User:Z5050801

From CellBiology

Joao Pedro Louzada Jaccottet

JP

Lab Attendance

--Z5050801 (talk) 16:34, 12 March 2015 (EST)

--Z5050801 (talk) 17:09, 19 March 2015 (EST)

--Z5050801 (talk) 16:08, 26 March 2015 (EST)

--Z5050801 (talk) 16:13, 2 April 2015 (EST)

--Z5050801 (talk) 16:15, 16 April 2015 (EST)

--Z5050801 (talk) 17:36, 23 April 2015 (EST)

--Z5050801 (talk) 16:43, 30 April 2015 (EST)

--Z5050801 (talk) 17:13, 7 May 2015 (EST)

--Z5050801 (talk) 16:12, 14 May 2015 (EST)

--Z5050801 (talk) 17:47, 21 May 2015 (EST)

--Z5050801 (talk) 17:01, 28 May 2015 (EST)

--Z5050801 (talk) 16:09, 4 June 2015 (EST)


--Mark Hill Thank you for maintaining your attendance record for this course.


http://www.ncbi.nlm.nih.gov/pubmed

Test page


Cells_Eukaryotes_and_Prokaryotes

PMID 25513760

<pubmed>25513760</pubmed>

Lab

Lab 1 Individual Assessment

Comparative transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803.png


Comparative Transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 Provide Insights into Mechanisms of Stress Acclimation[1]


Reference

  1. <pubmed>25340743</pubmed>

<pubmed>25340743</pubmed>

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.


Lab 2

Lab 2 - Image Referencing

Comparative transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803.png

Comparative Transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 Provide Insights into Mechanisms of Stress Acclimation[1]


Reference

  1. <pubmed>25340743</pubmed>


Lab 2 Individual Assessment

The referenced paper reveals the localization of STAT1 during the cell cycle. STATs, signal transducers and activators of transcription, are a group of factors that acts over the gene expression by transducing the signal given by citocines and other extracellular stimuli. The cellular localization of this factor and it`s nuclear traffic has an intrinsic relationship with the gene expression during the cell cycle - more specifically, during the interphase. The past studies about STATs, regarding their structure, signaling pathway used crystallology, biochemistry, immunofluorescence, and others methods. Nowadays, with the advent of the super-resolution fluorescence microscopy, the structure of the STATs can be better understood, as this method is able to generate images with lateral resolutions in the tens of nanometers range - much more accurate than the previous methods. Watching the cellular localization and the nuclear traffic of STAT1 can help us to elucidate more accurately it`s funcitons during the cell cycle.

The authors found, using the super-resolution super-resolution fluorescence microscopy, that the STAT1 distribution and expression is increased from G1 to G2 phase, and, then, is largely diminished during the mitosis. Furthermore, they found that EGF (epidermal growth factor) makes the amount of STAT1 increase. The EGF stimulation also promotes nuclear import of STAT1, which forms clusters in this part of the cell. The cluster amount during the S and G2 phases in the nucleus is higher than in the cytoplasm, without the EGF stimulation. Hence, the authors believes that STAT1 can form clusters of different sizes and different amounts during the cell cycle, and the cellular localization and distribution of STAT1 probably relates to the cell cycle. The authors also believes that this paper could be a first step in the development of specific therapies to STAT-triggered diseases. ==


References

<pubmed>25762114</pubmed>

Lab 3

Reference searching

Search term: Fibronectin


Recent PubMed articles:

<pubmed limit=5>Fibronectin</pubmed>


Material Safety Data Sheet for Formaldehyde

Lab 3 Individual Assessment

The referenced paper brings a technique to improve protein stability, wich leads to a better understanding of it's structure. This paper is important to our group topic because it increases the knowledge of the molecular mechanisms that govern stability and demonstrate the rising potential for enhancing stability via the consensus method, which could be obviously applicated to fibronectin. The structure of fibronectin 3 reveals significantly increased salt bridge interactions that are cooperatively networked, and a highly optimized hydrophobic core. Molecular dynamics simulations of FN3con and comparison structures show the cooperative power of electrostatic and hydrophobic networks in improving FN3con stability. Taken together, our data reveal that FN3con stability does not result from a single mechanism, but rather the combination of several features and the removal of non-conserved, unfavorable interactions


The second referenced paper shows that mechanical stretching of normal tissue-associated fibroblasts (NAFs) alters the structure of secreted fibronectin. This way it leads us to a much better understanding of the many functions of fibronectin, one of the most relevant proteins of the extracellular matrix. Results show that mechanical stretching of normal tissue-associated fibroblasts alters the structure of secreted fibronectin. Specifically, unstretched this tissue-associated fibroblasts deposit and assemble fibronectin in a random, mesh-like arrangement, while stretched tissue-associated fibroblasts produce matrix with a more organized, linearly aligned structure. Moreover, the stretched tissue-associated fibroblasts exhibited an enhanced capability for directing co-cultured cancer cell migration in a persistent manner. This also increases theproduction and liberation of PDGFRalpha. The comparison between stretched tissue-associated fibroblasts leads to the conclusion that they are very similar to cancer-associated fibroblasts. Hence, is licit to conclude that the mechanical stress is a critical factor in the activation of tissue-associated fibroblasts and it´s transformation into cancer-associated fibroblasts.


The third referenced article brings us a molecular target for therapeutics of hepatocellular carcinoma, which leads us to a better understanding of the role that fibronectin plays in this severe disease. The article states that ROBO1, fibronectin Type-III domain (Fn)-containing protein is a target for specific therapeutics. A monoclonal antibody, called B2212A, binds the third Fn (fibronectin) domain (Fn3) of ROBO1. The results of the study, according to the article´s text, promises to lead future researches towards a new antibody drug for the treatment of hepatocellular carcinoma.


The fourth referenced article presents a description offibronectin adsorption and adhesion to cells on poly(ethyl acrylate) (PEA) and poly(methyl acrylate) (PMA), two polymers with very similar physicochemical properties and chemical structure.The difference between this two polymers resides only in a single methyl group on the lateral chain. This paper also leads to a better understanding of the structure and function of the fibronectin.


References


<pubmed>25691761</pubmed>


<pubmed>25660754</pubmed>


<pubmed>25492858</pubmed>


<pubmed>25469314</pubmed>


Image

The complex of ROBO1 Fn3-B2212A Fab as determined by X-ray crystallographic analysis.jpg


<pubmed>25492858</pubmed>


Copyright © 2014 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society

This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Lab 4

Lab 5

Tm4.png

Lab 6

Lab 6 Individual Assessment

About the following article: <pubmed>25492858</pubmed>

1) Identify an antibody that can been used in your group's extracellular matrix project: B2212A

2) Identify the species deriving the antibody: mice

3) Identify the working concentration for the antibody: 5 mg/mL

4) Identify a secondary antibody that could be used with this antibody: anti-ROBO1 MAb

5) Identify a paper that has used this antibody: <pubmed>25006547</pubmed>


Lab 8

ATCC

Mouse cell line


Human Ccell line

Culture Medium: ATCC-formulated Dulbecco's Modified Eagle's Medium

Content of Media


ECACC

Human cell line

Culture Medium: EMEM (EBSS) + 2mM Glutamine + 15ug/ml Bromo-deoxy Uridine (BUdR) + 1% Non Essential Amino Acids (NEAA) + 10% Foetal Bovine Serum (FBS)

Mouse cell line

Antibiotics

Penicilin and Streptomicin


Groups Peer Review

Group 1 Peer Review: Hello, dear classmates!! I really liked your project!! There is a lot of information about the Small Leucine-Rich Proteoglycans, which can lead the reader to a good understanding about this molecule. The history part is very good, it follows a logical and chronological sequence which leads the reader to a very good understanding about how the Small Leucine-Rich Proteoglycans were discovered and how humanity reached today´s knowledge about this molecule. The Function and Structure parts are also clear, logical and easy to understand.

Despite being an excellent project, I think it would be great if you guys improved the introduction part: for me it does not seem very clear what a Proteoglycan, and improving the introduction will certainly lead to a much better understanding about the following topics. Furthermore, the Synthesis part it is not very clear, I could not have a good understanding about how the molecule it is produced. In this part, however, I think you guys should only rewrite the text, because it seems that you have enough information.

The following parts are very clear and the information provided is much more than enough to satisfy a curious reader. Also, I have to say that the page is very good looking, which attracts even more the reader´s attention.

Congratulations for your effort, if you guys correct the very few things that are not very good in your project, it will be undoubtedly an excellent one! Cheers!


Group 2 Peer Review: In general, your project looks very good, congratulations! It has not only good and beautiful images, but also a clear and comprehensive text. The organization and the appearance of the page are also pretty good!

The introduction is very clear, comprehensive and concise, which helps the reader to understand the following parts. The history section, however, seems to lack information, because it only says how the integrins were discovered, but it does not say what happened later. The diagram that shows how integrins relates to other proteins is very good and clear, and it shows that the one who draw it has potential to be an artist.

The structure part is very good, but the text in this section starts with information that should be present in other sections, such as introduction and function. Anyway, this section has a clear and rich text, and the images provided helps a lot in the understanding of the integrin’s structure.

The remaining parts look pretty good, but I think you guys should improve the look of the disease section: maybe putting some images there would be a very good thing to do. And the idea of putting a glossary at the end shows that you guys are interested in creating a clear and understandable project. Cheers!!!


Group 3 Peer Review: The project is amazing, guys, really!! The content is very rich, the text is clear. The images shown are good and helps a lot in the understanding of the content.

I cannot say that I found problems in what you guys have written… The only I can say is that a section with history would be an interest thing to add on the page. Furthermore, the section about clinical diseases could have more images, because the great amount of text makes the reading tiring. However, if the reader finds enough energy to go through this section, he or she will have plenty of information about the diseases involved with the elastic fibres. A section about current and future researches would also be great. Despite these little problems, the page is very good, I would give you high marks if I could! Congratulations, keep on!


Group 5 Peer Review: Guys, your project is pretty good. You have found a lot of information. However, there should be a lot of improvements regarding organization. The great amount of information you found – or tried to find – was not well structured in the page, which leads to an incomplete understanding about laminin. For example, talking about the function of the many laminins individually gave a messy look to the page. The introduction part seems to contain information that was repeated in other sections. I think you guys should improve this section, which is one of the most relevants, in my humble opinion. Furthermore, the idea of putting the references right after each section made the page look ugly, and it also like ‘’breaks’’ the flow of the page. The structure and the history part are very good! I would not change anything in these parts, as the text is comprehensive and rich. The abnormalities part should have more pictures, the great amount of text makes the reading tiring and hard, although the good information provided. But the biggest problem resides on the function part: what about trying to reduce the amount on ‘’laminins’’ to focus on the most relevant ones? I know you guys want to provide as much information as possible, but it can lead you to confusion sometimes.


Group 6 Peer Review: Hey, dear classmates! I see that your project has a lot of potential: this potential, however, should be explored. There is a serious lack of information in many topics has absolutely nothing written. There is no introduction for now, what makes the understanding of the subsequent headings pretty hard. Imagine if a reader with no biological background was to read your page? He would be completely lost. There is also a serious lack of information in the abnormalities section: in the sub-heading about rheumatoid arthritis, a disease that is so common, there is no more than a loose sentence, for instance. Hence, you guys should improve this section as well.

But let´s talk about what you have, as it is useless to talk about what is missing: the biosynthesis part is pretty good, there is enough information to understand how the process works and the text is clear. An image with the biosynthesis pathway would be excellent, if you guys can find it. In the function part, there are some loose sentences that makes the text a little bit confusing. The section about current understanding and ongoing researches is pretty good! You guys could show that there is many field to be discovered by these researches.

I am really sorry about what I just wrote. I did it because I wish that you do a great project in order to have very good marks. I believe you guys will have an excellent project if you work on this project! Keep going!!


Group 7 Peer review: Excellent project, guys!! I swear I did my best to find defects, your project is simply amazing. Very good looking, much more than enough information, excellent organization.

The introduction part truly introduces – many projects did not ´´introduce´´ appropriately the content in this section – what makes the understanding of the following parts pretty easy. The history section is very concise, but I know you guys have much to add. The ‘’formation, plasticity and regeneration´´ section has a rich and clear text, as well as a pretty good image. This part could be left like this. The idea of adding a ´´functional layers´´ heading was great, it makes the reader understand that the basement membrane is heterogeneous. The remaining parts are also very very good: I can´t find bad things to say.

Finally, the only thing I have tell you is that you should improve the history section. Besides that, the project is simply excellent! Congratulations!!!