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  • I have been present for all labs except on 17/04/14. I was unaware that adding a signature was an official indication of attendance

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Lab 1

This is prokaryotes [1]

Zhouqing Luo, Junbiao Dai [Synthetic genomics: the art of design and synthesis]. Sheng Wu Gong Cheng Xue Bao: 2017, 33(3);331-342 PubMed 28941334

Cristina Y Zamora, Nathaniel S Schocker, Michelle M Chang, Barbara Imperiali Chemoenzymatic Synthesis and Applications of Prokaryote-Specific UDP-Sugars. Meth. Enzymol.: 2017, 597;145-186 PubMed 28935101

Aharon Oren On names of genera of prokaryotes that are later homonyms of generic names with standing in the zoological or the botanical nomenclature. Proposal of Neomegalonema gen. nov. and Neomegalonema perideroedes comb. nov. as replacements for the prokaryotic generic name Meganema and the species name Meganema perideroedes. Int. J. Syst. Evol. Microbiol.: 2017; PubMed 28933323

this is a wonderful picture of 2 cells

Lab 2

1. On your own student page upload an image with the reference using the Pubmed formatting shown in the practical class tutorial last week.

Identification of a Plant Viral RNA Genome in the Nucleus[2]

2. Identify a recent research article (not review) that uses either confocal microscopy or super-resolution microscopy as one of the study's techniques. Explain briefly (1 paragraph) how the microscopy technique specifically contributed to the article's findings.

Researchers performed and compared applications of super-resolution, STORM and confocal imaging techniques to trace neural connectivity within wild, neonatal embryos of rats. Also, membrane labeling techniques and 2D vs. 3D neural process imaging were varied in order to obtain and compare the levels of trace accuracy. Results conveyed that super-resolution imaging provided the greatest tracing accuracy to allow the researchers in tracing neural processes within the cultured hippocampal neurons from the rat embryos compared to the other imaging techniques. Also, membrane specific labelling techniques (compared to cytoplasmic labelling) and 3D imaging at 116nm (compared to 44nm 2D) displayed higher image resolution. It was therefore concluded that membrane specific labelling coordinating with 3D, multicoloured super-resolution imaging will provide the most distinct and accurate tracing of neural processes. This type of imaging technique not only provides revolutionizing insight towards understanding brain activity and other neurological applications, but can be applied to many scientific research fields. [3]

Lab 3

Fast Axonal Transport --Mark Hill (talk) 14:39, 1 May 2014 (EST) These references and your descriptions relate to the group project. You should realise though that some of your references are "historic" and not part of the current research, you should have included this information in your descriptions.

1. Role of calcium in axonal transport

Development of the soma of a neuron without calcium will reduce the amount (but not the speed) of fast axonal transport of [3H] protein. Protein synthesis and energy metabolism will remain unaffected, but there will be less proteins to be used for axonal transport. Therefore, in order to generally increase the amount of proteins for axonal transport in calcium free somas, selected proteins are transported from their original polysomal sites of synthesis to the transport system for an initiation phase of fast axonal transport. [4]

2. Role of somal lipid synthesis in fast axonal transport

Initiation of fast axonal transport of protein is dependent on the presence and distribution of lipoprotein structures in the soma. In this study, inhibition of phosopholipid synthesis was directly proportional to the decrease in the amount of [3H] protein in the process of fast axonal transport. The lipid undergoing fast transport in the axon was unaffected by the inhibition of somal phospholipid synthesis, but the reduced amount of lipoproteins indicated its effect on the initiation (not ongoing) process of fast axonal transport. [5]

Kinesin-1 Returns To The Cell Body From The Neurite Tips[6]

3. Mediation of axonal transport

Fast transport is a type of microtubule-based mechanism of bidirectional movement of membranous organelles. Highly significant to fast axonal transport of individual cellular cargo along the microtubules is the motor-protein kinesin. Level of regulation of organelles and motor-proteins will determine the rate of axonal transport. [7]

4. Effect of a pressure barrier on fast anterograde axonal transport

A pressure barrier was applied to a small part of the nerve, with maximal pressure and gradients on each side of the maximum pressure (between 16-45 mmHg). This study indicated that the range of maximal pressure has a significant impact on the inhibition of axonal transport, but the pressure gradient insignificantly impacted the inhibition. Therefore, the results convey that at least one part of fast anterograde axoplasmic transport is functioning within collapsible canalicular structures. [8]

Lab 4

--Mark Hill (talk) 14:36, 1 May 2014 (EST) Where is the link to the Antibody data sheet? I cannot check your answer as correct or not without this link. For example the concentration you have given i probably the Antibody concentration that is shipped, not the final "working concentration" that would be in either the data sheet or one of the references. In your cited paper the information is " Immunogold labeling with the monoclonal antibody 13C4 (diluted 1/250)"

Identify an antibody that can been used in your group's transport project. Shigatoxin 1 (13C4)

Identify the species deriving the antibody. Mouse

Identify the working concentration for the antibody. 100 µg/ml

Identify a secondary antibody that could be used with this antibody. Anti-LAMP2 [H4B4]

Identify a paper that has used this antibody. Retrograde transport of KDEL-bearing B-fragment of Shiga toxin. [9]

Lab 8

Brief reviews of other group projects

Group 1

Introduction is good and easy to understand. It clearly highlights the key points relating to the topic without getting into too much detail. The format of this assessment is also good. The images relate to the text which allows the reader to gain visual understanding. A highlight of this assignment is the use of headings and sub-headings, it doesn’t chunk all the information together but divides into sections to make it easier to understand. However, perhaps a table would be beneficial. Overall this assignment is heading in the right direction. The references all appear to be valid, except I think the structure of the referencing may need to be altered, unless it is just structured this way as an early draft.

Group 2

At first glance the introduction appears to be very long, which isn’t a bad thing. However you may need to be cautious that you are not going into too much detail as it can make it very complicated for readers to understand. The assignment has great structure and format except there may be one thing you need to fix in relation to the formatting of headings and subheadings. At the top of the page where it says “contents”, everything is under “1. Transport from the Cytoplasm to the Mitochondria”, I think it would be better if you started a new heading for extra information (e.g. “2. What can go wrong…”, “3. Current or future research…”, “4. Glossary”). The “glossary” heading is excellent, allowing readers to identify a term that they’re not familiar with. The reference list is long which is good as you don’t seem to be sticking to one source, but getting information from many sources. Overall this assignment has great direction and the content is well written and accompanied by helpful images.

Group 3

At this stage, it appears that this assignment is going in the right direction. The overall structure is well structured as the headings and subheadings provides a quick glance of what the assignment is going to be about. The images are related to the text which allows further understanding for the reader. However there appears to be images within the references section, also a table would be beneficial. Also, there appears to be a lot of references within the content of the assignment which should be under the references section. Overall this assignment is well-structured, easy to understand and appears to be heading in the right direction.

Lab 9

Aim: to investigate which specific mechanism of apoptosis occurs in adipose tissue, in humans Hypothesis: adipose tissues in humans undergo the intrinsic pathway of apoptosis, rather than the extrinsic pathway Key techniques: Immunofluorescence techique Fas Ligand (CD95L) ELISA Kit Caspase-9 Human ELISA Kit

Write a hypothesis that you are going to test. adipose tissues in humans undergo the intrinsic pathway of apoptosis, rather than the extrinsic pathway

Write aims of your experiment. to investigate which specific mechanism of apoptosis occurs in adipose tissue, in humans

Identify key techniques and procedures used in your investigation (Spell these out in some detail). Immunofluorescence technique: fluorescence microscope. Uses the antigen and antibody specificity to target fluorescent dyes to specific biomolecule targets in a cell Fas Ligand (CD95L) ELISA Kit: for Ligand Binding Caspase-9 Human ELISA Kit: for activated caspase 9

Identify suppliers that have resources that you will need for your study (create links to the supplier resource pages, kits, antibodies etc). Abcam Fas Ligand kit Caspase 9 Human ELISA KIT

Now prepare a flow diagram of how the experiment will be carried out and analysed. Prepare tissue → Follow Protocol on use of Fas Ligand kit → Image tissue → Detect for presence of Fas Ligand

Repeat for Caspase 9 ELISA KIT

Prepare tissue → Follow Protocol on use of Caspase 9 ELISA kit → Image tissue → Detect for presence of Caspase 9

What will different experimental results (outcomes) mean. Staining that shows ligand binding indicate an extrinsic pathway. This is Activated caspase 9 (Caspase 9 Human ELISA KIT) that will indicate apoptosis formations and in essence the mitochondrial or intrinsic pathway.


  1. Ziga Zebec, Andrea Manica, Jing Zhang, Malcolm F White, Christa Schleper CRISPR-mediated targeted mRNA degradation in the archaeon Sulfolobus solfataricus. Nucleic Acids Res.: 2014, 42(8);5280-8 PubMed 24603867
  2. D J McKeever, H W Reid The response of the supramammary lymph node of the sheep to secondary infection with orf virus. Vet. Microbiol.: 1987, 14(1);3-13 PubMed 3498252
  3. Melike Lakadamyali, Hazen Babcock, Mark Bates, Xiaowei Zhuang, Jeff Lichtman 3D multicolor super-resolution imaging offers improved accuracy in neuron tracing. PLoS ONE: 2012, 7(1);e30826 PubMed 22292051
  4. R Hammerschlag The role of calcium in the initiation of fast axonal transport. Fed. Proc.: 1980, 39(10);2809-14 PubMed 6157571
  5. F M Longo, R Hammerschlag Relation of somal lipid synthesis to the fast axonal transport of protein and lipid. Brain Res.: 1980, 193(2);471-85 PubMed 6155973
  6. T Lynne Blasius, Nathan Reed, Boris M Slepchenko, Kristen J Verhey Recycling of kinesin-1 motors by diffusion after transport. PLoS ONE: 2013, 8(9);e76081 PubMed 24098765
  7. M P Sheetz, E R Steuer, T A Schroer The mechanism and regulation of fast axonal transport. Trends Neurosci.: 1989, 12(11);474-8 PubMed 2479151
  8. R W Hahnenberger Inhibition of fast anterograde axoplasmic transport by a pressure barrier. The effect of pressure gradient and maximal pressure. Acta Physiol. Scand.: 1980, 109(2);117-21 PubMed 6158830
  9. L Johannes, D Tenza, C Antony, B Goud Retrograde transport of KDEL-bearing B-fragment of Shiga toxin. J. Biol. Chem.: 1997, 272(31);19554-61 PubMed 9235960