14-CDK CDKs phosphorylate the Rb (Retinoblastoma) proteins http://en.wikipedia.org/wiki/Retinoblastoma_protein Alena: Extracting & Amplifying the p300 gene Extracting and Amplifying the p300 gene - buy p300
- use amino acid sequence to find mRNA
- mRNA used as probe Figure 1: Shows how the amino acid sequence can be
used to find the mRNA codons (W2). Southern Blotting Purpose: detect the p300's DNA sequence

1. Separate by molecular weight in RFLP
2. Denature DNA
2. Transfer to nylon membrane
3. Add mRNA probe
4. Detect DNA sequence Transfer DNA to membrane Figure 2: Shows the transfer of the DNA on the gel to the nitrocellulose membrane by capillary action (W3). Detect DNA with mRNA probe Figure 3: Shows how to detect the DNA of p300 using mRNA as a probe to form base pairs with the complementary DNA sequence and light up once bound (W4). Polymerase Chain Reaction (PCR) - amplify complementary strands of
p300's DNA sequence
- repeat cycles of separation & replication
- simple & inexpensive 1. Extract DNA from membrane
2. Move into test tube
3. Denature
4. Anneal
5. Elongate Figure 4: Shows the process of PCR where denaturation, annealing and elongation repeat to amplify the DNA fragment(W5). References: T1 - Di Giuseppe, Maurice, et al. Biology 12. Toronto: Nelson, 2003.
W1 - Davidson College. Department of Biology. 2001. 11 January 2013 <http://www.bio.davidson.edu/courses/genomics/method/southernblot.html>.
W2 - Buckley, Jim. Protein Synthesis Lab. 2011. 11 January 2013 <http://www.ekcsk12.org/faculty/jbuckley/lelab/proteinsynthesissimulationlableversion.html>.
W3 - Smith, Michael. The Science Creative Quarterly. 2011. 11 January 2013
W4 - Kaksonen, Anna. Environmental Engineering and Biotechnology. 2011. 11 January 2013. <http://wiki.biomine.skelleftea.se/biomine/molecular/index_20.htm>.
W5 - University of California Regents. Molecular Methods Web Module. 11 January 2013. <http://missinglink.ucsf.edu/lm/molecularmethods/pcr.htm>.
W6 - Genetic Science Learning Center. "PCR Virtual Lab." Learn.Genetics 11 January 2013. <http://learn.genetics.utah.edu/content/labs/pcr/>.. - Naturally occurring process
- Shaker baths are used to speed up the process Figure 1 displays plasmids moving from cell to cell Figure 2 displays a test tube shaker Francesca:
Transferring plasmid into the MVA virus Plasmids Drink Modified Vaccinia Virus Ankara
(MVA) your away - Weakened version of Vaccinia
- Bisafety level 2 required
- Cytoplasmic replication Figure 4 (B) Displays MVA as seen
under an electron microscope Figure 3 An electron micrograph
of the vaccinia virus Small circular, extrachromosomal DNA molecules.
Recombinant DNA; formed by joining different genetic segments from multiple sources.
Replicate independently of the genome
Antibiotic resistance, small size, and high reproductivity make plasmids indispensable to modern bio technology. Fig.1 depicts the pBR322 plasmid which was used in this experiment. It is useful because of its multiple antibiotic resistance sites, and has an extremely high copy number. Fig.2 shows a plasmid as observed under a Scanning Electron Microscope at the University Of Illinois. Fig.3 shows a petri dish with X chromosomes with nucleic matrial that had been introduced from plasmids. Modifying a Plasmid Restriction endonuclease's EcoRI and HindIII were used to cleave the gene creating sticky ends (w1)
DNA ligase will bind the sticky ends to the sticky ends on the plasmid (w2)
Selective plating is used to test the success of the transformation (refer to figure 5). Using Restriction Enzymes to insert P300 synthesizing gene Fig. 7 shows the introduction of genes onto a plasmid (circle) using 7 restriction enzymes producing a new vector. Paul Paul Paul Fig. 5 shows the selective plating technique used to distinguish the plasmids that have undergone sucessful gene transformation. Fig.4: Joshua and Esther Lederberg, founders of the Plasmid and the Plasmid Reference Center Stanford University. Emily:
Isolating the p300 Gene Figure 2: A naked mole rat Figure 1: The structure of p16 protein Codes for production of p16, a tumour suppressor protein
Inactive in most mammals, including humans
Activated in naked mole rats by the p300 protein, causing high cancer resistance The CDKN2A Gene Figure 5: Milking a Mongolian mare Figure 4: The Vaccinia virus Figure 3: A gene sequence in a DNA strand. 1. Isolate the gene coding for p300 protein in the mole rat
2. Transfer the gene to a virus that will inject its altered DNA into the Mongolian mares Objectives of Geneticists Website 1: “Scientists Discover Gene that ‘Cancer-Proofs’ Naked Mole Rat’s Cells”. ScienceDaily. October 27, 2009. January 11, 2013. http://<www.sciencedaily.com/releases/2009/10/091026152812.htm>
Website 2: “p16 Marker”. Roche Laboratories. January 11, 2013. <http://www.mtmlabs.com/us/index.php?option=com_content&view=article&id=10&Itemid=10?>
Website 3: Nelson, Brian. “Scientists Discover how Naked Mole Rats Stay Cancer-Free”. Mother Nature Network. October 27, 2009. January 11, 2013. <http://www.mnn.com/health/fitness-well-being/stories/scientists-discover-how-naked-mole-rats-stay-cancer-free>
Website 4: Oncol, Clin. “Role of p16 Tumour Suppressor Gene in Cancer”. PubMed. January 11, 2013. <http://www.ncbi.nlm.nih.gov/pubmed/9508208>
Website 5: “DNA Extraction Biotechniques Virtual Lab”. University of Utah.2006. January 11, 2013. <http://learn.genetics.utah.edu/content/labs/extraction/>
Textbook 1: Di Giuseppe et Al. “Biology 12” Nelson. 2003.
Figure 1:<http://upload.wikimedia.org/wikipedia/commons/thumb/3/3a/Protein_CDKN2A_PDB_1a5e.png/250px-Protein_CDKN2A_PDB_1a5e.png>
Figure 2:<http://i.telegraph.co.uk/multimedia/archive/02328/naked-mole-rat0_2328106b.jpg>
Figure 3:<http://www.bio.miami.edu/dana/pix/gene.jpg>
Figure 4: <http://www.redorbit.com/media/uploads/2004/10/70_8c49b7354584ec16683e38a21f19f6de.jpg>
Figure 5: <http://images.travelpod.com/tw_slides/ta00/9e7/520/kyrgyz-woman-milking-horse-tamga.jpg>
Figure 6: http://www.eppendorf.com/script/cms-newspic.php?tab=5&col=PICTUREFILE&id=1565>
Figure 7: http://www.therapak.com/catalog/img/lg/sk-2swab.jpg>
Figure 8: <http://www.et.byu.edu/~wanderto/homealgaeproject/centrifuge.jpg>
Figure 9: <http://www.funsci.com/fun3_en/dna/dna_11.jpg>
Figure 10: <http://pigeonracingpigeons.files.wordpress.com/2009/12/ecoli.jpg>
Figure 11: <http://media.historyofvaccines.org/images/000799_540.jpg>
Figure 12: <http://upload.wikimedia.org/wikipedia/commons/thumb/6/60/Gel_electrophoresis_2.jpg/250px-Gel_electrophoresis_2.jpg> References Figure 9: DNA clumps in ethanol solution Figure 8: A centrifuge machine Figure 7: a buccal swab Figure 6: Add substances using a micropipette. Extracting DNA from Naked Mole Rats Non-invasive cheek swab
Lyse the cells to expose DNA
Separate DNA from debris
Remove DNA from solution Isolating the p300 Gene Gel Electrophoresis EcoRI and HindIII restriction enzymes cleave DNA into fragments
Electrophoresis separates variously sized fragments into bands in an RFLP G | AATTC
TTCGA | A Figure 10: E.Coli bacteria and EcoRI recognition site Figure 11: Haemophilus influensae bacteria and HindIII recognition site Figure 12: RFLP shows bands of DNA segments separated by size from gel electrophoresis Lysogenic and Lytic Cycle Figure 1: An example of the structure of a bacteriophage. http://upload.wikimedia.org/wikipedia/commons/thumb/4/4a/PhageExterior.svg/300px-PhageExterior.svg.png lysogenic cycle lytic cycle Figure 2: The stages of the lysogenic cycle comparing to the lytic cycle. http://static.ddmcdn.com/gif/virus-human-lysogenic.gif Lysogenic Stages Absorption Entry Replication Assembly Lysis and Release http://www.zo.utexas.edu/faculty/sjasper/images/so23_02a.gif W1 - "07 Lytic vs Lysogenic Cycle." 07 Lytic vs Lysogenic Cycle. N.p., 11 Jan. 2012. Web. 13 Jan. 2013.

W2 - Anu Arora, Douglas Fraser, Laurice Di Giuseppe, Beth Lisser, Dr. Bob Ritter, Angela Vavitsas. Biology 12. Toronto, Ontario. Nelson, 2003.

W3- Freudenrich, Chris. "How Viruses Work." HowStuffWorks. N.p., n.d. Web. 12 Jan. 2013 Figure 5 (a) nucleo-cytoplasmic replication (b) cytoplasmic replication References Figure 1: "Bacteria." Society for General Microbiology. N.p., n.d. Web. 11 Jan. 2013. <http://www.microbiologyonline.org.uk/about-microbiology/introducing-microbes/bacteria>.
Figure 2: "Lab Equipment." Lab Equipment. N.p., n.d. Web. 11 Jan. 2013. <http://www.sciquip.co.uk/store/products/test-tube-rotating-shaker-3025/>.
Figure 3: Virol, J. "American Society for MicrobiologyJournal of Virology." Differences in Virus-Induced Cell Morphology and in Virus Maturation between MVA and Other Strains (WR, Ankara, and NYCBH) of Vaccinia Virus in Infected Human Cells. N.p., Oct. 2003. Web. 11 Jan. 2013.
Figure 4: Virol, J. "American Society for MicrobiologyJournal of Virology." The Block in Assembly of Modified Vaccinia Virus Ankara in HeLa Cells Reveals New Insights into Vaccinia Virus Morphogenesis. N.p., Aug. 2002. Web. 11 Jan. 2013.
Figure 5: Koonin, Eugene V., and Natalya Yootin. "Key Concepts:." Nucleo-cytoplasmic Large DNA Viruses (NCLDV) of Eukaryotes. N.p., May 2012. Web. 11 Jan. 2013. <http://www.els.net/WileyCDA/ElsArticle/refId-a0023268.html>. Paul: Transferring isolated gene for p300 into modified Plasmid http://media.photobucket.com/image/alcoholism%20in%20mongolia/melykin/mongolia-alcohol03_custom.jpg http://media.photobucket.com/image/alcoholism%20in%20mongolia/melykin/mongolia-alcohol03_custom.jpg http://sleepycity.net/1588.jpg http://files2.structurae.de/files/photos/wikipedia/Ulan_Bator_Parliament_Building_S_C3_BCkhbaatar_Square.JPG http://4.bp.blogspot.com/_j9sG9hFBYhA/TVDzUelQzjI/AAAAAAAAAVs/e-4G2q9LxM8/s1600/airag.jpg http://www.traveljournals.net/pictures/l/4/40565-drinking-airag-western-mongolia-mongolia.jpg References http://www.npr.org/templates/story/story.php?storyId=112485545http://ubpost.mongolnews.mn/?p=1583http://www.mad-mongolia.com/news/mongolia-news/mongolias-drowning-future-10593/http://www.mongolfood.info/en/recipes/mongol-arkhi.htmlhttp://en.wikipedia.org/wiki/Kumishttp://www.who.int/substance_abuse/publications/en/mongolia.pdfhttp://news.bbc.co.uk/2/hi/asia-pacific/3138806.stmhttp://www.mongoliatourism.org/mongolia-introduction/mongolia-public-holidays/independence-day.htmlhttp://thediplomat.com/2012/12/08/the-great-game-over-a-mongolian-mine/ Fig.6 shows the Plasmid-Bacterial cell complex. The cell will eventually be smeared with an agar gel containing Tetracycline and Chloramphenicol. http://www.scientificlegacies.org/esther-lederberg.html Nelson Biology 12 Textbook http://www.innovateus.net/science/what-bacterial-plasmid http://www.accessexcellence.org/RC/VL/GG/plasmid.php http://www.pnas.org/content/105/1/270/F9.expansion.html http://www.rpgroup.caltech.edu/courses/PBL/dna.htm Fig. 8 shows the importance of choosing a plasmid with a high copy number. As a geneticists, the higher number of recombinant DNA yields more reliable results. http://www.wwnorton.com/college/biology/microbiology2/ch/07/etopics.aspx Nick: What is p16? problems with Milk. The ultimate solution....
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