User:Z3332863

From CellBiology

-Z3332863 15:13, 8 March 2012 (EST) This is my first lab in cell biology.

Lab Attendence

Note: I have been forgetting to put my time signature in everytime I come to lab. Sorry about this. I am up to date all the lab assessments though.

--Z3332863 15:30, 8 March 2012 (EST)

--Z3332863 14:05, 29 March 2012 (EST)

--Z3332863 15:51, 19 April 2012 (EST)

--Z3332863 14:17, 26 April 2012 (EST)

--Z3332863 14:05, 10 May 2012 (EST)

--Z3332863 14:06, 17 May 2012 (EST)

--Z3332863 14:36, 24 May 2012 (EST)

--Z3332863 14:08, 31 May 2012 (EST)

Lab 1

Course_Timetable

YAHOO

Lab 2

Lack of c-Jun phosphorylation.jpg

Cagri G Besirli, Erwin F Wagner, Eugene M Johnson The limited role of NH2-terminal c-Jun phosphorylation in neuronal apoptosis: identification of the nuclear pore complex as a potential target of the JNK pathway. J. Cell Biol.: 2005, 170(3);401-11 PubMed 16061693



Rockefeller University Press Copyright Policy This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.jcb.org/misc/terms.shtml). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 3.0 Unported license, as described at http://creativecommons.org/licenses/by-nc-sa/3.0/).


Super Resolution Microscopy

Reference Article:

Martin Lehmann, Susana Rocha, Bastien Mangeat, Fabien Blanchet, Hiroshi Uji-I, Johan Hofkens, Vincent Piguet Quantitative multicolor super-resolution microscopy reveals tetherin HIV-1 interaction. PLoS Pathog.: 2011, 7(12);e1002456 PubMed 22194693



What did this Paper show that a normal microscope could not:

Lehmann et al used multicolour super resolution microscopy to show how restriction factor tetherin on our cells interact with the HIV-1 virions. This microscopy technique revealed the structural features of the HIV-1 virion and the clusters of 4-7 tetherin dimers at the HIV-1 budding sites. Their super-resolution microscopy findings led them to understand how tetherin inhibit the release of HIV-1 virions from our cell membrane.


Lab 3:

Acetone Link to Chem alert:

[ChemAlert Acetone]

The following information are retrieved from Chem Alert on 28/03/12 to 29/03/12.


Acetone Properties:

Appearance - clear, colourless liquid

Highly Flammable

slight odour

Vapour pressure = 185mmHg at 20°C

Soluble in water

Boiling point is 56°C

Melting point is - 98°C

Specific gravity 0.79

Upper explosion limit = 13%

Lower explosion limit = 3%

Flash point = - 29°C (oc)


Acetone Hazards:

Highly inflammable

Irritant: Irritating to the eyes - may cause lacrimation pain and redness

Repeat exposure may cause skin dryness or cracking, rash and dermatitis

Vapours may cause drowsiness and dizziness

Over exposure to central nervous system may cause Depression, nausea and unconciousness\

Inhalation may cause coughing, vomiting, headache

Ingestion may cause Gastrointesinal irritation, nausea and vomiting. Ingesting large amounts may cause kidney damage, unconsciuoness and coma.

Classified as Schedule 5 poison

Low to moderate toxicity (colour rating - amber)


Papers for group assignment:

Alem W Kahsai, Kunhong Xiao, Sudarshan Rajagopal, Seungkirl Ahn, Arun K Shukla, Jinpeng Sun, Terrence G Oas, Robert J Lefkowitz Multiple ligand-specific conformations of the β2-adrenergic receptor. Nat. Chem. Biol.: 2011, 7(10);692-700 PubMed 21857662

This paper talks about how the different conformations of the B adrenergic receptor can be induced by different ligands. This is important for our project because it explains the mechanisms underlying the activation and function of tis GPCR


A De Blasi Beta-adrenergic receptors: structure, function and regulation. Drugs Exp Clin Res: 1990, 16(3);107-12 PubMed 1974837

This paper gives a great overview of the structure and function of the B Adrenergic receptor. It talks about how cAMP acts as a secondary messenger and desensitisation of the receptor.


Haitao Li, Yu Liu, He Huang, Yanhong Tang, Bo Yang, Congxin Huang Activation of β3-adrenergic receptor inhibits ventricular arrhythmia in heart failure through calcium handling. Tohoku J. Exp. Med.: 2010, 222(3);167-74 PubMed 20975248

This paper talks about the B3 adrenergic receptor and its role in controlling Ca ion concentrations in cardiomyocytes. This is immportant as improper regulation of Ca ions can lead to chronic heart failure. This is useful for our section on abnormalities and disease associated with our receptor.


S D Tachado, R A Akhtar, A A Abdel-Latif Activation of beta-adrenergic receptors causes stimulation of cyclic AMP, inhibition of inositol trisphosphate, and relaxation of bovine iris sphincter smooth muscle. Biochemical and functional interactions between the cyclic AMP and calcium signalling systems. Invest. Ophthalmol. Vis. Sci.: 1989, 30(10);2232-9 PubMed 2551839

This article explains the inositol 1,4,5 triphosphate system of B adrenergic signalling and its role in muscle contraction. This gives more information about the downstream effects of the B adrenergic receptor.



Lab 4

--Z3332863 14:05, 29 March 2012 (EST)

--Z3332863 14:56, 29 March 2012 (EST)

What is Musashi:

Shinsuke Shibata, Masahiko Umei, Hironori Kawahara, Masato Yano, Shinji Makino, Hideyuki Okano Characterization of the RNA-binding protein Musashi1 in zebrafish. Brain Res.: 2012, 1462;162-73 PubMed 22429745


Musashi1 is real. This article says Musashi is an RNA binding protein that is expressed the Central Nervous system.

Musashi Function:

[ABCAM]

Angus M MacNicol, Anna Wilczynska, Melanie C MacNicol Function and regulation of the mammalian Musashi mRNA translational regulator. Biochem. Soc. Trans.: 2008, 36(Pt 3);528-30 PubMed 18481998


It interferes with signal transduction in the cell. Musashi regulates mRNA expression at translational level. regulates the expression of NOTCH-1

Musashi is detected in Fetal Kidney, brain, liver and lung, adult brain and pancreas.

There are 2 types of Musashi.

Musashi regulates Neural Stem cell self-renewal. It also activates maternal mRNA during meiotic cell cycle progression.


data for Musashi:

[Musashi data]

P Good, A Yoda, S Sakakibara, A Yamamoto, T Imai, H Sawa, T Ikeuchi, S Tsuji, H Satoh, H Okano The human Musashi homolog 1 (MSI1) gene encoding the homologue of Musashi/Nrp-1, a neural RNA-binding protein putatively expressed in CNS stem cells and neural progenitor cells. Genomics: 1998, 52(3);382-4 PubMed 9790759


It was discovered in 1998.

Musashi is 362 amino acids long.


Antibodies against musashi:

[ABCAM]

Anti-Musashi 1

supplied by Abcam : Sapphire Bioscience Pty Ltd Telephone: +61296982022, 1800062088

raised in rabbit

polyclonal antibodies

Isotype: IgG

works with humans and mouse Musashi

Concentration of Anti Musashi:

available at 1-1.4mg/ml

Applications:

Immunofluoresences, Western Blot, Immunocytochemistry


Secondary Antibody:

Alexa Fluor 488 goat Anti-rabbit IgG

concentration not available



Lab 5

Group 7 Project

Abnormal function of Beta 1

Two possible outcomes of abnormally functioning B 1 adrenergic receptor are over activity or insufficient activity. [1][2] Both lead to serious diseases in the heart or the kidneys where B 1 is prevalent.


Decreased activity of B1 in the heart:

In the heart, activation of B1 leads to increased cytosolic Ca2+ which stimulates the force and rate of contraction of the cardiomyocytes. [2] People with Primary Pulmonary Hypertension (PPH) are susceptible to right ventricular heart failure. [1] This is because these patients have decreased expression of B1 adrenergic receptors in the myocardium of their right ventricles compared to normal people. [1] Low B1 leads decrease in G protein α subunits, adenylate cyclase and PKA activation. [1]These aspects lead to decreased Ca2+ influx, causing weaker and slower contractions of Cardiomyocytes. [1] Due to high pressure in the pulmonary circulation in these PPH patients, the weak contractions of their right heart cannot force the blood into the pulmonary circulation. This results in right ventricular failure.


Increased activity of B1 in the heart:

Chronic activation of the B1 adrenergic receptor in the heart may cause ventricular tachycardia and heart failure. [3][4] Chronic activation of B1, causes G protein coupled receptor kinase (GRK) to phosphorylate the intracellular domains of B1 receptor and recruit B-arrestin to bind. [3] Binding of B-arrestin prevents G protein from interacting with B1-receptor and causes receptor endocytosis. [3] This is the mechanism the cell employs to turn off inappropriate Ca2+ release and over contraction of cardiomyocytes. However, in patients with tachycardia, B-arrestin acts as a scaffolding protein that brings 2 proteins Epac and Ca2+/calmodulin-dependent protein kinase II (CamKII) to the B1 receptor. [3] By bringing Epac to the plasma membrane where adenylatecyclase is, Epac is in close proximity to the cAMP produced by adenylatecyclase. Epac is a protein that can be activated (via phosphorylation) by cAMP. [3] Once activated, Epac starts a short signalling pathway that results in the phosphorylation and activation of CamKII. CamKII initiates downstream signalling to increase cytosolic Ca2+ via sarcoplasmic Ca2+ leaking and ryanodine receptor phosphorylation. [4] Ryanodine receptor phosphorylation allows influx of calcium from the sarcoplasmic reticulum. [4] This inappropriate Calcium release trigger tachycardias and arrhythmias that lead to cardiac failure. [4] see diagram for a schematic of this pathway.


B-arrestin CamKII induced heart failure.jpg

Supachoke Mangmool, Arun K Shukla, Howard A Rockman beta-Arrestin-dependent activation of Ca(2+)/calmodulin kinase II after beta(1)-adrenergic receptor stimulation. J. Cell Biol.: 2010, 189(3);573-87 PubMed 20421423



Rockefeller University Press Copyright Policy This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.jcb.org/misc/terms.shtml). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 3.0 Unported license, as described at http://creativecommons.org/licenses/by-nc-sa/3.0/). --Z3332863 15:53, 14 April 2012 (EST)


Autoantibodies against beta 1 can lead to Dilated Cardiomyopathy (DCM)

Dilated Cardiomyopathy (DCM) has been found to be caused by an antibody that targets the B1 receptor. [5] In DCM, many patients produce antibodies can bind to the extracellular domains of the B1 receptor and act as an agonist. One such antibody is the Anti-B1- ECII antibody. [5] This antibody binds to the second extracellular domain of the B1 receptor and stimulates the receptor. [5] One study has shown that when mice with the human B1 receptor were given this antibody, initially there was an increase in downstream B1 signalling molecules such as cAMP and PKA. [5] This suggested the anti-B1 antibody is acting as an agonist, over-stimulating B1 receptor. In an attempt to maintain homeostasis, the heart down-regulates B1 receptors. [5] Jahns et al, have found a 25 fold decrease in B1 receptors of anti-B1 stimulated mice. Over 9 months of exposure to the anti-B1 antibody, they found Left ventricular dilatations and dysfunction. [5] Whether it is the down-regulation of B1 receptors or the initial over stimulation of B1 that caused the ventricular dysfunction is unknown. It is possible that after down regulation of B1 receptors, the heart no no longer contracts properly and this leads to pooling of the blood in the left ventricles, causing dilations. It is also possible that B1 over stimulation may cause direct damage. [5] The exact mechanism is still yet to be discovered. Nonetheless, the LV dilations and contractile dysfunction that result from Anti-B1 antibodies are characteristic of DCM. [5]--Z3332863 11:26, 22 April 2012 (EST)

Clinical aspects

Sudden cardiac death may result from B1 over stimulation

Sudden cardiac death (SCD) is the unexpected death caused by cardiovascular abnormalities, within 1 hr after symptoms occur. [6] B1 receptor over activation causes ventricular tachycardia. [3][4] This ventricular tachycardia can degenerate into Ventricular arrhythmia and fibrillation. [3][4] Ventricular fibrillation (VF) is the major cause of SCD, as reviewed by Chugh. In this review, it was reported that the annual incidence of SCD in the US is 180000-250000. As summed up in the review by Chugh, in most age groups there is higher incidence in males and the age group with the highest incidence was 75-84. [7]. The reason why B1 induced tachyarrhythmias can lead to SCD is that when a heart undergoes tachyarrhythmia, it does not contract properly. [4] This means blood is not pumped into the aorta and coronary artery, causing the heart muscle to die.

--Z3332863 11:35, 22 April 2012 (EST)

Idiopathic Dilated Cardiomyopathy (DCM):


DCM is the continual dilatations and reduced contractility of the ventricles. [5] About 30-40% of cases are caused by toxic chemicals like alcohol but 60-70% of DCM is thought to be associated with production of anti-B1 antibody. DCM can lead to sudden cardiac death. [5] This is because in DCM, the contractility of the left heart is impaired and dilated so it cannot pump blood out into the aorta effectively. [5]

--Z3332863 11:35, 22 April 2012 (EST)


References for Abnormal Function and Clinical Aspects:

1. M R Bristow, W Minobe, R Rasmussen, P Larrabee, L Skerl, J W Klein, F L Anderson, J Murray, L Mestroni, S V Karwande Beta-adrenergic neuroeffector abnormalities in the failing human heart are produced by local rather than systemic mechanisms. J. Clin. Invest.: 1992, 89(3);803-15 PubMed 1311717

2. Neil J Freedman, Robert J Lefkowitz Anti-beta(1)-adrenergic receptor antibodies and heart failure: causation, not just correlation. J. Clin. Invest.: 2004, 113(10);1379-82 PubMed 15146232

3. Supachoke Mangmool, Arun K Shukla, Howard A Rockman beta-Arrestin-dependent activation of Ca(2+)/calmodulin kinase II after beta(1)-adrenergic receptor stimulation. J. Cell Biol.: 2010, 189(3);573-87 PubMed 20421423

4. Xun Ai, Jerry W Curran, Thomas R Shannon, Donald M Bers, Steven M Pogwizd Ca2+/calmodulin-dependent protein kinase modulates cardiac ryanodine receptor phosphorylation and sarcoplasmic reticulum Ca2+ leak in heart failure. Circ. Res.: 2005, 97(12);1314-22 PubMed 16269653

5. Roland Jahns, Valérie Boivin, Lutz Hein, Sven Triebel, Christiane E Angermann, Georg Ertl, Martin J Lohse Direct evidence for a beta 1-adrenergic receptor-directed autoimmune attack as a cause of idiopathic dilated cardiomyopathy. J. Clin. Invest.: 2004, 113(10);1419-29 PubMed 15146239

6. Douglas P Zipes, Michael Rubart Neural modulation of cardiac arrhythmias and sudden cardiac death. Heart Rhythm: 2006, 3(1);108-13 PubMed 16399065

7. Sumeet S Chugh, Kyndaron Reinier, Carmen Teodorescu, Audrey Evanado, Elizabeth Kehr, Mershed Al Samara, Ronald Mariani, Karen Gunson, Jonathan Jui Epidemiology of sudden cardiac death: clinical and research implications. Prog Cardiovasc Dis: 2008, 51(3);213-28 PubMed 19026856


--Z3332863 14:14, 12 April 2012 (EST)


lab 6

--Z3332863 15:51, 19 April 2012 (EST)

Tm4 group3.JPG


What we conclude from our count and explanation:

It seems that there were more 'stringed' and 'broken fan' phenotypes in the control than in the Tm4 expressing neurons. This was not expected. Broken fan and stringed phenotypes have neurites and lamella. These are features at the growth cone where Tm4 play an important role in the development of neurites and lamella. [1] Tm4 are found to be concentrated at regions where the neuron is growing such as at neurites.[1] Tm4 is involved in stabilizing the spatial organisation of actin filaments and controlling the interaction of actin and myosin motors. [1] The organisation of actin and its interaction with myosin drive neurite and lamella growth. It was expected that in Tm4 over-expressing neurons, there should be more neurite growth. Thus we expected to see more stringed phenotype in Tm4 expressing than in control neurons. The reason for the opposite results may be due to sample size. 10 images of each group (Tm4 expressing and control)was meant to be counted. However, due to time restraints only 3 images in each group were examined. There could be many stringed pheontype seen in the later images (images 4-10) of Tm4 but they were not included in the count.


Effect of Tm4 expression on db cAMP induced differentiation of B35 cells

Phenotype of A:

- more processes or neurites

- each process is medium to short in length

- neurites are shorter and wider

- the neurons appear green

- the nuclei seem less pronounced

Phenotype of B:

- Longer neurites

- fewer processes

- blue nuclei

- cytoplasm appears more red

Phenotype A is the Tm4 over expressing while control is group B. In Tm4 over-expression, there seems to be less neurite length growth in the presence of dB cAMP. This result was expected. DB cAMP is proven to reduce Tm4 transcript concentration by 35-52%. [2] Thus there shouldn't be much difference between control and Tm4 over-expression because dbCAMP inhibits Tm4 expression. [2] dbCAMP did not appear to affect the control as much as A. This is seen with processes of B being much longer. There also more pronged phenotypes seen in A (Tm4 over-expression) than B. This may be due to increased dbCAMP induced B35 differentiation of A. Since Tm4 is not over-expressed, B may be less affected and so fewer processes and differentiation are seen.


References:

1. L Had, C Faivre-Sarrailh, C Legrand, J Méry, J Brugidou, A Rabié Tropomyosin isoforms in rat neurons: the different developmental profiles and distributions of TM-4 and TMBr-3 are consistent with different functions. J. Cell. Sci.: 1994, 107 ( Pt 10);2961-73 PubMed 7876361

2. R Ferrier, L Had, A Rabié, C Faivre-Sarrailh Coordinated expression of five tropomyosin isoforms and beta-actin in astrocytes treated with dibutyryl cAMP and cytochalasin D. Cell Motil. Cytoskeleton: 1994, 28(4);303-16 PubMed 7954857


--Z3332863 11:18, 26 April 2012 (EST)




Lab 7

* Abnormal function of b1 in the heart.

  • How increase activity of B1 signalling, due to B arrestin not shutting down the pathway appropriately, can lead to tachycardia
  • How reduced expression of of b1 in the right heart can lead to right ventricular failure
  • How autoantibodies against b1 can lead to dilated cardiacmyopathy

* Clincial Aspects:

  • how ventricular tachycardia, stimulated by B1 over activity, can result in sudden cardiac failure.
  • dilated cardiac myopathy

* drugs to treat these diseases:

  • amiodarone treats tachyarrhythmias and prevents Sudden cardiac death
  • Immunoadsorption therapy removes antibodies against b1 to treat dilated cardiac myopathy

--Z3332863 13:07, 3 May 2012 (EST)

Referencing numbers have changed since I cut and pasted this from our group 7 page. Please refer to our group 7 page for list of references to these in text citations.

Abnormal function

Group 7 Project

Abnormal function of Beta 1

Two possible outcomes of abnormally functioning B 1 adrenergic receptor are over activity or insufficient activity. [1] [2]Both lead to serious diseases in the heart or the kidneys where B 1 is prevalent.


Decreased activity of B1 in the heart:

In the heart, activation of B1 leads to increased cytosolic Ca2+ which stimulates the force and rate of contraction of the cardiomyocytes. [2] People with Primary Pulmonary Hypertension (PPH) are susceptible to right ventricular heart failure. [1] This is because these patients have decreased expression of B1 adrenergic receptors in the myocardium of their right ventricles compared to normal people. [1] Low B1 leads decrease in G protein α subunits, adenylate cyclase and PKA activation. [1]These aspects lead to decreased Ca2+ influx, causing weaker and slower contractions of Cardiomyocytes. [1] Due to high pressure in the pulmonary circulation in these PPH patients, the weak contractions of their right heart cannot force the blood into the pulmonary circulation. This results in right ventricular failure.


Increased activity of B1 in the heart:

Chronic activation of the B1 adrenergic receptor in the heart may cause ventricular tachycardia and heart failure. [3] Chronic activation of B1, causes G protein coupled receptor kinase (GRK) to phosphorylate the intracellular domains of B1 receptor and recruit B-arrestin to bind. [3] Binding of B-arrestin prevents G protein from interacting with B1-receptor and causes receptor endocytosis. [3] This is the mechanism the cell employs to turn off inappropriate Ca2+ release and over contraction of cardiomyocytes. However, in patients with tachycardia, B-arrestin acts as a scaffolding protein that brings 2 proteins Epac and Ca2+/calmodulin-dependent protein kinase II (CamKII) to the B1 receptor. [3] By bringing Epac to the plasma membrane where adenylatecyclase is, Epac is in close proximity to the cAMP produced by adenylatecyclase. Epac is a protein that can be activated (via phosphorylation) by cAMP. [3] Once activated, Epac starts a short signalling pathway that results in the phosphorylation and activation of CamKII. CamKII initiates downstream signalling to increase cytosolic Ca2+ via sarcoplasmic Ca2+ leaking and ryanodine receptor phosphorylation. [4] Ryanodine receptor phosphorylation allows influx of calcium from the sarcoplasmic reticulum. [4] This inappropriate Calcium release trigger tachycardias and arrhythmias that lead to cardiac failure. [4] see diagram for a schematic of this pathway.

--Z3332863 15:37, 18 April 2012 (EST)


B-arrestin CamKII induced heart failure.jpg

Supachoke Mangmool, Arun K Shukla, Howard A Rockman beta-Arrestin-dependent activation of Ca(2+)/calmodulin kinase II after beta(1)-adrenergic receptor stimulation. J. Cell Biol.: 2010, 189(3);573-87 PubMed 20421423



Rockefeller University Press Copyright Policy This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.jcb.org/misc/terms.shtml). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 3.0 Unported license, as described at http://creativecommons.org/licenses/by-nc-sa/3.0/).

--Z3332863 15:53, 14 April 2012 (EST)


Autoantibodies against beta 1 can lead to Dilated Cardiomyopathy (DCM)

Dilated Cardiomyopathy (DCM) has been found to be caused by an antibody that targets the B1 receptor. [5] In DCM, many patients produce antibodies can bind to the extracellular domains of the B1 receptor and act as an agonist. One such antibody is the Anti-B1- ECII antibody. [5] This antibody binds to the second extracellular domain of the B1 receptor and stimulates the receptor. [5] One study has shown that when mice with the human B1 receptor were given this antibody, initially there was an increase in downstream B1 signalling molecules such as cAMP and PKA. [5] This suggested the anti-B1 antibody is acting as an agonist, over-stimulating B1 receptor. In an attempt to maintain homeostasis, the heart down-regulates B1 receptors. [5] Jahns et al, have found a 25 fold decrease in B1 receptors of anti-B1 stimulated mice. Over 9 months of exposure to the anti-B1 antibody, they found Left ventricular dilatations and dysfunction. [5] Whether it is the down-regulation of B1 receptors or the initial over stimulation of B1 that caused the ventricular dysfunction is unknown. It is possible that after down regulation of B1 receptors, the heart no no longer contracts properly and this leads to pooling of the blood in the left ventricles, causing dilations. It is also possible that B1 over stimulation may cause direct damage. [5] The exact mechanism is still yet to be discovered. Nonetheless, the LV dilations and contractile dysfunction that result from Anti-B1 antibodies are characteristic of DCM. [5]


Clinical aspects

Sudden cardiac death may result from B1 over stimulation

Sudden cardiac death (SCD) is the unexpected death caused by cardiovascular abnormalities, within 1 hr after symptoms occur. [6] B1 receptor over activation causes ventricular tachycardia. [3] This ventricular tachycardia can degenerate into Ventricular arrhythmia and fibrillation. [3] Ventricular fibrillation (VF) is the major cause of SCD, as reviewed by Chugh. In this review, it was reported that the annual incidence of SCD in the US is 180000-250000. As summed up in the review by Chugh, in most age groups there is higher incidence in males and the age group with the highest incidence was 75-84. [7] The reason why B1 induced tachyarrhythmias can lead to SCD is that when a heart undergoes tachyarrhythmia, it does not contract properly. [4] This means blood is not pumped into the aorta and coronary artery, causing the heart muscle to die.

--Z3332863 11:35, 22 April 2012 (EST)

Idiopathic Dilated Cardiomyopathy (DCM):


DCM is the continual dilatations and reduced contractility of the ventricles. [5] About 30-40% of cases are caused by toxic chemicals like alcohol but 60-70% of DCM is thought to be associated with production of anti-B1 antibody. DCM can lead to sudden cardiac death. [5] This is because in DCM, the contractility of the left heart is impaired and dilated so it cannot pump blood out into the aorta effectively. [5]

--Z3332863 11:35, 22 April 2012 (EST)


Pharmalogical relevance

Drugs/treatments for sudden cardiac death and tachyarrhythmias caused by over-stimulated B1 receptors:

Amiodarone

Amiodarone can be used to prevent Sudden cardiac death. [8] It reduces mortality from those at risk of SCD by 10-19%. People at risk of SCD include those suffering from B1 induced arrhythmias. [8] Amiodarone is also widely used to treat ventricular tachyarrhythmias. [8] It works by blocking both B1 receptors and calcium channels in the heart. [8] By reducing the B1-adrenergic signalling in cardiomyocytes, amiodarone counteracts the over-stimulation of B1 receptors seen in patients with ventricular tachyarrythmias. [8] Since ventricular tachyarrhythmia is the main cause of SCD, amiodarone can prevent the onset of SCD. Amiodarone can have serious side effects. [8] Long term use can result in pulmonary fibrosis.[8]


Drugs against DCM:

Immunoadsorption (IA) therapy can be used for DCM. This therapy removes the auto-antibodies against B1. [9] IA has been shown to increase heart function in patients suffering DCM due to anti-B1 antibodies. [9] In clinical trials, Anti-IgG columns are used to reduce the amount of IgG antibodies such as anti-B1 in DCM patients. [9] Patients were found to have increased Left ventricular ejection fraction after treatment. [9]

This table gives an overview of some of the serious diseases associated with Beta 1 and other beta receptors. For more information, please refer to the text below the table.

Abnormal Function Disease pathogenesis Treatment
Increased Beta 1 activity [6]

[3] [10] [4]

Tachycardia, tachyarrhythmia, Sudden Cardiac Death [6] [3] [10] [4]

B arrestin brings Epac and CaMKII to the Beta receptor C domain to activate CaMKII signalling. This increases intracellular Calcium to stimulate excessive heart contractions[6] [3] [10] [4]

Amiodarone, Metoprolol [8]

Autoantibodies to beta 1 receptor [5]

Dilated cardiomyopathy (DCM)[5]

Autoantibodies stimulates a down-regulation of beta 1 receptors. This leads to damage to cardiomyocytes and pooling of blood in the heart, causing DCM [5]

Immunoadsorption therapy [9]

Polymorphisms of Beta 2 receptor gene [11]

[12] [13]

Nocturnal Asthma [11] [12] [13]

Polymorphism changes arginine to glycine at position 16 of the Beta 2 receptor gene. This reduces expression of B2 receptors, leading to increased chance of bronchospasms[14] [11]

Salmeterol [12]


Lab 8

Link

ATCC mammalian Cell line: RK13

Cell line is from rabbit, Oryctolagus cuniculus

Tissue: kidney (normal - no disease)

Morphology: epithelial

Biosafety: level 2 (Cells contain Bovine Viral Diarrhea Virus (BVDV)

Paper it is discovered in:

22883: Bolin SR, et al. Survey of cell lines in the American Type Culture Collection for bovine viral diarrhea virus. J. Virol. Methods 48: 211-221, 1994. PubMed: 7989438 26192: . . Lancet 2: 593, 1963.


Growth properties: Adherent

cellular products: keratin

age: 5 weeks --Z3332863 15:05, 10 May 2012 (EST)



Lab 9

Peer Assessment of other group Assessment:

no signature, paste comments on discussion page, using the criteria.

--Z3332863 16:31, 12 May 2012 (EST)


group 1: testosterone:

what was done well:

  • the history section was very well organised and gave an insightful, yet brief summary of the discoveries over the last century
  • The biosynthesis was educational. It wasn't too detailed and easy to understand because of the table
  • The dot point structure of the signalling pathway made a complex section of this project easy to understand.
  • the PNAS image was correctly cited and relevant to text

what needs to be improved:

  • the introduction is too brief. Besides just adding in a table and some points about the properties, can you please add some linking sentences to tie the structure and pathway overview together? For example, 'there are two pathways for testosterone signalling as shown in the table below'
  • I feel you need more pictures and diagrams. For example flowcharts for the 2 pathways. Keep in mind you do need 1 student drawn diagram - maybe do that for the testosterone structure instead of using a non-copyrighted image
  • can you find some images besides wikipedia images?
  • Add some subheadings for Normal Function or a table summarising the functions at the start. Testosterone has many functions so it would be more easier to find information if it was better organised.
  • Add more in text citations - you can't put 1 reference at the end of each paragraph (seen in 'Normal function') because each sentence that includes idea from a paper needs an in-text citation.

Grp 2 VEGF:

what was done well:

  • very well written abnormal function section. It contained enough information and yet it was simple and clear. The images were also very relevant to text
  • The table summary for the VEGF receptor was great. It summarised the text well
  • Overall the page lay out is commendable. It was easy to find information because of the subheadings and dot points.

What needs to be improved:

  • what is exactly the signalling pathway for VEGF? There is a lot of information about the receptor but what are the chain of events after the ligand binding to receptor?
  • There are too many wikipedia images. I think we're only 1 or maybe 2 max. can you find some images from plos, JCB or PNAS?
  • there isn't a student drawn image.
  • where are the in text citations for oncogenes and hormones under the normal function section?

Grp 3 Extrinsic apoptosis

What was done well:

  • enjoyed your Introduction becasue it gave a great definition for apoptosis and extrisnsic apoptosis. It provided a great scope of the key ideas you are going to be reporting in the rest of your project

what needs Improvement:

  • You cannot leave no references. Even with technical difficulties you should still write the PMID and author at the end of each paragraph or section (at the very least)
  • Signalling pathway section was confusing. How do all these extrinsic apoptotic proteins interact with one another to give apoptosis? what is the actual pathway? I thought a pathway would be 'DISC activates caspase 8 which activates Caspase 3, etc' and not just a series of proteins given in no particular order.
  • There was a section under function where it was just dot points. I found this hard to understand. What does 'inactivate proteins involved in mRNA splicing' actually have anything to do with extrinsic apoptosis?
  • Only one image. need to add more
  • You need a section on Abnormal function and receptor structure

Grp 4 Notch

what was done well;

  • Normal Function section was very well written. I could understand the different roles of Notch in different tissues very easily. It gave a wide range of functions and picture is quite relevent to Notch in the CNS. This section had nice layout with the subheadings.
  • correct referencing and citations used
  • enjoyed the video

what needs Improving:

  • Your page seems rather short and many of your sections need expanding. In you intro, can you give an overview of everything you're going to talk about? The future research section doesn't appaer to have information - just the references to some literature.
  • You need a diagram for your Pathway. I find it hard to understand the text.
  • History section doesn't expalin what happened betweeen 30s and 1970s.

group 5 Wnt beta catenin

what was done Well:

  • Although I didn't get the Joke of the image just before the intro, it was guite creative and catchy. Gives this page that X factor.
  • Mechanism of action diagram clarified everything in the text and it was highly relevant. It was a student drawn image which is a rare sight on other pages.
  • The movie in Mechanism of Action was educational. I understood the text a lot better after viewing
  • The disease section gave a lot of detail but it clearly linked the mutations of Wnt with the pathogenesis of the diseases.

Improvements needed:

  • Disease section - can you give some background information for each disease - such as epidiomology and symptoms? what happened to the references?
  • 'Key players table' doesn't seem complete - what happened to the structures of Dsh, axin and Gsk-3B?

group 6 Insulin:

What was done Well:

  • signal pathway section was very well written. I understood the 2 different pathways by reading the text. I found it not too detailed or too long but it gave enough information for me to understand what was going on.
  • great Abnormal Function section - it linked the disease state to the abnormal function of receptor well. The set out with many subheadings made it very clear
  • Inspiring future current section too

What needs to be Improved:

  • The pictures (e.g. structure of receptor) need copyright and referencing added
  • Receptor section needs more information. I feel some of the information in signalling such as 'how the receptor is activated by ligand' should be in the receptor section
  • The schematic in the signalling pathway was very complicated. Can you add a paragraph underneath explaining the diagram?

group 8 Leukocyte Extravasation

What was done well:

  • Pathway was very clear. The ordered structure of the text explained exactly how extravasation occurred in a simple and brief way
  • Introduction was short and precise. It gave a great overview while it wasn't too long or boring

What needs to be improved:

  • Absent history and new research sections
  • The protein section was very dense. Can you please link some of these proteins to the normal pathway? What step of the extravasation process do they play a major role - can you please make this more clear? May be put in a table with headings; 'protein name', 'protein structure, ' function', 'step of extravasation involved'
  • Abnormal and Normal pathway - where are the references?
  • more pictures and diagrams, espcially in the Abnormal/Normal function sections, would make the opage more appealing and easier to understand.


Group 9 p53 Signalling:

What was done well:

  • Introduction gave a lot of information and the first paragraph was particularly relevant
  • History section was very well researched with a reference for each year and it was so up-to-date! Not many groups have history up to 2010.
  • Nicely set out Normal Function section. Clearly states what p53 does and briefly explains how it achieves these functions

What needs Improvement:

  • Absent receptor section made it hard to understand the pathway
  • There are 3 different pathways for p53 and without subheadings to separate them, it was really easy to get the 3 pathways mixed up. So adding subheadings would be helpful. A student drawn flowchart for the pathways would also be great
  • More Information needs for Anormal function and current research,such as the different cancers and treatments p53 may be involved in,would be interesting
  • more pictures needed

--Z3332863 10:45, 14 May 2012 (EST)

--Mark Hill 12:56, 17 May 2012 (EST) This has good critical comments about each project, with specific examples given.



lab 12

Identify a current technique used in gene sequencing.

Next generation sequencing


Identify a recent cell biology research paper that has used microarray technology.

Micah J Drummond, John J McCarthy, Mala Sinha, Heidi M Spratt, Elena Volpi, Karyn A Esser, Blake B Rasmussen Aging and microRNA expression in human skeletal muscle: a microarray and bioinformatics analysis. Physiol. Genomics: 2011, 43(10);595-603 PubMed 20876843


What aspect of the research findings were contributed by the microarray technique.

  • The miRNA Microarray was used to profile the MicroRNAs (miRNAs) in aging skeletal muscles of Aging
  • The results of this microarray showed:
  • 18 miRNAs were expressed in older human skeletal muscles but not in the younger ones
  • some Let-7 family members are up-regulated in aged muscle
  • Let-7 miRNA down-regulate genes, encoding proteins that promote cell divsion (Myc, CDK6)
  • this provides an explanation for age related sarcopenia
  • 1.0 1.1 1.2 1.3 1.4 M R Bristow, W Minobe, R Rasmussen, P Larrabee, L Skerl, J W Klein, F L Anderson, J Murray, L Mestroni, S V Karwande Beta-adrenergic neuroeffector abnormalities in the failing human heart are produced by local rather than systemic mechanisms. J. Clin. Invest.: 1992, 89(3);803-15 PubMed 1311717
  • 2.0 2.1 Neil J Freedman, Robert J Lefkowitz Anti-beta(1)-adrenergic receptor antibodies and heart failure: causation, not just correlation. J. Clin. Invest.: 2004, 113(10);1379-82 PubMed 15146232
  • 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 3.9 Supachoke Mangmool, Arun K Shukla, Howard A Rockman beta-Arrestin-dependent activation of Ca(2+)/calmodulin kinase II after beta(1)-adrenergic receptor stimulation. J. Cell Biol.: 2010, 189(3);573-87 PubMed 20421423
  • 4.0 4.1 4.2 4.3 4.4 4.5 4.6 Xun Ai, Jerry W Curran, Thomas R Shannon, Donald M Bers, Steven M Pogwizd Ca2+/calmodulin-dependent protein kinase modulates cardiac ryanodine receptor phosphorylation and sarcoplasmic reticulum Ca2+ leak in heart failure. Circ. Res.: 2005, 97(12);1314-22 PubMed 16269653
  • 5.00 5.01 5.02 5.03 5.04 5.05 5.06 5.07 5.08 5.09 5.10 5.11 5.12 5.13 Roland Jahns, Valérie Boivin, Lutz Hein, Sven Triebel, Christiane E Angermann, Georg Ertl, Martin J Lohse Direct evidence for a beta 1-adrenergic receptor-directed autoimmune attack as a cause of idiopathic dilated cardiomyopathy. J. Clin. Invest.: 2004, 113(10);1419-29 PubMed 15146239
  • 6.0 6.1 6.2 6.3 Douglas P Zipes, Michael Rubart Neural modulation of cardiac arrhythmias and sudden cardiac death. Heart Rhythm: 2006, 3(1);108-13 PubMed 16399065
  • Sumeet S Chugh, Kyndaron Reinier, Carmen Teodorescu, Audrey Evanado, Elizabeth Kehr, Mershed Al Samara, Ronald Mariani, Karen Gunson, Jonathan Jui Epidemiology of sudden cardiac death: clinical and research implications. Prog Cardiovasc Dis: 2008, 51(3);213-28 PubMed 19026856
  • 8.0 8.1 8.2 8.3 8.4 8.5 8.6 8.7 I Sim, K M McDonald, P W Lavori, C M Norbutas, M A Hlatky Quantitative overview of randomized trials of amiodarone to prevent sudden cardiac death. Circulation: 1997, 96(9);2823-9 PubMed 9386144
  • 9.0 9.1 9.2 9.3 9.4 S B Felix, A Staudt, W V Dörffel, V Stangl, K Merkel, M Pohl, W D Döcke, S Morgera, H H Neumayer, K D Wernecke, G Wallukat, K Stangl, G Baumann Hemodynamic effects of immunoadsorption and subsequent immunoglobulin substitution in dilated cardiomyopathy: three-month results from a randomized study. J. Am. Coll. Cardiol.: 2000, 35(6);1590-8 PubMed 10807465
  • 10.0 10.1 10.2 Cite error: Invalid <ref> tag; no text was provided for refs named PMID8239250
  • 11.0 11.1 11.2 Cite error: Invalid <ref> tag; no text was provided for refs named PMID7706471
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  • 13.0 13.1 Cite error: Invalid <ref> tag; no text was provided for refs named PMID1355640
  • Cite error: Invalid <ref> tag; no text was provided for refs named PMID21385652