ANAT2341 Lab 2 2013

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Introduction To Group Projects

This 2013 course is divided into the lecture content and the laboratory practicals and assessment is divided equally between these components. The short answer/ multiple choice tests that are conducted during the laboratories will constitute 20% of the final mark. The group project work conducted and supported during the laboratories will constitute 30% of the final mark. The remaining 50% will be by examination at the end of the course and will focus on lecture content and the course textbooks.

Group projects - "Using mouse models to understand human genetic developmental abnormalities"

This series of practicals has been designed to complement the lecture material by providing an opportunity to examine human embryology in the context of modern medical research aimed at understanding the cellular and molecular basis of human developmental abnormalities that are caused by genetic mutations. Since students may have a variable understanding of human genetics, mouse model development and cellular and molecular analytical techniques, each laboratory will provide tutorials on these topics and make use of a series of examples to support the research process as it progresses.

Objectives of this laboratory

  1. First short answer/ multiple choice test of last week's lecture material
  2. Describe the group project process and assessment procedure
  3. Provide time for the formation of groups and begin selection of the group project topic

First short answer/ multiple choice test on Lectures - Fertilization and Week 1 and 2 Development

The laboratories for this 2013 Embryology course support the lecture material by reviewing the content of the previous week using short answer questions and multiple choice tests to ensure that the material is understood and students are staying up to speed. Paper answer sheets will be provided at the beginning of the laboratory and the questions will be delivered by Powerpoint. It is important that students are on time for laboratory classes as the test will take place in the first minutes of the class. Questions arising from this test can be addressed immediately afterwards.

The group project process and assessment

Forming a group

Groups should ideally have 3 members but 2 is also allowable to take into account the final class size. Groups of 4 are not permitted. Groups should be formed during this 2nd laboratory either voluntarily or by random selection.

Selecting a topic

Below is a set of approved topics for group projects. Groups can select one of these but once it has been selected no other groups can make the same choice. Groups can also select their own topic but it must be approved by the course coordinator.

Human disease
Relevant mouse models
Skin Gorlin Sydndrome/Basal Cell Nevus Syndrome 109400 PTCH1 K14-Cre Ptc mutants
Craniofacial Treacher-Collins Syndrome 1 154500 TCOF1 Tcof1 mutants
Limb development Split-hand/foot malformation 1 with sensorineural hearing loss 220600 DLX5 Dlx5/6 mutants
Gonadal development Campomelic Dysplasia 114290 SOX9 Sox9 transgenics/LOF mutants
Heart development Holt-Oram Syndrome 142900 TBX5 Tbx5 mutants
Kidney development Polycystic kidney disease, adult type I 173900 PKD1 Pkd1,2 mutants
Multisystemic DiGeorge Syndrome 188400 TBX1 Multiple
Eye Aniridia 106210 PAX6 Small eye (Sey)
Blood Omenn Syndrome 603554 RAG1 and RAG2 Rag1 mutant and Rag2 knockin
Bone Cleidocranial Dysplasia 119600 RUNX2 Runx2 mutant and knockout
Neural tube Neural tube defects including spina bifida 182940 T Tailless Brachyury mutants
Sexual differentiation Androgen Insensitivity Syndrome 300068 AR Tfm mice
Neural Crest Derivatives Waardenburg Syndrome Type 4 277580 EDNRB Endothelin-B receptor mutant

Researching the topic

  1. Perhaps the most useful online resource is the website Online Mendelian Inheritance in Man
  2. Access to the human and mouse genomes can be found via the UCSC Browser or the Ensembl browser
  3. Information regarding mouse strains and genetically modified mouse lines is available at the Mouse Genome Informatics database
  4. Analysis of gene expression through RNA in-situ hybridization is available at Genepaint
  5. However, database entries often do not contain the most up-to-date research and reference lists are often incomplete or give unnecessary prominence to the least important papers. Therefore, it is essential to research papers from primary peer-reviewed research via Pubmed
  6. As a means to assist in the understanding of human genetics, mouse genetics and the analysis of mouse models of human genetic disease, we will be presenting a series of practicals/tutorials on these topics over the next few weeks during which, specific questions can be addressed. So make sure that you begin your research early and bring your queries to class for discussion.
  7. Don't forget that the ANAT2341 web pages have detailed descriptions of organ systems that may be relevant to your disease-of-interest.
  8. Remember this is an embryology course and your work should focus on embryological issues:
  • What anatomical structures or physiological functions have been affected in human patients?
  • What cell types constitute these structures?
  • What is the embryological origin of these cells/organs?
  • How does the genetic insult create these features?
  • What is the cellular and molecular basis of the disease?
  • What sort of protein does the mutated gene encode and what is its normal function?
  • Where is the gene expressed spatially and what is the temporal pattern of expression?
  • What embryological mechanisms are disrupted? signalling, patterning, growth, differentiation, etc?

Dividing the tasks

The oral and written reports should be divided into 3 equal sections.

  1. Developmental abnormalities of the disease, diagnosis and human genetics
  2. Genetics of the relevant mouse mutants and the resulting developmental abnormalities
  3. Using the mouse mutants to understand the developmental, cellular and molecular basis of the disease

Each member of the group should assume responsibility for one of these sections. The marks will be divided into 2 parts. A mark for the overall project and a mark for the section for which you have taken responsibility. Therefore, it is important to edit each others work and ensure that the overall product is integrated and well finished. Each person should identify which section they have taken chief responsibility for.

Groups that only have 2 members should divide their work by one student taking responsibility for part 1 and the other part 2, then part 3 should be shared equally. During the oral presentation, only one student should present part 3.

Oral presentations

The oral presentations will be 15 minutes long for each group and each member of the group will present their own section of the project in the order listed above. Therefore, each person will have 5 minutes for their section. The whole talk should be integrated into a single Powerpoint file and each section should begin with a title slide that includes the name of the person presenting. It is recommended that the total number of slides for the whole presentation is between 12-20. The talks should be practiced as a group to ensure that it doesn't exceed 15 minutes and that it communicates the essential information in a clear and concise way. A final summary slide is recommended highlighting the essential points discussed.

There will be 5 minutes allocated to questions following each presentation during which students from other groups or lecturing staff can ask questions of the presenters. This is designed to test the depth of knowledge that has been acquired during the research process and to identify areas of weakness that may need more work before submission of the final report.

Final report

The final report is a 3000 word essay that is divided into the same 3 equal sections

  1. Developmental abnormalities of the disease, diagnosis and human genetics
  2. Genetics of the relevant mouse mutants and the resulting developmental abnormalities
  3. Using the mouse mutants to understand the developmental, cellular and molecular basis of the disease

Word count: Title page, figures, figure legends, tables and the References section will not be included in the word count. Penalties will apply to reports that are outside a 10% margin of 3000 words. Each section does not have to be kept to 1000 words, only the total word count will matter. However, the in-text references will be counted as words.

Figures: Figures are important to communicate concepts efficiently. However, do not overdo figures. The report should have a maximum of 10 figure items (this includes tables). The figure legends should be numbered consecutively and have a title that states what the figure shows to the reader; e.g. (Figure 2. Sagittal section through a mouse head at E14.5 showing the position of the developing pituitary gland). The text should then describe what the figure shows in detail without the reader having to refer to the main text.

References: Reference style will be according to the APA system

This is a brief guide to referencing a variety of information sources, both print and electronic, according to the APA style. Referencing needs to be accurate and consistent. For a comprehensive guide, please refer to:

   American Psychological Association. (2009). 
   Publication manual of the American Psychological Association (6th ed.). Washington DC: APA.
   [Located in the UNSW Library at 808.06615/1 U]

or the American Psychological Association's APA Style webpage

or obtain a copy of

   Perrin, R. (2010). Pocket guide to the APA style (4th ed.). Boston: Houghton Mifflin.

Why reference?

   To avoid plagiarism by acknowledging the source of your information;
   To enable the reader to verify your information, including quotations;
   To inform the reader of the source of your ideas or information which he/she may choose to locate and read more fully.

References are often cited within the text of an assignment and are listed in the References list on a separate page/pages at the end of the assignment.

This guide includes examples of in text citations as well as referencing formats for print and electronic sources of information to create a list of references. In-Text Citations

In text citations are also known as parenthetical notes. Generally the APA format requires citing the author's surname and its year of publication.

In general, there are two forms of in-text citation accepted in the APA style of referencing.

The first format of in-text citation, includes author's surname and year, separated by a comma enclosed in brackets. e.g. (Marieb, 1989).

The second format is done by mentioning the author's surname in the text, immediately followed by the year of the published work (e.g., Researches such as those presented by Marieb (1989) has...)

Reference List

The reference list must be in alphabetical order by author and should use the hanging indent format.

For multiple works by the same author, arrange in chronological order. e.g. Byrnes, J.M. (2007) precedes Byrnes, J.M. (2010)

For authorless works, alphabetise by the first significant word in the title.

Submission of the final report Reports should be submitted electronically in word format. This is to enable checking for evidence of plagiarism using the Turnitin system. Final report is due in no later than midnight of Sunday 20th October.

Marking Criteria

For oral and written work, the marking criteria will overlap to a large extent and will include many of the following elements:

  • Focused introduction to the genetic disease with sufficient detail but able to be understood by a non-expert audience
  • Clear and concise description of the features of the human disorder and means of diagnosis
  • Demonstrated understanding of the human genetics of the disease and what is known of the human embryology
  • Focused introduction to relevant mouse models and methods of construction or identification
  • Clear description of the mouse phenotypes, correlations of mouse phenotypes with the human disease and analysis of phenotype through development
  • Focused introduction to the cellular and molecular analysis of the mouse model
  • Clear description of insights into the molecular and cellular mechanisms revealed by analysis of the mouse model
  • Description of gene expression and potential impact on target organs
  • Concluding summary that highlights the essential impact of the mouse model on the understanding of the human disease
  • Clear presentation style with minimal grammatical or typographic errors
  • Good use of figures with clear labeling, attribution and explanation of what the figure shows
  • Clear and logical structure with a single thread that presents a compelling scientific argument.
  • Accurate and comprehensive use of appropriate referencing
  • Demonstration of depth of understanding through response to feedback or questioning.