From CellBiology

Question Lab 1 - What Cell Biology Journals allow reuse of acknowledged and correctly cited content?

-The Journal of Cell Biology -BMC Cell Biology, and -All on the Public Library of Science site

--z3255926 06:45, 10 March 2010 (UTC)

Question Lab 2 - What are the "light" regions of DNA within the nucleus called?


--z3255926 06:05, 17 March 2010 (UTC)

Question Lab 3 - How do we know the hazards associated with research chemicals?

-there should be clear labels on research chemicals.

-Comprehensive information is found in Material Safety Data Sheets (MSDSs). These provide standardised OH&S information for specific substances. Labs must have these available for all the chemicals that they will be using, and those using the chemicals should be aware of their properties before using them. The data contained in MSDSs include ingredients, chemical and physical properties, health hazards, how to correctly use and store the chemicals etc.

-MSDSs for specific chemicals can be queried using the Chem Alert database.

--David Williamson 06:49, 24 March 2010 (UTC)

Question Lab 4 - Identify a commercially available antibody to an adhesion junction protein, and also add a link to the antibody page on your own student page.

- This is a monoclonal antibody that binds to an epitope near the C-terminus on human desmoplakin. Desmoplakin is a protein that is part of the desmosomes that form cystoskeleton-involving junctions between adjacent cells, in particular between the (lateral) cell-cell domains of epithelial cells. It has been raised using goat IgG. Its antigen binding site will identify the human form of desmoplakin, but the other parts of the antibody are goat-derived so any other antibodies used for tagging will need to be from others species (eg: and set up to recognise goat Ab's). - desmoplakin mAb

--David Williamson 06:17, 31 March 2010 (UTC)

Note: Question 5 answer handed in during lab.

Lab 6 Chart


--David Williamson 08:12, 21 April 2010 (UTC)

Note: Question 6 questions answered on handout that was returned to the PhD student.

Question Lab 7: Lab 7 - From today's confocal tutorial, identify an advantage to using each of the following objectives: Air, Water or Oil.

  • Air: Using an air objective is the most convenient and easiest of the three, (though it will not work at high magnification).
  • Water: Water is advantageous because most cell cultures are done in water/aquesous solution of the same refractive index as water, so a water objective allows high power magnification of these live specimens without distorting the image.
  • Oil: When a specimen can be fixed to a slide and stained (eg: a gram stain) then an oil objective can be used. Oil objectives allow the greatest resolving power.

--David Williamson 13:46, 3 May 2010 (UTC)

Lab 8- Peer Assessments

Group 1: Fluorescent PCR

  • The outline of headings and subheadings is very clear and logical.
  • The many pictures are helpful in understanding. The pictures you guys did yourselves are very impressive!
  • The level of depth is good and appropriate for the page.
  • The meaning of the first sentence wasn’t immediately clear to me, maybe this could be reworded? Does it mean Genetic expression has become the basis of clinical diagnosis? Or that our ability to measure genetic expression has become the basis of clinical diagnosis?
  • The tense is a bit mixed in some sections making it a little hard to read—eg: “Gene amplification accounts for the high sensitivity of PCR (present tense) where single copies of genes could be analysed” (future tense). If “can” was used instead of “could” this would read more smoothly (in my opinion). Or “Basic PCR, invented in 1984, generated large quantities of DNA sequence (past tense) if the DNA sequences of the primer molecules are known” (present tense). This sentence could use “were known” instead of “are known” to make the whole sentence past tense, or “generates” instead of “generated” to make the whole sentence present tense.
  • A glossary could be helpful

Group 2: RNAi

  • The layout of headings and subheadings are well thought out.
  • Good clarity of expression- well written in a way that is easy for people that aren’t experts to understand.
  • Impressive student drawn diagram!
  • I’m not sure if you need to reference anything in the first 2 paragraphs of “What is RNAi”?
  • I think the mechanisms section needs to be referenced?
  • Something I’m not sure about- in the opening section it mentions that RNAi gene silencing involves inhibition of transcription through cleavage and degradation of mRNA... if mRNA is already present hasn’t transcription already occurred? And won’t cleavage and degradation of the mRNA only prevent the subsequent translation of that mRNA, with transcription occurring independently?
  • The descriptions of ideas behind medical applications is good- but for some diseases it isn’t clear whether RNAi is used clinically or only in development?

--David Williamson 06:46, 6 May 2010 (UTC)

Group 3: Immunohistochemistry

  • Only an opinion- but I wonder if the introduction could do without the details about the immune system, and leave the focus on immunohistochemistry?
  • The student drawn diagrams are helpful. I’m not sure if he might penalise you for not making it more obvious that they’re your own work though?
  • I really like the way the page is written- it’s clear and simple to understand even for people that aren’t experts.
  • I think the structure could be changed a little- to me it makes more sense to put history, then the generalised method, then the specific methods, then the notes about controls and blocking.
  • The glossary is handy but I think it could do with some extra terms like all the abbreviations (PAP, ABC,LSAB etc). I know these are spelled out the first time they’re mentioned which is good- but if someone skips ahead to a different section they might not know what they are.
  • I think your reference list might need a little consolidation- like some of the same articles are given a few times, and I’m not sure if more detail is needed for the website references?

Group 4: Cell Culture

  • I like the layout and headings, but I wonder if ‘potential cell culture problems’ could be merged with ‘limitations’?
  • I think the applications, limitations, current research and advances sections need to be referenced? And some other sections seem like they need more citations...
  • I like the introduction as a good clear summary of the main points.
  • Helpful links is a great idea and the glossary is handy.
  • I think the history section could be clearer if it was arranged chronologically or possibly chronologically for subtopics?
  • I think this page is well written- explained appropriately for people at our level, and manages to keep readers aware of the big picture rather than getting bogged down in details.

--David Williamson 04:41, 7 May 2010 (UTC)

Group 5: EM Really good work guys.

  • The intro reads very well but I wonder if you could also summarise in a sentence in there what an electron microscope actually is? If you’re anything like me, often when you go to a Wikipedia page you just read the first sentence to get a basic idea of what a word might mean.
  • If those microscope schematics are by you guys they’re really good! But I think you might need to make it a bit more obvious they’re your own work or he might penalise you...
  • I really like the way the history is done- with the bold headings giving a nice summary of the whole process.
  • The comparison table between TEM and SEM is very effective- a great way of showing both similarities and differences.
  • Applications are well done with really clear layout and good examples.
  • The “uses at UNSW” is a great idea- relating the topic to the page’s audience.
  • Good collection of references, but some of the references appear a few times... I’m not sure if this is something to do with the wiki system because I’ve seen this a couple of times but it would be good if it could be consolidated.

Group 6: Confocal Microscopy Very good work guys.

  • Your page could do with an introduction summarising as simply as possible what confocal microscopes are and what they’re used for. I don’t know about you but often when I look up a Wikipedia page this is often all I’m looking for...
  • The layout seems well thought out, but all the glossary points in the contents it makes it really long... You can still make the terms bold without them being section headings, but I don’t know if there’s a way to do this and maintain all the links to the glossary words in the text? Because the links to glossary points are maybe the best idea ever.
  • The student diagram is epic. In the description I think you need to put your student number where it says “I, (student number)” though?
  • I think the page is well written, making it possible for non-physics experts to understand what’s going on as well as why it matters. One tiny thing I noticed- Under CLSM where you say “Another use of the CLSM is the aperture size which is adjustable”, do you mean aperture size is a use, or like a property or an advantage of CLSM?
  • Some bold subheadings would help drive home the main stages in the timeline.

--David Williamson 03:17, 9 May 2010 (UTC)

Group 8: Microarray.

  • Good project guys, and I’m sure it’ll be even better by the time you guys are done with it.
  • The choice of subheadings and layout seems logical and well thought out.
  • Good choice of pictures- they’re useful in aiding understanding.
  • I liked the way the project was written- the language is clear and direct
  • Going through the project as a whole and making it flow a bit better between sections could further improve this project (I know our group has this problem too as we haven’t really integrated everyone’s work that well yet).
  • It could be worth including some extra words in the glossary, eg: I didn’t know what ‘perturbations’ meant.
  • In the introduction- I think it could be good to give a single sentence at the start saying what microarrays are, or it might be worth merging the intro and ‘definition and use’? The intro gives readers a great sense of applications and types of microarrays but not what they physically are, and often someone visiting a page will only want to know what the technique is in a very basic sense.
  • The table in ‘protein microaray’ section is a great idea, but I found it a little confusing to read. Would it be possible to have clearly laid out rows that directly compare the types eg: a row for what it measures, a row for significance, a row for uses etc.

Group 9: Fluorescent proteins

  • All in all I think you guys have done a really good job- the amount and choice of info you have is really sensible, and it’s well expressed in a readable way.
  • The pictures you guys have are really helpful. Even more could be good though- eg: a picture/schematic for the theory of fluorescence.
  • I think you guys still need to make your own diagram?
  • The advantages, disadvantages and limitations of both GFP and fluorescent proteins in general are good but I think some of them may need elaboration- eg: why is gene transfection a disadvantage of GFP? Or oligomerisation a limitation of fluorescent proteins?
  • I think some of your sections need referencing- eg: there aren’t many references in the “current research section”
  • Some places where you have numbers you could change to be wiki number lists rather than 1) etc? This would save space and make the numbers more obvious. You do this by putting a # next to it in the editing section.

--David Williamson 06:24, 10 May 2010 (UTC)

Group 10: Hey guys, really great project on the whole, with just a couple of things that could make it even better:

  • Great introduction- a good summary of what SCNT is and why it’s important.
  • Good use of pictures including the student drawn one.
  • A very minor point but I think the plural of embryo is embryos not embryoes?
  • The “SCNT Research in Australia” section is a great idea but I think you need a bit more specific information about what they are researching? And could this section possibly be integrated to the links to research labs and researchers section?
  • The choice and number of references is really good, but some of the references appear a few times... I’m not sure if this is something to do with the wiki system because I’ve seen this a couple of times but it would be good if it could be consolidated.
  • I think some of the dot points in the ‘Future Directions’ section need to be elaborated on if they are to be included? For instance what are ‘serial transfer’ and ‘activation procedure’, and how do they relate to the future of SCNT? I also don’t quite understand the first sentence in the ‘Future directions’ section… I think this may need rewording?
  • If the ‘ethics’ section drew on any ideas other than your own you may need a few citations in there?

--David Williamson 02:06, 11 May 2010 (UTC)

Question lab 9: What is the technological bottleneck common to all next generation sequencing (NGS) platforms?

  • Next generation sequencing platforms generate multiple sequences at once, leading to colossal amounts of data. The bottleneck/limitation is in the processing of the huge amounts of data produced- both for the computers to handle the output, and for researchers to be able to analyse and draw meaningful conclusions from it.

--David Williamson 07:47, 19 May 2010 (UTC)