User:Z3411306

From CellBiology

Lab Attendance

First Lab

1. Add your signature to your own work page.

--Z3411306 15:29, 8 March 2012 (EST)


2.Add a correctly formatted internal link to your page.

Lab 1


3. Add a correctly formatted external link to your page.

JOVE


Second Lab

Lab 2

--Z3411306 14:40, 15 March 2012 (EST)

Workflow.jpg


1. Identify a reference article that uses the "superresolution" microscopy technique.

Lothar Schermelleh, Rainer Heintzmann, and Heinrich Leonhardt A guide to super-resolution fluorescence microscopy J Cell Biol 2010 190:165-175. Published July 19, 2010, doi:10.1083/jcb.201002018


2. What did the paper show that normal microscopy could not show.

The article stresses the advancement for Cell Biology that is made with the invention of the fluorescence microscopy. Since then not only the image resolution but also the possibility to follow complexes in the size range of macromolecules like tens or hundreds nm or the customized illumination due to fluorescence opened new possibilities. Moreover the technical development allowes to follow subcellular structures and win new insights.

Third Lab

--Z3411306 15:29, 22 March 2012 (EST)

1. Locate a current SDS for one of the fixatives described in today's lab. Identify the properties and hazards associated with that chemical.

SDS Formaldehyd

Properties:

Appearance: colorless gas

Molar mass: 30,3 g mol^-1

Density: 0, 8153 g/cm^3 (-20 °C)

Boiling point: -19 °C

Melting point: -92 °C

Solubility in water: 400g dm^-3

Log P: 0,350


Hazards:

Potential Acute Health Effects

Potential Chronic Health Effects


2. Identify 4 papers required for your group work project. Cite on the Group Project discussion page and also on your own Individual page. Add one sentence for each as too why they are relevant to your group topic.


[1] Wayne Stallaert, Jonas F Dorn, Emma van der Westhuizen, Martin Audet, Michel Bouvier Impedance responses reveal β₂-adrenergic receptor signaling pluridimensionality and allow classification of ligands with distinct signaling profiles. PLoS ONE: 2012, 7(1);e29420 PubMed 22242170

This paper provides a good overview about G protein-coupled receptors.


[2] Nina Wettschureck, Stefan Offermanns Mammalian G proteins and their cell type specific functions. Physiol. Rev.: 2005, 85(4);1159-204 PubMed 16183910

This paper shows an overview about the functions that G protein-coupled receptors fulfill, for example modulation of synaptic transmission, hormone release and actions, regulation of cell contraction and migration,cell growth and differentiation.


[3] Steven M Foord, Tom I Bonner, Richard R Neubig, Edward M Rosser, Jean-Phillipe Pin, Anthony P Davenport, Michael Spedding, Anthony J Harmar International Union of Pharmacology. XLVI. G protein-coupled receptor list. Pharmacol. Rev.: 2005, 57(2);279-88 PubMed 15914470

This paper gives information about diseases in relation with GCPb receptors.


[4] Johan Duchene, Joost P Schanstra, Christiane Pecher, Anne Pizard, Christiane Susini, Jean-Pierre Esteve, Jean-Loup Bascands, Jean-Pierre Girolami A novel protein-protein interaction between a G protein-coupled receptor and the phosphatase SHP-2 is involved in bradykinin-induced inhibition of cell proliferation. J. Biol. Chem.: 2002, 277(43);40375-83 PubMed 12177051

This paper provides information about interactions between G protein-coupled receptors and other enzymes. It is important to get an overview about the different influences and interactions between GPCR and other factors.


Fourth Lab

--Z3411306 14:04, 29 March 2012 (EST


Musashi is a real protein that is expressed in nervous system of zebrafish. 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


It is a stem cell marker and is involved in cell division. The human Musashi homolog is a 362 aa protein. [[5]] It was first discovered in 1998.[[6]]


Primary Antibody to Musashi: Anti-Musashi 1

Clonality: polyclonal to Musashi 1

raised in rabbit

Cross reactivity: Mouse, Human

Isotype: IgG

Tested Applications: ICC/IF, WB

concentration: 100 µg at 1-1.4mg/ml [[7]]


Secondary Antibody:

Goat anti-rabbit Alexa Fluor 488

Incubation for Western Blots: Dilution 1/200; at 4 degrees Celsius gentle shaking over night [[8]]

Fifth lab

Add a picture to group's page.


Sixth lab

Seventh lab

My task in our project is to care about the introduction. I wrote a text about the GPCR in general. In future I will contribute to the table that C. put in, I will fill the introduction with more details to give a greater overview and I will draw a picture to visualize the page. I copied the introduction here:

Introduction

GPCR process.

G protein is the short form for guanine nucleotide protein. It is involved in physiological effects such as signal transfer.

The signal transfer takes place between a receptor and a second messenger system.

A receptor is a protein that has the ability to bind certain particles due to its special binding side and starts a process of signal transfer inside of the cell.

The second messenger system is a substance in the cell whose concentration is changed depending of the primary messenger, the above described process. It forwards a signal within the cell.


source picture


GPCR

GPCR is short term for G-protein coupled receptor. It is the biggest and most diverse group of membrane proteins. The main function of GPCR is to forward signals from GTP-binding proteins into the cell.

It plays a big role in inflammation processes, cell movement, and transport of particles through the membrane or cell growth and differentiation. Moreover it handles with attractions and completes the final structure of hormones and therefore their later impact.

An activated G-protein coupled receptor affects by introducing the breakup between α and βγ subunit. This takes place because the α-subunit becomes stimulated by the heterotrim G-protein to change GDP against GTP. These subunits will transmit signals then.

--Z3411306 21:57, 14 April 2012 (EST) Wayne Stallaert, Jonas F Dorn, Emma van der Westhuizen, Martin Audet, Michel Bouvier Impedance responses reveal β₂-adrenergic receptor signaling pluridimensionality and allow classification of ligands with distinct signaling profiles. PLoS ONE: 2012, 7(1);e29420 PubMed 22242170


Adrenoceptors
Adrenoceptors


Adrenergic receptors within the human body
--Z3333208 19:36, 30 April 2012 (EST)





V can u add some information here! thanks






(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))



Eihgth lab

--Z3411306 14:15, 3 May 2012 (EST)


Identify a cell line from the ATCC which was derived from the mouse.

1. Identify a mammalian cell line in the ATCC catalogue (and add a link)

/ ATCC cell line

Designations: M-MSV-BALB/3T3


2. Identify the original tissue of origin of that cell line.


ATCC® Number: CCL-163.2™ Price: $551.00 (for-profit list price) $459.17 (non-profit list price)


See New Benefits of ATCC Culture Designations: M-MSV-BALB/3T3 Depositors: S Aaronson Biosafety Level: 1 Shipped: frozen Medium & Serum: See Propagation Growth Properties: adherent Organism: Mus musculus Morphology: fibroblast

Source: Organ: embryo

Strain: BALB/c

Cell Type: fibroblastMoloney murine sarcoma virus (Mo-MSV) transformed

Permits/Forms: In addition to the MTA mentioned above, other ATCC and/or regulatory permits may be required for the transfer of this ATCC material. Anyone purchasing ATCC material is ultimately responsible for obtaining the permits. Tumorigenic: Yes

Antigen Expression: H-2d

Age: 14 to 17 day gestation embryo

Comments: Do not produce M-MSV. Derived from BALB/3T3 (CCL-163).

Propagation: ATCC complete growth medium: Dulbecco's modified Eagle's medium, 90%; bovine calf serum, 10%

Temperature: 37.0°C

Subculturing: Protocol: Remove medium, add fresh 0.1% trypsin for 3 to 5 minutes, remove trypsin and let the culture stand at room temperature for 10 to 20 minutes. Add fresh medium, aspirate and dispense into new flasks. Subculture every 5 to 7 days.

Subcultivation Ratio: A subcultivation ratio of 1:4 to 1:10 is recommended

Medium Renewal: Every 2 to 3 days

Related Products: parental cell line:ATCC CCL-163


3. Identify the original paper that characterised the properties of that cell line.

References: 22253: Aaronson SA, Rowe SP. Nonproducer clones of murine sarcoma virus transformed BALB-3T3 cells. Virology 42: 9-19, 1970. PubMed: 4318987

Ninth lab

--Z3411306 14:11, 10 May 2012 (EST)


Group 1:

The first sentences you have, they start all almost the same. Moreover I can’t really find copyright for the picture. You should work on the references in the introduction part, too. I liked the colorful table in the History part but I think it would be better to lighten the dark purple, so that it’s easier to read the letters. To illustrate the History part it might also be nice, to insert some pictures. To the Biosynthesis part I might refer to my critic from the introduction: also here most of the sentences have the same beginning “this”. You should correct that, because then it is more exciting to read as when it starts always same. The part “Non-clinical pathway” contains information about studies, which could either occur into another part “further research” or brought more into context; you mention different studies or points of research throughout also in other parts- I would prefer reading about all them in one part then every time a little. Furthermore, you should improve the part “normal function”: here are sentences that are not yet finished. In the second paragraph, you should correct the capital letters after punctuation and leave a space in between them! However, I like how you built up this part from a baby to a grown-up. Throughout your page you mention, that Testosterone affects women and men but then you only relate to men. In my eyes, you should either at least mention how it concerns women or leave it out. By mentioning it multiple times the reader becomes curious, by not giving explanations then the reader becomes disappointed. Another point is that you refer to articles and studies in your research part but you do not name them. I think you should mention it once and correspond to it afterwards, to make it easier to follow. All in all I think your group should over read the whole page themselves. There are a couple of little things that can be made better by rereading it. There are a lot of repetitions in words or structuring which are pretty obvious when you put in a little effort.

Group 2:

You could define better in the introduction what vascular endothial is and why it is dependent on growth factors. I think the introduction could be made more interesting and a little more detailed. It is important not to mention too many details but you should provide the reader at least with an great overview about the topic. The History part could be illustrated with some pictures. Also, there are punctuation mistakes throughout. Especially the part about Oncogenes should either be explained better and/or illustrated with the help of a picture. The Hormones part is not yet ready and should be formulated. Although I would try to avoid question marks on your page because it stresses insecurity from your site about your own theme- which let it look unprofessional. Further, I don’t understand why you have subheadings when you don’t use them (“Vascular Endothelial Growth Factor”). I do like the idea with the table in the part Vascular Endothelial Growth Factor Receptors but I think when you say “induces other factors” at the first effect, you should give examples or name some. In the part “VEGFR-3” you should maybe explain how it works and why it is important. The part about the receptors is very confusing from my point of view. I suggest, you should correct the structure. The table that lists diseases gives a good overview. Nevertheless, there are some parts which would fit better into “further research”.


Group 3:

In your introduction, the first thing that I realized was that you named the combination of genes “wonderful”. In my eyes it is not very scientific to give your opinion about anything on a theme like this. I liked that you give an overview in the introduction about what you deal with and concentrate on, but it is a page and not a “paper”. In the last sentence of the first paragraph it is said, that relevant literature indicates to concentrate on extrinsic and intrinsic pathways and not anything else. I think you should try to formulate this in another way because there might be people who research on stuff that you name to be not important although you say that “relevant literature” indicates it, there might be another opinion on that. Either I would just say on what you concentrated for any reasons or not mention the other fields of research. Since you do not yet have a glossary it is hard to understand various shortening that you used throughout your whole page. From my point of view, especially in the last part of the history, it is very difficult to follow you with all these short termini. There are also four question marks behind a word in the Introduction- that’s a no-go! You should be expert on your field, you should be able to answer questions and you should not show your insecurity already in your introduction- Readers might stop following from this point because they don’t take you serious anymore. In the History part you mention a couple of papers and reviews; when they are so important that they occur in your list of historic events, I guess you should give the name of them. The sentence you wrote in the part of “1972” concerning inflammation does not make sense to me. There is no final dot after the sentence from 1991. The last paragraph contains a lot of repetitions. It would be easier if you would list all of the events together instead of trying to separate them. In the next part you mention different enzymes; I do not understand why they are mentioned under the headline “Signaling pathway”. Also the signaling pathway is not obvious for me at all. Maybe you should insert a table and describe where the enzymes appear to give an overview. Just listing 15 enzymes leads to confusion. The Fas-Mediated Apoptosis part is very confusing. I propose, that you read all over this part again. Also you could take use of a graph or flow-chart to make it easier to follow. Especially all the short forms make it even harder to understand, in the last paragraph. Another point is, that references should not appear behind the text but under the part “references” where they connect your text with the detailed source. Under the part “Function” there are quotation marks. They only do appear once, so is it a quote? Is it copied? What does that mean? Later you make new paragraphs for each sentence- why? I, as a reader, would prefer to follow a fluent text or at least see the concept why it is better to have single paragraphs. There are unformed bullet points, the letters in the beginning of the sentences are not capitalized- it is really a mess!!! Also, you mention throughout your page, that some parts of your theme are not yet well understood. By the time I read it the third time, I knew it! I think you should try to over correct your whole page. To me it looks like everyone did his own little work without connection, thus, there are so many repetitions and no relation between the single parts. Later, there are again plenty of reference mistakes or you name the third example “one example of current research”. To me it looks like as if you got different information from different sources and just used them but did not bring them into context with each other. It is really hard to understand what you want to say. To put it in a nutshell, for the reader it is confusing, difficult and boring to read this page. For the future, you should try to get a better overview. Better less but better structured!


Group 4:

First of all, you should start your page with a headline: What is your theme? After reading the introduction, I have still no idea about what you are doing. In the History part you could use some pictures to illustrate your page. All in all, I really like your page. It is structured and well written.

Group 5:

Introducing your theme with a picture is a good idea! It creates curiosity for the reader and makes him reading more. I do not understand why you have a picture of the overall structure in your history part. Nevertheless, the History part is very nice. You just mention the most important events and do not overload the reader with too much. It is easy to follow- good! I also like the self made picture a lot! What I do not really understand are the bullet points below the picture. Maybe you should either bring them in context or make them into a text format. The table about the key players in signaling is a nice idea. I do think that you should try something new, because due to the big pictures, the last column is very tiny and it is annoying to read only one or two words in one line. Some of your references repeat- you should bring that to perfection. But all in all, I really like your page- I think it is the best so far.

Group 6:

First of all, you should start your page with a headline about what your project is about. I do not really understand your concept giving each part a new introduction. I would like to get a better overview in the first introduction instead of everywhere a little bit. I think I would prefer some pictures and maybe a greater overview about the single parts. There are some spelling mistakes in your page too. It seems like you mention different things multiple times a little. You should try to avoid repetitions but bring your information into a flowing. In the part “Current Research” you mention Research Institutes but maybe you should specify where it is. Later on your page, you refer to an article about Diabetes, Insulin and Cancer- if you stress it like that, I would be interested to know the name and have the possibility to read through it.


Group 8:

In your History I would suggest to make a colon after function. In the introduction there are different sentences that I cannot understand from their logic. The third sentence has two verbs after each other, and is written in an unscientific way- people who read your page about leukocyte extravasations are probably not interested in the fact how wounds come into being; either on the playground or in a traffic accident. Moreover you should work on the space gaps between words and punctuations throughout the whole page. There are plenty of word repetitions (“recruit”, “recruitment”, “activated”, “sense” etc.) which cause irritation. Summarizing the first part, I ask myself if this work is written on a phone or in a five minute break. It contains many spelling, punctuation, and tenor mistakes. The text for Selectins could be better understood, when you superscripted the picture. Then there would be a connection between both, text and image which in turn would be easier for the reader to follow. All in all, your group should work on references (especially there is a gap for reference 5), and reread the whole page for repetitions and tenor mistakes.


Group 9:

From the first point of view, you table of content looks different, compared to other groups. You should maybe try to get the number 1 in front of p53 away. Then, I think your sentence in the third paragraph of the Introduction, which is over 4 lines, is a little too long and could be cut into smaller pieces. I don’t understand why you write some Headings all capitalized out of sudden. Although it looks good, it does not give your page a red line. Also, there are a lot of repetitions and shortenings which make it confusing for the reader to follow. The way you are referencing is not obvious. The themes Receptors, Proteins and History need still to work on.

--Z3411306 00:15, 17 May 2012 (EST)


--Mark Hill 13:30, 17 May 2012 (EST) You have made a peer assessment for each project, these are brief but specific in their assessment of content. You may in future consider structuring your assessment so that it can be easily reviewed by each group and including some +/- critical assessments. I appreciate the formatting comments, in terms of clarity of expression, but analysis of the scientific content is generally more useful.


Tenth lab

--Z3411306 14:09, 17 May 2012 (EST)

Eleventh lab

--Z3411306 14:05, 24 May 2012 (EST)

Twelfth lab

--Z3411306 14:06, 31 May 2012 (EST)


Microarray

1. Identify a current technique used in gene sequencing.

"Next generation sequencing"


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

Paul M Ruegger, Elizabeth Bent, Wei Li, Daniel R Jeske, Xinping Cui, Jonathan Braun, Tao Jiang, James Borneman Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technology. J. Microbiol. Methods: 2012, 90(3);235-40 PubMed 22640891


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

The aspect of the research finding in the above mentioned paper by microarray technique is that through improvements it is able to fingerprint oligonucleotide of rRNA genes (OFRG). This is achieved by implementing polony microarray technology, which analyizes the microbial community composition. This technique contains certain aspects that amends it from other techniques.