Difference between revisions of "Talk:Group 9 Project - Fluorescent Proteins"
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--[[User:Z3217043|Jessie Tomkins]] 04:34, 12 May 2010 (UTC)Hey guys, you have a lot of content here. It just isn't presented in a way that does it justice. Here are some ways you could improve it.
--[[User:Z3217043|Jessie Tomkins]] 04:34, 12 May 2010 (UTC)Hey guys, you have a lot of content here. It just isn't presented in a way that does it justice. Here are some ways you could improve it.
* Condense some of the material you have written. It seems like it goes on for way too long. In particular the history section.
* Condense some of the material you have written. It seems like it goes on for way too long. In particular the history section.
Revision as of 15:42, 12 May 2010
--z3252833 04:42, 12 May 2010 (UTC) You’ve obviously done a lot of research into this, so well done on that front. The text is comprehensive but quite dense, so it might be worth thinking about summarising it a bit more with tables or something; maybe you could summarise the advantages and limitations of fluorescent proteins in a table. Also, with your glossary – I’m guessing you’ll work on that before final submission, because there are terms in the text that aren’t there and some terms have no definitions. It might be worth moving the glossary above the references, too, so it’s easier for readers to find. Also in-text referencing might be a good idea rather than just a reference list (are you going to combine your two lists?), and you might want to think about getting rid of some of those gaps of white space between paragraphs in “current research”.
In terms of pictures, I’ve got just a few points that you might want to consider. On the whole, you’ve used them well to illustrate text, but you might want to find some pictures to put at the beginning of the page, because it’s just black text on white right now for big areas. Also, maybe play around with positioning them on the left and right of the page instead of just the right – and maybe move that mosquito larvae picture son it’s in the text not randomly in the middle of the screen. (I noticed some of your pictures weren’t cited but said ‘copyright to be updated real soon’, so I know it’ll all be fixed before final submission.) With a bit of work I think this page will look really good.
--Jessie Tomkins 04:34, 12 May 2010 (UTC)Hey guys, you have a lot of content here. It just isn't presented in a way that does it justice. Here are some ways you could improve it.
- Condense some of the material you have written. It seems like it goes on for way too long. In particular the history section.
- Add some more pictures to make the page more appealing.
- Perhaps summerise the advantages/ disavantages in a table.
- Make some of your headings into bolder larger headings to that your info is broken up more and is more logical to understand.
- In text referencing should be used.
- Your glossary needs to be finished properly.
I think with a little more work you'll have a great project!
--Mark Hill 04:29, 12 May 2010 (UTC) Lab 8 Assessment - 22 student reviews.
--Erika Unsworth 03:51, 12 May 2010 (UTC) Group 9,
- Its great how you've incorporated dot points etc. to try and break up the information
- Some more pictures would be good
- Glossary and References need some work (But you guys probably already know that)
- Overall, I'm pretty happy with your page- looks like a lot of time has been put into it.
--Paula Ordonez 03:45, 12 May 2010 (UTC) Hi group 9, Upon first glance, this page does not seem well organised as the number of subheadings is too minimal, and the numerous paragraphs of text could use with pictures to break it up and make it more interesting. Furthermore, the history section is too long and the glossary section needs to be completed. I really liked the advantages and disadvantages section which clearly explains the information.
--Joanne Raffel 02:01, 12 May 2010 (UTC) Your page was lacking in images and subheadings and it was rather long. Your history section was also long, the nobel prize section did not seem relevant, your paragraphs did not flow and your referencing within the information was incorrect. I liked the thoroughness of the development sections but I think more pictures would be good. Your current research section was too spaced out and the advantages and limitations sections should be before the current research. Your referencing needs to be condensed into one and there were no helpful links. Otherwise ice work.
--Julianna Lam 01:55, 12 May 2010 (UTC) great page guys. might contain too much information, having said that the content of the information is very informative. the use of pictures is good although it would be good to see pictures at the start of the page to make it look more appealing to read. some of the information under the historys heading, would be good to put it under a separate heading so it doesnt look as cluttered.
--Darren Dizon 23:26, 11 May 2010 (UTC)Page is good as the content and diagrams were very easy to understand, however the formatting seems to be a little off in terms of headings, and some headings don't have information under them. Needs more referencing too, especially for the applications. peace out
--z3254509 22:18, 11 May 2010 (UTC)
Hey, the information on this page is really good, but it seems a little dense, and the overall impression of the page is that it is a little dry. Some helpful points:
- You may want to look over your headings and make some of them double dash instead of triple. Also check that the headings have capital letters.
- The glossary section needs to be completed, and referenced.
- As far as referencing goes, please refence the pictures, they are lacking any sort of permission statement.
- Consider breaking up the text somehow, as it is very hard to read.
--z3269335 14:40, 11 May 2010 (UTC)
Honestly, I think your group may need to put extra effort into the project. Although your group have included quite a lot of information about fluorescent protein and some colourful photos, some of them like, Gfp mouse1.JPG, Malaria.jpg and Prion coverting protein.jpg, have not been properly referenced. Also, please noted that our project is required to include at least one self- drawn diagram.
Additionally, the way of referencing is not consistent. More work should be done on correct citations.
Moreover, the Links to Current Research and Glossary have not been completed.
Sorry if I have been made a harsh comment on your project, however, please do not feel disappointed as we still have 1-2 weeks to finalize our project. Wishing you all the best.
--Dougall Norris 07:13, 11 May 2010 (UTC)
Hey guys, i feel like this is a solid page that needs a bit of work. You have some really quality information, but it has a poor flow. I think you need to go through as a group and re-structure your page.
- For starters, you have two disadvantages and advantages sections,
- As previously mentioned, there is so much content under the history heading that could do with new headings, it also needs to be referenced
- The development of FP's is great but future resarch could also be put under its own heading.
- Current reseacrh and needs to be referenced and i think there is too much spacing in this part.
- The references of the whole piece should be regular wiki style too, because it would make it much easier to verify the statements and get some further knowledge.
- A few of the images need permission info as well and i dont think you have a student drawn image either
Sorry if this sounded harsh but i think its better that you know, because you could have a really good composition on your hands.
--z3178608 04:40, 11 May 2010 (UTC) Hello Group 9
Your project page is detailed and informative about the use of fluorescent proteins in different aspects of research. These are the points after reading your project page:
- Information on fluorescent proteins is covered extensively in the theory and different types of fluorescent proteins.
- However, the organization of the project could be improved by the proper usage of subheadings and appropriate font size of the subheadings. Alternatively, you could use a horizontal line to segregate other sections of the page.
- I think the time should be more appropriate to be classified under the development of GFP.
- Appropriate use of graphics with the accompanying text.
- Referencing could be improved by having a more proper order.
It is apparent that your group has put in great effort for this page. Good job!
--Jae Choi 11:54, 10 May 2010 (UTC) Hi Guys, You guys have made a great project page. I can guess how much effort you have spent for this. This page looks really good. But in terms of the order, this project still needs to be organised. For example, History part contains not only the ‘timeline/discovery of GFP’ but also has ‘structure and classification’ and ‘advantages and disadvantages’ and extra. Also, as others mentioned, it would be better if you use wiki referencing style. Cheers.
--z3252005 10:31, 10 May 2010 (UTC) Hey Group 9. Your project is great and has a good structure to it. The choice of information used is appropriate as well. Some points I could suggest to help improve your project are:
- I would suggest to switch the timeline and nobel prize press release around to keep the history section in chronological order.
- Make sure to write what an abbreviation stands for the first time you use it then you can mention it as an abbreviation later on in your text like GFP, BFP EGFP and FRET.
- I wasn't sure what this was "Links original steps used;". I think you guys may have left this in by mistake. It's not a big thing just wanted to let you guys know.
- I would also suggest that you guys place both the links to research and glossary before the references section.
- In-text references where not there for all sections. Also have a look at project referencing to see how Mark would like us to reference our projects.
- I would also suggest you guys put the advantages and disadvantages section into a table format. This is just a preference and I think would help to break up the text.
- More images would also be helpful both to understand this technique and to break up the text.
- I couldn't see a student drawn diagram. Don't forget to put one up.
Overall I think you guys have done a done a good job. You have helped me expand my knowledge of Fluorescent Proteins. Well done.
--Angama Yaquobi 08:25, 10 May 2010 (UTC) Hi group 9, your page looks amazing and very informative indicating the hard work you lot have put in. Here are few points that I would like to mention:
- Intro is concise and easy to read
- History is very well structured
- However there is a large amount of text so using a table or dot points would help to break up the text and also an image can make your webpage even more appealing.
- The dot points under ADVANTAGES & DISADVANTAGES are very helpful and easy to understand.
- Adding few more words in glossary and also placing the glossary before referencing will make your webpage complete and perfect other than that well done guys.
--Joseph Chuk 07:52, 10 May 2010 (UTC) Your project is intersting and I have leanrt a lot about fluorescent proteins. The project starts with a precise history timeline. The advantages and limitations are clearly described. Good job! I think you should add a subheading for the theory part because the principle of how it works is relatively important. The applications are too detailed, which seemed to form the major part of the project but I think it should be more precise. Overall well done!
--David Williamson 06:28, 10 May 2010 (UTC)
- All in all I think you guys have done a really good job- the amount and choice of info you have is really sensible, and it’s well expressed in a readable way.
- The pictures you guys have are really helpful. Even more could be good though- eg: a picture/schematic for the theory of fluorescence.
- I think you guys still need to make your own diagram?
- The advantages, disadvantages and limitations of both GFP and fluorescent proteins in general are good but I think some of them may need elaboration- eg: why is gene transfection a disadvantage of GFP? Or oligomerisation a limitation of fluorescent proteins?
- I think some of your sections need referencing- eg: there aren’t many references in the “current research section”
- Some places where you have numbers you could change to be wiki number lists rather than 1) etc? This would save space and make the numbers more obvious. You do this by putting a # next to it in the editing section.
--Katiana Shaw 03:32, 10 May 2010 (UTC) Hey group 9 - Here are my thoughts on your project:
- The introduction and history parts are good; I like how you have a section on Nobel Prize winners. Just note that you have spelt Nobel as "noble".
- There is a lot of really good information, though I find the use of subheadings makes it seem like a really big slab of text. I would have liked to see you break up the sections on theory, structure & classification, Advantages, Disadvantages, etc into sections with their own headings, not just subheadings as these look as though they come under the history. It makes the project a bit more readable and by separating into sections it makes it easier to jump to specific areas.
- I think you could eliminate some of the text by using tables for advantages and disadvantages - that way you don't have to cut any information but still makes it easy to read.
- A few more pictures would also help break it up.
Overall it looks as though you have researched your topic very well. Apart from the few structural things listed above, you have done really well!
Hi group 9, your page is really quite good. it is evident that you have all put in a lot of work on the page and the information that you have come up with is very informative. A few points to note though:
- There is no initial reference to what GFP is. when you are going to use an abbreviation you should put it in brackets after the actual name e.g Green Fluorescent Protein (GRP)
- The history is very good - I particularly liked the timeline, however I felt that the theory part could have its own section.
- There are massive amounts of text - perhaps use tables to break up the text.
- The glossary is a little empty - you have put in a couple of terms but there are no definitions for them.
- There was no methodology section - perhaps revise some sections and see if any of the information would fit into a section on the method
--Emily Wong 22:25, 9 May 2010 (UTC)
--z3256682 07:39, 9 May 2010 (UTC) Hi,
There is a lot of good research and work here, however there seems to be some issues in terms of structure, and referencing. As a previous reviewer indicated, you have no student-drawn image anywhere. I have placed my opinions below, however they are for your consideration, and I hope you will not take any offence from them at all.
- the theory of fluorescence bit onwards should be put into its own section, and not included as a subsection of the History part.
- be consistent: Consistency is needed eg. sometimes you use GFP and other times you use gfp - use either one consistently so you don't confuse your readers.
- Shorthand usage: Amino acid shorthands such as Thr, Ala etc should be avoided when you first introduce them to us in theory of fluorescence.
- Referencing: Overall referencing really needs improvement in theory of fluorescence, since you state a lot of research-related things which isn't your own study, but there are no citations at all. Furthermore, you write 'Tsien has classified GFPs...' - who is Tsien, where is his citation?
- Advantages/Disadvantages in theory of fluorescence could be placed in a table for presentation and comparability reasons. Also, these adv/disadv should be integrated with the adv/disadv you placed under Section 5 (Advantages) and Section 6(Limitations) - if something applies only to GFP, just indicate it so you don't repeat yourselves.
- since GFP is the foundation of all FPs, your extraction and purification methods could be put as a separate methods part, possibly integrated with transgenic organism part. then development of new FPs and the way to obtain these could be illustrated following the methods bit.
- cancer, malaria, prion sections should be further summarised allowing the reader a brief concise idea of the applications, but also allowing you to indicate other possible uses outside just the 3. Proper referencing is again needed eg. 'In one study by Barmada and Harris, scarpie prions were..' A short sentence or two on what Cancer, malaria and prions are should be enough for the reader.
--Begum Sonmez 00:41, 8 May 2010 (UTC) Hello Group 9. I had a quick look at the whole page first and I felt that there is a problem with structure. Here are some changes that you might like to make:
- The introduction made special mention of GFP, and under History it was metioned in greater detail. It seems to me that it is a chosen example of FP (amoung all the other type of FP). There is nothing wrong with this, but as a reader I would like to know about this focus on GFP in the intro, and why it is chosen by all of you. Great coverage on GFP though and so should be given that extra credit by being placed under its own heading just before the ‘New Fp Colours’ heading. (‘Links original steps used;’ should be fixed as a reminder).
I hope I’m not confusing anybody. But basically, have the Heading ‘Types’, say that you will be looking at GFP in detail, and then have the sub-headings ‘GFP’, and ‘New Colours’.
- Put the Major Milestone timeline directly under ’History of FP’, and ‘The recipients of the noble prize’ straight after. The general overview (which is more specific to the technique of FP) should come first, than the Recipients of the Nobel prize (which is less significant to technique itself should come after).
- In regards to the reference: ‘(timeline referenced from here http://www.conncoll.edu/ccacad/zimmer/GFP-ww/timeline.html and the textbook.’ The textbook is not mentioned. The website can be linked to in a better way, for example, by putting it in brackets so it appears as a number (?)
- I like The theory of fluorescence because it was interesting. I think it should be a sub-heading on its own.
- I like the ‘New FP Colours’ part
- Current research:
- There is mention of a ‘specific technique’-What is this technique?
- The format under Protein Synthesis looks out of place compared to the rest of the page (just remove the gaps I’d say)
- Have the Title of each stage of Protein Synthesis as ‘Transcription’, ‘Amino acid activation’, and ‘translation’ and have them numbered. Just clears extra text, making it look neater.
- There is too much text under Cancer, Malaria, and Prions. Try to summarise further and remove unnecessary information. But I love the images.
- Tick to advantages and tick to Limitations. Great work with the summary!
- Combine the refernces
- Put the Glossary before the references
- Remove the Heading (Located before the Glossary heading) ‘Links to Current Research’.
I think that was too much review from me, hope It is helpful though. Good effort Group 9.
Hey guys. This is a very good project in terms of explanation of concepts and a comprehensive look at florescence proteins. However, some areas of improvement are the references which are not using the wiki format that mark explained. The in text citations are also quite scarce and stuff that isn't common knowledge isn't referenced. A hand drawn image is also needed. Once these are put in, the project will be flawless.--z3253199 04:13, 7 May 2010 (UTC)
Just letting you know I may not make it into the lab until about 1 today, but I will be there! --Louisa Frew 00:32, 5 May 2010 (UTC)
I guess you can take a few notes on disadvantages, i'll take some on advantages and Shoahaib can make some notes on intro. Then we discuss our findings on Tuesday. --Vishnnu Shanmugam 14:20, 1 May 2010 (UTC)
I'll definately be there from 12. Also, should I write up the disadvantages section or do you want to do the intro/advantages/disadvantges together so we can each contribute things we've picked up from our sections? I've put what i've done so far down the bottom, but it's still a work in process. --Louisa Frew 12:10, 1 May 2010 (UTC)
Hey gang, so the plan is everyone have their written material posted up by Tuesday. We then meet on Tuesday (12pm-3pm) at cell bio lab for a discussion on where we go from there. Remember to bring your image collection on Tuesday. --Vishnnu Shanmugam 02:27, 30 April 2010 (UTC)
Sounds fine to me Louisa. Good idea dividing the different fluorescent proteins based on their emission spectra. "What makes a good fluorescent protein" could come under the "advantages" section, this will allow you to describe what good properties the FP has and why this is an advantage. Photoactivatable FPs and the development of infra-red FPs sounds good. See ya at lab, we discuss this more. --Vishnnu Shanmugam 08:55, 27 April 2010 (UTC)
Hi Guys. I've had a look how i'm going to do the "new FP" section, and i have a few different options which i thought i'd run past you. It's looking like the best way to approach it is to look at the variants of GFP and split them into Yellow, Blue, Orange and Rec spectrum categories to discuss the properties, advantages/disadvantages and uses of each. Does this sound like an ok approach? This will probably also need some info on what makes a "good" fluorescent protein- brightness, photostability etc. Do you think this would fit under any of the existing headings?? I have a couple of really good review articles that look specifically at this stuff so it shouldn't be very hard. Also, apart from colour variants there are lots of other types of FPs so i might just focus on photoactivatable FPs and the development of infra-red FPs if that sounds ok?!? Anyway, if you don't get this, then I'll catch you both in the lab tomorrow. --Louisa Frew 03:58, 27 April 2010 (UTC)
Hi! I had a look and completely agree we were a little over enthusiastic with the number of subtopics! Given the changes, we should defintately sort out a new distribution of sections in the lab today so we can get properly started. --Louisa Frew 01:57, 31 March 2010 (UTC)
Hi folks, I had a look at some of last year's cell biology group projects (can be found on the 2009 student link after clicking on 2010 projects). I propose that we consider revising some of our subtopics as they seem to cover the same thing. Eg. 3)Early/Historical Uses of GFP and 4)History development (GFP). Another is 6)Contemporary/commercially available fluorescent proteins and 7)Uses in current research which once again is the same thing as it is not possible to write about current research without writing about Contemporary/commercially available fluorescent proteins. We probably don't need this many topics but make each one detailed. Example:
- History of fluorescent proteins- this includes all GFP (development,nobel prize, historical uses)-------S
- Development of new fluorescent proteins - new proteins since GFP and how they were developed---write detailed about most important fluorescent proteins-----L
- Current research - How the new fluorescent proteins are used and to what purpose in research projects today eg. nuclear staining-------V
- Advantages of fluorescent proteins-------V
- Limitations of fluorescent proteins-------L
- Links to current research sources (people and organisations)
Have a look at the 2009 projects and tell me what you guys think. --Vishnnu Shanmugam 01:31, 30 March 2010 (UTC)
Project outline: (please add suggestions)
- Introduction- define fluorescent proteins
- The fluorescence process- general explanation L
- History- development (GFP)- Nobel Prize etc S
- Early/Historical Uses of GFP L
- Developments that followed GFP- new proteins (colours, variations etc) S
- Contemporary/commercially available fluorescent proteins- different brands, uses etc V
- Uses in current research V
- Future ??
- Links to current research sources (people and organisations)
Some Subtopics for Fluorescence techniques:
- Fluorescence in situ hybridization
- Fluorescence Microscopy
- Fluorescence trangenesis
- Flow Cytometric Fluorescence
- Fluorescent marking and labelling
- Fluorescent Proteins
Hello! Fluorescence is still looking like a good option. We've added a few to the list! See you next week. --Louisa Frew 07:00, 17 March 2010 (UTC)3 .
hey i found great articles but 1 of them is german i have an exam soon so ill get on to translating it.
Cancer (malignant neoplasm) is a class of diseases in which a group of cells display uncontrolled growth (division beyond the normal limits), invasion of surrounding tissues and metastasis (spread via the circulatory or lymphatic system). The first use of GFP to visualize cancer cells in vivo was by Chishima et al. They stably transfected tumour cells with GFP and transplanted these into several mouse models, including orthotopic models that have a high metastatic capacity. They showed that in excised live tissue, with no additional preparation, metastases could be observed in any organ at the single-cell level. In addition, cells were visualized in the process of intravasation and extravasation. The visualization of single metastatic cells in tissue is beyond the capabilities of standard histological techniques and so such ex vivo studies enabled, for the first time, micrometastases (including dormant cells) to be visualized in unfixed or unprocessed tissue.
Researchers can attach the fluorescent molecules to a protein inside a dividing cancer cell, then by shining a light of the appropriate colour, scientists can watch as a cell divides uncontrollably. Fluorescent proteins (FPs), because of their endogenous expression, allow the observation with minimal disturbance to the subject (Hoffman and Yang, 2006). For example, cancer cells can be engineered to carry FPs stably and implanted into the subject to allow monitoring of metastasis and the effectives of cancer treatment.
Previously developed fluorescent compounds that are activated inside the body's cells have the limitation that, once they are turned on, they continue to fluoresce even after they diffuse to new locations, making it difficult to distinguish viable tumor cells from normal tissue or dead or damaged tumor cells. The research team, led by Hisataka Kobayashi at the Molecular Imaging Program of NCI's Center for Cancer Research (CCR), in collaboration with Yasuteru Urano at the University of Tokyo, created an imaging compound that is turned on only when it is inside a living cell and stops fluorescing when it leaves the cell, as would happen when the cell dies or becomes damaged. The compound also can be engineered to target specific types of cancer cells.
Fluorescent imaging based on the specific marking of tumors is widely used in experimental oncology. The possibility to introduce genes of a particular class of fluorophores [fluorescent proteins (FPs)] into cells enabled the development of a new method: genetic marking. The fluorescence ability of FPs persists for the whole life of a cancer cell and remains after cell division. As a result, it becomes possible to estimate tumor growth rate, to study the mechanism of carcinogensis and metastasis formation, and to investigate the safety and efficacy of intervention using novel therapeutics. Recently, a new group of FPs - red fluorescent proteins (RFPs) - was isolated, and they became useful as markers for whole-body biological imaging. The fluorescence spectrum of these proteins is in the relatively long-wave part of the spectrum (580 to 650 nm), a region that is promising for object visualization at depths up to 1 to 2 cm with millimeter resolution. Therefore, RFP-labeled tumors can be regarded as the most appropriate model for whole-body investigations.
Malaria is caused by a parasite called Plasmodium, which is transmitted via the bites of infected mosquitoes. In the human body, the parasites multiply in the liver, and then infect red blood cells. The disease is caused by infection with one of four species of the genus Plasmodium: Plasmodium falciparum, P. vivax, P. malariae, and P. ovale. The first two are the most common.
Malaria is one of the most widespread of all human parasitic diseases, and in the early part of the last half century more than two-thirds of the world's population lived in endemic areas. WHO estimates that 3.3 billion people (half of the world's population) are at risk of malaria. Every year, this leads to about 250 million malaria cases and nearly one million deaths. People living in the poorest countries are the most vulnerable. Malaria is especially a serious problem in Africa, where one in every five (20%) childhood deaths is due to the effects of the disease. An African child has on average between 1.6 and 5.4 episodes of malaria fever each year. And every 30 seconds a child dies from malaria. In Australia, malaria has been endemic, but was declared eradicated from the country in 1981. Although malaria is no longer endemic in Australia, approx. 700-800 cases occur here each year in travellers infected elsewhere, and the region of northern Australia above 19oS latitude is the receptive zone for malaria transmission.
A possible breakthrough in curtailing the spread of malaria carrying mosquitoes was reported in October 2005 the creation of mosquitoes with green fluorescent testicles. Now male mosquito larvae can easily be separated from female mosquito larvae. Without green fluorescent gonads it is impossible to separate mosquito larvae based on their sex. Now a laser sorting machine has been developed that can sort 180,000 larvae in 10 hours. Once separated from the females it is trivial to sterilize the males and release them into the environment where they will mate with wild females. Female mosquitoes only mate once in their two-week cycle, so if they chose a sterilized male they will produce no offspring. If a large enough population of sterilized males is released into the wild population should be eradicated in a fairly short time.
A prion is an infectious protein particle similar to a virus but lacking nucleic acid. An infectious prion can affect a normal prion protein. Whenever a prion comes in contact with a normal prion protein, it causes the normal protein to 'flip' into an abnormal shape, thereby becoming a prion (ie, the rogue form of the protein). Any other normal prion protein that a rogue prion touches will also be converted, creating a domino effect. Prions have been known to cause neuro generative diseases such as spongiform encephalopathy (mad cow disease and Creutzfeldt-Jakob disease), fatal familial insomnia and Gerstmann-Straussler-Scheinker Syndrome, chronic wasting disease and Scrapie.
Humans can be infected by two modes:
1. Acquired infection (diet and following medical procedures such as surgery, growth hormone injections, corneal transplants) i.e. infectious agent implicated.
2. Apparent hereditary mendelian transmission where it is an autosomal and dominant trait. This is not prima facie consistent with an infectious agent.
We need to know more about how PrPc is expressed and treated in cells in order to understand how the misfolding of PrPc occurs and why cells die as a result. By means of green fluorescent protein (GFP) cloned into PrP, PrP in cell cultures can be studied under a microscope. In addition, genetically manipulated variants of PrP have been made in order to uncover important factors regarding the localisation of PrP in cells and the enzymatic cutting of PrP.
PrP is normally cut into fragments in the course of its cellular lifespan. Lund et.al has studied one of these cutting processes, the α-cut. Where the PrP α-cut occurs in the cell, and to what purpose, is unknown. Through his studies, Lund has shown that PrP is cut in the same place, even when the amino acid composition at the place of cutting is changed. PrP is also cut at the same place, irrespective of whether it is joined to the outside of the cell membrane or whether it is localised in the cell cytoplasm. Lund's findings indicate that the cutting occurs at the same place in PrP, but that the cutting is caused by different mechanisms, depending on where the PrP is localised in the cell. A phenomenon associated with PrP's localisation in cells that is still poorly understood is that in some types of cells, PrP is positioned in the cell's cytoplasm instead of on the cell membrane, where it most likely fulfils its function. A predominant theory on why proteins may be found in the cytoplasm instead of on the cell membrane is that the cell in question is in a state of stress. Furthermore, PrP has been shown to have an inefficient signal sequence compared to other proteins and may therefore be less efficient at following its natural route out onto the cell membrane, even under normal cellular conditions. Lund's work reveals that a completely different mechanism related to the actual translation of PrP may also be the reason why a proportion of the PrP molecules end up in the cytoplasm. By studying different mutated variants of PrP, Lund has demonstrated that a cytoplasmic variant of PrP can emerge after PrP molecules have been synthetised from a downstream start codon in the PrP gene. The result of this translation is a shortened form of PrP which lacks large portions of the signal sequence and therefore ends up in the cytoplasm of the cell.
Research also focuses on how prions travel from the digestive tract and other sites in the body and pass into the brain? Scientists have found that organs involved in immune cell development and maturation—such as lymph nodes, spleen, and bone marrow—actually serve as the prions’ staging area, where they propagate. Subsequently, researchers speculate, peripheral nerves that stimulate these organs serve as conduits that transport prions to the spinal cord and brain. Investigators will test these hypotheses by using a novel technology that takes advantage of mice genetically engineered to produce prions that are fluorescent and will glow green under the microscope. First, researchers will analyze the distribution of fluorescent prions in the intestine, spleen, lymph nodes, and involved peripheral nerves. Next, they will analyze dissemination of prions within the spleen using a cell transplantation technique. Finally, they will study prions that are selectively generated in specific immune cells and nerve cells, to analyze the processes involved in transporting prions from the immune system to the brain. Significance: Learning how prions travel to the brain could lead to development of methods for blocking this process and preventing deadly prion infection in the brain.
GFP Variants Section- Louisa
Since the revolutionary development of GFP, extensive research has been conducted with the aim of producing fluorescent proteins (FPs) which cover a broader colour spectrum. These colour mutant FPs are also being genetically engineered to exhibit faster maturation rates, greater photostability, increased brightness, pH insensitivity and reduced oligomerisation and toxicity (Shaner et al. 2007, Shaner et al. 2005).
Enhanced BFP (EBFP) was one of the first spectral variants engineered from Aquorea GFP, but due to its low brightness and poor photostability it is now unappealing for most research (Shaner, 2007). New blue Aquorea GFP variants Azurite, SBFP2 and EBFP2 show improved brightness and photostability in comparison to EBFP, offering a promising means of imaging live cells in this region (Ai et al., 2007 & Kremers et al. 2007). EBFP2 is the most photostable and brightest blue FP (Shaner et al., 2007).
The cyan FPs (CFPs) began with the production of enhanced CFP (ECFP) from Aequorea GFP (Cubbit et al. 1995). mCerulean followed in 2004 offering a brighter and better general-purpose CFP (Rizzo et al. 2004). In 2006, a monomeric teal-coloured variant mTFP1 was obtained from a Clavularia soft coral protein (Ai et al, 2006). mTFP1 is brighter, less pH sensitive and more photostable than the traditional CFPs, making it an excellent alternative to its predecessors (Shaner et al. 2007). Most recently, site-directed mutagenesis of ECFP has produced super CFP (SCFP) which is twice as bright as ECFP when expressed in bacteria. SCFP shows promise for use as a fusion tag or as a biosensor for the detection of calcium ion fluctuations, pH changes, metabolites or enzyme phosphorylation (Shaner et al. 2007).
GREEN Following the discovery of the original Aequorea GFP discussed previously, many other proteins which express in the green region of the spectrum have been isolated from other Aequorea species, copepods, amphioxus and reef corals (Shaner 2007).
Most of these novel GFPs exhibit no discernable advantage over EGFP (Shaner 2007) and hence will not be discussed. Emerald, a derivative of EGFP, is currently the best choice for live-cell imaging due to its more efficient folding than EGFP at 37°C (Shaner 2007. Cubitt 1999)
Yellow FPs (YFPs) are among the brightest and most versatile probes developed in any of the spectral classes (Shaner 2007). EYFP was developed in 1999 (Miyawaki et al, 1999) and is still widely used despite its high pKa and sensitivity to halides (Shaner et al 2007). EYFP has proved effective in tracking the distribution patterns of single proteins on the membranes of live cells (Ober et al. 2004). mCitrine, derived from the addition of a single mutation in EYFP, is less halide sensitive and twice as resistant to photobleaching as its predecessor (Griesbeck et al, 2001). mVenus is a popular YFP mutant with a greatly reduced maturation time, however it has low photostability. The fact that mVenus requires only two minutes in vitro or seven minutes in vivo to produce fluorophores makes it ideal for monitoring cellular processes with fast dynamics such as gene expression (Nagai et al., 2002). Super YFP (SYFP), the product of site-directed mutagenesis of EYFP, may hold similar applications as those discussed previously for SCFP. Yellow fluorescent protein for energy transfer, YPet, is the brightest YFP variant. YPet is also reported to have very good photostability and superior acidic resistance to mVenus and other YFP derivatives (Nguyen and Daugherty, 2005).
Compared to the other areas of the spectrum, few probes have been constructed to emit in the orange and red wavelengths. Probes such as DsRed, TagRFP and tdTomato actually have emission profiles in the orange range of the spectrum and not the red range as suggested by their names (Shaner, 2007). mOrange, a member of the ‘Fruits’ series (see ‘Red’ section for details), once dominated this spectrum in terms of brightness, but has average photostability and is unstable at low pH (Shaner, 2007). In an attempt to overcome these problems mOrange2 was engineered from mOrange and shows significantly improved photostability but is still pH sensitive and shows an almost doubled maturation time. Kusabira Orange (KO), derived as a tetramer from the mushroom coral Fungia concinna, was later modified to give monomer KO (mKO) (Karasawa et al. 2004). mKO demonstrates extremely good photostability and brightness similar to that of EGFP, making it a good candidate for long-term and wide-fluorescence illumination experiments (Shaner 2007 and Shaner 2004) In 2007 TagRFP was cloned as a dimer from Entacemaea quadricolor sea anemone and appears to be a useful tool for localisation and FRET studies (Merzlyak et al 2007). Random mutagenesis of Tag RFP produced the highly photostable, bright and pH resistant TurboRFP. Many of the problems associated with Discosoma DsRed FP- including slow maturation, an intermediate green state, and tetrameric character- have been the target of many attempted modifications of this protein through both random and site-directed mutagenesis. The production of the monomeric mRFP1 from DsRed was promising, but reduced emission and quick photobleaching still means that it is less useful than monomeric GFPs and YFPs (Campbell et al. 2002) tdTomato, another of the 'Fruits' proteins, is the brightest of all available FPs, emits at closer to the true red range and is very photostable (Shaner et al 2004). The major drawback in the use of tdTomato is its comparatively large size which is proposed to interfere with fusion-protein packing (see reference 66 from the paper pp62).
FPs that emit in the far red area of the spectrum are the holy grail of this area of development, due to this wavelength of light being less phototoxic and able to probe deeper into biological tissues (Shaner 2007). The most promising develops have arisen from the site directed mutagenesis of mRFP1 to give monomeric FPs which emit in the 560-610nm wavelength which are collectively referred to as the ‘Fruit’ proteins (Shaner, 2007). Despite their improved emission colours, many Fruits lack the brightness and photostability needed for most experiments (Shaner 2005)). According to Shaner and team, mStrawberry and mCherry are the best reds, with brightness levels of 75% and 50% of EGFP (Shaner 2007). mCherry is more photostable than mStrawberry (Shaner 2005) and as well as a better alternative to mRFP1 for long-term imaging experiments (Shaner 2007).
Developed in 2004, mPlum is one of the first true far-red probes, emitting at 649nm (Wang et al 2004). mPlum has limited brightness (10% of EGFP) but good stability and is recommended for use in multicolour imaging experiments, the imaging of thicker tissues and as a FRET partner for GFPs and YFPs (Shaner 2004, Shaner 2007).
Kutushka, a dimeric protein that emits at 635nm, was developed in 2007 and is commercially available from Evrogen as TurboFP635 (Shcherbo et al 2007). Despite being less bright than EGFP, Kutushka has the highest brightness level of any of the FPs in the 650-800nm wavelength area.
mKate (Evrogen, TagFP635) has similar spectral characteristics to Kutushka, brightness on par with mCherry and is reported to be very photostable, making it a good candidate for localisation experiments in this area of the spectrum (Shcherbo et al. 2007). mKate has been reported to exhibit complex photobleaching behaviour which is yet to be well characterised and it is suggested that mCherry remains a more reliable choice for single-molecule imaging (reference book).
Other Novel FPs
These proteins display negligible fluorescence until excited by irradiation at a specific wavelength (Lippincott-Schwartz and Patterson 2003). This allows for the highlighting of molecules within a discrete region of a cell as well as a way to study the lifespan and behaviour of proteins independently of other newly synthesised proteins. (EXAMPLES)
This class of FPs show “light-driven modulation of fluorescence properties” (Wiedenmann et al, 2009 pp1032), allowing !!!!!!!!! Green-to-red photoconvertable proteins (such as Kaede, KikGR, EosFP, Dendra2, mKikGR, tdEosFP, mEosFP and mEosFP2) are useful for the tracking of fusion proteins, organelles or the fate of embryonic cells during development!!!!!!!!!
Destabilised GFP variants
These FPs allow the characterisation of the expression timing or lifetime of a target protein due to their rapid turnover by proteolysis resulting in only younger protein chimeras fluorescing (Li et al 1998)
"Fluorescent Timer" Protein
This protein, similarly to the destabilised GFP variants, allows the measurement of protein turnover and expression timing (Lippincott-Schwartz and Patterson 2003). It initially fluoresces in green area of the spectrum before conversion of the fluorophore after several hours leads to emission in the red (Terskikh et al.2000). Using the ratio of green to red fluorescence allows the age of the tagged protein to be determined.
Future aims for new mutants suggested by Shaner et al. : • Brighter • Monomeric • High contrast • Easily photoconverted • Reversible photoactivation • Red-to-green photoconversion • Improved expression in the far-red or near-infrared regions
--Louisa Frew 12:10, 1 May 2010 (UTC)
1565 N. Monardes, he observed emission of light by an infusion of wood lignum Nephriticum (first reported observation of fluorescence)
1640 Licetus, study of Bolognese stone. First definition as a non-thermal light emission
1842 E. Becquerel , observed emission of light by calcium sulfide upon excitation in the UV. First statement that the emitted light is of longer wavelength than the incident light
1853 G. G. Stokes Introduction of the term fluorescence
1858 E. Becquerel, created the first phosphoroscope
1929 F. Perrin Discussion on Jean Perrin’s diagram for the explanation of the delayed fluorescence by the intermediate passage through a metastable state First qualitative theory of fluorescence depolarization by resonance energy transfer
1944 Lewis and Kasha Triplet state
1955 Green fluorescent substance in jellyfish first described. (1)
1962 GFP identified as protein, extracted from 10,000 jellyfish - "a protein giving solutions that look slightly greenish in sunlight though only yellowish under tungsten lights, and exhibiting a very bright, greenish fluorescence in the ultraviolet of a Mineralite, has also been isolated from squeezates." Called "green protein." (2)
1979 Shimomura characterized structure of chromophore. (6)
1985 Prasher clones aequorin. (7)
1993 Structure of GFP chromophore confirmed, flanking amino acid residues corrected from Shimomura's 1979 structure. Still "apoGFP". (9)
2000 Fluorescent timer protein. (20) The biggest difference between green fluorescent protein and its red analog, DsRed, is that the chromophore of DsRed has an extra double bond (drawn in yellow) which extends the chromophores conjugation and causes the red-shift. (21) The Olympus web-site has a java tutorial that shows how the DsRed chromophore is formed. Check it out.
2002 Monomeric DsRed (mRFP) (22), first photoconverible (Kaede (23,24), and photoactivatable (PA-GFP (24)) FPs created.
2004 New "fruit" FPs generated by in vitro (26) and in vivo (27) directed evolution.
Hey guys shaib i can't talk about cloning gfp as vishnu's doing it, hes talking about transinfection and thats well the only ways of doing on a large scale.--Shoahaib Karimi 04:37, 4 May 2010 (UTC)