User:Z3459996

From CellBiology

User page for Z3459996, an otherwise anonymous and overbearingly enthusiastic ANAT3231 student. Check out our Project Page on Small Leucine-Rich Proteoglycans!

Attendance

Lab 1
--Z3459996 (talk) 16:34, 12 March 2015 (EST)
Lab 2
--Z3459996 (talk) 16:52, 19 March 2015 (EST)
Lab 3
--Z3459996 (talk) 16:08, 26 March 2015 (EST)
Lab 4
--Z3459996 (talk) 16:33, 2 April 2015 (EST)
Lab 5
--Z3459996 (talk) 16:03, 16 April 2015 (EST)
Lab 6
--Z3459996 (talk) 17:02, 23 April 2015 (EST)
Lab 7
--Z3459996 (talk) 17:14, 7 May 2015 (EST) I was here but too polite to log in to list attendance. z3459996 does not miss classes.
Lab 8
--Z3459996 (talk) 17:14, 7 May 2015 (EST)
Lab 9
--Z3459996 (talk) 16:09, 14 May 2015 (EST)
Lab 10
--Z3459996 (talk) 16:01, 21 May 2015 (EST)
Lab 11
--Z3459996 (talk) 16:08, 28 May 2015 (EST)
Lab 12
--Z3459996 (talk) 16:06, 4 June 2015 (EST)

Individual Assessments

Lab 1

C callunae SEM 001.jpg
Scanning Electron Micrograph of Corynebacterium callunae [1]

Lab 2

Spatial Covariance Reconstructive (SCORE) Super-Resolution Fluorescence Microscopy[2]

Super-resolution microscopy overcomes the physical limitation of the diffraction of the objective aperture using a variety of techniques, each with their own restrictions. For example, Stimulated Emission Depletion (STED) microscopy uses a set of techniques which may damage some biological systems, while Stochastic Optical Reconstruction microscopy (STORM) requires 1 000 to 10 000 individual images to be taken (by necessity) over a period of minutes to produce a decent final composite, thereby rendering it a poor option for live-cell imaging. In this article, the authors propose an new algorithm for super-resolution microscopy, which they call the Spatial Covariance Reconstructive (SCORE) algorithm, which can achieve a lateral resolution of 100 nm in 5 to 7 seconds of imaging.

Like STORM, SCORE combines data on the fluorescent intensity covariance of each pixel with the shape of the overlapping point spread function (PSF) data to compile a composite image representing the probability distribution of each emitter. In less technical language, a series of images of the subject is taken, the difference in light intensity between corresponding pixels in different images is measured, and the resulting data run through a set of algorithms to compensate for optical phenomena in order to "pinpoint" the source of light emission. In this case, resolution is limited not by the diffraction of the objective lens, but by the quality of the fluorescent label being used. Several comparisons between SCORE and STORM are given, and it is concluded that SCORE produce superior quality images with less noise and closer resemblance to actual structure, but maintaining a similar processing time to existing techniques. A most incredible example is shown in 2(e), where simulated data depicting a sub-diffraction ellipse is parsed using both STORM and SCORE algorithms with various volumes of data and duty cycles.

Lab 3

Article 1: Small leucine-rich proteoglycans in the vertebrae of Atlantic salmon Salmo salar.[3]

The distribution of small leucine-rich proteoglycans (SLRPs) across different tissues in various organisms other than humans is poorly-understood. This study analyses small leucine-rich proteoglycan distribution in S. salar vertebral columns. It had previously been demonstrated that decorin mRNA is present in S. salar vertebral columns, and this study established that decorin, biglycan and lumican are all present in regions of intermembranous and endochondral ossification, suggesting a role in mineralisation of bone. It was found that the developmental expression of SLRPs is similar to that of mammals, hinting at the evolutionary origin of proteoglycans as a biochemical family.

Article 2: A comparative evaluation of the small leucine-rich proteoglycans of pathological human intervertebral discs[4]

In intervertebral discs, SLRPs have multiple functions. Decorin, fibromodulin and lumican have been reported as being present in intervertebral discs. These interact with fibrillar and other collagens, fibronectan, elastin, and various growth factors. This study finds that all SLRPs in pathological intervertebral discs exhibit fragmentation to some extent, which is contrasted to the findings of an earlier study indicating little fragmentation of normal post-mortem intervertebral tissue. Only lumican was left unfragmented, indicating that it does not undergo enzymic cleavage in disc pathology as other SLRPs do. This was noted to differ from osteoarthritis, where fragmentation of lumican does occur. The reverse effect is reported for fibromodulin: there is little fragmentation in osteoarthritis, but significant fragmentation in intravertebral disc pathology. Fragmentation of different SLRPs may be used clinically in the future to determine the pathway of joint degradation, therefore improving treatment of affected individuals.

Article 3: The role of small leucine-rich proteoglycans in osteoarthritis pathogenesis[5]

As an important component of the extracellular matrix, SLRPs and the genes that encode them have been implicated in many the pathogenesis of many conditions, particularly degenerative contitions. These is emerging evidence that SLRP may play a role in osteoarthritis pathogenesis. This article proposes mechanisms by which this may occur. Some SLRPs have been implicated in differentiation of mesenchymal progenitor cells, which are important players in osteoarthritis pathogenesis. Single- and double-SLRP knockout mice have shown increased osteoarthritis biomarkers, and this is postulated to be a result of one or more of the following: changes in extracellular collagen network, TGF-β signalling, or roles in innate immune inflammation, muscle weakness, or subchondral bone.

Article 4: Lumican-derived peptides inhibit melanoma cell growth and migration[6]

Just as underexpression of SLRPs seems to have a negative effect on degenerative disease processes within the organism, so too is overexpression correlated with positive effects. Lumican in particular exhibits potent anti-tumor properties which are explored in this article. Migration of tumor cells causes progression of melanoma by tissue invasion and metastasis. This study finds that lumican decreases melanoma progression in vivo, and elucidates that it prevents migration in vitro. A complex mechanism by which this occurs is postulated in the article, which ends by proposing two mechanisms of melanoma cell migration inhibition (inhibition of phosphorylation and decrease of MMP-14 activity).

Image:

Lumicans melanoma 001.png

Figure 2: Lumcorin inhibits melanoma motility.[6] This is relevant as it not only indicates a pathology that may result from underexpression of a specific SLRP, but also because it indicates a potential therapeutic application of SLRP expression modulation.

Lab 5

Counts from the images here, compiled into a convenient graph:

B35 phenotype count 3459996.png

Lab 6

  1. Monoclonal antibody 2B6 (anti-CD73) is an anti-chondroitin sulfate antibody that targets small leucine-rich proteoglycans such as biglycan.
  2. Raised in mice (Mus musculus; BALB/c).
  3. 1/100 for Western Blotting; 1/20 for Immunohistochemistry.
  4. Anti-Mouse IgG1 VHH Single Domain Antibody (ab193651)
  5. The following article uses 2B6 antibodies: <pubmed>23801333</pubmed>

Information for this section taken from Cosmo Bio Co., Ltd.'s 2B6 listing.

Peer Reviews

Group 2

Overall, the Integrins wiki is looking quite nice. The biggest thing you need to do going forward is try to eliminate content duplication (ie stuff from one paragraph appearing again later in the page), which will be a matter of checking each other’s work.

There’s a bit of formatting stuff that needs to be cleaned up, also. For example, there’s a random sciencedirect link that I guess is meant to be part of a reference tag at the end of the first section. You also need to decide whether you place the ref tag after the full stop (as in [3]) or before (as in [2]). The timeline in the history section obviously needs some work.

The hand drawn integrins diagram is very well drawn but you really need to scan it rather than taking a photo with a phone. It looks terribly out-of-place as it is at the moment.

Overall, the fact that I need to nit-pick this so much probably means you’re doing a good job so far! Your notes indicate that you know where you need to go next – continue to work hard and you should have a good product at the end!

Group 3

In terms of content, I’m very pleased with the page. It’s not overly long (but could do with some trimming down), but all the relevant and expected information is present. There’s a little too much text, so I’d recommend replacing some of your larger concepts with a picture equivalent. For example, much of the discussion on microfibrils could be discussed with a diagram. The Clinical Significance subheading also desperately needs a picture or two. I understand that it’s probably difficult to track down a picture on the role of elastic fibres in Ebola or thrombosis, so you may have to draw it.

The biggest problem here is with readability. I really had to force myself through this because, while it was interesting, it was fairly difficult to interpret. There are widespread grammatical abnormalities that need to be addressed. These are especially prevalent in the Introduction and Structure and Components sections, but do infiltrate other sections as well. I strongly recommend you go over each other’s sections with a fine-toothed comb to try and get all the grammatical errors out, because it really affects the readability of your page.

Also, small thing: get rid of Dr Hill’s "please have something ready for the next lab" notice. You also have some empty references (23-25) – that’s probably due to an easily fixed bug in your code.

Overall, I think the wiki page is very good in terms of content, but needs some work as far as presentation goes. The only real changes that need to be made to the content is addition of more pictures and the corresponding excision of unnecessary details. Most of your focus now, however, should go into making your page as easy-to-read as possible.

Group 4

My biggest gripe with this page is the amount of text. There’s hardly any graphical augmentation or subheadings to break it up into easily readable chunks. You’re currently sitting at 2 652 words, which I think is a little excessive. Probably time to bring that number down by converting some of the larger paragraphs into easy-to-digest pictures.

The text is, however, well-written, which really reflects well on the page’s professionalism and readability. Some sentences could do with a little bit of rewording and adjusting, but that will be a matter of making sure you each read over the whole page and adjust what you feel is necessary. Having another (three) sets of eyes looking over your work can do wonders for readability.

There are some minor formatting woes that are detrimental to the presentation of the page. Make sure your ref tags are placed appropriately and consistently. You have a couple of references flanked by a full stop on both sides, and a bunch of others that don’t have a space between them and the next word. A couple of your references (16 and 17) are empty for some reason, also.

I may be coming off as overly harsh, but there’s a lot of good stuff here. I’m now halfway through the peer assessments and this is definitely the most complete and well-written wiki page I’ve looked at so far, so well done! It’s now just a matter of polishing the page up and trimming off the excess text.

Group 5

Please don’t take this the wrong way. I’m not trying to be a jerk or put you down, just provide helpful suggestions. This page needs a lot of work. There’s a lot of content on the page, but most of it could be moved to another section, shrunk in length, or eliminated entirely. For example, why is there a brief, poorly-formatted list at the end of your introduction section? It seems completely out of place.

Let’s take the Function section as an example: why is there an exhaustive list of laminins? Could you not just give a more integrated, rounded overview of what laminin function is all about? What is their basic biochemical and cellular function? Perhaps start with something like “Laminins have diverse roles in the ECM, including smooth muscle contractility, structural support of the basement membrane, melanin synthesis…” A diagram should be used to explain this, and to break up the text a little.

There are text walls everywhere that are very hard (and extremely boring) to read on a computer screen. More visual aids are required and shorter paragraphs should be used. The actual quality of writing is good (except for where sentences are incomplete), but again, efforts should be focused on reducing the overall size of the page by making everything more concise.

Formatting needs a lot of work. You definitely, definitely need to compress your references into one, easy-to-keep-track-of section. It makes comfortable navigation of your page extremely difficult. You should also get rid of Dr Hill’s comment from 16 April. It’s cluttering your page! You need to make sure your pictures are formatted properly as well. There are copyright statements and references on the page that should be nested within the page for the image itself.

There’s a lot to be done to this page. It’s simply far too long to be comfortably readable, and is currently poorly formatted. My ultimate problem with it can be summarised with the observation that the Function section has 16 subheadings beneath it. That’s not something that the average undergraduate would be comfortable reading.

Group 6

While a history section isn’t 100% necessary if you don’t get around to it, it is very important to have a captivating introduction to your topic. It is probably a good idea to leave that until you’re all but finished though, so good job planning ahead.

The biggest problem is that your page isn’t as well-developed as it should be by this stage. There are still raw journal article references and lists that need to be formatted properly, as well as headings with no content. You should also convert the glossary into a table, or at least make the headword of the entries bold.

Remember that you’re writing a wiki page, not an essay, so your aim is to communicate concepts rather than specific results. Some of the language in the “Abnormalities” section is extremely technical (which is good) and causes the reader to skip over most of the details (which is bad). Keep your target audience in mind!

Your paragraphs aren’t overwhelming in size, which is good (though some are a little long – try splitting the “Biosynthesis” paragraph at “After the glycosylation…”). They are also written fairly well. Your page almost has the best layout of any of the project pages. Small suggestion, however: change “Type II Collagen” to a title by enclosing it with 1 equals sign instead of 2:

=Type II Collagen=

Ultimately, you seem to be on the right track. You have the perfect balance of pictures and text, and the progression of the page and division into subheadings is pretty much perfect. It’s now just a matter of actually fleshing out those sections that haven’t been written yet and making sure you check each other’s work for errors.

Group 7

This is my favourite project page overall. It’s an excellent balance of text and images, the formatting is mostly good, and the expanded sections are absolutely fantastic. The style of writing is spot on – there’s enough technical detail that it’s worth reading but at the same time, it’s written in a more relaxed, easy-to-read manner than a typical essay. There are some minor gripes with wording, but if you carefully read over the whole page, that issue should be resolved.

The list of issues with the page are mostly minor, and you’re probably aware of most of them: the current research needs to be distilled into actual words rather than a list of journal articles; make sure your lists are formatted properly so that they appear as the pretty MediaWiki-style bullet lists. It makes everything look much more professional (this is most applicable to the Formation, Plasticity and Regeneration section).

The notes scattered throughout your page indicate that you know what needs to be done now. Some sections need to be expanded, your longer sections (such as Basement Membrane Functions) could be made a little more concise with the aid of diagrams, and sources need to be added in some places. Other than that, you’re definitely on the path to success!

Lab 12

The following is a research article on microarrays. Microarrays are an older technique used at the centre, and newer gene sequencing methods (next-gen long/short read) and the ~$3.5 million dollars in machines to carry out this task (excluding the bioinformatic power behind it) were focused on. Unfortunately, a pubmed search turned up 0 relevant articles for short read or long read sequencing in SLRP research.

<pubmed>22345433</pubmed>

Paraformaldehyde

MSDS (Sigma-Aldrich Australia)

Use:

Cytological preservative that functions by cross-linking proteins.

Hazards:

  • Flammable.
  • Harmful if swallowed.
  • Causes skin irritation (potentially allergic skin reaction).
  • Serious eye damage on contact.
  • Respiratory irritation.
  • Suspected to cause cancer.

Lab 9 Cell Lines

ATCC

American Type Culture Collection

Human
A101D, a melanoma cell line from a 56 year old male caucasian. To be grown in Dulbecco's Modified Eagle's Medium.
Mouse
NMuMG, epithelial cells from the mammary gland of a mouse.

ECACC

European Collection of Cell Cultures

Human
DD1076, a chorionic villus cell line from chromosome 14 a female foetus affected by cystic fibrosis. Culture medium is Ham's F10 + 20% FBS.
Mouse
10T½, fibroblast-like mouse embryonic tissue cell line.

Growth Media Components

Ham's F10 + 20% FBS

Ham's F10:

  • Various inorganic salts.
  • Essential L-amino acids.
  • Vitamins.

20% FBS means that the medium contains 20% fetal bovine serum.

Dulbeco's Modified Eagle's Medium

This is Minimal Eagle's Medium which has been modified to contain:

  • 4 mM L-glutamine
  • 4500 mg/L glucose
  • 1 mM sodium pyruvate
  • 1500 mg/L sodium bicarbonate

Antibiotics

Penicillin

Active against:[7]

  • Gram-positive aerobic cocci.
  • Gram-negative aerobes.
  • Anaerobes.

Streptomycin

Active against:[8]

  • Aerobic gram-negative bacilli.
  • Gram-positive aerobes.


References

  1. Marcus Persicke, Andreas Albersmeier, Hanna Bednarz, Karsten Niehaur, Jörn Kalinowski, Christian Rückert Genome sequence of the soil bacterium Corynebacterium callunae type strain DSM 20147T. Standards in Genomic Sciences: 2015, 10(5) doi:10.1186/1944-3277-10-5
  2. <pubmed>24788039</pubmed>
  3. <pubmed>24062553</pubmed>
  4. <pubmed>22358337</pubmed>
  5. <pubmed>24795272</pubmed>
  6. 6.0 6.1 <pubmed>24098450</pubmed>
  7. http://www.uic.edu/pharmacy/courses/pmpr342/itokazu/penicillins.html
  8. http://www.uic.edu/pharmacy/courses/pmpr342/itokazu/aminoglycosides.html

2015 Course Content

Lectures: Cell Biology Introduction | Cells Eukaryotes and Prokaryotes | Cell Membranes and Compartments | Cell Nucleus | Cell Export - Exocytosis | Cell Import - Endocytosis | Cytoskeleton Introduction | Cytoskeleton - Microfilaments | Cytoskeleton - Microtubules | Cytoskeleton - Intermediate Filaments | Cell Mitochondria | Cell Junctions | Extracellular Matrix 1 | Extracellular Matrix 2 | Cell Cycle | Cell Division | Cell Death 1 | Cell Death 2 | Signal 1 | Signal 2 | Stem Cells 1 | Stem Cells 2 | Development | 2015 Revision


Laboratories: Introduction to Lab | Microscopy Methods | Preparation/Fixation | Cell Knockout Methods | Cytoskeleton Exercise | Immunochemistry | Project Work | Confocal Microscopy | Tissue Culture | Stem Cells Lab | Microarray Visit

2015 Projects: Group 1 | Group 2 | Group 3 | Group 4 | Group 5 | Group 6 | Group 7

Dr Mark Hill 2015, UNSW Cell Biology - UNSW CRICOS Provider Code No. 00098G