Talk:2009 Group 8 Project
--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: 
--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.
--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)
- 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 , 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.”  However, they do distinguish the process of both types of cell death from the consequences, as those are very different.
 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
 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
Re: What are the causes of necrosis? Date: Sun Mar 19 12:10:32 2000 Posted By: Kenneth Mitton, Post-doc/Fellow, Molecular Development Retina, Cataract, Dept Ophthalmology / U. Mich Area of science: Cell Biology ID: 951760497.Cb
Necrosis, is simply a cell dying, all of its coordinated activities going wrong and things shut down. Necrosis is best understood if you compare it to another way cells shut down called apoptosis: Cells these days, are seen by biologists as dying in two major ways: necrosis or apoptosis. Cells can undergo programmed cell-death or "apoptosis", where the cell triggers special metabolic, signal transduction and gene regulation pathways or "programs" that systematically shut down and disassemble the cells components. Apoptosis is not death the way necrosis is. If a cell gets too much heat, or is poisoned by a toxic substance or exposed to chemicals that damage its proteins and membranes or radiation that breaks its DNA molecules, that cell can just stop functioning.
In necrosis, the cell dies as damage leads to loss of control of ion gradients between the outside and the inside of the cell, and also loss of the proton gradient across the membranes of mitochondria (where alot of our ATP is made for energy). A toxic insult that damages a cell and causes it to loose energy (ATP levels fall down), and to loose control of ion gradients (Na+ and Ca++, which are low in the cell, rush into the cell and rise in levels), are causing necrosis. In Apoptosis, cells chop up their DNA, disassemble their organelles (mitochondria, ER, golgi) and break themselves up into little peices of cells. But in programmed cell death, apoptosis, this is meant to happen and is under control of the cell...the cell breaks down its proteins and DNA and membranes to eventually be recycled. During apoptosis, in contrast to necrosis, the cell and eventually the fragments of the cell all maintain their ion-gradients and energy levels. In other words, ATP levels are high, and Na+ and Ca++ levels remain low in the cell fragments because the membrane ion pumps are still working (they need ATP for energy). So cells can recycle(die) on purpose by using the apoptosis systems, eventually they fragment into small fragments of cell remains that are phagocytosed (eaten up) by neighboring cells. When tadpoles lose their tails, the tail seems to shrink day after day, that is because the cells are being recycled. Leaves fall from trees in the autumn, because apoptosis shuts the leaves down where they connect to the branch. These are programed cell deaths, and they are good for the organism to develope as it should. In the womb, our hands start off as paddles, and the skin separates into fingers, as the paddles are remodeled by apoptosis. Some cells go away, and new ones are made somewhere else.
In necrosis, damage from toxic compounds or oxidation damage often harms the mitochondria or membrane ion pumps and causes the energy levels in the cells to drop. ATP levels fall and this also means that cell glutathione levels drop (important antioxidant in cells), and a vicious cycle of damage starts. Lower glutathione levels make the mitochondria even sicker and less able to make ATP and on and on. When mitochondria are damaged in the cell electron transport does not work well, and more oxygen reacts at the wrong place in the chain, leading to formation of superoxide. (a very reactive free radical) The cell and mitochondria have superoxide dismutase, to quickly convert this into H2O2 (hydrogen peroxide) which is less reactive (toxic). However, lots of H2O2 can build up, and react with metal ions to create hyroxy radicals .OH that react and damage proteins and membranes. Catalase gets rid of H2O2 to make water, but it can become overwhelmed. If the cell is in a state of lower energy too, it also cannot make more of these proteins to protect itself either. Therefore when cells are undergoing a necrotic type of cell death from some toxic insult, they often show increased oxidation damage etc in the tissue where this is happening.
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.
· Necrotic insult initiating the irreversible cell death eg - ischemic injury - chemical (toxic) injury
- 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
- 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)
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? [][]
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)