Talk:2009 Group 8 Project

From CellBiology

References for hand drawn diagram

(The diagram should go under the apoptosis vs necrosis section, next to the table)

This student hand drawn image was adapted by z3219606 from the following sources:

  • Apoptosis, oncosis, and necrosis. An overview of cell death. Majno G, Joris I. Am J Pathol. 1995 Jan;146(1):3-15. Review. PMID: 7856735
  • Necrosis: a specific form of programmed cell death? Proskuryakov SY, Konoplyannikov AG, Gabai VL. Exp Cell Res. 2003 Feb 1;283(1):1-16. Review. PMID: 12565815
  • http://www.susanahalpine.com/anim/KubyHTML/Celdeath.htm

This image illustrates the distinct morphological differences between apoptosis and necrosis. The different pathways that lead to necrosis or apoptosis after an event of cellular stress are shown.


Peer Review

BTW z3219606, there WAS a hand drawn image on group 3's page. if you cared to CLICK onto the first image shown on the page you would CLEARLY have known that, it was "hand-drawn" with photoshop.


Group 7. (we've done this as a group rather than individually) The project as a whole is quite long - Consider finding areas which have overlapped so that you can condense the project.

  1. Intro: repetition of 'irreversible' and 'can be fatal' to what? "There are several types of necrosis classified based on morphological criteria, coagulative necrosis, liquefactive necrosis, caseous necrosis, fibrinoid necrosis and fat necrosis." needs to be worded better.
  2. History: Good, however it would be good to discuss what happened between 1972 and 2009.
  3. Apoptosis vs Necrosis: "Condensation of chromatin to form sharply circumscribed, uniformly dense, cresentic masses that abut the nuclear envelope." - This sentence seems quite dense and it's a bit hard to understand. Also, consider making the sentences longer to this section flowing. Try to condense the part on apoptosis as it's not that relevant to your project - the table explains the differences well. Also, please read over this section with regards to grammar.
  4. Cellular processes: The text at the beginning is repeated by the dot points below. The dot points look good so maybe you can just write a general overview at the beginning for this section. Pictures - good, but there needs to be explanation at which particular pictures we're looking at. If the ones not explained in the legend aren't relevant, consider cutting them out. Good explanation of changes in the nucleus.
  5. Causes: First part sometimes repeats what was said in Apoptosis vs Necrosis section (try not to repeat too much info on apoptosis). "necrosis is said to be accidental and uncontrolled" this repeats the definition of necrosis. Also, large amounts of text would look better in dot points.
  6. In Causes: The whole section needs condensing down because the reader might lose interest when reading through the large chunks of text which are not necessary, e.g. section on proteases is probably far to in-depth for the overview of necrosis. In saying that, this section is a bit better set out than the previous sections with the use of subheadings and dot-points. perhaps it could be condensed by using images to explain the more complex ideas more succinctly.
  7. Patterns of necrosis: very good use of the images, clearly displaying the different morphologies. The text is again probably a bit too long, so consider maybe only mentioning a paragraph on each. reads well.
  8. Glossary is great!
  9. overall, the different sections show great research and in-depth knowledge but some is lost through the dense text and incorrect grammar, which just needs some proof-reading and deleting repeated sections, so that each major heading has a clearly defined content which you're trying to convey.
  10. with links to individual projects, try to put them so they are in the text and/or more relevant. (and make sure they're all there! sorry wasnt sure about the troponin one)
  11. well done!!


A. (was reviewed as a group)

  • Content - as necrosis was the focus of the research, i dont think that your section "necrosis vs apoptosis" needed to be as long. Perhaps the table on its own would have been sufficient? In addition to a bit of text. good descriptions with regards to the types of necrosis. The structure was really good. It has a logical flow and is pretty well spaced out. I think you need a few more images in the middle section. There is heaps of text there, a few images in the middle will break up the text and make it easier to read.
  • Diagrams - Well use of diagrams. The table illustrating the differences between apotosis and necrosis is a good aid in understanding the topic. Images under "Patterns of Necrosis" is very helpful. However, it would be ideal if you can find some diagrams to illustrate the processes under "Causes" of necrosis.
  • Glossary - The glossary is very thorough; clear explanation of words.
  • Links - The links are very applicable, especially the animated video. The links to the individual member's pages were also placed appropiately.
  • Images are good but where is your student drawn image/diagram? Is the table in place of this?


B- • Like the use of tables and some sections such as the on the different types of necrosis looks good with images but the introduction/ causes looks too text heavy. Also, too many horizontal lines – just the use of sub headings should be sufficient.

• References need to be edited and signatures within the page needs to be taken out. There is no links section and no link back to the individual project.

• Glossary is well organised and informative

• Labelling of figures need to consistent – there are two figure 1, and some not labelled...

• No student drawn figure/ diagram on the page...


  • Feedback on our assignment was fair and useful - we were given an idea of how our project was looking in terms of its structure and content from suggestions provided as well as from the viewing other group projects. We were able to take on board and implement some of these suggetsions, such as correcting spelling/grammar, including links to our individual projects, shortening paragraphs and including a paragraph on current research, and have thus come up with our final product!!



--Mark Hill 13:43, 19 March 2009 (EST) Adjusted your title format and moved your microscopy information to the discussion page (here). Note, only single square bracket for external links.

microscopy services offered at SOMS UNSW: [1]

--Bridget Josephs 20:01, 29 March 2009 (EST)Hi all just posting a timeline of the necrosis process that we can start working from:

--Leone Chare 14:15, 1 April 2009 (EST) Thanks Bridget! Since our group meeting today fell through lol, we decided it was probably best to post on to this discussion board what proteins we're interested in doing for our individual projects and also which parts of the group project we're keen to do. But we can discuss this more tomorrow during the lab.

--Gurkiran Flora 21:25, 1 April 2009 (EST)I found some really interesting information about Ischemia and how it leads to necrosis... Bridget touched on this too. It is Necrosis caused by hypoxia resulting from local deprivation of blood supply. There is also some nice brief information on necrosis on this site http://books.google.com.au/books?id=kD9VZ267wDEC&pg=PA23&lpg=PA23&dq=ischemia+%2Bnecrosis+%2Bcell&source=bl&ots=lK1CoDNJNw&sig=8vXuBOEe-B1I1EmpQSadith-1WU&hl=en&ei=jUDTSb1vpN7oA-SmpJoE&sa=X&oi=book_result&resnum=1&ct=result#PPA23,M1

--Leone Chare 22:45, 12 April 2009 (EST) I found this textbook which is a tad old, but I found it to be pretty comprehensive in explaining the fundamental differences between apoptosis and necrosis. It has some good stuff on cellular mechanisms affected by necrosis and there are also some good references we could use. It's called Cell Death and Diseases of the Nervous System By Vassilis E. Koliatsos, Rajiv R. Ratan - you can just paste that into google and there's a preview version on googlebooks.


--Mark Hill 23:44, 12 April 2009 (EST) Good to see your group working on your project. Time line is a good start. You now need some images of necrotic cells (EM or light) and some details about the process itself.


Wow, that is something we should touch upon. Apoptosis and Necrosis do have similarities. I like the general overview. The self drawn diagram can be made for either oxidative stress or the calpain pathways. what do you think?--Gurkiran Flora 19:53, 4 May 2009 (EST)

--Leone Chare 21:58, 4 May 2009 (EST) Yep, I think the drawn diagram should be used for either of the pathways-- possibly for the calapin/cathepsin pathway because it's quite complicated. I've already started on a diagram for this pathway so I'll post a draft as soon as I'm done and we can decide whether to use it or not. Plus, I've started to fill in the glossary, let me know if you think they're too brief.


--Leone Chare 15:18, 15 May 2009 (EST) by the way, i had a look at the 'patterns of necrosis', just thought it may be worth adding (don't have to) that coagulative necrosis is caused by ischemia: with ischemia resulting from decreased ATP, increased cytosolic calcium leading to membrane damage.

  • decreased ATP causes an increase in anaeorobic glycolysis, accumulation of lactic acid which then decreases the pH.
  • decreased ATP causes less activity of Na/K pumps leading to indreased Na anf water in the cell--> leading to cell swelling

A video illustrating the differences in apoptosis and necrosis. this is something you can incorporate into morphological changes http://www.susanahalpine.com/anim/KubyHTML/Celdeath.htm

--Gurkiran Flora 17:12, 17 May 2009 (EST)GUYS!! I am just rearranging our outline so that we have an idea of what goes where. If you want to talk on the discussion page, do it in this area. Bridget, I copied your information onto the main page so we can have an some real stuff up there. I wasn't sure where to paste your stuff Leone. My part will be up later tonight. I have also made up a section for references so please post any additional references in alphabetical order. Henry, the timeline and introduction is still pending, our project is due soon and we haven't seen a draft as yet. Please work on that


--Hon Cheung 17:31, 17 May 2009 (EST)I did try to find some information about the history of necrosis, but I couldn't find much about that. Are you sure we are still going with timeline? I have also done some of the cause part and I will do the introduction part as well.

--Gurkiran Flora 18:16, 17 May 2009 (EST)If you can't find information about the timeline, then we can leave that out. But please post up whatever you have got so we can start adding to it and editing the the project as a whole.

--Leone Chare 20:28, 17 May 2009 (EST) I put the final version of cellular processes on the main page and tidied it up a bit.

--Gurkiran Flora 17:31, 27 May 2009 (EST)

--Bridget Josephs 21:22, 23 May 2009 (EST)Hi guys! How are you all going with your parts? Lets try to have everything up by Monday so we can review it as a group before Wednesday. Remember to go through your parts and see if there are any words to be included in the glossary. We still need to draw a picture too.... & Oh, Henry maybe you could do a brief summation of the key differences between necrosis and apoptosis? I've constructed a table on it for you.


--Hon Cheung 20:06, 25 May 2009 (EST)---- I have done the part of Apoposis vs Necrosis and recontructed a table. Also I have added some findings in the timeline and cause part.

--Gurkiran Flora 21:28, 25 May 2009 (EST)Thanks Bridget and Henry. your stuff looks great! I love the pictures Bridget. I am sorry I haven't posted my stuff up yet. I do have stuff to put up though. I am fixing it all up. everything will b there and we can do last minute editing on wednesday. Also, please put up any additional references you have used.

--Leone Chare 23:32, 25 May 2009 (EST) hey guys finally found some TEM pictures of necrotic cells! i will post them up tomorrow. plus i have added to cellular processes.

--Gurkiran Flora 12:07, 27 May 2009 (EST)Hey guys, I'm adding to my causes part. I added more to Henry's post on mitochondrial dysfuntion. I am also goin around fixing grammatical errors.

--Gurkiran Flora 17:31, 27 May 2009 (EST)Hey Guys!! I only have one really important thing to say! REFERENCE REFERENCE REFERENCE!

--Gurkiran Flora 19:43, 1 June 2009 (EST) Heya!! I have edited the causes section, i took out alot of the unnecessary detail. it still looks like a chunk of information though. suggestions?



--Leone Chare 13:33, 1 May 2009 (EST) Here’s a simplified overview of the causes of necrosis (feel free to correct)—thought it may be useful for organising the research into easy to understand sections. The first part is the simplified overview and each subsequent section goes into more detail. (the numbers correspond to the ones in the general overview)

General overview

  • 1) stimulus
  • 2) stress
  • 3) activation of first messengers
  • 4) activation of second messengers
  • 5) release of killers
  • 6) necrotic cell death

Lack of oxygen and/or glucose

  • 1) lack of oxygen and/or glucose
  • 2) acute energy depletion
  • 3) resting potential of neurons collapse
  • 4) glutamate release at synaptic clefts
  • 5) excitation of neurons
  • 6) necrotic cell death

The calpain/cathepsin pathway

  • 1) exposure to ROS (reactive oxygen species—usually caused by ischemia etc.)
  • 2) oxidative stress
  • 3) increase in intracellular Ca2+
  • 4) calpain activation -- eventually leads to cytoplasm collapse
  • 5) lysosome membrane damage -- leads to cathepsins release
  • 6) necrotic cell death

--Leone Chare 17:39, 1 May 2009 (EST) Was thinking we could mention some finds that go against the consensus of what necrosis is..if we have space at the end.

While the consensus is that “apoptosis and oncosis are therefore pre-mortal processes, while necrosis is a post-mortal condition” as stated in a journal article on morphological differences between apoptosis and necrosis [1], there was a study conducted soon after that questioned this statement. This particular article found that necrosis could in fact be a specific form of programmed cell death as indicated by several “examples of necrosis during embryogenesis, a normal tissue renewal, and immune response.” [2] However, they do distinguish the process of both types of cell death from the consequences, as those are very different.


[1] Morphological and biochemical aspects of apoptosis, oncosis and necrosis. Van Cruchten S, Van Den Broeck W. Anat Histol Embryol. 2002 Aug;31(4):214-23. Review. PMID: 12196263

[2] Necrosis: a specific form of programmed cell death? Proskuryakov SY, Konoplyannikov AG, Gabai VL. Exp Cell Res. 2003 Feb 1;283(1):1-16. Review. PMID: 12565815



Chronology of the pathologic process of necrosis

· Necrotic insult initiating the irreversible cell death eg - ischemic injury - chemical (toxic) injury

In general:

Macroscopic (visible) level:

0-24hrs: necrotic tissue undergoes a colour change and becomes firm (note however that this does not include necrotic tissue within the brain)
2-3 days: a border demarcated by an inflammatory response can be observed. A fibrinous exudate may additionally be observed
> 1week: healing by fibrosis begins to take place: observe a grey/white periphery zone
After several months: fibrous scar


Microscopic level:

Observation of an acute inflammatory infiltrate in the effected tissue (vasodilation of blood vessels, neutrophils predominating in early stages and later replaced by macrophages, edema etc)
2-3 days: vascular granulation
1 week: fibrous granulation tissue
Months: fibrosis

· Consequence: death of the affected tissue. Sometimes this can result in the death and loss of function of an entire organ

Necrosis is classified as Type III cell death--Bridget Josephs 12:55, 30 April 2009 (EST)


causes

I am going to put emphasis on Ishcemia in necrosis. What do you guys think?--Gurkiran Flora 19:53, 4 May 2009 (EST) For the types of Necrosis, I found a really good websitw with images of necrosis vs apoptosis. I found it to be good. Maybe we can use them .. copyright?! http://library.med.utah.edu/WebPath/CINJHTML/CINJIDX.html#2 --Gurkiran Flora 20:00, 4 May 2009 (EST)

--Hon Cheung 01:29, 7 May 2009 (EST) I have found some recent researches suggesting necrosis can be regulated by a network of genes and is called "necroptsis". Do you think we can put this research in our website? [[2]][[3]]


Patterns of Necrosis

Morphologically, the process of tissue necrosis can be categorized into several distinct types. Such types may provide both pathologists and clinicians with clues about the underlying cause of the necrosis.


• Coagulative necrosis

  • most common pattern of tissue necrosis
  • is a result of protein denaturation
  • even though the cells are dead the basic cell shape and tissue architecture remains preserved; the ‘ghostly’ outline of the anucleate cells can be observed under the light microscope as well as an acute inflammatory infiltrate
  • the affected tissue is firm in texture
  • the necrotic cells are eventually removed by phagocytosis
  • if there are enough labile cells around the affected tissue, regeneration can occur ie healing by fibrosis
  • granulation tissue is replaced by fibrosis after a few months
  • occurs in all tissues except the brain
  • caused by ischemia
  • characteristic of infarcts eg myocardial infarction


Liquifactive necrosis

  • occurs as a consequence of enzymatic degradation often due to focal bacterial or fungal infections
  • such infections attract inflammatory cells, specifically polymorphonuclear leukocytes. These leukocytes release enzymes to fight the offending microbes, but as a result the enzymes also digest (liquefy) the surrounding tissue
  • the tissue is ultimately transformed into a solid viscous mass
  • if caused by acute inflammation this material is known as pus
  • common type of necrosis observed in the brain
  • eg abscess


• Caseous necrosis

  • characteristic of mycobacterial infections eg tuberculosis
  • a form of coagulative necrosis
  • the name ‘caseous’ arises from the fact that the dead tissue has a distinctive white, cheesy appearance
  • the tissue architecture is completely destroyed
  • the necrotic focus is agranular and contains cells
  • granulomatous inflammation occurs
  • microscopically the lesion is observed as a granuloma with four different layers; the centre is the caseous necrosis, which surrounded by a layer of giant and epitheloid cells. The third layer consists of leucocytes and the outer layer, fibrosis


• Fibrinoid necrosis


Fibrinoid necrosis is a type of necrosis associated with injury, often immunologically mediated reactions, to blood vessels. As a response to the injury sustained, plasma protein complexes of antigens and antibodies are deposited on the walls of affected vessels. Fibrin which leaks out from the blood vessels is also deposited. These depositions result in its characteristic fibrinoid (‘fibrin-like’) appearance when viewed under the light microscope. Fibrin is easily identified by the fact it stains brightly with eosin

Polyarteritis nodosa is an example of a disease in which fibrinoid necrosis is observed.


• Fat necrosis

  • occurs in tissues with a high content in fat, for example the pancreas
  • caused by acute pancreatitis (inflammation of the pancreas) or by direct physical trauma to fat (eg as a result of surgery or by a physical blow)
  • the necrosis is ultimately due to the action of lipases, enzymes that digest fat
  • the lipases act on fat cell membranes, splitting triglyceride esters and causing free fatty acids to be released
  • the fatty acids may combine with calcium to produce soapy deposits in the tissues. This is called fat saponification

--Bridget Josephs 11:49, 7 May 2009 (EST)


Cellular Processes

--Leone Chare 20:41, 10 May 2009 (EST) This is a revised version of the bits of information I posted on the actual page (not final version, I still need to expand on cytoplasmic changes). I'll just post it on here before I replace the old stuff with this so you guys can have a look and let me know if there should be any changes. by the way, if your wondering the references are on the actual page for now.(doing the cellular characteristics of necrosis)

The first paragraph I'm thinking can be used for the introduction instead (just so we don't repeat ourselves)

The term ‘necrosis’ is used for the presence of dead tissues or cells and is the total of the transformations which have occurred in cells after they have died. It is currently thought to be a type of cell death that is accidental as opposed to programmed. Necrosis this therefore thought of as a passive form of cell death because it does not require the complex regulatory mechanisms such as protein synthesis that are characteristic of programmed cell death. In addition to this, the process of necrosis has minimal energy requirements, whereas cell death by apoptosis requires energy in the form of ATP.


The full process of necrosis is complete only after 12-24 hours. Therefore, cells are dead long before any necrotic changes can be seen through a light microscope. Necrosis, therefore, refers to morphological features noticed after a cell has already died and attained equilibrium with its surroundings. Necrosis is typified by rapid cell swelling and eventually lysis of the cell. It’s associated with loss of cell membrane integrity and the subsequent leakage of cytoplasmic contents and generation of an inflammatory response. This specific form of cell death is also characterised morphologically by intracellular swelling and condensed nuclear chromatin, which are associated with loss of membrane integrity.

Indicators of Necrosis

Light microscopy level

  • Early mitochondrial swelling
  • Loss of plasma membrane
  • Nuclear membrane preserved


Ultrastructural level

  • Proliferation of the endoplasmic reticulum
  • Disaggregation of polyribosomes
  • Dilation of organelles
  • Intranuclear vacuoles
  • Breakdown of cell membrane (plasmalemma)


Changes in the nucleus

  • Clumping and swelling of chromatin
  • Pyknosis
  • Kayorrhexis
  • Karyolysis

In general, the death of a cell is accompanied by severe swelling, distension of organelles, clumping of nuclear DNA, “plasma membrane endocytosis and autophagy”[1]. The morphological changes that occur within the nucleus can be observed over time.

Nuclear changes - appear in three patterns (as indicated above) and all due to nonspecific breakdown of DNA. The first pattern identified as karyolysis. This is essentially the fading of basophilia of the chromatin which results in the dissolution of the nucleus by action of deoxyribonucleases. The second pattern is pyknosis, characterised by nuclear shrinkage and condensation of the nucleus which is mainly due to increased basophilia. In the third pattern, karyorrhexis, the nucleus which has already undergone pyknosis then undergoes fragmentation. Over time, the nucleus eventually disappears.

[1] Death by necrosis. Uncontrollable catastrophe, or is there order behind the chaos? Syntichaki P, Tavernarakis N. EMBO Rep. 2002 Jul;3(7):604-9. PMID: 12101090