User:Z3333865

From CellBiology

Lab Attendance

Lab 1

This is my first lab in Cell Biology! YAY!

External link: JoVE

Internal link: Lecture 2


--Z3333865 15:13, 8 March 2012 (EST)


Lab 2

Second lab in cell biology :)

Actin acrosomal reaction.jpg Actin drives the acrosomal reaction (left to right).

Reference

L G Tilney, S Hatano, H Ishikawa, M S Mooseker The polymerization of actin: its role in the generation of the acrosomal process of certain echinoderm sperm. J. Cell Biol.: 1973, 59(1);109-26 PubMed 4356568


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/).


PMID 4356568


--Z3333865 14:39, 15 March 2012 (EST)


Lab question

Michael Hofmann, Christian Eggeling, Stefan Jakobs, Stefan W Hell Breaking the diffraction barrier in fluorescence microscopy at low light intensities by using reversibly photoswitchable proteins. Proc. Natl. Acad. Sci. U.S.A.: 2005, 102(49);17565-9 PubMed 16314572


Improved view of separation of protein clusters was due to superresolution microscopy techniques used. In this paper, the gain in resolution can be explained by the fact that, thanks to the reversible photoswitching of a fluorescent protein between two conformational states, diffraction is no longer a limiting factor.


Liberalization of PNAS copyright policy: Noncommercial use freely allowed (Note original Author should be contacted for permission to reuse for Educational purposes) "Our guiding principle is that, while PNAS retains copyright, anyone can make noncommercial use of work in PNAS without asking our permission, provided that the original source is cited."

--Z3333865 17:43, 16 March 2012 (EST)


Lab 3

Lab question 1

Physical and Chemical Properties

Appearance: Clear, colourless liquid.

Odour: Slight alcohol odour. Detectable at 2000-8800ppm

pH: Not available

Vapour pressure: 92 mmHg @ 25°C

Vapour density: 1.1 (air = 1.0)

Boiling point: 64.5°C

Melting point: -97.8°C

Solubility: Complete

Specific gravity: 0.79

Information for flammable materials - Flashpoint : 11°C

Upper and lower flammable limits in air: Flammable (Explosive)Limit - Upper: 36%; Flammable (Explosive)Limit - Lower: 7%

Auto-ignition Temperature: 385°C

Additional Properties: Evaporation Rate: 500 (n-Butyl Acetate); Molecular Weight: 32.04; Volatile Organic Compounds Content (VOC): (as specified by the Green Building Council of Australia) 100%; % Volatiles: 100%


Hazards

Acute:

Eye contact: Vapour and liquid can irritate the eyes resulting in redness, pain and swelling. Substantial acute poisoning, or chronic long term abuse, can lead to temporary or permanent loss of sight.

Skin contact: Brief skin contact may cause minor and short-lasting irritation. Prolonged contact (e.g. Repeated daily contact, or working in clothing saturated with the product) may cause drying and cracking of the skin due to the de-fatting action. Dermatitis may also occur in some individuals.

Inhalation: Vapour may cause irritation of the nose, throat and upper respiratory tract. Higher concentrations can cause drowsiness, nausea, dizziness and eventually unconsciousness. Harmful if aspirated into the lungs, may cause chemical pneumonitis.

Ingestion: Unlikely under normal occupational exposures, but methanol is very toxic by mouth and 60-120ml (1 g/kg) may be a fatal dose. Initial symptoms resemble ethanol intoxication (drunkenness) and may include fatigue, dizziness, headache, nausea, vomiting. Ingestion may cause acute poisoning with initial narcosis, progressing to coma and death where sufficient dosage has been ingested. Lesser dosage may lead to damage to liver, heart, kidneys, lungs and other organs including the retina and optic nerve.

Chronic:

Repeated exposure at over the occupational standard may lead to damage to liver, heart, kidneys, lungs and other organs including the retina and optic nerve.


Lab question 2

1) Ron O Dror, Albert C Pan, Daniel H Arlow, David W Borhani, Paul Maragakis, Yibing Shan, Huafeng Xu, David E Shaw Pathway and mechanism of drug binding to G-protein-coupled receptors. Proc. Natl. Acad. Sci. U.S.A.: 2011, 108(32);13118-23 PubMed 21778406


This primary article investigates G-protein coupled receptors and the mechanism of binding of drugs to these receptors at an atomic level. One of the pathways for travel includes association with a vestibule on the extracellular surface of the receptors; a method used by several different drugs, including beta-blockers binding to beta-adrenergic receptors.


2) Ron O Dror, Daniel H Arlow, Paul Maragakis, Thomas J Mildorf, Albert C Pan, Huafeng Xu, David W Borhani, David E Shaw Activation mechanism of the β2-adrenergic receptor. Proc. Natl. Acad. Sci. U.S.A.: 2011, 108(46);18684-9 PubMed 22031696


This primary article investigates an activation mechanism for the β(2)-adrenergic receptor. It is known that G-protein coupled receptors change from active to inactive states and vice versa due to drug actions, though recent crystalline structures do not reveal the mechanism of transition. Atomic simulations in this paper that the first structural changes during receptor activation often take place on the intracellular side of the receptor, far from the drug-binding site.


3) Jillian G Baker, Stephen J Hill, Roger J Summers Evolution of β-blockers: from anti-anginal drugs to ligand-directed signalling. Trends Pharmacol. Sci.: 2011, 32(4);227-34 PubMed 21429598


This review article addresses the development of Beta-blockers, the way in which they have evolved up until now and the direction in which we are headed regarding their future uses. Some concepts include receptor selectivity, agonistic and antagonistic actions, ligand-directed signalling, and how these characteristics could be useful in fighting diseases related to beta-adrenergic receptors, such as cardiac failure and osteoporosis.


4) Nobuyuki Hizawa Pharmacogenetics of β2-agonists. Allergol Int: 2011, 60(3);239-46 PubMed 21681016


This review article addresses the possible relationship between polymorphisms in the β2 adrenoceptor gene and various individual responses to short-acting and long-acting Beta2-agonists. These drugs are used in the treatment of asthma and chronic obstructive pulmonary disease to dilate the airways and protect them, despite their associated side-effects, such as increased mortality. Although currently genetic testing is very limited, it is hoped that in the future we can predict the individual responses to these drugs based on the genotype of the β2 adrenoceptor gene.

--Z3333865 10:35, 28 March 2012 (EST)


Lab 4

In class exercise

--Z3333865 14:57, 29 March 2012 (EST)

M Szabat, T B Kalynyak, G E Lim, K Y Chu, Y H Yang, A Asadi, B K Gage, Z Ao, G L Warnock, J M Piret, T J Kieffer, J D Johnson Musashi expression in β-cells coordinates insulin expression, apoptosis and proliferation in response to endoplasmic reticulum stress in diabetes. Cell Death Dis: 2011, 2;e232 PubMed 22113197


Musashi is in fact a real protein. Musashi-human

It is a stem cell marker, can also be found in Beta-cells and neuronal cells. 362 amino acids long - approx. 10 kD

First published in Genomics journal in 1998.


Function

RNA binding protein that regulates the expression of target mRNAs at the translation level. Regulates expression of the NOTCH1 antagonist NUMB. Binds RNA containing the sequence 5'-GUUAGUUAGUUAGUU-3' and other sequences containing the pattern 5'-[GA]U(1-3)AGU-3'. May play a role in the proliferation and maintenance of stem cells in the central nervous system. UniProt-MSI1


Commercial antibody available:

Anti-Musashi 1 / Msi1 antibody (ab21628) Rabbit-ab21628

Rabbit polyclonal to Musashi 1 / Msi1

ICC/IF: Use at a concentration of 1 µg/ml.

WB: Use at a concentration of 1 µg/ml. Detects a band of approximately 39 kDa (predicted molecular weight: 39 kDa). Can be blocked with Musashi1 peptide (ab23870).

Is unsuitable for IHC-P.

Not yet tested in other applications.

Reacts with: Mouse, Human

Predicted to work with: Rat, Xenopus laevis

Clonality: Polyclonal

Isotype: IgG


Second antibody:

Goat anti-rabbit Alexa Fluor 488 Anti-rabbit

Conjugation: Alexa Fluor® 488


Alexa Fluor® 488 Goat Anti-Rabbit IgG (H+L) *2 mg⁄mL*

Provider: Molecular Probes®

The Alexa Fluor 488 goat anti—rabbit IgG is labeled with our bright, photostable, green-fluorescent Alexa Fluor 488 dye and is prepared from affinity-purified antibodies that react with IgG heavy chains and all classes of immunoglobulin light chains from rabbit. To minimize crossreactivity, it has been adsorbed against human IgG, human serum, mouse IgG, mouse serum and bovine serum. We also provide a version of the same antibody that has been cross-adsorbed against additional species (A-11034).


--Z3333865 15:38, 29 March 2012 (EST)

Lab 6

Z3333865 lab 6.JPEG


What changes were observed between group A (overexpression of Tm4) and group B (control)?

Over-expression of Tm4 seemed to favour ‘stumped’, ‘pronged’ and ‘stringed’ cell phenotypes, indicated by an increase of those phenotypes by 2%, 10% and 8% respectively. Consequently, ‘fan’, ‘broken fan’ and ‘pygnotic’ phenotypes decreased in expression by 4%, 14% and 2% respectively.


What changes were observed between the phenotypes of the two groups?

Fan: decreased in expression when Tm4 was over-expressed, though the cells did seem to have a larger diameter than the control ‘fan’ phenotype.

Broken fan: highly expressed by the control group, however, when Tm4 was over-expressed the cells seem to have a larger diameter than the control ‘broken fan’ phenotype. The ratio of the nucleus to the lamellum for the control group was significantly smaller than the ration observed for the Tm4 group.

Stumped: a slight increase in the ‘stumped’ phenotype was observed for the Tm4 group, compared to the control group. Both the size of the entire cell and the size of the nucleus seemed smaller for the control group compared to the Tm4 group.

Pronged: this phenotype is significantly more common when Tm4 is over-expressed, compared with the control group. Furthermore, increased branching was observed for the Tm4 group, as well as an increase in the number of connections between cells.

Stringed: the most common phenotype observed when Tm4 is over-expressed. More branches were observed for the Tm4 group as compared with the control group, the length of the branches was generally longed and the nuclei were larger.

Pygonic: found to be present in the control group, despite being absent when Tm4 was over-expressed. This phenotype is rarely observed.


How does Tm4 mediate these changes?

The protein tropomyosin has different isoforms which act upon the regulation of the cytoskeleton and the actin filaments. It is found in various cell types and influences neurite development and synaptic plasticity, as explained in the lab class. When Tm4 was overexpressed, observations indicated that increased number of branches and increased number of connections between cells had formed. The control group had a decreased number of cell phenotypes with branches and less connections between cells. These results indicate that the increase in cell-cell connections, as well as branch number and length, and other differences in phenotype between the two groups was caused by an overexpression of Tm4.


--Z3333865 16:00, 19 April 2012 (EST)


Lab 7

--Z3333865 14:18, 26 April 2012 (EST)

My contribution to the group project up until now:


Group 7 - G-protein coupled receptors: Beta-adrenergic receptors with a focus on Beta1-adrenoceptors


Introduction

Comment: Suggestion to V: a quick mention of the differences, eg. location in the human body where they are found most often - to some extend expand upon table.

Happy to help out if you're experiencing difficulties finding info, M --Z3333865 20:59, 1 May 2012 (EST)


History of pathway

1854-1915: The idea that drugs bind to specific sites or receptors on cell surfaces - Paul Ehrlich [1]

1852-1925: Use of the term ‘receptive substance’ - John Langley, further developed by Sir Henry Dale [1]

1949, 1956: Development of concepts of affinity and efficacy. Development of the quantitative methods by which the properties of agonists, partial agonists and antagonists can be evaluated from the measurement of functional responses in isolated tissues - Arunlakshana and Schild, Stephenson [1]

1962: The discovery of cyclic AMP as the factor mediating the effect of epinephrine on glycogenolysis and of cAMP mediating the effects of other hormones - Sutherland and Rall. [1]

Early 1970s: Growing realisation that the receptor structures responsible for stimulating cyclic AMP formation involved separate proteins for agonist recognition (receptor), cyclic AMP synthesis (adenylyl cyclase) and the transduction of information from the receptor to adenylyl cylase (heterotrimeric G-protein). [1]

1994- Gilman and Rodbell shared the Nobel Prize in Physiology or Medicine in 1994. This was "for their discovery of G-proteins and the role of these proteins in signal transduction in cells". Nobel Prize 1994

1997: Development of the concept of GPCRs and the vital role of G-proteins in signal transduction processes - Research teams of Gilman and Rodbell [1]

--Z3333865 10:13, 4 April 2012 (EST)

--Z3333865 18:02, 12 April 2012 (EST)


Gene description

Adrenergic receptors can be classified into different subtypes, namely alpha and beta.

This group project places a specific focus on beta-adrenergic receptors, which can be further classified into different subtypes, each of them being coded for by a different gene.


Beta 1

The gene coding for Beta-1 adrenergic receptors is located on chromosome 10, 10q24-q26.

The gene is protein coding for 477 amino acids. Beta-1 adrenoceptor gene

--Z3333865 09:00, 6 April 2012 (EST)


Beta 2

The gene coding for Beta-2 adrenergic receptors is located on chromosome 5, 5q31-q32.

The gene is protein coding for 413 amino acids. Beta-2 adrenoceptor gene


Beta 3

The gene coding for Beta-3 adrenergic receptors is located on chromosome 8, 8p12.

The gene is protein coding for 408 amino acids. Beta-3 adrenoceptor gene

--Z3333865 19:31, 10 April 2012 (EST)


Receptor agonists

Suggested the following: Hey, what about combining this with the gene description? Cause we already have the 3 different Beta receptors listed with chromosomal location and a quick mention of defect.. Just a thought so we'll have less headings and more information per heading.. M.--Z3333865 22:11, 1 May 2012 (EST)


Pathway and normal function - my section specifically

Stimulatory Pathway

β-adrenergic receptors are activated specific agonist compouds. These include direct agonists such as dobutamine (specific for β-1 receptors) and endogenous catecholamines like adrenaline and noradrenaline. As depicted in the illustration, we will consider the binding of an endogenous catecholamine which leads to initiation of the stimulatory pathway. The first step in signalling is accomplished by activation of the heterotrimeric G protein Gs, promoting dissociation of its α and βɣ subunits. Next, the α-subunit binds to the membrane-bound effector protein adenylate cyclase, stimulating the synthesis of cyclic AMP from ATP. As a second messenger, cyclic AMP causes the dissociation of regulatory and catalytic subunits of protein kinase A. The catalytic subunits of protein kinase A are now able to phosphorylate numerous substrate proteins including ion channels, myofilament proteins, and metabolic enzymes[2]. Protein kinase A-dependent phosphorylation mediates many of the physiologic consequences of β-adrenergic receptor signaling. Phosphodiesterases eventually degrade the cyclic AMP and protein phosphatases dephosphorylate protein kinase A substrates, consequently terminating and reversing the previous events.

β-adrenergic receptor signaling has been thought to have four main functional roles in the heart: to increase the heart beating rate, contractility, relaxation rate, and to modulate metabolism as required by those increased energetic demands. Cardiac myocytes express two main β-adrenergic receptor isoforms, β1-adrenoceptors and β2-adrenoceptors (75%:25%)[3].

β-adrenergic receptor pathway - student image

Phosphorylation of the Ryanodine receptor 2 on the sarcoplasmic reticulum due to the catalytic subunits of protein kinase A leads to an elevated Ca2+ flux to cytoplasm. Elevated Ca2+ in cardiac muscles causes an increase in heart rate. Increased contractility is primarily due to protein kinase A-mediated phosphorylation of the L-type calcium channel located in the cell membrane, and phospholamban located in the cytosol. β-adrenergic receptor signaling increases the Ca2+ current, bringing additional calcium into myocytes for larger contractions. 2,3 Phosphorylation of phospholamban releases its tonic inhibition of the Ca2+ pump located in the membrane of the sarcoplasmic reticulum, sequestering more Ca2+ into the sarcoplasmic reticulum for larger subsequent contractions. Furthermore, the increase in Ca2+ flux from cytosol to sarcoplasmic reticulum accelerates relaxation of the myofilaments. To keep up with the energy demands, protein kinase A also activates phosphorylase kinase, a metabolic enzyme that increases rates of glycogen breakdown. Additional glucose and increased cellular ATP are provided to retain the rate and force of cardiac contractility.[4]


Inhibitory pathway

--Z3333865 12:04, 7 April 2012 (EST)

Inhibition of the pathway mentioned above can occur due to binding of Beta-adrenergic receptor antagonists, more commonly known as Beta blockers to the receptors. These compounds block in particular the action of the endogenous catecholamines adrenaline and noradrenaline. Levels of cAMP will decrease as a result and further pathway signalling has been prevented. Main effects are to reduce excitement caused by the sympathetic nervous system, however they have minimal effects on subjects that are in a resting state.

Experimental findings have indicated that attenuation of the production of cAMP is insufficient as the only signal for educing the many effects observed. Despite additional biochemical and electrophysiological changes which must occur, we will solely focus on the role of beta-adrenergic receptors in this process.[5]


Beta-2 adrenoceptors have been linked to the heterotrimeric G protein Gi. As with the Gs protein, the Gi protein is made up of an alpha, beta and gamma subunit which can dissociate. Dissociation occurs once energy is provided by conversion of GTP to GDP. This will cause the alpha subunit to interact with adenylate cyclase. Instead of causing a stimulatory effect, this mechanism causes an inhibitory effect. Less ATP is converted to cAMP, hence the separation of regulatory and catalytic subunits of protein kinase A has been prevented. As a consequence, no phosphorylation of cell signalling constituents occurs and the effects normally observed by activation of adenylate cyclase are now diminished.

--Z3333865 21:47, 1 May 2012 (EST)


Regulatory mechanisms

Comment: I'll include this in my section :) M.

Regulation of the adrenergic signalling pathway can be achieved in many ways.


1)Control of cAMP levels

Signalling complexes can be formed between adrenergic receptors and cAMP-specific phosphodiesterase (PDE). The beta2-adrenergic receptor forms a complex with both Beta-arrestin and the PDE4D5 isoform. Agonists are required to bind to the beta2-adrenergic receptor in order to form this complex [6].

On the other hand, beta1-adrenergic receptors form a direct signalling complex with a cAMP-specific phosphodiesterase isoform, namely PDE4D8. Furthermore, binding of agonists to the receptor will result in dissociation of the complex. Our current understanding is that this complex might allow for the control of cAMP levels in proximity of the receptor [7].


2)Regulation by Beta-arrestin

Currently working on this.

[8]

[9]


Glossary of terms

  • ATP: Adenosine-5'-triphosphate, a good energy source for metabolic processes, is a multifunctional nucleoside triphosphate used in cells as a coenzyme.
  • Cyclic AMP (cAMP): a nucleotide generated from ATP by adenylyl cyclase in response to stimulation of many cell-surface receptors. cAMP acts as an intracellular signaling molecule by activating cyclic-AMP-dependent kinase (protein kinase A, PKA)
  • Cytosol: the intracellular fluid found inside a cell
  • Dissociation: disuniting or separating an object into parts
  • Gi: inhibitory G-protein
  • Gs: stimulatory G-protein
  • Heterotrimeric protein: a protein made up of 3 different subunits
  • Phosphodiesterase: an enzyme that breaks a phosphodiester bond
  • Phospholamban: a 52-amino acid integral membrane protein that regulates the Ca2+ pump in cardiac muscle and skeletal muscle cells
  • Phosphorylate: to cause (an organic compound) to take up or combine with phosphoric acid or a phosphorus-containing group
  • Protein isoform: A protein that has the same function as another protein but which is encoded by a different gene and may have small differences in its sequence
  • Sarcoplasmic reticulum: a system of membrane-bound tubules that surrounds muscle fibrils, releasing calcium ions during contraction and absorbing them during relaxation
  • Synthesis: a combination of two or more entities that together form something new

PLEASE NOTE: I'm not exactly sure of which terms I added, but as far as I recall, I added about 12 or 13 terms.


''Here's what I'm currently working on''

Still to edit!!


The activated βAR is phosphorylated resulting in binding of β-arrestin that physically interdicts further G protein coupling leading to receptor desensitization. The phosphorylated βAR is internalized and undergoes resensitization by dephosphorylation mediated by protein phosphatase 2A in the early endosomes. Desensitization and resensitization are two sides of the same coin maintaining the homeostatic functioning of the receptor.

PKA or PKC whether activated as a consequence of βAR stimulation (homologous desensitization) or via other GPCRs (heterologous desensitization) can phosphorylate βARs to reduce G protein coupling.18 Differential regulation indicates that GRKs mediate phosphorylation of agonist occupied βAR while PKA/PKC can phosphorylate βARs independent of their occupancy or activity status.

Phosphorylation of agonist occupied βARs by GRKs results in recruitment of β-arrestin to the receptor complex.

Recruitment of β-arrestin to agonist occupied βAR following GRK phosphorylation not only sterically hinders G protein coupling but also prepares the receptor toward internalization.20 In addition, β-arrestin also initiates G protein-independent signaling. 4,16 It is important to note in this context, that βAR belongs to class A family of receptors wherein recruited β-arrestin falls off the βAR complex prior to internalization.20 While, β-arrestin remains bound to the GPCRs of class B family (e.g., angiotensin II type 1A receptor) and is internalized along with the receptor into early endosomes.20 Despite the transient nature of β-arrestin interaction with βAR, it plays a critical role in linking desensitized receptors to the endocytic machinery.21 Internalized βARs are directed to recycling endosomes wherein, they are dephosphorylated and recycled back to the plasma membrane as naïve receptors ready for new stimulation (resensitized) or trafficked to lysosomes for degradation.1,21 In addition to the critical role of β-arrestin in receptor function, β-arrestin through its scaffolding function provides a platform for formation of multifunctional signaling cascades. These cascades or signalsomes can initiate a variety of cellular responses

[10]

Lab 8

--Z3333865 14:23, 3 May 2012 (EST)

Mammalian cell line:

ATCC number: CCL-242

Please follow this link to go to this mammalian cell line: ATCC CCL-242 Mammalian cell line GPC-16


Designation: GPC-16

This is an epithelial cell from the colon of a guinea pig. It is associated with colorectal adenocarcinoma.

The following article was the first paper to characterise the properties of GPC-16:


R W O'Donnell, G L Cockerell Establishment and biological properties of a guinea pig colonic adenocarcinoma cell line induced by N-methyl-N-nitrosourea. Cancer Res.: 1981, 41(6);2372-7 PubMed 7237435


Lab 9

--Mark Hill 13:30, 17 May 2012 (EST) You have not completed the peer assessment process yet. If you have made comments on each project page they need also to be pasted here today for me to include in your individual assessment.

Group 1

In the introduction the sentences can be rearranged to sound more logic and to make it easier to read.

Please provide copyright details on your picture “Testosterone structure”.

Your history is expansive and well-organised in a colourful table. This encouraged me to read it! Well done!

I found your biosynthesis section a little difficult to read. Some of the terms mentioned there should be explained in the glossary of terms. Another option would be to edit that section and make it more understandable for those who have not put the research into this topic and hence have less knowledge regarding testosterone signaling and the various elements involved.

Your picture on “Steroidogenesis” does seem relevant but please make sure you provide the copyright statement.

Regulation is well-explained and the steps are easy to follow. Just as a suggestion: maybe provide a picture showing where these organs are located in the body. But besides that well done.

The signaling pathway contains the “structure of the receptor”. You might be better of putting this near the introduction and including a schematic picture of the receptor.

The picture “binding of testosterone to an AR within a cell” is very helpful in this section. One thing to notice is that you’re only allowed to use one image from wikipedia. "Steroidogenesis" was also a wikipedia image. I would encourage you to change the binding of testosterone image – maybe make it a student-drawn image as you don’t have one yet.

The image “testosterone induced phosphorylation” has the correct information provided – including copyright - so that's great.

From normal function onwards you have a lot of information, which is excellent! However, without pictures this does make it a little less encouraging to read. Put in some images relevant to the text, for example provide a picture on prostate cancer where you explain the abnormal function.

Clinical uses looks organized and is well-written to make it understandable for the audience. The video link provided is also an excellent attribute!

Current and ongoing research contains a lot of text with insight into recent studies which were undertaken. All the information is good, however, if you could include an image this would make it more attractive for the audience to read it.

You used a good range of sources but do make sure your references are correct. In particular have a look at 20, 22, 26 and 27 as I can only see a website in the reference list.

Overall, well done. There is a lot of information regarding testosterone signaling. Please do check your spelling and grammar and take into account the copyright statement for the images. Notice that we are allowed to use only 1 wikipedia image and we are required to provide at least 1 student image. More images makes it look more attractive and would persuade the audience to read it.

Kind regards


Group 2

The introduction is short and clear. It gives a good preview of what will be discussed in the other sections. You might want to expand upon this, for example listing a few names of diseases associated with it. It might also be good to mention what VEGF actually is - a signalling protein - and provide a crystal structure image.

The images you have are relevant, however, please display them as 'thumb' so you can add a description to it on your main page. It would also be advisable to have the copyright text displayed instead of just the link. T In regards to the history: this section is well-organised in a table, which makes it easy to read.

I am a little confused when it comes to the normal function. It seems like you are focussing on the production of VEGF and what factors influence this, not on the function of VEGF in the body. All that is mentioned is that it can 'initiate a cascade of signal resulting in vasculogenesis, angiogenesis and lymphangiogenesis in cells. It is a heparin-binding glycoprotein that also promotes mitogenesis and vascular permeability in endothelial cells'. You might want to expand upon this and change the subheading to 'Normal production of VEGF and factors affecting this' or 'Production and functioning of VEGF' etc.

Signalling Pathway seems to be well-written and covers pathways when different receptors are involved. Please delete the first subheading which does not have any information to it. Also, make sure you put the picture in 'thumb' so you can add a description to it and have the copyright text there (not just the link). The table is simple and clear, which I like.

Abnormal function looks amazing! It is well set-out in the table and pictures are all relevant. Do make sure you only have 1 image from wikipedia on your page - in this section both arthritis and breast cancer are from wikipedia. It would also be advisable to list the copyright text instead of the link.

The research section looks interesting and it encourages me to read it. The pictures have the copyright statement and a thumb description, which is good. The table and other information is relevant and the many links are a plus!

Your references seem to be fine, however please put them last. With this I mean switch it around with the glossary of terms. When it comes to the glossary of terms you might want to expand upon this. Also note that you will need to provide us with at least one student image.


Group 3

The introduction is well-written. It given a really good layout of what is involved. One of my issues though is that you have not provided any references - not just this section but other parts of your project as well. Because of this, it makes me wonder how much of this is written by you as a group and how much is simply pasted from the original source and rearranged. Also, when you use abbreviations etc (like TNF), please do write out the full name first.

History is quite expansive and easy to read. A reference is provided at the end of this section, which I don't think is acceptable. I don't know which sentences came from that reference and the style of referencing is incorrect. Please improve this.

Signalling pathway: it might be an idea to use subheadings here. You list many different proteins which are involved in the signalling pathway, however you only talk about FasL (Fatty acid synthetase ligand) in more detail. It might be better if you shorten your list or give more information on the other proteins mentioned, as this seems a bit irrelevant now. The pathway itself sounds a little complex (as it would be) so I would advise you to get a simplified picture to complement your text. Adding student-drawn images would also be good. Again, the issue with references; you have all the APA style in-text citations, but please put them in as little numbers so we can see all the sources in the reference list.

The function section has a lot of information, which looks a bit boring now that I've read so much of your project without being engaged by colourful images and tables. Please provide (student-drawn) images to encourage the audience to continue reading. Sub-headings within this section will also make it easier to understand and look more attractive, eg. a subheading for 'cellular disassembly'. As we are about to start week 11, I really hope you can soon provide us with the references. At the moment it is unclear whether you plagiarised or not! Another little point to notice: the 'function' does not relate to the apoptotis function as much - it is more so the function of caspases on apoptosis. Maybe change the heading to 'Function of caspases within this signalling pathway'.

Current research has quite a lot of information to it, which is good. Also, I'm happy to finally see an image! The image has the copyright information, though please provide a description on your main page. Cardiovascular disease is mentioned, however no further information is provided so please expand upon this. The section on leukaemia was very interesting though. Please do check your spelling and provide correct citations. It might be advisable to put this information into a table, thereby explaining the disease, current research and provide a picure.

Please expand upon the glossary and references (most importantly!)


Group 4

First of all, please put down your signalling pathway as your heading. All that I can see now is the introduction - only by reading your text it becomes clear which signalling pathway you have chosen to discuss.

The introduction does not provide me with too much information as to what 'notch signalling' is. In your introduction you are supposed to give us a general overview of what you will be covering in the other sections. Most important would be to briefly mention the normal function, not solely the organs which they target. Because I did not get this information from your introduction I had a quick look at wikipedia. Now please be careful with your information! The first few sentences from the wikipedia page were very similar to what you wrote. When I looked at the reference in wikipedia and the reference you provided me with I could see that they were the same! To me this seems like you simply rearranged wikipedia text and copied their reference. I would advise you to re-write your introduction. Use wikipedia as a guideline only and give us a general (but not too general) overview of what is coming.

History looks good and is well-presented in the table. Please provide some more recent discoveries to it - I am sure some research has been done on notch signalling between 1995 and today.

The pathway sections has some good information to it, however it might make it more understandable if you put this in dotpoint form. An image/student-drawn image would also be helpful here.

It is nice and clear which proteins and receptors are involved. I did notice that there are 3 links which 'do not exist'. The picture caught my eye, which is positive. Do make sure you have the copyright statement provided.

Normal function was very expansive and had a good layout with the use of subheadings. It seems like a lot of research has been done on this section and the majority of your references are indeed listed here. When it comes to the picture, please provide us with the correct information - title and description, reference, copyright statement, etc.

Building upon function you could now discuss abnormal function, current research etc. This has not been provided yet.

It seems like you made a good attempt to start the glossary, however you could probably expand this a little. Similarly with your references, you could use a wider range of sources to get a more holistic idea of what is involved (normal/abnormal function etc). The references you do have seem to be cited correctly.


Group 5

The introduction is clear and well-written. It gives a good overview of what will be discussed in further details throughout your project.

The history has an incredible amount of information. Credit on those who researched it all! When it comes to the picture displayed in the history section, please provide information whether or not you are classified as being an 'authorised user', as the copyright statements mentions 'Authorized users of Genes & Development may view, reproduce, or store copies of articles for the purposes of scholarly, research, educational, and individual use only'.

The mechanism of action is easy to understand and has a good amount of detail to it. The student picture in particular gives me as a reader a clear comprehension of what happens during the 'on' and 'off' state. This complements the text well. Please do note that you got inspiration for this picture from another source, hence the copyright statement will need to be provided. Your subheading on tumour cells might seem more logical in the abnormal function section, as I expect to read only the normal function in the mechanism of action.

The section on diseases looks very attractive with the table and 2 pictures. You might want to expand upon the treatment subheading - only to a minor extend though. Maybe give us some more information (if available) on what step of the abnormal signalling it affects in order to help relieve or cure the disease.

Great idea to provide the readers with the key players in the signalling pathway! However, to me it would make more sense if you were to put this section behind your history and in front of your mechanism of action. Just so that we get a general overview of what is involved before we read how they are involved. Also, some parts of the table were not visible, eg. structure of Dsh, Axin, GSK3beta, diversin. If information is unavailable then please mention this. Pictures in the table were very helpful.

Embryonic development is very important when it comes to the functioning of the WNT/beta-catenin pathway. Again, it might be good to rearrange your format - most ogical to me would be reading this section after reading about the mechanism of action and before the diseases section.

Your section on future directions seemed a bit rushed. There is no paragraph format, only dotpoints. If you are planning on listing them, then at least provide a brief statement saying what it is exactly that you are listing, eg. current research being undertaken, future research and hypotheses yet to be attempted, etc.

Your glossary seems good, although you could always expand upon that. With regards to the references I can see that a lot of research has been done. Please be aware of cite errors (eg. #63) and references which have been listed twice (eg. #74 and #75).

Overall, well done.


Group 6

First of all, it might be a good idea to put your signalling pathway as the title for your group project - at the moment you simply start with the introduction and only by reading your information do I realise you are discussing insulin.

The introduction has quite a bit of information to it. I would advise to delete your subheadings in the introduction and put everything into one paragraph. You might want to be a bit more brief with the normal and dysfunction paragraphs and simply give the reader an idea of what will be discussed later on in your project.

The structure of insulin: the picture is a good attribute, however, make sure you put it as 'thumb' with a description and provide the source details and copyright statement. You could upload an image of the active monomer for comparison (if available). I do have the feeling you could mention a little more about insulin itself - maybe mention the gene, gene location etc. At the moment this section is mainly made up by the picture.

You provided a fair amount of history and I like the links you added in as well. If you want you could put it in a colourful table, however it looks organised and is easy to read the way it is now. With some of the discoveries you might want to mention the person/team who discovered it. As you do have a section on current research, you should provide us with some history from 1998-now.

The student picture in the insulin receptor section is very helpful. Please do put is as 'thumb' with a description on your main page. Also put your student number in the copyright statement. I am not sure whether or not inspiration for this image has been taken from another source, so please make that clear. When it comes to the text in this section on the insulin receptor, you might want to expand upon that. At the moment it is very basic and does not seem to be finished. For example, provide gene information on the insulin receptor, explain its dimerisation and what dimerisation is, give us more information on the different aspects of the beta-subunit, etc.

The signalling pathway is well-covered and the picture complements your text well. Again, I would advise you to change it to 'thumb', add a description and provide a copyright statement. I can also see by the number of references that more time and effort has been put into this section.

Normal function seems to have been created by using one source only.. I would use different sources to at least check the accuracy of the information used. Within this section you could give us some more information on the regulatory mechanisms and how this assists the normal function.

There is quite a lot of information in abnormal function as well, which demonstrates more effort has been put into this section. You could provide us with a table which briefly summarises the different abnormalities. Pictures could also make it look more attractive. Please do provide references on diabetes 1 and 2. Overall, this is a good section, but it could be more engaging for the reader.

I found it very interesting to read what is currently being researched. You could provide some direct links to the specific research institutes and their current projects.

You might want to add a few more terms to your glossary as you expand upon your text. The references seem to be fine. Overall, add a little more information to your project and make it more enjoying to look at by using tables/pictures/etc.


Group 8

Introduction is brief but clear. It gives me a good general idea of what your project is all about.

The pathway section is excellent apart from the lack of referencing. The steps are very easy to follow and the student picture is an invaluable addition! Please do provide the student copyright statement for this image and make clear whether or not you used inspiration for another source - if yes, provide a reference and copyright statement for that source.

You have no information in the history section, so please add to this. I would also advise you to rearrange your sections. Here is a suggestion: intro, history, pathway, proteins (as they are involved in the pathway), normal function, abnormal function.

Normal function has quite a lot of good information. My big issue with this section is the lack of references! I don't think we have been taught all of this knowledge yet at school/uni, so you must have used other sources. Please provide them to avoid being accused of plagiarism. Another point is that pictures would make this section look more attractive, hence encouraging me to continue reading. A simplified image of leukocyte recruitment, activation and microbe killing would really help.

Abnormal function is well done with the introduction to the different LADs, and then further detail under the different subheadings. A brief and colourful table summarising LAD 1, 2 and 3 could be useful in this section. Another option is to provide the reader with pictures to engage them. Thankfully, references are provided in this section.

I mentioned before that you could put the protein section in a different location. The section itself has a lot of information and I can see the effort that has been put into this. Most of the focus seems to be related to the cell adhesion receptors themselves, not the interaction with the leukocytes. Your integrin section does not even mention leukocytes and leukocyte extravasation! Maybe focus on that a bit more. Please change the first image next to integrins to 'thumb' and provide a description below it. Copyright statement is present, as is the source. However, the second image only has a copyright statement - no source/reference is provided when looking at the image file (when I click on the image).

No information has been provided on current research, so please add to this.

You've made a good initial list with terms in your glossary, however you could expand upon this. Especially some of the abbreviations used. The references seem to be fine.


Group 9

The introduction is fairly good. Quite a number of references are used to give the reader some initial information before getting more detail. You could tailor the information a bit though, and make it more of a preview of what is coming later on.

The pathway section has good information in it. The one thing I'm not impressed iwth is the lack of references. Only one reference is provided all the way down the end of this section. I am sure you consulted sources for the other information you wrote down. Even if you did only use the one reference, you should be citing specific sentences. The picture could be enlarged slightly and it would be helpful if specific dotpoints could link the text with this image.

Receptors and Proteins do not have any information provided. Please add text to these sections.

Apart from the fact that the history should come after the introduction, it does looks really good. It is very well presented in the table and gives a good overview of what has happened over the past few decades. One minor thing: I would advise you to provide us with some of the people/teams who contributed to the specific discoveries.

Current research should probably come after abnormal function - the following order seems more logical to me: normal, abnormal, current research. You have made an attempt to start on this section, but it is nowhere near complete. Please provide some more information, eg. mention 3 current projects and future directions. Links to the institutions/projects could also be helpful.

Normal function has quite some text presented. Your use of different subheadings is good, however, please do write more than 2 lines per subheading (eg. for DNA repair). In that case it will be easier to use this information and compare it with abnormal function. Pictures would also be helpful and make the page look more attractive.

A lot of work will have to be put into the abnormal function. At the moment, there simply is not enough information. Also, the reference (- ref 63) will need to be fixed. Provide dotpoints to explain and incorporate the image.

You're well on your way with the glossary of terms, and I am sure that you will expand upon this as you add text to your project. The references will need to be checked though. Some of them are listed more than once, but nor under the same number. This is mainly towards the end of your project.

My main advise would be to add more text, and include pictures and tables to engage the reader.

Lab 10

Very interesting lab class on stem cells --Z3333865 15:41, 17 May 2012 (EST)

Lab 11

Forgot to log in and put down my signature last time.. I was present though.

--Z3333865 14:23, 31 May 2012 (EST)

Lab 12

--Z3333865 14:23, 31 May 2012 (EST)

  • Identify a current technique used in gene sequencing

Next-generation sequencing:

Next-generation micro-array sequencing has developed a lot over the past few years. There was and is a need for techniques which give us fast, inexpensive and accurate genome information. One of the main advantages of next-generation sequencing is the inexpensive production of large volumes of sequence data. Various strategies and techniques are used that involve a combination of template preparation, sequencing, alignment of the genome, methods of assembly and imaging of the product.


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

Miguel Angel Rodriguez-Milla, Isabel Mirones, Luis Mariñas-Pardo, Gustavo J Melen, Isabel Cubillo, Manuel Ramírez, Javier García-Castro Enrichment of neural-related genes in human mesenchymal stem cells from neuroblastoma patients. Int. J. Mol. Med.: 2012, 30(2);365-73 PubMed 22641458

To obtain genetic evidence about the interaction between mesenchymal stem cells (MSCs) and metastatic neuroblastoma (NB) cancer cells in bone marrow (BM), this research team isolated ΒΜ-derived MSCs from children with NB and compared their global expression patterns with MSCs obtained from normal pediatric donors, using the Agilent 44K microarrays.


  • What aspect of the research findings were contributed by the microarray technique
As stated by Rodriquez-Milla et al. (2012), significance analysis of microarray results with a false discovery rate (FDR) <5% identified 496 differentially expressed genes showing either a 2-fold upregulation or downregulation between both groups of samples. Comparison of gene ontology categories of differentially expressed genes revealed the upregulation of genes categorized as 'neurological system process', 'cell adhesion', 'apoptosis', 'cell surface receptor linked signal transduction', 'intrinsic to membrane' and 'extracellular region'. Among the downregulated genes, several immunology-related terms were the most abundant. These findings provide preliminary genetic evidence of the interaction between MSCs and NB cancer cells in ΒΜ as well as identify relevant biological processes potentially altered in MSCs in response to NB.
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