From CellBiology

My Student Page

Group Projects
This year's main topic is Blood Cell Biology. Each group should discuss with group members the specific sub-topic that will be covered by their project.

Here is a list of some of the cell types (Structure and Function)

Cell Type (PuMed citations)

Below are the groups to which students have been randomly assigned. You should now on the project discussion page add your own suggestion for a specific topic. Once your group has agreed on the topic, add this as a heading to the project page before Lab 3.

2016 Projects: Group 1 | Group 2 | Group 3 | Group 4 | Group 5 | Group 6 | Group 7

Group 1: User:Z5017493 | User:Z3330991 | User:Z5020043 | User:Z5020175 | User:Z3489355

Group 2: User:Z5018320 | User:Z5015980 | User:Z3376375 | User:Z3461106

Group 3: User:Z5019595 | User:Z5019962 | User:Z5018925 | User:Z3461911

Group 4: User:Z5020356 | User:Z3463895 | User:Z3376502 | User:Z3423497 | User:Z5021149

Group 5: User:Z5015719 | User:Z3462124 | User:Z3463953 | User:Z5017292

Group 6: User:Z5018866 | User:Z3329177 | User:Z3465531 | User:Z5105710

Group 7: User:Z5021060 | User:Z5016365 | User:Z5016784 | User:Z3414546 | User:Z3417773

Group Assessment Criteria

Group Assessment Criteria

  1. The key points relating to the topic that your group allocated are clearly described.
  2. The choice of content, headings and sub-headings, diagrams, tables, graphs show a good understanding of the topic area.
  3. Content is correctly cited and referenced.
  4. The wiki has an element of teaching at a peer level using the student's own innovative diagrams, tables or figures and/or using interesting examples or explanations.
  5. Evidence of significant research relating to basic and applied sciences that goes beyond the formal teaching activities.
  6. Relates the topic and content of the Wiki entry to learning aims of cell biology.
  7. Clearly reflects on editing/feedback from group peers and articulates how the Wiki could be improved (or not) based on peer comments/feedback. Demonstrates an ability to review own work when criticised in an open edited wiki format. Reflects on what was learned from the process of editing a peer's wiki.
  8. Evaluates own performance and that of group peers to give a rounded summary of this wiki process in terms of group effort and achievement.
  9. The content of the wiki should demonstrate to the reader that your group has researched adequately on this topic and covered the key areas necessary to inform your peers in their learning.
  10. Develops and edits the wiki entries in accordance with the above guidelines.
Individual Lab Assessments
Lab 8 Assessment
2016 Lab 8 - Lab 8 Assessment (to be completed before Lab 9)
  1. Add your peer assessment to your own student page to the site.
  2. Add your peer assessment to each project discussion page to the site.
Lab 6 Assessment
2016 Lab 6 -
  1. Identify an antibody against your group blood cell protein that is commercially available.
  2. Add a link to the original data sheet page and identify the type of group blood cell protein.
  3. Include the following information: type of antibody (polyclonal, monoclonal), species raised in, species reacts against, types of application uses, and if available any reference using that antibody.
Lab 2 Assessment
2016 Lab 2 - Super resolution microscopy
  1. Find a recent research article (not review) that uses super resolution microscopy technique.
  2. Write a brief summary of the paper (referenced) and what the super resolution microscopy technique showed.
    1. This should not simply be the abstract of the paper.
    2. This can be 2-3 paragraphs no longer.
  3. Include a super resolution microscopy image from the paper.
    1. Therefore the paper must be from a source that you can reuse.
    2. Image uploaded as in Lab 1 (summary box - description/reference/copyright/student image)
    3. Image should appear as a "thumbnail" (thumb) next to your paper summary (with citation legend) See Test page
Lab 1 Assessment
2016 Lab 1 - Lab 1 Assessment (to be completed before Lab 2) The test page I set up in the Lab
  1. Add your own student page to the site.
  2. Add your signature for Lab attendance.
  3. Add a sub-heading.
  4. Add an external Link.
  5. Add an internal Link.
  6. Add an image from PubMed, PloS or BioMed Central journal related to prokaryote cellular component. Make sure it includes both the reference and copyright information, with the file and where it appears on your page.


Z5018866 (talk) 11:53, 10 March 2016 (AEDT)

Z5018866 (talk) 12:37, 17 March 2016 (AEDT)

Z5018866 (talk) 11:11, 30 March 2016 (AEDT) - Sorry I forgot to add this last week, promise I was here

Z5018866 (talk) 11:12, 7 April 2016 (AEST)

Z5018866 (talk) 11:11, 14 April 2016 (AEST)

Z5018866 (talk) 11:12, 21 April 2016 (AEST)

Z5018866 (talk) 11:05, 28 April 2016 (AEST)

Z5018866 (talk) 11:11, 5 May 2016 (AEST)

Z5018866 (talk) 11:08, 12 May 2016 (AEST)

Z5018866 (talk) 12:27, 19 May 2016 (AEST)

Z5018866 (talk) 11:12, 26 May 2016 (AEST) - added late, I was here I did the presentation :)

Z5018866 (talk) 11:12, 2 June 2016 (AEST)

Peer Reviews

  • Z8600021 Useful to have section names in your assessments. these are very good peer assessments going the groups some feedback that would be useful for them to revise and complete the projects. (17/20)

Group 1: Megakaryocytes

Introduction: Gives a really nice overview however, it would be good to know what megakaryocytes actually do straight away rather than later in the introduction.

History: I found this section really long and also lacked references, not being the main focus of the assignment I think cutting down to the major events or making it collapsible so if someone is interested they can click to read it.

Structure: I think it has a good amount of content and is structured well. It would be nice to have a couple of pictures to show the different zones though.

Development and maturation: This section was really easy to read however, I had to go back and forth a little to figure out where RhoA fitted in, so maybe mention that in development section and have the elaboration as well below (which was also good).

Signaling: The JAK/STAT signaling section could be worded a little better but I liked the signaling section. The TPR explained well.

Function and role: Platelet production section is great! However, I think all the platelet stuff should be together (platelet function is later on – I feel like it jumps back and forward). In the regulation of skeletal homeostasis I’m left with the question is there another functioning life stage other immature and mature that isn’t involved in this regulation process? A concern in maintenance of hematopoietic stem cells is that it is mentions studies – but only one reference.

Pathology: The second last paragraph on essential thrombocytosis is quite poorly worded and a bit hard to understand. The referencing for this section is also not to format. CAMT section is nice and I assume that the osteoporosis section is not yet complete.

Future: Good, gave me something to think about and was relevant.

Overall I really like this project page! It was well written and easy to understand, with the more complex concepts where explained in a comprehensible manner. The paragraphs broken up so it wasn’t too overwhelming and links were made back to structures covered in the course.

Group 2: RBC

Introduction: Good introduction that told me a brief overview of what was ahead and introduced related diseases too. A good addition may be a picture in this section of the cell or the heam group. Also there is an unfinished sentence, which I’m sure you’ll fix.

Structure: The difference between fetal and adult RBCs is broken up across a couple of paragraphs and reads a little disjointed. The information on the action of drugs I feel could go in its own section potentially after structure, as whilst it relates it is not ‘the structure of the cell’ (but still interesting and should be included). Also left asking what happens when ATP levels are depleted? What does this change in shape mean for the fate of the cell? The first paragraph on cytoskeleton is a little repetitive; ‘traverse through the microvasculature’ is used twice. Are there pictures of the cryo-electron tomography that we have access too? Diagram of haem structure would also be good here, potentially one showing the binding to oxygen. For the ABO section I really want to know more, I feel this is a subtopic that could be expanded on. Additionally, do you talk about these certain increased risk diseases later on? If so, mention this or at least give an example.

Function: Gaseous exchange paragraphs have good informative content but are a little hard to read at times. In terms of inflammation what do these ROS mean for the surrounding tissue? Buffering ability topic should be expanded a lot more.

Synthesis and regulation: Good overview given in life cycle section. In the production section I wonder how the nucleus is lost as this is a major feature of a RBC? Filtering and destruction and the recycling of Iron are clear however, eryptosis is a little harder to read and gain a full understanding. Also does eryptosis result in the loss of iron? Is that why we need it in our diet?

Disease and abnormalities: Good content however, I think each disease could be broken up into subsections or even just smaller paragraphs. Current research: really interesting topic! I was wondering whilst reading for a while what it had to do with RBC so maybe introduce that first.

Overall a really informative page, major thing to look at would just re-wording the great content so it’s more readable and dividing up some sections. Good links were made to course content as well.

Group 3: B cells

Introduction: Good overview, just left asking what in the body do they elicit an immune response to? Is it something specific or just any pathogen?

History: Nice and short, give key points at a glance.

Development: the 1st and 3rd paragraphs are good, the second is a little hard to read and understand. Also the order of the paragraphs seems odd, it would make more sense to have the 1st one last so it is chronological.

Location and activation: In first paragraph second sentence there is repetition. A picture showing the zones of the lymph node would be a great addition here, and would help to make clear of the content. The second paragraph I feel should be reworded introducing the interaction with B-cells as I was a little confused as to why it jumped to macrophages. In the t-cell dependent activation section state that class switching is mentioned as this is something I immediately questioned and started scrolling the page for. The T-cell independent activation is good in content however, could be a little more concise.

Types: What causes the plasmablast to die or differentiate into a plasma cell? The section of regulatory B cells could be expanded on and how they work.

Structure: I found most of the section difficult to follow, breaking it up into just structural features and the function would be good keeping how they do it in another section. “How cell surface markers vary in different stages of differentiation” was particularly hard to read, I feel like it was meant to be in dot points but not formatted correctly. The inclusion of some diagrams of these receptors would help too. The structure of antibodies section is much easier to follow again however, again a diagram would be good.

Function: I feel this should be more towards the top of the page as it is a section I want to know about straight away. Also some of the first paragraph is repetitive. I found it a little confusing talking about the function in terms of an experiment, I feel it would be best just to take the most accepted recent findings and tell me about the function not the experiment. Could the antibody isotypes be put into a table, it would be much easier to compare that way. It also may be useful to add how the receptors carry out their function on the cell, in terms of activation and binding.

Role in disease: The autoimmunity section seems more fitting to the function section. Rheumatoid arthritis section gives a good overview of disease and B cell roles. I assume this section is not finished and more will be added.

Applications: Good section, potentially add current and future works into this section.

Overall you’re on track, major thing is references there seems to be a lot of unreferenced material and some not in the wiki format. The addition of diagrams and pictures is needed throughout. Other than that, just minor grammatical corrections and rewording of some paragraphs needed. Also the banner is really big with B lymphocytes written really small this could be made more proportional. Great work though!

Group 4: Natural Killer Cells

Introduction: Great introduction, short and sweet could say where they are though, whole body? Or localized?

History: History is good with only key points included, resulting in me actually wanted to read it and not just scroll past, as it isn’t the main focus.

Structure: I really liked the 3-dot point to divide them however; I think further use of sub dot points could be used to make it really clear on what is classifying them. It would be good to know more about the NKp46, maybe a diagram. I assume you’re going to add information on the activating and inhibitory receptors, which would be good. Also I think the pictures is a tiny bit small, I can’t really see what it is showing to know if I want to click into it for further detail.

Function: I like the 3 main functions section however, I feel it doesn’t relate to the information below. I feel a few sentences could be reworded for ease of reading, as I am a little confused about the relation to MHC1. It would be nice to have a chronological sequence of how they carry out their function. Also some information on CD65 as this is mentioned numerous times but not explained. As well as what NKp46 does being the characteristic features, as I don’t even know what it is, I just know it is there. Paragraph on pregnancy is good and interesting, makes to topic relevant to everyday life. Again the picture needs to be a little bigger, I have no idea what its showing.

Abnormalities: The table gives a great summary, I really like this. The RA section is quite long and a lot of receptors and chemokines are introduced here without explaining them making it quite hard to understand. If they are 100% necessary introduce them in the above topics or omit them and only talk about key points relating to NK cells. The cancer section I felt was more related to treatment rather than an abnormality in the cell, potentially go in the current research section? I felt the asthma section gave me no information at all and needs to either be expanded on or deleted. The anemia paragraph was good and informative. The section on schistosome japoncium wasn’t exactly clear on what role NKc played, I think it would be better not to mention the results of the experiment but just their conclusion.

Current research: I didn’t really know what was going on in the section, maybe some subheadings would help, but overall I wasn’t given a clear understanding of what was currently being researched in relation to NKc.

Overall, a good project that is coming along nicely. I’d focus more on the NKc themselves rather than pathology, as I was left with a lot of questions about the cell. Try to expand on the features of the cell and link them to the function. The banner at the top is really big, and could probably be made a little smaller.

Group 5: Mast cells

Introduction: Good introduction gives good overview of the cell explaining what, when, where and why however, I feel that their functions of “communicate the presence of pathogens to the lymph nodes and other immune cells.”etc. should be one of the first things I read.

History: Formatting of table is nice, nicely spaced and easy to read.

Physiology: Morphology: The picture coding has an error, shows 300px. Also would be good to have pictures of different morphologies.

Function: Very clear section that outlines the key functions. Is there any information on how they are protective in regards to tumor growth?

Origin and migration: What makes the mast cell go to different areas? What are these corresponding molecules? Also what chemokine receptors are present? Otherwise section has good content potentially rewording some of the sentence for ease of reading as a final touch up.

Activation and mediators: I really like this section, straight to the point and clear. Degranulation: Good table however, and introduction to it might be helpful and explain what degranulation is.

Pathology: Great introduction to topic ran over everything again to refresh what I needed to know for below. For the MACD I think the subsets should be bullet pointed, as it can be a little confusing to read all in one line. Also potentially making the criteria and treatments collapsible as you have done with signs and symptoms. I feel the parathyroid bone disease and other disease paragraphs could be made more concise as there is quite a number of them.

Glossary: I think may be best in a table.

Overall a really great page! I found it quite difficult to find major faults, only minor rewording and a few things to add.

Group 7: Eosinophils

Initially I wonder why there is no introduction giving me a basic overview of Who? (eosinophils) What they do? When the do it? Where? And why? I also notice there is no function section, whilst their function may be incorporated into other sections I think it is important to at least have a function heading for navigational purposes and then have subheadings beneath it.

History: some points are quite long I think sticking to key points and if there is more information that is essential incorporate into introduction

Birth, life and death: Hematopoietic progenitor cells need explaining, not everyone knows what they are. The second paragraph is really good, tells a chronological story that is easy to follow. The third paragraph almost seems like an introduction to section on function.

Structure: I really like the picture however it could be positioned on the left side with corresponding text next to it rather than below. I am confused in the paragraph is the enzyme catalyzing 3 different things? If so use of commas or dot points rather than +, or is it an equation? This isn’t clear. I really like the breakdown of granules it makes it super clear and easy to read and understand! The surface markers section definitely needs to be elaborated on and use of diagrams helps to show interaction between cells. What markers are present on the cell should be at the start of the paragraph not at the end, as this is the whole point of the paragraph.

Role in disease: In the helminth section I have no idea what is going on, what is a helminth? This needs introducing and then relating to eosinophils. Section on fungal infection is great, follow this format for other sections and elaborate when needed. I feel bacterial could also be expanded on, what happens next? “Eosinophilic Esophagitis, Eosinophilic Gastritis, and Eosinophilic Gastroenteritis” could be worded “Eosinophilic esophagitis, gastritis and gastroenteritis”. I also find the table on eosinophilia quite large for such a small section; it makes me assume it is really important when it is more of a minor addition. Overall this section needs to follow a common structure within each disease and have more equal amounts of content for each subheading if possible.

Overall good project! Just needs some work in having everything structured in a consistent manner and the addition of an introduction and function sections.

Lab 6 Assessment

Anti-T-Cell Receptor Antibody, clone C305

Type of group blood cell protein:

  • Jurkat T Cell receptor

Type of antibody:

  • Monoclonal

Species raised in:

  • Mouse

Species reacts against:

  • Human

Types of application uses:

  • Multiplexing
  • Immunoprecipitation

Reference using that antibody:

PMID 6208306

PMID 11395491

PMID 12913111

  • Z8600021 multiplexing? this could have had more explanation, the rest is fine. (5/5)

Lab 5 Assessment

Phenotype of undifferentiated B35 cells.png

Cell counts of the morphological phenotypes of group A: TM4 over expression and group B: Control

Images sourced from 2016 Lab 5

Lab 4 Assessment


It may be possible that cellular prion protein (PrPC), associated with Creutzfeldt–Jakob disease, is related to other neurological disorders in which prions are implicated. Our hypothesis is that PrPC and its activity within the cell is instrumental in the proposed replicative characteristics, and thus pathogenicity, of alpha-synuclein protein. CRISPR will successfully knock out the gene for PrPC,[1] and it is hypothesised that the resulting mice will display less pathogenic symptoms than the infected mice with the gene for PrPC knocked out.


To determine if knocking out the (PrPC) gene affects susceptibility to multiple system atrophy (MSA)

  • Successfully knock out (PrPC) gene
  • Infect all non-control mice with prion form of Alpha-synuclein
  • Quantify the amount of misfolded alpha-synuclein protein in knock out and healthy mice


CRISPr/Cas 9 kit was obtained through Australian bioresources

Mice neuroblastoma cells were obtained through ATCC

"CRISPR design tool" was used to determine appropriate target sites within the (PrPC)

Generation of gRNA Expression Vectors, Cell Culture and Transfection, Generation of stable knockdown cell clones, Genetic analysis, Western blot analyses were done as in CRISPR-Cas9-Based Knockout of the Prion Protein and Its Effect on the Proteome [2]

As in *Neuropathology in mice expressing mouse alpha-synuclein*[3], for all three groups, control, PrPc and koPrPC we will use an anti alpha synuclein antibody from (Syn-1, 1∶500; S63320, Transduction Laboratories and 4D6, 1∶800; Abcam) which we will visualize with avidin-biotin peroxidase method (Elite standard kit SK6100, Vector) and DAB substrate (1718096 Boehringer). And use a confocal microscope (Leica TCN NT) to infer fluorescence and compare the fluorescence of all three group.


We have three different groups, which are Control, PrPC with prion form of alpha synuclein disease causing agent, and KO PrPC with prion form of alpha synclein disease causing agent.

We believe that a prion form of the alpha-synuclein protein causes multiple system atrophy, and also research supports that PrPC function can play role in pathogenesis of prion diseases [4].

The results that we can expect are that the amount of alpha-synuclein protein found in mice with active PrPC protein will be greater than the mice with KO PrPC protein. However, we expect that both of the alpha-synuclein protein groups will report more amount of alpha-synuclein than the control group. This result could show that PrPC is involved in the function of the pathogenesis of prion diseases.


  1. <pubmed>20056882</pubmed>
  2. <pubmed> 25490046</pubmed>
  3. <pubmed>21966373</pubmed>
  4. <pubmed>1986710</pubmed>

Lab 3 Assessment

1. Summary: Folate-mediated chitosan nanoparticles containing the IP-10 gene enhance melanoma-specific cytotoxic CD8+CD28+T Lymphocyte responses, He, J., “et. al.” [1]

In the study promising combination treatments for malignant melanomas are explored using adoptive immunotherapy with Cytotoxic T lymphocytes (CTL).

The study aimed to increase the CTL anti-tumor response by inducing melanoma TRP2-specific CD8+CD28+T cell in combination with folate-modified chitosan nanoparticles containing Interferon-y-inducible protein-10 (IP-10). IP-10 plays a role in chemotaxis particularly for CD8+ T cells towards the tumor [2][3]. The chitosan molecules where prepared with a IP-10 gene from a mouse and the TRP2-specific CD8+CD28+ T cells co-cultured with artificial antigen presenting cells, due to cost and efficiency. Affected mice were treated with one therapy, both or a saline control, with tumor size and survival times measured. Other immune cells were measured and TUNEL techniques used to determine proliferation and angiogenesis.

Overall the combination of the two therapies increased the anti-tumor response and hindered the advancement of the melanoma in vivo. Inhibiting growth and proliferation whilst promoting apoptosis of tumor cells leading to an extended survival time for the mice than either therapy alone. With the chitosan nanoparticles creating a chemotaxic by inducing IP-10 secretion, resulting in recruitment of CD8+ t cells in the tumor area angiogenesis and proliferation were reduced.

2. Summary: Delivery system of CpG oligodeoxynucleotides through eliciting and effective T cell immune response against melanoma in mice, Sun, W., “et. al.” [4]

Through the addition of a C-class CpG ODN-685 (oligodeoxynucleotides) the study aims to explore the effects on anti-tumor activity in melanoma inoculated mice as well as prophylactically in healthy mice to ultimately improve the immunogenicity of the whole tumor cell lysate developed as a vaccine for tumors, whilst. The CpG ODNs are involved in stimulating the early immune responses with T cell activation occurring during their transport to the immune system. There were two groups of study, prophylactic – which were given tumor cell lysate, CpG ODN, tumor cell lysate plus CpG ODN or PBS as control. At a later stage were given tumor cells. The other therapeutic group was inoculated with melanoma tumor cells and then received a treatment. Tumors were either inoculated in hind leg or peritoneum of mice. Subcutaneous and intraperitoneal melanoma affected mice did not respond to tumor lysate or CpG ODN but when combined an immune response was triggered. This led to longer survival time and prevented tumor spread to through the abdominal cavity. Upon analysis of splenocytes the lysate only group displayed anti-tumor effects whilst the CpG ODN alone did not however, when used in conjunction an enhanced response was displayed. Suggesting assistance from CpG ODN in stimulating a cytotoxic immune response. CD4+ / CD8+ T cells increased significantly after tumor inoculation signifying their involvement in immune response and when CpG ODNs where combine with tumor lysate a strong specific Cytotoxic T lymphocyte response was generated. It was concluded that CpG ODN-685 could be effective in increasing immunogenicity of tumor vaccines against melanoma.

3. Summary: Spinal cord T-cell infiltration in the rate spread nerve injury model: a time course study, Gattlen, C., “et. al.” [5]

Infiltration of the spinal cord by T-cells after SCI [5]

In this study Gattlen et. al. explored the immune response following a spared nerve injury (SNI) [6] in mice, in particular microglia, T-lymphocytes and cytotoxic T-lymphocytes responses. The study looks at the relation between different immune cell types and their role in pain and chronic pain. Levels of microglia (Iba1), T-lymphocyte (CD2) and cytotoxic T-lymphocyte (CD8) were measured through various techniques such as measuring gene expression and immunofluorescence.

Microglial reactivity gene expression was unregulated for a prolong period, whilst microglial proliferation measured through immunofluorescence was only increased sharply on day 2. Inflammatory genes were regulated following the SNI with pro-inflammatory factors such as interleukins being increased soon after injury and typical anti-inflammatory factors began to increase at a later stage. Following the SNI CD2 and CD8 cells were counted in the dorsal horn to detect T-cell infiltration into the spinal cord however, a significant difference was not found. This is comparable to a spinal cord injury where T-cell infiltration is displayed.

The increase of anti-inflammatory factors could be a factor in the resolution of the inflammation [7]. Increased excitability in the lamina neurons of the spinal cord has been linked to the increased presence of Pro-inflammatory factors [8]. From this the study concluded that further study should focus on the transition from pro- to anti- inflammatory phases of the microglial cells.

4. Summary: Eliciting cytotoxic T lymphocytes against human laryngeal cancer-derived antigens” evaluation of dendritic cells pulsed with a heat-treated tumour lysate and other antigen loading strategies for dendritic cell based vaccination, Wei, F., “et. al.” [9]

With the goal of improving the antitumor immunity though optimizing antigen loading of current dendritic cell (DC) vaccinations, Wei et. al. explore the value of various dendritic cell vaccinations comprised of whole tumor cells or their derivatives. Through antigen loading DCs tumor-associated antigen (TAA) specific t-cells and cytokine production can be induced. DCs pulsed with tumor cell supernatant (DC-TCS), whole-cell tumor stressed lysate (DC-TSL) and irradiated tumor cells (DC-ITC) where the three different types. It was found that DC-TSL induced strongest responses for TAA-specific T-cells, Th1 cytokine production, and cytotoxic T lymphocyte activity. Making it the most efficient of the three tested for laryngeal squamous cell carcinoma. DC-TCS and ITC inhibited T cell activation however, had limited capacity for CTL activity.

DCs have a potent antigen presenting capacity, which are taken advantage of in the vaccines that have shown promising clinical results [10]. However, a percentage of patients remain insensitive to the therapy, where further research can develop the immunogenicity of these current vaccinations.


  1. <pubmed>27022421</pubmed>
  2. <pubmed>18723067</pubmed>
  3. <pubmed>21802343</pubmed>
  4. <pubmed>26918036</pubmed>
  5. 5.0 5.1 <pubmed>27005622 </pubmed> Cite error: Invalid <ref> tag; name "PMID27005622" defined multiple times with different content
  6. <pubmed>19923276</pubmed>
  7. <pubmed>10767254</pubmed>
  8. <pubmed>18480275 </pubmed>
  9. <pubmed>26795730</pubmed>
  10. <pubmed>12633662</pubmed>

Lab 2 Assessment

Mouse brain slices using SeeDB2 and comparison[1]

The article seeks to address the challenge of imaging deep inside tissues (in particular brain neuronal circuits), where limitations have arisen in the techniques to prepare specimens. Alterations in cell size and loss of cellular material affect the fine cellular morphology aiming to be imaged. Due to the sensitivity to light scattering and spherical aberrations high resolution can only be obtained at the surface of the specimens.

In the article optical clearing and index matching are used to reduce light scattering and spherical aberrations. In addition to this using the developed various SeeDB protocols that focus on maintaining fine morphological structure. Finally, various bright and stable fluorophores were used as high-resolution fluorescence imaging obtains photons from smaller volumes per pixel.

Deep tissue super-resolution images of intact samples where established with depths of up to 100um scale, opposed to the typical few micrometers. The SeeDB2 imaging was also useful for other fragile samples in cell biology, such as oocytes, with fine structures being maintained. SeeDB had some advantages over the SeeDB2 in that it was detergent free, which can affect plasma membrane integrity. In the SeeDB2 a small amount of a weak non-ionic detergent was used to optimize clearing of the sample. Overall a limitation of the SeeDB and SeeDB2 is a reduction in transparency compared to other techniques however, these do not maintain fine structure.


<pubmed> 26972009 </pubmed>


© 2016 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license [1]

Note - This image was originally uploaded as part of a student project and may contain inaccuracies in either description or acknowledgements. Please contact the site coordinator if the uploaded content does not meet the original copyright permission or requirements, for immediate removal.

Lab 1 Assessment

Search PubMed

Prokaryotic Cytoskeleton

Eukaryotic Cytoskeleton

PMID 26756351




Cell Biology Introduction

What I've learn't so far...

Today I have refreshed my knowledge of basic coding, as well as learning more specific details for a wiki page. I've also learn't how to make references for PubMed through this coding, which is extremely helpful and time saving.

How to make an in-text citation

Bacterial division protein FtsZ.[2]

Individual assesment

Lab 1

Pili-induced clustering of N. gonorrhoea bacteria.PNG

Pili-induced clustering of N. gonorrhoea bacteria[3]

Pili-induced clustering of N. gonorrhoea bacteria[3]


<pubmed> 26355966 </pubmed>


© 2015 Taktikos 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

Note - This image was originally uploaded as part of a student project and may contain inaccuracies in either description or acknowledgements. Please contact the site coordinator if the uploaded content does not meet the original copyright permission or requirements, for immediate removal.


  1. <pubmed>26972009</pubmed>
  2. <pubmed>26756351</pubmed>
  3. 3.0 3.1 <pubmed> 26355966</pubmed>