BM 506/2011:Schedule

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(New page: {{Template:BISC110/F11}} <div style="padding: 10px; width: 725px; border: 5px solid #397D02;"> ==BISC110/112 Fall 2011 Lab Calendar== <BR> {| border="2" |+ ! Monday !! Tuesday !!...)
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(Bahan Ketrampilan Dasar Ilmu Biomedik)
 
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{{Template:BM 506/2011}}
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==BISC110/112 Fall 2011 Lab Calendar==
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==Jadwal Kuliah dan Praktikum Ketrampilan Dasar Laboratorium 2011==
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Lihat jadwal praktikum  [http://openwetware.org/images/c/c5/Jadwal_Praktikum_Biomedik_2011.pdf di sini.]
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==Bahan Ketrampilan Dasar Ilmu Biomedik==
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Bahan praktikum maupan kuliah bisa Anda dapat [http://openwetware.org/wiki/Magister_Ilmu_Biomedik:Notebook/Ketrampilan_Dasar_2011 di sini.]
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! Monday    !! Tuesday    !! Wednesday !! Thursday  !! Friday 
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|-
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| August 29 <br>
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| August 30 <br>'''Lab 1'''<br>Classes Start || August 31  <BR> '''Lab 1''' || September 1  <br> '''Lab 1''' || September 2 <br>'''Lab 1''' ||
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|-
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| September 5 <br>'''Labor Day <BR> NO CLASSES'''
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| September 6 <br>'''Lab 2'''|| September 7 <br>''' Monday Schedule'''<BR>'''Lab 1''' || September 8<br>'''Lab 2'''|| September 9 <br>'''Lab 2''' || 
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|-
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| September 12 <br>'''Lab 2'''
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| September 13 <br>'''Lab 3''' || September 14 <br>'''Lab 2''' || September 15 <br>'''NO LAB''' || September 16 <br>'''Lab 3''' || 
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|-
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| September 19 <br>'''Lab 3'''
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| September 20 <br>'''Lab 4'''<br> || September 21 <br>'''Lab 3''' ||  September 22 <br>'''Lab 3''' || September 23 <br>'''Lab 4'''  || 
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|-
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| September 26 <br>'''Lab 4'''
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| September 27 <br>'''Lab 5''' || September 28 <br>'''Lab 4''' ||  September 29 <br>'''Lab 4''' || September 30 <br>'''Lab 5''' || 
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|-
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| October 3 <br>'''Lab 5'''
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| October 4 <br>'''Lab 6''' || October 5 <br> '''Lab 5'''  ||  October 6 <br> '''Lab 5'''|| October 7 <br>'''NO LAB''' || 
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|-
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| October 10 <br>'''FALL BREAK <BR> No Classes'''
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| October 11 <br>'''FALL BREAK <BR> No Classes''' || October 12 <br>'''Lab 6''' ||  October 13 <br>'''Lab 6''' || October 14 <br>'''Lab 6'''|| 
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|-
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| October 17 <br>'''Lab 6'''
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| October 18 <br>'''Lab 7''' || October 19 <br>'''Lab 7'''|| October 20 <br>'''Lab 7''' || October 21<BR>'''Lab 7'''|| 
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|-
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| October 24 <br>'''Lab 7'''
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| October 25 <br> '''Lab 8''' || October 26 <br> '''Lab 8''' || October 27 <br> '''Lab 8'''|| October 28 <br> '''Lab 8'''|| 
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| October 31 <br> '''Lab 8'''
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| November 1 <br>'''Tanner Conference <BR> No Classes''' || November 2  <br>'''Lab 9''' || November 3 <br>'''Lab 9''' || November 4 <br>'''Lab 9'''|| 
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|-
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| November 7<br> '''Lab 9'''
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| November 8 <br>'''Lab 9''' || November 9  <br>'''Lab 10''' || November 10 <br>'''Lab 10''' || November 11 <br>'''Lab 10'''|| 
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| November 14<br> '''Lab 10'''
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| November 15 <br>'''Lab 10''' || November 16  <br>'''Lab 11''' || November 17 <br>'''Lab 11''' || November 18 <br>'''Lab 11'''|| 
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| November 21 <br> '''NO LAB <br> Photosynthesis paper due'''<br>
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| November 22 <br>'''NO LAB'''<br>'''Photosynthesis paper due''' || November 23  <br>'''Thanksgiving Break<BR> No Classes''' || November 24 <br>'''Thanksgiving Break <BR> No Classes'''|| November 25 <br> '''Thanksgiving Break <BR> No Classes'''|| 
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|-
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| November 28 <br>'''Lab 11'''
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| November 29 <br>'''Lab 11''' || November 30 <br>'''Lab 12'''  || December 1 <br>'''Lab 12''' || December 2 <br>'''Lab 12'''|| 
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|-
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| December 5 <br> '''Lab 12'''
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| December 6 <br> '''Lab 12''' || December 7  <br>'''Last Day of Classes<BR> NO LAB''' || December 8 || December 9 || 
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|}
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<br>
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=='''Schedule of Experiments'''==
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Bahan kuliah dan materi tugas kuliah lainnya bisa didapat [http://openwetware.org/wiki/User:Donny_Nauphar/Notebook/Program_Magister_Biomedik_FK_USU di sini.]
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! Section !! Lab # !! Activities
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! 1
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| 1-5 || Boot Camp: Metric Measurement;<BR> Using Basic Lab Equipment;<BR> Making Solutions and Dilutions;<BR> Microscopy; Scientific Investigation;<BR> Designing & Executing Experiments;<BR> Data Analysis & Display; <BR>Statistical parameters; Scientific Writing
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|-
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!2
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| 6-8
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|Genetics: DNA extraction, Visualization by agarose gel electrophoresis;<BR> Genotype/phenotype via Taster SNP data collection and analysis;<BR> Scientific Writing & Effective figure design
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|-
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!3
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|8-10
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|Photosynthesis: Spectrophotometry: Beer-Lambert Law, Linear regression analysis;<BR>  Hill Reaction: Self-designed investigation of factors <BR>affecting photosystems
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|-
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!4
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|11
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|Gene Regulation/Enzymology: Invertase enzyme assay
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!Lab Practical
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|12
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|Hands-on skills assessment:
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|}
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<br>
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== '''BISC110/112 Assignments/ Weekly Lab Planner''' ==
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{| border=1px
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|'''Series'''
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|'''Lab #'''
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|'''LAB DATES'''
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|'''LAB DESCRIPTION'''
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|'''Assignment/Notes'''
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|--
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| colspan="6" |
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|--
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| 1
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| 1
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| Aug.30 to<br> Sept. 7
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| Practice metric conversions; <BR>Practice pipetting; <BR>Making Solutions; Microscopy; <BR>Examination of ''Tetrahymena pyriformis''<br>
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| '''Homework''': Familiarize yourself with the wiki, particularly the information in the [[BISC110/F11:Resources]] section of the Lab wiki; <BR>Lab 1 Practice Problems downloadable here [[Media:Lab_1_Practice_Problems110.doc]];<br>
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Read about the process of endocytosis in your textbook;<BR> familiarize yourself with phagocytosis in ''Tetrahymena''<BR> from the following reference articles:<BR> '''*Gronlien HK, Berg T, Lovlie AM.''' In the polymorphic ciliate ''Tetrahymena vorax'',<BR> the non-selective phagocytosis seen in microstomes <BR>changes to a highly selective process in macrostomes.<BR> (2002), Journal of Experimental Biology 205, 2089-2097; <BR>
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'''*McLaughlin NB and Buhse HE, Jr.,''' Localization by indirect immunofluorescence of tetrin, actin,<BR> and centrin to the oral apparatus and buccal cavity of the macrostomal form of ''Tetrahymena vorax''., (2004), J Eukaryot. Microbiol., 51(2), 253-257.
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|--
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| 1
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| 2
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| Sept. 6 to<br> Sept. 14
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| ''Tetrahymena'' Behavior: Phagocytosis; Observations; Data Analysis;<BR> Accuracy vs. Precision; Statistical Parameters;<BR> Data Presentation; Effective Figure Design and Legends<BR> using the Gronlien article as a model.
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| '''Homework''': Study dilution making for Lab 3; <BR>Generate two figures with legends from your ''Tetrahymena'' experiment:<BR> one or more microphotographs of Tetrahymena and a graph or table of data.
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| 1
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| 3
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| Sept. 13 to<br> Sept. 19
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| Making Dilutions; Determination of toxicity of Heavy Metals on ''Tetrahymena'';<BR> Design your own experiment exploring<BR> inhibitors and ''Tetrahymena'' phagocytosis
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| '''Homework''': There are animated tutorials on dilution<BR> available at the following link:<BR> [http://www.wellesley.edu/Biology/Concepts/Html/dilutions.html Dilution Help Tutorials]; <br> Finalize your experimental design for Lab 4; have it approved by your lab instructor;<br> Write a results section of a scientific report<BR> on your findings in the ''Tetrahymena'' toxicity experiment <BR>including a narrative portion and integrated figure(s) with legend(s);<br>
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Solve the dilution problems found at<BR> [[Media: Lab_3_110_Dilution_Problems.doc]] and hand them in<BR> by the beginning of Lab 4.
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| 4
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| Sept. 20 to <br> Sept. 29
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| Student Designed Experiments:<BR>Potential Inhibitors of Vacuole Formation;
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| '''Homework''': 5 minute oral presentation in PowerPoint™ of your data,<BR> including at least one figure with legend, of your Lab 4 experimental results. <br>Read assigned journal article for science writing discussion <BR>'''* Gronlien, H.K., Berg, T., Lovlie, A.M.''' (2002).<BR> In the polymorphic ciliate ''Tetrahymena vorax'', the non-selective phagocytosis seen in microstomes changes<BR> to a highly selective process in macrostomes, J. Exp. Biol. 205, 2089-2097
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|--
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| 1
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| 5
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| Sept.27 to <br> Oct. 6
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| Scientific Writing Workshop with Journal Article Discussion
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| '''Homework''': '''''Tetrahymena'' Partial Scientific Research Report: DUE AT THE BEGINNING OF LAB 6'''<BR> Title Page, Results, Discussion and References sections. <BR>Guidelines at:[[BISC110/F11:Resources | Resources]]; <BR>Science Writing peer-tutor appointment scheduling at: <BR>[http://www.wellesley.edu/Writing/Program/tutors.html Wellesley College Writing Program Resources].<br>
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Have Lab notebooks ready to be turned in for inspection after Lab 6.
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<br> Read Lab 6 (first lab in Series 2, Genetics)
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<br>Prepare a flow chart in your lab notebook of all Lab 6 experimental procedures.
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| 2
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| 6
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| Oct.  12 to<br> Oct. 17
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| Genetics: Taster SNP 1-Test PTC Taster Phenotype;<BR> Isolate and digest DNA; PCR;
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| '''Homework''': Read the following background information on<BR> [http://serc.carleton.edu/files/genomics/units/snp_restriction_enzymes.pdf restriction enzymes] <BR>and on [http://serc.carleton.edu/files/genomics/units/snp_gel_background.pdf gel electrophoresis] <br>
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Read the following background information on ethical issues in genetic testing:<br>
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'''[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2710700/?tool=pubmed Direct-to-Consumer Genetic Testing,'''<BR> Two Sides of the Coin] by Farkas and Holland, J Mol Diagn. 2009 Jul;11(4):263-5. Epub 2009 Jun 18. <BR>
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[http://0-www.sciencemag.org.luna.wellesley.edu/cgi/reprint/320/5872/53.pdf PUBLIC HEALTH: <BR>A Case Study of Personalized Medicine] by S. H. Katsanis, G. Javitt, and K. Hudson,<BR> published in ''Science'', 4 April 2008 320: 53-54 [DOI: 10.1126/science.1156604](in Policy Forum)<BR>
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[http://www.dnapolicy.org/news.enews.article.nocategory.php?action=detail&newsletter_id=35&article_id=156 AMA DTC testing policy recommendations] <br>
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Draw the expected migration locations of the Fnu4H1 digested PCR product<BR> obtained from a homozygous taster (left lane), a homozygous nontaster (center lane)<BR> and a heterozygote (right lane) on a diagram of an agarose gel; <br>
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Answer the questions found at:<BR>[[Media:Taster_DTC_questions110.doc‎]] <BR>to use as a template for your answers.'''
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| colspan="6" |
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|--
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| 2
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| 7
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| Oct. 18 to <br> Oct. 24
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| Genetics: Taster SNP 2: Prepare and perform agarose gel electrophoresis;<BR> Determine PTC Taster Genotype; Scientific Writing: <BR>Introduction & Discussion
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| '''Homework:
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Prepare draft figures/tables from the preliminary course data<BR> for the taster investigation paper and an skeleton outline<BR> of your introduction & discussion sections.<BR> (Refer to the handout on How to Prepare a Skeleton Outline in Sakai.)
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|--
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| 2 & 3
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| 8
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| Oct. 25 to<br> Oct. 31
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| Data Analysis of Taster investigation; Science Writing Workshop:<BR> Effective Figure Design, Introduction, Discussion; Photosynthesis 1:<BR> Chlorophyll pigment investigation, Spectroscopy,<BR> The Beer-Lambert Law and Creating a Standard Curve
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| '''Homework''': Write a scientific research report (all sections except M&M)on your PTC Taster SNP study.'''<BR> For help, see the [[BISC110/F11:Resources | Resources]] section of this wiki.<br>
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In your lab notebook, prepare a flow chart for the Hill Reaction (Lab 9);<br>
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Review the mechanisms of electron transport and proton flow in photosynthesis (use your textbook).<br>
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| 3
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| 9
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| Nov. 2 to<br> Nov. 8
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| Photosynthesis 2: Hill Reaction
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| '''Homework''': Finalize your self-designed experiment<BR> testing a variable affecting the Hill Reaction;<br> Write a Materials and Methods style version of the Hill Reaction<BR> experiment that you did this week in Lab 9
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| 3
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| 10
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| Nov. 9 to <br> Nov. 15
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| Photosynthesis 3: Investigation of variables affecting the Hill Reaction
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| '''Homework''': Plot your A580 data (y-axis) versus time in seconds (x-axis)<BR> for the different treatments (with the treatments on the same graph).<BR>See([[Appendix_E/F11 |Appendix E]]). <BR> Determine regression equations for the linear part of each data plots<BR> to get slope (m) values (slopes represent the rates of electron transport). <BR>Calculate the rates (change over time of the linear portion of your graphs)<BR> and plot those values against your variable (x-axis);<br>
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'''A full paper on your experiment, in the form of a scientific research report,<BR> is due at beginning of Lab 11 (or on day indicated in Lab Calendar).'''<BR>  Discuss your results in terms of how the factor that you chose to investigate<BR> affects the electron transport rate in photosynthesis.<BR> Compare your results to other investigations published in the primary literature.<BR> Refer to the "[[BISC110/F11:Guidelines for Science Writing | '''Guidelines for science writing''']]" information<BR> found in the [[BISC110/F11:Resources | Resources]] section of the wiki.
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| 4
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| 11
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| Nov. 16 to<br> Nov. 29
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| Enzymology<BR>Answer the following questions (5 points) <BR>and hand them in to your instructor before you leave lab. <BR>Download a Word document form of these questions here:[[Media: Lab_11_Questions_110_112.doc]]
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| '''Homework: Prepare for a Lab Practical Skills Assessment in lab 12.'''<br>
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<br> Make sure Lab Notebook is ready to turn in for grading at the beginning of LAB 12
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| Skills Assessment
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| 12
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| Nov. 30 to <br> Dec. 6
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| '''Lab Practical'''; <br>Turn in Lab Notebook
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| End of lab
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|--
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<br>
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=='''Lab Graded Assignments'''==
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! Lab Assigned !! Lab Due !! Assignment<br> description !! Point Value <br>(Total 200)
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! 1
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| 2
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| Practice Problems
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| 5
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! 2
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| 3
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| Fig. Design
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| 5
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! 3
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| 4
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| Dilution Problems (5);<br>Fig.& Results (10)
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| 15
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! 4
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| 5
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| Oral presentation: Results, original figure & legend;<br> Journal article discussion
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| 10
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! 5
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| 6
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| Lab notebook check (ungraded);<br> Partial Scientific Paper(25)
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| 25
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! 6
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| 7
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| SNP Taster Questions
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| 5
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! 7
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| Draft figures/tables & outline of Taster paper
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! 8
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| Taster Scientific Paper (all but M&M)
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| 35
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! 9
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| 10
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| M&M (5pt);<br> Finalize Self-Design <br>Experiment Hill Rxn.(ungraded)
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| 5
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! 10
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| 11 (or on day indicated in calendar)
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| Full Scientific Paper: Factor Affecting Rate of Photosynthesis
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| 35
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! 11
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| 11 (In Lab)
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| Concept Questions Enzymology/Gene Reg.
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| 5
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! 12
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|12
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|Lab Notebook Check (10) <BR>Lab Practical:Hands-on skills assessment (35)<br>
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| 45
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! Other
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| Discretionary Points <br> Preparation & Participation
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| 5
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Ilmu Biomedik FK USU BM 506/2011

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