From CellBiology

Lab Attendance

Lab 1: 12th March I was there but I wasn't connected with Wiki.

Lab 2: --Z5050795 (talk) 16:54, 19 March 2015 (EST)

Lab 3: --Z5050795 (talk) 16:06, 26 March 2015 (EST)

Lab 4: A

Lab 5: --Z5050795 (talk) 16:06, 16 April 2015 (EST)

Lab 6: --Z5050795 (talk) 16:32, 23 April 2015 (EST)

Lab 7: A

Lab 8: --Z5050795 (talk) 15:59, 7 May 2015 (EST)

Lab 9: --Z5050795 (talk) 16:17, 14 May 2015 (EST)

Lab 10: --Z5050795 (talk) 16:04, 21 May 2015 (EST)

Lab 11: --Z5050795 (talk) 16:24, 28 May 2015 (EST)

Lab 12: --Z5050795 (talk) 16:06, 4 June 2015 (EST)

Individual Assessments

Lab 1

Respiration of intracellular nitrate.jpeg

Respiration of stored intracellular nitrate by eukaryotes and prokaryotes. Pone.0104517.g005.jpg

The Fate of Nitrate in Intertidal Permeable Sediments

Marchant HK, Lavik G, Holtappels M, Kuypers MMM. The Fate of Nitrate in Intertidal Permeable Sediments. Vopel KC, ed. PLoS ONE. 2014;9(8):e104517. doi:10.1371/journal.pone.0104517.


Copyright notice This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Lab 2 - Image Referencing

Respiration of intracellular nitrate.jpeg

Respiration of stored intracellular nitrate by eukaryotes and prokaryotes [1]


  1. <pubmed>4134218</pubmed>

Lab 2 - Article Referencing

The article talks about the membrane budding process and also its components focusing on this process at HIV cells. Some HIV cells can hijack some structures such as ESCRT, which is the cellular endosomal sorting complex required for transport, to maintain the virus survival. As we all know, these cells interact with various host cell factors to achieve its functional purpose and there's a lot of microstructures that contribute to the virus-host membrane fission. Some of them were already seen, an example is the various geometries of ESCRT-III (multimer protein connected to the membrane, presumed to be the central driving force for membrane remodeling during fission process), but the mechanisms of membrane constriction and fission are not fully understood. There's where the super-resolution fluorescence microscopy appeard to help. The size and structure of some components involved in the cell interaction and process to fission were elucidated. Their measured size and localization of endogenous ESCRT and also the HIV assembly sites and they concluded that the membrane scission process is directed by these proteins. The study used super-resolution florescence microscopy to measure sizes and also relations between components, using the antibodies for immunodetection.

Super-Resolution Imaging of ESCRT-Proteins at HIV-1 Assembly Sites [1]

Copyright notice This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited


  1. <pubmed>4339578</pubmed>

Lab 3

Commercial Example: Paraformaldehyde

Lab 3 - Searching References

Search term: Collagen

<pubmed limit=5>Collagen</pubmed>

BioMed Central

Lab 3 - Assesment

Collagen type II: Structure

Article One: The authors of this article were studyind the relation with cancer progression and collagen disposition in the extracellular matrix. For this, they built a 3D computational model of collagen network to study the mechanic properties of a single molecule and also fibrils and fibers. They review the tripe-helix strucutre briefly and focus on the collagen gel (collagen fibers, interconnected into a three-dimensional fiber network), measuring the distance between the cross-link interactions, the density of fibers and creating models to vary the fibers geometry and see the dinamics alterations. They found that the network geometry is a determinant key in the mechanical properties of the fiber, even more significant than the density. The stiffer and denser crosslinkers increase the mechanical stiffness of the whole network and stress can be acumulated along fibers, which is an ideia to the collagen aligment that occurs in tumor progressions.


Article two: This article links chemical properties of individual tropocollagen molecule (length) and strenght of intermolecular attractions to macroscopic mechanical response of fibril. They studied deformation in two scales to see when it changes from homogeneous intermolecular shear to propagation of slip pulses and when covalent bons within tropocollagen molecules begin to fracture and one of the conclusions is that collagen's properties are scale-dependent (the strength of an individual tropocollagen molecule is different than the strength of a collagen fiber). Although the nanoscale distribution of crosslinks give additional strenght to the fibers, extremely large crosslink densities lead to negative effects.


Article three: In this study, the authors discuss how deformation can change the microstructure at the fiber scale. For this, they simulated a stretching strain to see the evolution of both the fiber and the network and verify the presence of cell-induced aligments. At low strains, no particular aligment was observed but above some levels both fiber aligment and network density increased. In uncrosslinked networks, this aligment is found to be irreversibly imprinted, however, in crosslinked networks the similar fiber aligment and the same geometrical properties are found but with full reversibility. Strain-induced alignments were known to be a combination of reversible elastic effect and irreversible inelastic effects, but now we know that it is primarily an elastic effect.


Article four: This study uses scanning transmission electron microscopic mass mapping to develop an image of the structure of collagen fibrils from embryonic cartilage. Cartilage fibrils were harvested from 14-day-old chicken embryo sterna. These samples were then prepared for examination via electron microscopy. The results demonstrated that collagen type II in conjunction with type XI formed 10+4 microfibril structures. Evidence suggested that as long as some collagen type XI was present, over expression or mutations in collagen type II did not affect the assembly of thin fibrils. It is also apparent that microfibrils that contain XI are the nucleus for the accretions of collagen type II microfibrils.




(A) Single U87 glioblastoma cell in a collagen network 10 hours after gel polymerization. bar = 50 µm. (B) Several U87 cells on the surface of a collagen gel 10 hours after gel polymerization. bar = 200 µm. (C) Two cell colonies embedded in a collagen matrix 48 hours after gel polymerization. bar = 200 µm. Fibers (artificial red color) are imaged through confocal reflectance; cell nuclei (green) are labeled with a GFP-histone heterodimer.

Collagen gel morphological changes induced by presence of cells. [1]

Copyright Vader et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


  1. <pubmed>19529768 </pubmed>

Lab 5 - Assesment

Lauras graph.jpg

Lab 6 - Assesment

MAB8887 | Anti-Collagen Type II Antibody, clone 6B3

Anti-Collagen Type II Antibody, clone 6B3 is a mouse anti-chicken monoclonal antibody against Collagen Type II for use in immunohistochemistry, immunohistochemistry & Western Blotting.

Brand Family: Chemicon®

Trade Name: Chemicon

Host: Mouse

Isotype: IgG1

Concentration: 200 μg/mL

Dudek KA1, Lafont JE, Martinez-Sanchez A, Murphy CL. "Type II collagen expression is regulated by tissue-specific miR-675 in human articular chondrocytes." J Biol Chem. 2010 Aug 6;285(32):24381-7. doi: 10.1074/jbc.M110.111328. Epub 2010 Jun 6.

Lab 9 - Assesment

Mouse Cell Line: "B6H12.2 (ATCC® HB-9771™)"

Human Cell Line: "(ATCC® CRL-11554™)"

"Dulbecco's Modified Eagle's Medium" with 4 mM L-glutamine that is modified by ATCC to contain 4.5 g/L glucose and 1.5 g/L sodium bicarbonate and supplemented with an additional 2 mM L-glutamine, 2176 ng/ml Aminopterin, 0.00978 mg/ml Thymidine, 0.0136 mg/ml Hypoxanthine, 0.025 mg/ml Mycophenolic acid, 0.250 mg/ml Xanthine and 10% dialyzed fetal bovine serum.

"Penicillin-Streptomycin, What it is?"

The antibiotics penicillin and streptomycin are used to prevent bacterial contamination of cell cultures due to their effective combined action against gram-positive and gram-negative bacteria. Penicillin was originally purified from the fungi Penicillium and acts by interfering directly with the turnover of the bacterial cell wall and indirectly by triggering the release of enzymes that further alter the cell wall. Streptomycin was originally purified from Streptomyces griseus. It acts by binding to the 30S subunit of the bacterial ribosome, leading to inhibition of protein synthesis and death in susceptible bacteria. This solution contains 10,000 units/mL of penicillin and 10,000 µg/mL of streptomycin.

Lab 10 - Assesment

Group 1 Nice work. The page is well organized, the topics are well exposed. I didn't understand some images, they seem to be ilustrative but not completely inserted on the context of the topics.. Your own draws are awsome, very good idea, very good draw. The "The role of SLRPs in disease" topic is very interesting, with a lot of usefull information and good diagrams and images. Your text is concise and informative, easy to read. Congratulations!

Group 2 Good set of images, those 3D perceptions are useful to clarify the structure. Smart initiative add one video to the project, the more interactive the more people pay attention. Maybe formatting the text of the project would be nice, more spaces between big texts and some images in the "disease" section, the texts and images are condensed maybe spread them and create a balance. I would edit the first image too, the draw is perfect but maybe some bright and contrast to make it more evident. The page is very informative and practical, congratulations!

Group 3 Very nice job! Your page is clear, concise, organized and well formatted. Your own image is outstanding, very nice draw and paint. Maybe would be a good idea to add some pictures to the "Clinical Significance" section, is nice when we have something to illustrate the problem. I also noticed that some references are missing, make sure you will fix this before the submission. Congratulations!

Group 4 The text is good, the information is well organized and good to read. The current images are big and they need to be exposed like that, but maybe add some other images to break the text flow would be nice. Maybe format que images in a way that they fit between the texts so there would not be a blank space beside the images, of necessary adjust the size of them. There's also some references missing, better fix this before the submission. Good luck and congratulations!

Group 5 Your page have a lot of information, which is good, shows that you worked hard on your searchings. I think you should format your page before the submission, put all the references in the end of the page, leave spaces between texts and organize the images. The images that were used are very good to illustrate the page, but some of them dont need to be so large, you could try to decrease its size and fix them with the text, left or right. I also see there's some information missing on the function section, but maybe is possible to summarize the information so your page won't be so long. Congratulations!

Group 7 Good work! Your page has a good balance between text and images. In the "History" section the table has a good layout but perhaps is missing some information. Maybe would be nice to add some picture in the "structure" section, but the "function" one is very complete and explanatory with a good image to illustrate. The sections to expand are very well done and your own drawn is clear and practical. Congratulations!