BIOMO512-23B (HAM)

Molecular Techniques for Environmental Science

15 Points

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The University of Waikato
Academic Divisions
Division of Health Engineering Computing & Science
School of Science
Biomedical, Molecular and Cellular Biology

Staff

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Convenor(s)

Charles Lee

Charles Lee
4241
TRU.G.17
See Moodle
charles.lee@waikato.ac.nz

Lecturer(s)

Craig Cary

Craig Cary
4593
TRU.G.23
See Moodle
craig.cary@waikato.ac.nz

Brendan Hicks

Brendan Hicks
4661
R.2.14
See Moodle
brendan.hicks@waikato.ac.nz

Huw Richards

Huw Richards
4029
TRU.G.01
See Moodle
huw.richards@waikato.ac.nz

Administrator(s)

: klaus.reiter@waikato.ac.nz

Placement/WIL Coordinator(s)

Tutor(s)

Student Representative(s)

Lab Technician(s)

: charlotte.king@waikato.ac.nz

Librarian(s)

: anne.ferrier-watson@waikato.ac.nz
: melanie.chivers@waikato.ac.nz

You can contact staff by:

  • Calling +64 7 838 4466 select option 1, then enter the extension.
  • Extensions starting with 4, 5, 9 or 3 can also be direct dialled:
    • For extensions starting with 4: dial +64 7 838 extension.
    • For extensions starting with 5: dial +64 7 858 extension.
    • For extensions starting with 9: dial +64 7 837 extension.
    • For extensions starting with 3: dial +64 7 2620 + the last 3 digits of the extension e.g. 3123 = +64 7 262 0123.
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What this paper is about

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This paper introduces students of diverse scientific backgrounds to current and emerging molecular analytic and diagnostic techniques (with an emphasis on DNA-based methodologies) used across biological and environmental sciences. It is designed to provide a practical and theoretical overview of molecular techniques (particularly those based on DNA and RNA) used in various aspects of ecology, evolution, and environmental science. It targets postgraduate students with diverse knowledge bases and places emphasis on the intended use, strength, and weakness of various techniques. The techniques will be discussed in the context of real-life research and diagnostic applications, particularly focusing on ecology, systematics, and monitoring.

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How this paper will be taught

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This paper is taught through lectures, interactive seminars, practical laboratory sessions, and student-led roundtable discussions. Attendance at all lectures and seminars is required. This paper is 100% internally assessed. Depending on the number of students present, the first presentation session may be unnecessary and cancelled, which may affect the timing (but not the order) of preceding seminars.

All laboratory sessions take place in Week 35 (Teaching Recess week starting 28 August). Labs (with embedded seminars) will run from 9 am to 5 pm (should finish around 3 pm on most days). Please contact the Paper Convener prior to enrolling in this paper if you cannot fully participate in the laboratory sessions.

Anticipated Workload:

  • Seminars: 24 hours
  • Laboratory Sessions: 12 hours
  • Assignments (non-contact): 60 hours
  • Presentation Preparation (non-contact): 12 hours
  • Test Preparation (non-contact): 24 hours

PLEASE NOTE: Moodle will be used for class notices etc, and it is your responsibility to check the site regularly. Instructions provided on Moodle and in lectures are considered to be given to the class as a whole.

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Required Readings

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Required reading will be supplied in the forms of PDFs or web links through Moodle.

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Learning Outcomes

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Students who successfully complete the course should be able to:

  • Communicate scientific concepts and findings in an efficient and accurate manner
    Linked to the following assessments:
  • Describe the theoretical underpinning and experimental details of a broad range of modern molecular technologies
    Linked to the following assessments:
  • Evaluate studies utilising molecular techniques and offer articulated and thoughtful critique of the methodology and findings
    Linked to the following assessments:
  • Gain practical experience in the laboratory relevant to future career opportunities
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  • Understand the advantages and limitations of variour molecular techniques and how they affect the techniques' suitability for various applications
    Linked to the following assessments:
  • Understand the basics of cutting-edge DNA-based methods, such as quantitative PCR (qPCR), DNA sequencing, and genomics
    Linked to the following assessments:
  • Understand the use of molecular genetic tools to address questions broadly in the fields of ecology, evolution, and systematics
    Linked to the following assessments:
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Assessments

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How you will be assessed

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Assessment consists of the following components:

  • [15%] an essay on a published study
  • [5%] an assignment on molecular phylogenetics (details announced in class)
  • [15%] a technical summary of the laboratory component
  • [20%] a 10-minute presentation on a published study
  • [20%] a "mock" study design (three pages + citations) that incorporates one or more of the techniques discussed in this paper
  • [25%] an in-class test at the end of the semester (not an Exam)

Assessment items should be formatted in 12-­point Helvetica or Arial and 1.15X line spacing. Please submit the assessment items through Moodle in an editable format (i.e., not PDF) so that feedback on the work can be provided.

  • Essay: two A4 pages + one A4 page for citations
  • Technical Summary: See Moodle for guidelines
  • "Mock" Study Design: three A4 pages + two A4 pages for citations

For the 10-minute presentation, each student will select a unique article from a peer-reviewed publication that incorporates a technique covered in this paper (i.e., no two students should present the same study). Students must email a PDF for the article of their choice to Charlie one week before their presentation. The presentation will be assessed based on (but not limited to) the following criteria:

  • The slides should contain enough information for the audience to understand the key ideas
  • Aim for a good balance of text and images
  • The information must be "presented" (i.e., do not read direct quotes from the paper)
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The internal assessment/exam ratio (as stated in the University Calendar) is 100:0. There is no final exam. The final exam makes up 0% of the overall mark.

The internal assessment/exam ratio (as stated in the University Calendar) is 100:0 or 0:0, whichever is more favourable for the student. The final exam makes up either 0% or 0% of the overall mark.

Component DescriptionDue Date TimePercentage of overall markSubmission MethodCompulsory
1. Essay
18 Aug 2023
No set time
15
  • Online: Submit through Moodle
2. Assignment on Molecular Phylogenetics
5
  • Other: TBA
3. Technical Summary of Laboratory Component
8 Sep 2023
No set time
15
  • Online: Submit through Moodle
4. Presentation - Paper of Choice
20
  • Presentation: In Class
5. Study Design
20 Oct 2023
No set time
20
  • Online: Submit through Moodle
6. Test
25
  • In Class: In Lecture
Assessment Total:     100    
Failing to complete a compulsory assessment component of a paper will result in an IC grade
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