Difference between revisions of "Talk:3158969"

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==Individual Project==
 
  
==Apoptosis Inducing Factor (AIF)==
 
  
==What is AIF?==
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==individual comments==
The [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=9131&ordinalpos=2&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum AIF] gene has been conserved throughout the eukaryotes, making this protein a phylogenetically old flavoprotien (Cande et al, 2002). It is called a flavoprotein because it is able to be stably bound to FAD (flavin adenine dinucleotide). AIF is a positive intrinsic regulator of apoptosis. It is a mitochondrial [http://www.britannica.com/EBchecked/topic/436732/oxidoreductase oxidoreductase]. Resides in two locations, within the intermembrane space or within the innermembrane space of the mitochodria (Klein et al, 2002).
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z3217578: The layout of the page is a little messing so kind of confusing. The info is really good, maybe just rearragne the titles, and use some bold headings or something
  
==Topology and Gene location==
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* here, sorry to mess up your setup, had to make space for discussion....
 +
There's a few typos..."Fig. 2. Schematic of the structuraal chnages of AIF"... also i'm not sure if the reference used in point one of "what is..." lines up correctly; the article discribes a different function to that in the source... unless it was in the introduction, in which case you should track down where ''they'' got it from.
 +
Also, your final ref presentation is a bit rough... perhaps arrange it into points as some refs overlap in formatting.
  
===Crystal structure===
 
  
[[Image:ZAIF crystal structure.JPG]]
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that considered, i think its tops :D i love the diagrams etc etc, good job.
 +
--[[User:Z3187854|Peter Kehoe]] 12:28, 21 May 2009 (EST)
  
* AIF consists of a three domains, a mitochondrial localization sequence (MLS), a spacer sequence, and a oxidoreductase amino acid domain (Cande et al, 2002). 
 
  
===Gene location===
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'''B''' : The page was properly referenced with sufficient diagrams, easily comprehend, and overall it suited a wiki kind of style.Probably you can talk about how the three domains interact with each other? And why the protein needs to have seperated domains? Because it does not really explain further about it. But other parts showed a very well structured page and the flow went really nicely. (3222840)
[http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&CHR=X&maps=genes-r,pheno,morbid,genec&R1=on&query=AIFM1&VERBOSE=ON&ZOOM=3 Xq25-q26]. The gene is made up of 17 exons.
 
Image:
 
  
==How it works==
 
  
There are two proposed functions in which AIF has been associated with, free radical scavengers and DNA fragmentation in apoptosis. The first has been well documented in AIF knockout mice, which has seen resulting in neuronal degeneration (Klein et al, 2002). It should be mentioned that mouse AIF has strong 92% amino acid similarity homology to human AIF (Cande et al, 2002). This study by Klein et al (2002) demonstrated that without AIF expression there is oxidative stress from too many free radicals. The second is a caspase independent pathway via which apoptosis is induced. AIF in this pathway contributed to the fragmentation of DNA and chromatin condensation (Millan et al, 2007). The later pathway is the focus of this report. 
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** Sorry for the late peer reviewing. Your individual project is well structured, very organized and easy to understand with the help of images. I think your explanation of how the cell death and cell survival works should be written under a subheading right under “how it works”. I think it would be clearer like that. (3221652)
  
===Arriving in the mitochondria===
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==Peer assessed==
AIF is transcribed from X chromosome gene within in the nucleus. It is translated to the cytosol of the cell where if forms a precursor protein (Modjtahedi et al, 2006).  It was mentioned that AIF resides within the mitochondrion, and it does. AIF is translocated to the inner membranous region of the organelle where it truncated to become matures. Here the AIF is responsible for metabolite redox and vital bioenergetics within the mitochondria (Modjtahedi et al, 2006). It remains within the mitochondria until sufficient stimulus has altered the mitochondrial outer membrane allowing translation of the AIF back into the cytosol.
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* 3187854
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* 3219393
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* 3221652
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* 3219261
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* 3207164
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* 3132868
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== Lecture Feedback ==
 +
=== Lecture 4 - Nucleus===
  
===Getting out of the Mitochondria===
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Nucleosomes- Formed by DNA wrapped around histones.
The exact mechanism by which the outer membrane of the mitochondria becomes more permeable to AIF is not fully understood.  It has been suggested that death stimuli such as oxidative stress and DNA damage begin the cascade. There are two mechanisms which have been hypothesised to induce AIF translocating out of the mitochondria from death stimuli (Vosler et al, 2009). Recent studies by Volser et al (2009) show that PARP-1, and calcium dependent cystien protease calprin are the triggers of AIF release from the mitochondria as well as nuclear translocation (Wang et al., 2004; Culmsee et al., 2005; Moubarak et al., 2007). This study showed that calprin activity is dependent on that of PARP-1. This downstream regulation was shown to be modulated by calcium levels within the mitochondria; however this exact mechanism is not known (Vosler et al, 2009).
 
  
===In the cytosol===
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=== Lecture 5- Exocytosis===
Once in the cytosol AIF cleaves into a smaller protein, catalysted by the enzymatic reaction with the activated from of calprins and cathepsin. The AIF in the cytosol can be inhibited by Heat shock protein 70 family (Hsp70). If it is not inhibited the AIF translocates to the nucleus. One hypothesis made by Daugas et al (2000) suggested that this translocation may be due to ATP depletion or NAD+ depletion. It must be emphasised that many of these AIF pathways are speculations.
 
  
===To the nucleus===
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How does the synthesis from amino- to carboxy- terminal of protein happen in the Ribosome?
Once the AIF is within the nucleus, it has been shown to bind to [http://www-nmr.cabm.rutgers.edu/photogallery/proteins/htm/page22.htm cyclophilians A] (Cyp A). The AIF and the Cyp A bind to DNA where there is the formation of a trimolecular complex. This interaction allows for the degeneration of the DNA (Modjtahedi et al, 2006).  Images from Ye et al (2002) immunostaining showed colocalization of AIF with DNA during the first stage of chromatin condensation. This process converts chromatin to high molecular weight segments (Bajti et al, 2006). This idea that AIF binding to DNA is significant for cell death has been shown in AIF mutants. Studies have indicated that AIF mutants are defective in DNA binding and in consequence are defective at inducing cell death.
 
  
The overall mechanism of DNA degeneration via AIF has not been fully uncovered. Like many of the other processes ideas of their workings have been hypothesised. One idea is that the AIF binding to DNA recruits the enzymes proteases and nucleases inducing the chromatin condensation. Another idea is that the binding of AIF to DNA may displace specific chromatin-associated proteins, disrupting the normal structure and leading to a collapse of the DNA.
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===Lecture 7- Mitochodria===
 +
What types of cellular processes require lots of energy from the mitochondria?
  
==Signalling==
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*Muscle cells (cardiac, skeletal and smooth muscle cels), for contraction.
 +
*Sperm, within the tail for motility.
 +
*Hepatocytes, for liver detoxification.
  
===Image===
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===Lecture 8- Cell Junctions===
 +
*L-CAM; liver cell adhesion molecule
 +
*I-CAM; intercellular cell adhesion molecule
 +
*Ng-CAM; neuron-glia cell adhesion molecule
 +
===Lecture 10- Intermediate Filaments===
  
==Abnormalities==
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* Stratum Spinosum; this web-like system contain intmediate filaments which attach to desmosomes.
  
==Research today==
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===Lecture 15- Cell Cycle===
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* S- Phase: synthesis phase.
  
The use of animal models in research.
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== Lab 6: Effect of Tm4 expression on db cAMP induced differentiation of B35 cells ==
Mouse model for AIF knock out.
 
  
==A current finding== 
 
  
===AIF in Colon Cancer===  
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=== Description of phenotype: B35 cells===
  
===Conclusion===
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Both genotype A and genotype B share similar morpholology. The cells were primarily pronged or stringed.
  
===Terms===
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'''Genotype A:'''
*oxidoreductase
 
*free radical
 
*redox
 
*bioenergetics
 
*PARP-1
 
*calprins
 
*cathepsin
 
*ATP
 
*NAD+
 
*immunostaining
 
*chromatin
 
  
===References===
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* showed higher concentration of cells all together, and primarily pronged.
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* more neurites in the cells, but shorter and thinner.
  
Candé C, Vahsen N, Kouranti I, Schmitt E, Daugas E, Spahr C, Luban J, Kroemer RT, Giordanetto F, Garrido C, Penninger JM, Kroemer G (2004) AIF and cyclophilin A cooperate in apoptosis-associated chromatinolysis. Oncogene. 26;23(8):1514-21.
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'''Genotype B:'''
  
Candé C, Cohen I, Daugas E, Ravagnan L, Larochette N, Zamzami N, Kroemer G (2002). Apoptosis-inducing factor (AIF): a novel caspase-independent death effector released from mitochondria. Biochimie. 84(2-3):215-22.
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* showed lower number of cells, but primarily stringed.
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* less neurites within the cells but longer and thinner.
  
Millan A, Huerta S (2009) Apoptosis-inducing factor and colon cancer. J Surg Res. 151(1):163-70. Epub 2007 Dec 3
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From these results we can suggest that the Tm4 mutant cells compared to the WT (wild type) B35 cells, influence the nutrites of the cells, influencing the morphology of the cells. Thus showing that tryptomyosin specificity differs to suit the cytoskeletons specific role.
  
Modjtahedi N, Giordanetto F, Madeo F, Kroemer G (2006) Apoptosis-inducing factor: vital and lethal. Trends Cell Biol. 16(5):264-72. Epub 2006 Apr 18.
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==Lab 7: Confocal Microscopy==
  
Joza N, Susin SA, Daugas E, Stanford WL, Cho SK, Li CY, Sasaki T, Elia AJ, Cheng HY, Ravagnan L, Ferri KF, Zamzami N, Wakeham A, Hakem R, Yoshida H, Kong YY, Mak TW, Zúñiga-Pflücker JC, Kroemer G, Penninger JM.(2000)''Essential role of the mitochondrial apoptosis-inducing factor in programmed cell death''.Nature.410(6828):549-54
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Two methods:
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* Laser.
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* Spinning Disc.
  
Lorenzo HK, Susin SA, Penninger J, Kroemer G.(1999). ''Apoptosis inducing factor (AIF): a phylogenetically old, caspase-independent effector of cell death''.Cell Death Differ.6(6):516-24.
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==Feedback==
 
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--[[User:Z3158969|Beatrix Palmer]] 15:52, 11 May 2009 (EST) mark, could you please remove an uploaded pic, z crystal structure AIF. thanks.
New Articles:  
 
 
 
Porter AG, Urbano AGL. (2006) ''Does apoptosis-inducing factor (AIF) have both life and death functions in cells?''. BioEssays 28:834-843.
 
  
Knockout AIF mice:
 
The embroyoid cavity fails to form killing mice before birth. Demonstrating the need for apoptosis in tissue morphology.
 
 
 
===Feedback===
 
--[[User:Z3158969|Beatrix Palmer]] 15:52, 11 May 2009 (EST) mark, could you please remove an uploaded pic, z crystal structure AIF. thanks.
 
 
--[[User:S8600021|Mark Hill]] 09:22, 16 April 2009 (EST) All on track, kee up the good work!
 
--[[User:S8600021|Mark Hill]] 09:22, 16 April 2009 (EST) All on track, kee up the good work!
  
 
--[[User:S8600021|Mark Hill]] 18:13, 19 March 2009 (EST) Thank you for your feedback. Yes nucleosomes are important, not only for DNA packing, but also in our initial understanding of how apoptosis works.
 
--[[User:S8600021|Mark Hill]] 18:13, 19 March 2009 (EST) Thank you for your feedback. Yes nucleosomes are important, not only for DNA packing, but also in our initial understanding of how apoptosis works.
 
  
 
* Formed by DNA wrapped around histones.
 
* Formed by DNA wrapped around histones.

Latest revision as of 20:17, 24 May 2009


individual comments

z3217578: The layout of the page is a little messing so kind of confusing. The info is really good, maybe just rearragne the titles, and use some bold headings or something

  • here, sorry to mess up your setup, had to make space for discussion....

There's a few typos..."Fig. 2. Schematic of the structuraal chnages of AIF"... also i'm not sure if the reference used in point one of "what is..." lines up correctly; the article discribes a different function to that in the source... unless it was in the introduction, in which case you should track down where they got it from. Also, your final ref presentation is a bit rough... perhaps arrange it into points as some refs overlap in formatting.


that considered, i think its tops :D i love the diagrams etc etc, good job. --Peter Kehoe 12:28, 21 May 2009 (EST)


B : The page was properly referenced with sufficient diagrams, easily comprehend, and overall it suited a wiki kind of style.Probably you can talk about how the three domains interact with each other? And why the protein needs to have seperated domains? Because it does not really explain further about it. But other parts showed a very well structured page and the flow went really nicely. (3222840)


    • Sorry for the late peer reviewing. Your individual project is well structured, very organized and easy to understand with the help of images. I think your explanation of how the cell death and cell survival works should be written under a subheading right under “how it works”. I think it would be clearer like that. (3221652)

Peer assessed

  • 3187854
  • 3219393
  • 3221652
  • 3219261
  • 3207164
  • 3132868

Lecture Feedback

Lecture 4 - Nucleus

Nucleosomes- Formed by DNA wrapped around histones.

Lecture 5- Exocytosis

How does the synthesis from amino- to carboxy- terminal of protein happen in the Ribosome?

Lecture 7- Mitochodria

What types of cellular processes require lots of energy from the mitochondria?

  • Muscle cells (cardiac, skeletal and smooth muscle cels), for contraction.
  • Sperm, within the tail for motility.
  • Hepatocytes, for liver detoxification.

Lecture 8- Cell Junctions

  • L-CAM; liver cell adhesion molecule
  • I-CAM; intercellular cell adhesion molecule
  • Ng-CAM; neuron-glia cell adhesion molecule

Lecture 10- Intermediate Filaments

  • Stratum Spinosum; this web-like system contain intmediate filaments which attach to desmosomes.

Lecture 15- Cell Cycle

  • S- Phase: synthesis phase.

Lab 6: Effect of Tm4 expression on db cAMP induced differentiation of B35 cells

Description of phenotype: B35 cells

Both genotype A and genotype B share similar morpholology. The cells were primarily pronged or stringed.

Genotype A:

  • showed higher concentration of cells all together, and primarily pronged.
  • more neurites in the cells, but shorter and thinner.

Genotype B:

  • showed lower number of cells, but primarily stringed.
  • less neurites within the cells but longer and thinner.

From these results we can suggest that the Tm4 mutant cells compared to the WT (wild type) B35 cells, influence the nutrites of the cells, influencing the morphology of the cells. Thus showing that tryptomyosin specificity differs to suit the cytoskeletons specific role.

Lab 7: Confocal Microscopy

Two methods:

  • Laser.
  • Spinning Disc.

Feedback

--Beatrix Palmer 15:52, 11 May 2009 (EST) mark, could you please remove an uploaded pic, z crystal structure AIF. thanks.

--Mark Hill 09:22, 16 April 2009 (EST) All on track, kee up the good work!

--Mark Hill 18:13, 19 March 2009 (EST) Thank you for your feedback. Yes nucleosomes are important, not only for DNA packing, but also in our initial understanding of how apoptosis works.

  • Formed by DNA wrapped around histones.

--Mark Hill 15:25, 25 March 2009 (EST) The complete ribosome does not exist unless attached to a messenger RNA, it occurs as the 2 major subunits in the cytoplasm. Initial binding of a subunit occurs at the 5' amino- encoding end of the mRNA and the other subunit now assembles to form the complete ribosome. t-RNA now docks and brings the first amino acid and protein synthesis at AA1 has begun.The next AA is added and synthesis occurs as the ribosome translocates (moves) along the mRNA to the 3' carboxy- terminal at the end of the forming protein.

--Mark Hill 22:44, 31 March 2009 (EST) Yes both these processes, but I had told you these in the lecture, so it was not as if you have tried to find additional cellular processes that require lots of energy. --Beatrix Palmer 15:56, 5 April 2009 (EST) I did look on the internet after class as well, i just thought you wanted a couple of examples. sorry.

  • Muscle cells (cardiac, skeletal and smooth muscle cels), for contraction.
  • Sperm, within the tail for motility.

--Mark Hill 09:39, 3 April 2009 (EST) Correct for CAM terms, lots of science today uses acronyms (because the terms or gene names are very long), but what this means is that several acronyms can mean different things to different people.