Updated: 13 April, 2007
 

Genetics Lab - sections

Lab Resources

 

A. Recombinant DNA
  i) Restriction Enzymes & Ligases
  ii) Gel Electrophoresis
RESULTS - Latest gel image is here NOW!

For Lab report 1 ONLY - if you want to fix the issues, then I will regrade it just this once for you.

 

B. Detection of Human Polyporphic Alleles
 

i) PCR

WATCH what PCR is about here...

Many PCR MOVIE 1 PCR MOVIE 2 PCR MOVIE 3 and many more here

  ii) STRs
  iii) Profiler & Cofiler
RESULTS <<<<<<< now activated
 
C. Enzyme Essays
  Learn about enzyme induction here and here and here
How to calculate the results - check here now!
 
D. Human Karyotypes
  i) Phase contrast microscope
 
E. Linkage Mapping in Drosophila melanogaster
  i) Probability
  ii) Pedigree Primer
  iii) Linkage Analysis
 
Lab Report Writing & Good sample report
Information on Group Presentations
Grades

Group Presentations

A brand new format devised by Prof Holland applies this year. It gives you a more rounded experience into real scientific research and presentation.

GROUP PRESENTATION GUIDELINES – BIO 184

Note: this document contains many web links, and is most useful when viewed on a computer with an internet connection.

Purpose

  • To gain valuable experience giving oral presentations.
  • To investigate ethical issues stemming from biotechnology and genetics.
  • To experience using digitally based presentation technology.
  • To gain exposure to various types of information/resources available on the web, and to experience searching for information on the web.
  • To develop skill in evaluating the quality and accessibility of information presented in various categories of websites.

Members of each presentation group will implement the following guidelines

Cooperation and communication: Group members will:

  • Work together to divide responsibilities among themselves (an essential skill).
  • Prepare slides that are coordinated and presented in the same format within one PowerPoint file.
  • Meet early in the semester to schedule meeting times and exchange contact information.

Subject: Your presentation will be on a specific subject of your choice, within the general framework of ethical issues stemming from biotechnology and/or genetics. 

Research methods

  • You will conduct Web searches to obtain material from three types of information sources found on the Web:
    • General news: What many people are most accustomed to seeing on the Web, because it is often tied to a service or subscription.  Examples:
      • Yahoo: http://www.yahoo.com/
      • MSNBC http://www.msnbc.msn.com/
        • These sites will give a brief, often poorly rendered, summary of anything that will put the most eyes on the page.  You may use only one general news site, primarily for the purpose of contrasting it to the other sources.  Do not devote a lot of time on this source during your presentation.  General sources may give you a reference to the original research from which the news report was developed.  However, you will find some of technical aspects of the original research report extremely difficult to understand.  This is one reason to use the following category of sites:
    • Non-professional specialty: Such sites are extremely valuable because they usually are authored by professionals, but are often written for the thoughtful layperson, or for other professionals, but in a manner that is more reader friendly (less jargon, less terse).  This is a medium in which you can find extremely useful commentaries and essays with references and links to professional: peer-reviewed literature, societies, and databases. 
      • Blog: web-log, which is usually shortened to blog.  Blogs are usually authored by one, or a few, authors. 
      • Wiki: a type of website that allows an unlimited number of contributors to easily add, remove, or otherwise edit some available content, sometimes without the need for registration.  This ease of interaction and operation makes a wiki an effective tool for collaborative authoring, but may also make them more variable in the quality of their content.  The most famous wiki is wikipedia, a free encyclopedia.  However, I am asking you to not use wikipedia (or if you do, to include an additional wiki) because I want you to explore more specialized wikis, for example:
    • Professional (peer-reviewed):  Once you have identified a specific topic and introduced yourself to it at a comfortable level (above), it is time to use peer-reviewed articles.  Theseare generally published by professional journals, almost all of which are now available online (sometimes at no cost).  Only a very small fraction of peer-reviewed journals is available at the CSUS library.  The advantage of the library, however, is that it contains the most widely read and intensely scrutinized journal articles (e.g., from Science and Nature) and they are free to borrow.  Here are examples of some relevant journals that are available free online:
  • Searching for information:  There are varieties of ways to approach searches, based on your goals and experience with the subject.
    • General search engines
      • The best is Google: http://www.google.com/ both because of the search superior algorithms and because of vast diversification of categorical searches it offers.  For example, go to:  http://www.google.com/intl/en/options/
        • You will find specific search categories that greatly improve the efficiency of common searches, e.g., scholarly papers and blogs.
    • Deep search engines
      • These are engines search the “Deep Web”, which usually refers to two types of content that often are not seen by standard search engines (e.g., Yahoo).  It has been estimated that content on the Deep Web may be 500 times larger than the fixed Web.  Deep Web content:
        • Databases: contain information stored in tables created by such programs as Access, Oracle, SQL Server, and DB2.  Information stored in databases is accessible only by query.  This is distinct from static, fixed Web pages, which are documents that can be accessed directly.  A significant amount of valuable information on the Web is generated from databases.  
        • Non-text files such as multimedia files, graphical files, software, and documents in formats such as Portable Document Format (PDF).
      • Several useful Deep Web sites are listed below.
      • The line between general search engines and deep search engines has been blurred by Google, which now can search some of the same sources as deep engines.
    • Specific databases: these are the kinds of sites whose contents are accessed through a deep web search engine.  However, there is an advantage to mastering specific databases that you will use often, and that exclude material you will not need.

For an interactive version of this figure: http://www.ncbi.nlm.nih.gov/About/primer/

  • Downloading information
    • If you prefer not to download something that you want to read (e.g., an expensive journal article at a publisher’s site), you may be able to find a free copy of the article at the author’s web site.  How do you find that web site?  Google him/her!

Content of your presentation

  • You willinclude at least one source from each of the three information sources: Research methods: 1: a), b), and c), into a presentation with the following goals:
    • Introduce the topic: this starts with a brief, interesting title and ends within a few slides, and several sentences, that briefly:
      • Describes your topic.
      • Describes why this topic should be interesting to your audience.
      • Overviews (e.g., an outline on a slide) what your talk will cover.
    • Organize the material: For an example of organizing material:
      • Notice, below, how the ordering and description of non-professional specialty and professional web sites, is very different then the actual order in which I found the information (described above).  I reorganized them, from general-to-specific.  This is one of the qualities of a good presentation. 

1-6, above, took about 5 minutes.

    • Interpret: do not simply copy the authors’ words, but instead, convey their meaning, reasoning, and evidence. 
    • Edit: Do not try to present everything:
      • Summarize the authors’ main points, so that the class can get an overall understanding of the work.
      • Focus on those points that you think are particularly important.
    • Evaluate the strengths and weakness of the various source materials used.
      • Integration to a larger question or subject
      • Accuracy
      • Clarity
      • Comprehensiveness
    • Slides: Your slides should outline your talk, remind you of what you want to say (through practice), summarize important information, and make complex ideas easily understood.  Slides should NOTcontain anything that will distract your audience (repeating animation or sounds, etc.) from your content.  Generally, such presentations are trying to distract the audience from a lack of content.  The audience is usually not fooled.  Your instructor (and most future employers) will not be fooled.
      • Figures are a major component of good presentations.  Make sure to define the components (e.g., axes of graphs) and orient us to the figure so that we can understand what is shown.  These may be created by you or downloaded, or some combination.  Ideal uses of figures:
        • Summarize data.
        • Simplify complicated information or concepts.
    • Search methods: In the penultimate content slide (one prior to the last) slide, show an outline of the search that led to one of each of the three categories of information sources:
    • Research methods: 1: a), b), and c).  You do not have to do this for every information source, just a representative one from each category that best illustrates your use of search engines and/or databases.
    • Reference your sources of information in two ways:
      • Within the talk itself: any source used by you should be cited on the slide in which it is presented.  This should be done in a way that does not interfere with the content (e.g., numbers). 
      • In the last content slide, there should be a complete list of full references that correspond to the summary citations used in the talk. 
        • Guidelines for both of these can be found here, or at the course website “Referencing in PowerPoint Presentations”.
    • Acknowledgments: following the references slide you have the option to add an additional slide, acknowledging anyone outside of the group who helped you with any aspect of your project.

Style

  • Speak to your audience in a clear but conversational style.  Reading your notes or slides will put your audience to sleep like a dose of anesthesia.  If you are nervous, ask them to hold any non-urgent questions to the end of the entire presentation.
  • Speak loud enough to be heard at the back of the room.
  • Show enthusiasm (enjoy yourself), despite the situation, and you will be far more successful.  Try to accept your nervousness.  It is okay, and usually helpful, to admit to your audience that you are nervous.  Even the best speakers get nervous at some point.

Discussion following the formal presentation

  • Immediately following the presentation, ask if there any questions.
  • If there are no questions, or after audience’s questions have been exhausted, members of the presentation group are responsible for directing discussion by raising several thoughtful questions that they contemplated during the creation of the presentation.  This is very important as it will solidify the fact that you gave due consideration to your topic.  Do not shy away from asking negative or controversial questions.

What each group should bring to the presentation and submit

  • Bring a CD, or USB memory stick containing your presentation as PowerPoint file (sometimes it is also a good idea to bring both or duplicates).
  • Submit an .html formatted email, that contains a copy of the active links (such that clicking takes you to the site) shown on,  both, your search methods and references slidesThe search methods list should be and organized chronologically so that your instructor can quickly recreate your steps (for the search).  The references source-links should then follow (one link for each reference that takes your instructor directly to the actual source).  If you were unable to download the referenced source freely, then simply provide the web site at which you located the reference.
    • Do not send PowerPoint files unless requested.
    • The electronic submission of you search method and reference links may be made any time prior to, or during, the day of your presentation.  Note, this is mandatory to complete the assignment.

Time for presentation: 45 minutes, plus 15 minutes for discussion, unless announced otherwise by your instructor at the beginning of semester.

Grades: are based on your adherence to the above guidelines, with weight given to the following areas:

Presentation component

Percent of total score

Research methods

30

Content of your presentation

30

Style

10

Discussion following the formal presentation

10

What to bring to the presentation

10

Time for presentation

10

Your lab instructor may provide you with a different point breakdown at the beginning of the semester.

Material from this section was modified from: http://www.internettutorials.net/deepweb.html

 

 

Lab Reports

Lab reports are the foundation of scientific communication. Students MUST learn how to write proper reports. We have incorporated this very important aspect into this lab in a big way.

Each student is required to write his or her own reports. The formats to follow can be viewed here. The reports are due as exactly two weeks after the conclusion of a lab experiment. Late reports will be subject to deduction of scoring (grade) points.

Each report is now worth 15 points. As there are 6 experiments, and thus 6 lab reports, there are available a total of 75 points. Prof. Holland has included a scoring matrix with the course syllabus. It shall shortly be replicated below, with his permission.


 

copyright , Dr. Kamal Dulai. all rights reserved

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