Difference between revisions of "User:Z3378012"

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--[[User:Z3378012|Z3378012]] ([[User talk:Z3378012|talk]]) 15:12, 20 March 2014 (EST)
 
--[[User:Z3378012|Z3378012]] ([[User talk:Z3378012|talk]]) 15:12, 20 March 2014 (EST)
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--[[User:Z3378012|Z3378012]] ([[User talk:Z3378012|talk]]) 15:15, 10 April 2014 (EST)
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I have been here every week to date but was unaware that this would be our method of roll attendance. If there are any issues please let me know
 +
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--[[User:Z3378012|Z3378012]] ([[User talk:Z3378012|talk]]) 15:07, 1 May 2014 (EST)
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--[[User:Z3378012|Z3378012]] ([[User talk:Z3378012|talk]]) 15:30, 15 May 2014 (EST)
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Add a sub-heading.
 
Add a sub-heading.
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==Lab 2 Individual Assessment==
 
==Lab 2 Individual Assessment==
  
[[File:Schistosoma mansoni Eggs in the Gut of Mice.png|300px]]
+
'''Confocal Laser Scanning Microscopy for Detection of Schistosoma mansoni Eggs in the Gut of Mice<ref><pubmed>21533168</pubmed></ref>'''
Schistosoma mansoni Eggs in the Gut of Mice <ref><pubmed> 21533168</pubmed></ref>
+
 
 +
[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018799 PLoS One]
 +
 
 +
[[File:Schistosoma mansoni Eggs in the Gut of Mice.png|thumb|Schistosoma mansoni Eggs in the Gut of Mice<ref><pubmed>21533168</pubmed></ref>]]
 +
Background
 +
 
 +
[[File:Protein_in_the_nucleus_and_cytoplasm_of_S._mansoni_cells.png|thumb|Protein in the nucleus and cytoplasm of S. mansoni cells<ref><pubmed>21887276</pubmed></ref>]]
 +
 
 +
As the name of the journal entails, confocal laser scanning microscopy (CLSM) is used and compared to other imaging techniques. The aim is to detect Schistosoma mansoni eggs in the gut of mice and conclude whether CLSM is a viable and more effective and efficient method than other imagine techniques.
 +
 
 +
Schistosoma mansion eggs are direct indicators of schistosomiasis. schistosomiasis infects the urinary tract or intestines. Symptoms may include: abdominal pains, diarrhea, bloody stool, or blood in the urine. For long term sufferers and late diagnosis the effects can be liver damage, kidney failure, infertility, or bladder cancer.
 +
 
 +
The current and best way to detect schistosomiasis is detecting eggs which possess a characteristic spine from urine, stool, or rectal and bladder biopsy specimens. As sound as the current methods are, urine and stool samples do not always test positively to indicate schistosomiasis due to the viability of eggs. The dissected specimen undergoes various staining methods which can reveal different levels of egg maturity.
 +
 
 +
The results showed CLSM had a much better detection rate of all different egg maturities and thus, can be used as a more effective method of detecting schistosomiasis.
 +
 
 +
==Lab 3 Individual Assessment==
 +
--[[User:Z8600021|Mark Hill]] ([[User talk:Z8600021|talk]]) 14:43, 1 May 2014 (EST) Good brief descriptions of papers that relate to group topic. Your descriptions though are a little to close to the actual paper abstracts. Good image.
 +
 
 +
'''Mechanism of axonal transport: a proposed role for calcium ions<ref><pubmed>47182</pubmed></ref>'''
 +
 
 +
[http://www.sciencemag.org/content/188/4185/273.long Science]
 +
 
 +
A good article as to the introduction of the mechanisms for axonal transport.
 +
Macromolecules and organelles are transported in a systems known as axonal or dendritic transport. This study looked at transport of protein in a calcium free medium to conclude that calcium plays a role in the initiation of axonal transport.
 +
 
 +
'''Relation of somal lipid synthesis to the fast axonal transport of protein and lipid<ref><pubmed>6155973</pubmed></ref>'''
 +
 
 +
[http://www.sciencedirect.com/science/article/pii/000689938090178X Science Direct]
 +
 
 +
This study inhibited phospholipid synthesis in dorsal root ganglia to show a decreased proportional effect on amount of protein undergoing fast axonal transport. Exposing an unmyelinated nerve trunk to a certain cation had no effect on protein translocation. This helps conclude that phospholipid synthesis is not required to maintain ongoing transport in the axon. Inhibiting cholesterol synthesis in the ganglia also resulted in depression of protein transport. So both phospholipid and cholesterol are required at the level of the ganglion. Drawing from these results they suggested that the initiation of fast axonal transport of protein is dependent on the assembly of lipoprotein structures in the soma.
 +
 
 +
'''Axonal transport of microtubules: the long and short of it<ref><pubmed>16643272</pubmed></ref>'''
 +
 
 +
[http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0854.2006.00392.x/abstract;jsessionid=441432D80838EA84B6F408CBC1523CAC.f04t04 Wiley]
 +
 
 +
Specific to the transport of microtubules. The study proposes a model as to how microtubules are transported within the axon, which they term 'cut and run'. Longer microtubules are mobilized by enzymes that sever them into shorter mobile polymers. Previous studies have already shown that microtubules are transported down the axon in the form of these short polymers. The shorter microtubules are transported via cytoplasmic dynein by generating forces against the actin cytoskeleton. This was one mechanism thought to be transporting shorter microtubules after they were 'cut'. The study then talks about what mechanisms organise the longer microtubules to be then cut and transported.
 +
 
 +
[[File:Hippocampal neurons.png|thumb|Hippocampal neurons are differentiated and present distinct morphology for both the axon and dendrites<ref><pubmed>23894274</pubmed></ref>]]
 +
 
 +
'''Molecular motors and mechanisms of directional transport in neurons<ref><pubmed>15711600</pubmed></ref>'''
 +
 
 +
[http://www.nature.com/nrn/journal/v6/n3/full/nrn1624.html Nature]
 +
 
 +
This article studies the role of motor proteins in directional axonal and dendritic transport and the mechanisms associated with them. As a basis, motors proteins seem to recognise cargoes of mRNAs and large protein–RNA complexes through adaptor complexes or scaffolding proteins. Motors can intrinsically distinguish between axons and dendrites, perhaps as a result of cues from microtubules.
 +
 
 +
==Lab 4 Individual Assessment==
 +
--[[User:Z8600021|Mark Hill]] ([[User talk:Z8600021|talk]]) 14:42, 1 May 2014 (EST) Where are your answers to this exercise?
 +
 
 +
Identify an antibody that can been used in your group's transport project.
 +
 
 +
Identify the species deriving the antibody.
 +
 
 +
Identify the working concentration for the antibody.
 +
 
 +
Identify a secondary antibody that could be used with this antibody.
 +
 
 +
Identify a paper that has used this antibody.
 +
 
 +
==Lab 7 Individual Assessment==
 +
 
 +
===Group 1===
 +
Introduction has good structure and with knowledge of the subject is easy to read. If this is a general informative page it may be helpful to not use too much jargon.
 +
The structure of the membrane is probably able to be put into the introduction and inserting an image would probably benefit the reader.
 +
Receptor sections needs to have more detail about PRRs and PAMPs rather than branching into the subsections. Probably a vital part of the topic that solidifies the introduction.
 +
Mechanism of phagocytosis has good amount of detail but seems disjointed. Better sentence structure will give this section more flow and make it easier to read. The first heading phagocytosis is probably unnecessary as this is done in the intro.
 +
When talking about the zipper model might be worthwhile to bold the text to place emphasis on the idea.
 +
Diseases Related to Phagocytosis and Current/Future Research subsections are great ideas that help give more information to the reader. Adding a little more to the Current/Future Research would benefit everyone greatly.
 +
One consistent issue is the referencing throughout the project. Under each section is a huge chunk of references that make it look very disjointed and messy. Should look into referencing each sentence with the appropriate reference.
 +
Overall a good job so far with some minor adjustment to make it even better.
 +
 
 +
===Group 2===
 +
The introduction provides a clear understanding of the topic. There is good sentence structure and flow which then gives a good lead up to the next subsections. The rest of the project builds well on the introduction. Every section you have set as heading gives good detailed information. The only real improvement I would recommend is more images and maybe even a more broad outlook on the transport system. The quality of what you have so far is amazing but the amount of information is very select.
 +
 
 +
===Group 3===
 +
 
 +
 
 +
The project is lacking an introduction which is vital in providing background to such a big topic.
 +
It may be worthwhile embedding an image rather than providing a link to the image for ease of reading. The link to further information on the nuclear envelope is a good way of reducing unnecessary information and making the intro succinct. Not particularly sure what the Function heading is there for if you have provided this link. Would be better if you moved the NPC section before the Nucleoporins. The explanations of each model is easy to understand and provides what's necessary. If there are any images for each model it would be good to get a visual. Nucleoporins has a table which helps with the interpretation of data. This information is hard to understand in the table though as none of the headings are really explained. RanGTP and RanGDP section seems there is a lot of jargon without any real explanation of what each is. The images helps greatly with processing information and when on the image page the subtext for the image is explained well. The rest of the project seems to be in dot points so I won't critique it. Overall the project has great images and references where necessary. I feel with the intro completed this will give the reader and much better background for reading the rest of the page. Might be worthwhile moving the sections around to go along with for mentioned intro.
 +
 
 +
==Lab 9 Individual Assessment==
 +
 
 +
1. Write a hypothesis that you are going to test.
 +
 
 +
2. Write aims of your experiment.
 +
 
 +
3. Identify key techniques and procedures used in your investigation (Spell these out in some detail).
 +
 
 +
4. Identify suppliers that have resources that you will need for your study (create links to the supplier resource pages, kits, antibodies etc).
 +
 
 +
5. Now prepare a flow diagram of how the experiment will be carried out and analysed.
 +
 
 +
6. What will different experimental results (outcomes) mean.
 +
 
 +
Answers
 +
 
 +
1. The apoptosis of adipocytes follows the intrinsic pathway
 +
 
 +
2. The aim of the experiment will be to investigate the mechanism of apoptosis for adipocytes in adipose tissue. Also to identify whether it follows the intrinsic, extrinsic or both pathways.
 +
 
 +
3. Immunohistochemistry that has Fas Ligand kit (CD95L) which will staining for Ligand Binding. Another stain for activated caspase 9 (Caspase 9 Human ELISA KIT).
 +
 
 +
4. [http://www.abcam.com Abcam], [http://www.abcam.com/fasnbspligand-cd95l-human-elisa-kit-ab45892.html Fas Ligand kit], [http://www.abcam.com/caspase-9-human-elisa-kit-ab119508.html Caspase 9 Human ELISA KIT]
 +
 
 +
5. Prepare tissue → Follow [http://www.abcam.com/fas-ligand-cd95l-rat-elisa-kit-ab100759-protocols.html Protocol] on use of Fas Ligand kit → Image tissue → Detect for presence of Fas Ligand
 +
 
 +
Repeat for Caspase 9 ELISA KIT
 +
 
 +
Prepare tissue → Follow [http://www.abcam.com/caspase-9-human-elisa-kit-ab119508-protocols.html Protocol] on use of Caspase 9 ELISA kit → Image tissue → Detect for presence of Caspase 9
 +
 
 +
6. Staining that shows ligand binding indicate an extrinsic pathway. Activated caspase 9 (Caspase 9 Human ELISA KIT) that will indicate there are apoptosome formations and in essence the mitochondrial or intrinsic pathway.
  
 
==References==
 
==References==

Latest revision as of 18:49, 21 May 2014

Demo


Add your own student page to the site.

Add your signature for Lab attendance.

--Z3378012 (talk) 15:44, 13 March 2014 (EST)

--Z3378012 (talk) 15:12, 20 March 2014 (EST)

--Z3378012 (talk) 15:15, 10 April 2014 (EST)

I have been here every week to date but was unaware that this would be our method of roll attendance. If there are any issues please let me know

--Z3378012 (talk) 15:07, 1 May 2014 (EST)

--Z3378012 (talk) 15:30, 15 May 2014 (EST)


Add a sub-heading.

Sub-heading

Add an external Link.

PubMed

Add an internal Link.

INTERNAL LINK

this is awesome

This is about prokaryote. [1]

This is also about prokaryotes. [2]

<pubmed limit=2>mitochondria</pubmed>

Images

Ecoli [3]

Journal.pone.0091915.g003.png[4]

Lab 2 Individual Assessment

Confocal Laser Scanning Microscopy for Detection of Schistosoma mansoni Eggs in the Gut of Mice[5]

PLoS One

Schistosoma mansoni Eggs in the Gut of Mice[6]

Background

Protein in the nucleus and cytoplasm of S. mansoni cells[7]

As the name of the journal entails, confocal laser scanning microscopy (CLSM) is used and compared to other imaging techniques. The aim is to detect Schistosoma mansoni eggs in the gut of mice and conclude whether CLSM is a viable and more effective and efficient method than other imagine techniques.

Schistosoma mansion eggs are direct indicators of schistosomiasis. schistosomiasis infects the urinary tract or intestines. Symptoms may include: abdominal pains, diarrhea, bloody stool, or blood in the urine. For long term sufferers and late diagnosis the effects can be liver damage, kidney failure, infertility, or bladder cancer.

The current and best way to detect schistosomiasis is detecting eggs which possess a characteristic spine from urine, stool, or rectal and bladder biopsy specimens. As sound as the current methods are, urine and stool samples do not always test positively to indicate schistosomiasis due to the viability of eggs. The dissected specimen undergoes various staining methods which can reveal different levels of egg maturity.

The results showed CLSM had a much better detection rate of all different egg maturities and thus, can be used as a more effective method of detecting schistosomiasis.

Lab 3 Individual Assessment

--Mark Hill (talk) 14:43, 1 May 2014 (EST) Good brief descriptions of papers that relate to group topic. Your descriptions though are a little to close to the actual paper abstracts. Good image.

Mechanism of axonal transport: a proposed role for calcium ions[8]

Science

A good article as to the introduction of the mechanisms for axonal transport. Macromolecules and organelles are transported in a systems known as axonal or dendritic transport. This study looked at transport of protein in a calcium free medium to conclude that calcium plays a role in the initiation of axonal transport.

Relation of somal lipid synthesis to the fast axonal transport of protein and lipid[9]

Science Direct

This study inhibited phospholipid synthesis in dorsal root ganglia to show a decreased proportional effect on amount of protein undergoing fast axonal transport. Exposing an unmyelinated nerve trunk to a certain cation had no effect on protein translocation. This helps conclude that phospholipid synthesis is not required to maintain ongoing transport in the axon. Inhibiting cholesterol synthesis in the ganglia also resulted in depression of protein transport. So both phospholipid and cholesterol are required at the level of the ganglion. Drawing from these results they suggested that the initiation of fast axonal transport of protein is dependent on the assembly of lipoprotein structures in the soma.

Axonal transport of microtubules: the long and short of it[10]

Wiley

Specific to the transport of microtubules. The study proposes a model as to how microtubules are transported within the axon, which they term 'cut and run'. Longer microtubules are mobilized by enzymes that sever them into shorter mobile polymers. Previous studies have already shown that microtubules are transported down the axon in the form of these short polymers. The shorter microtubules are transported via cytoplasmic dynein by generating forces against the actin cytoskeleton. This was one mechanism thought to be transporting shorter microtubules after they were 'cut'. The study then talks about what mechanisms organise the longer microtubules to be then cut and transported.

Hippocampal neurons are differentiated and present distinct morphology for both the axon and dendrites[11]

Molecular motors and mechanisms of directional transport in neurons[12]

Nature

This article studies the role of motor proteins in directional axonal and dendritic transport and the mechanisms associated with them. As a basis, motors proteins seem to recognise cargoes of mRNAs and large protein–RNA complexes through adaptor complexes or scaffolding proteins. Motors can intrinsically distinguish between axons and dendrites, perhaps as a result of cues from microtubules.

Lab 4 Individual Assessment

--Mark Hill (talk) 14:42, 1 May 2014 (EST) Where are your answers to this exercise?

Identify an antibody that can been used in your group's transport project.

Identify the species deriving the antibody.

Identify the working concentration for the antibody.

Identify a secondary antibody that could be used with this antibody.

Identify a paper that has used this antibody.

Lab 7 Individual Assessment

Group 1

Introduction has good structure and with knowledge of the subject is easy to read. If this is a general informative page it may be helpful to not use too much jargon. The structure of the membrane is probably able to be put into the introduction and inserting an image would probably benefit the reader. Receptor sections needs to have more detail about PRRs and PAMPs rather than branching into the subsections. Probably a vital part of the topic that solidifies the introduction. Mechanism of phagocytosis has good amount of detail but seems disjointed. Better sentence structure will give this section more flow and make it easier to read. The first heading phagocytosis is probably unnecessary as this is done in the intro. When talking about the zipper model might be worthwhile to bold the text to place emphasis on the idea. Diseases Related to Phagocytosis and Current/Future Research subsections are great ideas that help give more information to the reader. Adding a little more to the Current/Future Research would benefit everyone greatly. One consistent issue is the referencing throughout the project. Under each section is a huge chunk of references that make it look very disjointed and messy. Should look into referencing each sentence with the appropriate reference. Overall a good job so far with some minor adjustment to make it even better.

Group 2

The introduction provides a clear understanding of the topic. There is good sentence structure and flow which then gives a good lead up to the next subsections. The rest of the project builds well on the introduction. Every section you have set as heading gives good detailed information. The only real improvement I would recommend is more images and maybe even a more broad outlook on the transport system. The quality of what you have so far is amazing but the amount of information is very select.

Group 3

The project is lacking an introduction which is vital in providing background to such a big topic. It may be worthwhile embedding an image rather than providing a link to the image for ease of reading. The link to further information on the nuclear envelope is a good way of reducing unnecessary information and making the intro succinct. Not particularly sure what the Function heading is there for if you have provided this link. Would be better if you moved the NPC section before the Nucleoporins. The explanations of each model is easy to understand and provides what's necessary. If there are any images for each model it would be good to get a visual. Nucleoporins has a table which helps with the interpretation of data. This information is hard to understand in the table though as none of the headings are really explained. RanGTP and RanGDP section seems there is a lot of jargon without any real explanation of what each is. The images helps greatly with processing information and when on the image page the subtext for the image is explained well. The rest of the project seems to be in dot points so I won't critique it. Overall the project has great images and references where necessary. I feel with the intro completed this will give the reader and much better background for reading the rest of the page. Might be worthwhile moving the sections around to go along with for mentioned intro.

Lab 9 Individual Assessment

1. Write a hypothesis that you are going to test.

2. Write aims of your experiment.

3. Identify key techniques and procedures used in your investigation (Spell these out in some detail).

4. Identify suppliers that have resources that you will need for your study (create links to the supplier resource pages, kits, antibodies etc).

5. Now prepare a flow diagram of how the experiment will be carried out and analysed.

6. What will different experimental results (outcomes) mean.

Answers

1. The apoptosis of adipocytes follows the intrinsic pathway

2. The aim of the experiment will be to investigate the mechanism of apoptosis for adipocytes in adipose tissue. Also to identify whether it follows the intrinsic, extrinsic or both pathways.

3. Immunohistochemistry that has Fas Ligand kit (CD95L) which will staining for Ligand Binding. Another stain for activated caspase 9 (Caspase 9 Human ELISA KIT).

4. Abcam, Fas Ligand kit, Caspase 9 Human ELISA KIT

5. 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

6. Staining that shows ligand binding indicate an extrinsic pathway. Activated caspase 9 (Caspase 9 Human ELISA KIT) that will indicate there are apoptosome formations and in essence the mitochondrial or intrinsic pathway.

References

  1. <pubmed>24603758</pubmed>
  2. <pubmed>24601599</pubmed>
  3. <pubmed>24603758</pubmed>
  4. <pubmed>24637574</pubmed>
  5. <pubmed>21533168</pubmed>
  6. <pubmed>21533168</pubmed>
  7. <pubmed>21887276</pubmed>
  8. <pubmed>47182</pubmed>
  9. <pubmed>6155973</pubmed>
  10. <pubmed>16643272</pubmed>
  11. <pubmed>23894274</pubmed>
  12. <pubmed>15711600</pubmed>