2016 Lab 1

From CellBiology

Introduction

Welcome to your first practical in Cell Biology.

  1. We will begin by working through the Health and Safety (HS) information required for the practical component of this course.
  2. We will identify available Cell Biology resources for your study and project work.
  3. Then there will be an introduction to your individual and group assessment work for this course.
  4. A tutorial will be worked through on online editing and referencing.


Moodle

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Student Health and Safety

Computer Lab Wallace Wurth G08 - Student Risk Assessment


Emergency Assembly Area: Chancellery Lawn SOMS Evacuation Map | Google Maps | Latitude 33°54'59.67"S Longitude 151°14'4.34"E


Links: SOMS H&S for Students | SOMS Health and Safety


Research Laboratories Health and Safety The information below is general in nature. Specific information should always be supplied by the responsible laboratory personnel before commencing work in a research laboratory.

Cell Biology Textbooks

I have brought along a range of cell biology textbooks that we will look through and determine the main issues identified within the texts.

Online Journals and Resources

Today there are a range of online cell biology textbooks and resources that we will identify.

Journals

What’s Happening in Cell Biology and Cell Biology Methods

Using the UNSW journal connections we will look at the key journals and identify current research concepts and techniques.


Journal of Visualized Experiments (JoVE) Technique Examples

Individual and Group Assessment Work

Your individual and group assessment in this course will all be submitted in an online format. I will spend some time assisting you in working in this online media.


Here is the test page I generated in Lab 1 Test page. You can look at my page in edit mode to see how the code works.


Editing Basics: Project Referencing | Image Tutorial | Copyright Tutorial | One page Wiki Reference Card


I will let students know when access to the website is available again (or you can let me know if you can set up your student page.


Individual Assessment

Promoters for Ecoli.[1]
  • A small number of questions will be set in class each week based upon the practical content.
  • You will need to complete these questions by the end of the practical class (unless instructed of an alternate deadline for submission).

Lab 1 Handout - One page Wiki Reference Card

  1. Add your own student page to the site.
  2. Add your signature for Lab attendance.
  3. Add a sub-heading.
  4. Add an external Link.
  5. Add an internal Link.
  6. Add an image from PubMed or PloS journal related to prokaryote cellular component. Make sure it includes both the reference and copyright information.
  1. Tomohiro Shimada, Yukiko Yamazaki, Kan Tanaka, Akira Ishihama The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli. PLoS ONE: 2014, 9(3);e90447 PubMed 24603758

Group Assessment

  • The Group project is designed to be worked by group members mainly in times outside the Practical class.
  • Time will be available within class for your group to discuss progress, problems and allocate work to be done.
  • There will also be tutorials provided in how to prepare your online submissions.


2016 Projects - Topic TBA

Project Archive

2015 Extracellular Matrix: Group 1 - Small Leucine-Rich Proteoglycans | Group 2 - Integrins | Group 3 - Elastic Fibres | Group 4 - Fibronectin | Group 5 - Laminin | Group 6 - Collagen | Group 7 - Basement Membrane

2014 Cell Transport: Group 1 - Phagocytosis | Group 2 - Cytoplasm to the Mitochondria | Group 3 - Nucleocytoplasmic Transport | Group 4 - Neuron Soma to Processes

2013 Cell Division: Group 1 - Regulation of Cell Division | Group 2 - Cytokinesis | Group 3 - Golgi Apparatus | Group 4 - Spindle Apparatus | Group 5 - Nuclear Envelope | Group 6 - Anaphase | Group 7 - Mitochondria

2012 Signaling: Group 1 - Testosterone | Group 2 - Vascular Endothelial Growth Factor | Group 3 - Extrinsic Apoptosis | Group 4 - Notch | Group 5 - Wnt-Beta catenin | Group 6 - Insulin | Group 7 - G protein (beta adrenergic) | Group 8 - Leukocyte Extravasation | Group 9 - p53

2011 Junctions: Group 1 - Synaptic Junctions | Group 2 - Gap Junctions | Group 3 - Tight Junctions | Group 4 - Desmosomes | Group 5 - Adherens Junctions | Group 6 - Neuromuscular Junction

2010 Cell Methods: Group 1 - Fluorescent-PCR | Group 2 - RNA Interference | Group 3 - Immunohistochemistry | Group 4 - Cell Culture | Group 5 - Electron Microsopy | Group 6 - Confocal Microscopy | Group 7 - Monoclonal Antibodies | Group 8 - Microarray | Group 9 - Fluorescent Proteins | Group 10 - Somatic Cell Nuclear Transfer

2009 Cell Topics: Meiosis | Cell Death - Apoptosis | Cell Division | Trk Receptors | The Cell Cycle | Golgi Apparatus | Mitochondria | Cell Death - Necrosis | Nucleus | Cell Shape


Lab 1 Individual Assessment

This will test if you have understood some of the basics for your group project work.

Upload an image from a Journal listed on the References page or from PLOS One or Biomed Central (http://www.biomedcentral.com) or PLOS Journal (http://www.plos.org/publications/journals) from a recent article image that relates to the difference between prokaryotes and eukaryotic cells.

  • Using the format outlined in the assessment tutorial show below.


Assessment Tutorial

This tutorial can also be found in an email sent to each student at the end of the first lecture week.


A. Uploading the Image

1. Log-in to the Cell Biology website (http://php.med.unsw.edu.au/cellbiology).

2. From a Journal (any PLOS Journal) listed on the References page ( http://php.med.unsw.edu.au/cellbiology/index.php?title=ANAT3231_References) identify a recent article image that relates to prokaryoteic cells.


Hint - bookmark the page and it is easier to do in a new browser tab or window so you can refer back to the original page when adding information later.


3. Download the image to your computer.

4. Open the menu item Toolbox - > Upload file (http://php.med.unsw.edu.au/cellbiology/index.php?title=Special:Upload). Using "Choose File" find the image on your computer you have downloaded from the Journal and click "Choose". This will return you to the Upload file page. In the "Destination filename:" window the original image file name will now appear.

DO NOT click "upload file" yet.

  • Firstly, copy the original image file name and paste it into the Summary: window.
  • Secondly, go back to the article window and paste the web address, paper title and figure legend also in the Summary: window.
  • Thirdly, RENAME the "Destination filename:" to a name that best describes the image.


Hint - The filename can be based upon the figure legend title, should be a maximum of 3-4 words. Must clearly identify the content of the image. Leave the file extension (.jpg, .jpeg, .gif, etc) on the file name.


DO NOT include in the filename:

  • The original figure name downloaded to your computer.
  • The figure number.
  • Your student number.
  • Useless information (figure 1, image 1, student image 1, file 1, exercise 1, etc.)
  • Special characters or punctuation for example (, < > " { } [ ] ' : ; | \ ? / ^ % $ # @ ! * & =) that are not part of the basic keyboard letters and numbers.


Hint - If someone else has already uploaded this image or used your selected file name, a warning will prevent you from duplicating the image or file name. Do not replace the other image with your own. Find another image or rename your own image. I do not want the same image uploaded more than once.


Now you can click "upload file".

Depending on the size of the image file it will now upload to the website and when completed the File page will be open with your image title as the page name.


B. Adding the correct image information to the Summary window.

1. Now at the top of your image page select the "Edit" tab, and the file summary window will open. It should already contain the image you had previously pasted in the summary area.

2. Add a Sub-heading title at the top of the summary window space. This title can be the same as the figure title or now be a more complete description of the image.

3. Add a brief comment in your own words as to how this image relates to Prokaryotic/Eukaryotic cells. and add your signature after the text.

4. Below this paste the original figure legend.

5. Below this add a sub-sub heading:

===Reference===

and paste the full reference below this heading.

6. Below this add a a sub-sub-sub heading:

====Copyright====

and paste the copyright information from the paper/Journal.

7. Finally add the template:

{{Student Image}}

and click save page button.


Hint - If you have made a mistake you can edit the summary information as many times as you need. If the image has been uploaded by mistake or misnamed, you can delete the image by using the triangle button next to "View history" tab at the top of page, and start again.


C. Adding the image to your own student page.

1. Select the full file name (everything after the = symbol in the web address), copy and click your student number at the top of the screen.

2. When your own page opens, click the edit tab and add a new sub-heading;

==Individual Assessments==

and a sub-sub-heading

===Lab 1===

3. Now add your image as 500px wide.

4. Beneath the image paste the figure title, reference and copyright information without any subheading formatting.


You have now completed the online image exercise for Lab 1!


Here is the course co-ordinator's example Image and Test student page.

Assessment Criteria

  • Full marks will be given for completing the exercise correctly before 9 am of the day of the next practical class.
  • Marks are deducted for: image not relevant to topic or not described relevance in your own words, late submission, incorrect file naming, not including any of the relevant information or formatting required in the summary box or on your student page.




2016 Course Content

Lectures: Cell Biology Introduction | Cells Eukaryotes and Prokaryotes | Cell Membranes and Compartments | Cell Nucleus | Cell Export - Exocytosis | Cell Import - Endocytosis | Cytoskeleton Introduction | Cytoskeleton - Microfilaments | Cytoskeleton - Microtubules | Cytoskeleton - Intermediate Filaments | Cell Mitochondria | Cell Junctions | Extracellular Matrix 1 | Extracellular Matrix 2 | Cell Cycle | Cell Division | Cell Death 1 | Cell Death 2 | Signal 1 | Signal 2 | Stem Cells 1 | Stem Cells 2 | Development | 2016 Revision


Laboratories: Introduction to Lab | Microscopy Methods | Preparation/Fixation | Cell Knockout Methods | Cytoskeleton Exercise | Immunochemistry | Project Work | Confocal Microscopy | Tissue Culture | Stem Cells Lab | Microarray Visit


2016 Projects: Group 1 | Group 2 | Group 3 | Group 4 | Group 5 | Group 6 | Group 7

Dr Mark Hill 2015, UNSW Cell Biology - UNSW CRICOS Provider Code No. 00098G