- 1 Lab Attendance
- 2 Lab 1 Activities
- 3 Individual Assessments
- 3.1 Lab 1
- 3.2 Lab 2
- 3.3 Lab 3
- 3.4 Lab 4
- 3.5 Lab 5
- 3.6 Lab 8: Peer Assessments
- 4 References
Lab 1 Activities
- point 1
- point 2
- point 3
The Origin of Eukaryotes from Prokaryotes by Time and Genetic Distance
Nick Lane Energetics and genetics across the prokaryote-eukaryote divide. Biol. Direct: 2011, 6();35 PMID:21714941
Copyright ©2011 Lane; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Endosymbiotic origin of eukaryotes by time and genetic distance 
Research Article Using Confocal Microscopy
The aim of this study was to investigate and provide evidence to support the migration and morphological change of mesothelial cells during tissue injury response. By using confocal microscopy imaging Nagai and peers, 2013, were able to observe clearly delineated mesothelial cells within ex vivo mouse abdominal wall tissue culture, as well as transformed mesothelial cells (MeT5A) in in-vivo tissue culture and witness their morphological transition from flat cells to cuboidal cells. This transition was able to be observed as confocal microscope analysis allows for the control in the depth of field and eliminates/reduces background matter, so that mesothelial cells positioned on top of each other can be differentiated. In addition, these confocal microscopy techniques also allowed the researchers to observe the horizontal migration of these mesothelial cells across the tissue culture, moving through gaps between surrounding cells. These findings provided evidence in support of the change and migration of mesothelial cells during injury response. 
--Mark Hill (talk) 12:05, 11 April 2013 (EST) This is good explanation as to how the confocal microscope was used in this research paper, the Pubmed referencing format is correct, you should have inserted at the beginning of paragraph (after study) rather than at the end. Your link at the top does not work.
Nuclear envelope breakdown in starfish oocytes proceeds by partial NPC disassembly followed by a rapidly spreading fenestration of nuclear membranes 
Lenart and co-workers (2003)examined the breakdown of the nuclear envelope in live starfish oocytes using various techniques involving fluorescently labeled dextrans (polysaccharides), membrane dyes and green fluorescently tagged proteins (GFP-tagged proteins), in conjunction with confocal time-lapse microscopy and electron microscopy which allowed them to view the changes in the oocyte nuclear envelope. Through the use of different sized fluorescently labelled dextran fractions experimenters were able to analyse the changes in the permeability of the nuclear envelope in maturing starfish oocytes. They firstly observed a sequential entry of dextran molecules, beginning with the smaller molecules entering the nucleus followed by larger molecules with diameters up to 40nm. The use of GFP-tagged nucleoporins revealed a corresponding gradual loss of peripheral nucleoporins from Nuclear Pore Complexes (NPC) (selective aqueous channels that span both nuclear membranes, connecting the nucleus with the cell cytoplasm) which resulted in the dilation of these channels from 10 to 40nm and a gradual release of import substrates. It was clearly noted, however, that the core of NPCs remained intact. Another key observation which was made was that the nuclear envelope structure remained unaffected. Next a rapid complete permeabilisation of the nuclear envelope that spread throughout the nuclear surface was noted, allowing macromolecules of diameters up to 100nm to enter the nucleus, this proposed the complete removal of the remaining core of the NPCs. It was also found that at the electron microscope level the nuclear envelope was fenestrated in the end. These experimenters therefore concluded that the breakdown of the nuclear envelope occurred in two distinct sequential phases:
-Phase 1 involves the gradual disassembly of the NPCs, which coincides with an increase in nuclear membrane/envelope permeability allowing for some macromolecules to enter the nucleus and nuclear import substrates to leave. At the end of this first phase the nuclear envelope remains intact.
-Phase 2 is characterised by an increase and rapid spreading nuclear envelope permeability as well as apparent fenestration of the nuclear envelope and hence its breakdown resulting from the removal of the core of NPCs. 
This research paper is relevant to the nuclear envelope breakdown section as it provides an experiment which clearly shows evidence of how the nuclear envelope gradually breaks down and explores the role of NPCs in this.
This paper explores the importance of the Nuclear Pore Complex (NPC) transmembrane nucleoporin, gp210, in the breakdown of the nuclear envelope. Galy and his colleagues subjected Caenorhabditis elegans (worm) egg extracts to RNAi-mediated deletion or mutation of the gp210 nucleoporin which resulted in the prevention of lamin depolymerisation, a late event which aids in the breakdown of the nuclear envelope. The prevention of lamin depolarisation results in the inability of the nuclear envelope to breakdown and also blocks pronulclear chromosome mixing that ultimately leads to the formation of two nuclei after mitosis. This implied that gp210 was key in nuclear envelope breakdown.
The block of gp210 phosphorylation which is conducted by cyclin-B-cdc2 (proposed to be an important trigger for the initiation of mitosis) was also explored. Depletion of the cyclin-B-cdc2, achieved through RNAi, resulted in the inability of the gp210 nucleoporin to be phosphorylated and achieve nuclear envelope breakdown. Hence, this provided further evidence that gp210, particularly its phosphorylation, was indeed an early step in the breakdown of the nuclear envelope.
This research article is relevant to the subheading Nuclear Envelope Breakdown as it suggests one of the nucleoporins involved in the breakdown of the nuclear envelope. 
In this study, Makhnevych et.al (2003) revealed a new mechanism for regulating transport into the nuclear compartment during closed mitosis in yeast. This mechanism involved specific molecular rearrangements in the nuclear pore complex (NPC). Karyopherins (kaps) are soluble transport factors that facilitate the transport of distinct cargo molecules into the nucleus by binding to NPCs. This transport can be regulated so as to conduct changes in gene transcription, DNA replication and chromosome segregation. Previous studies identified posttranslational modifications to the cargo molecules (including phosphorylation and acetylation), resulting in an increased or decreased affinity to their kap transporters, as a way of inhibiting or enhancing their transport into the nucleus. A mechanism which is less commonly examined as a form of import regulation of cargo molecules is the alteration of the kaps transport machinery and one of these mechanisms is explored in this paper. Makhnevych and peers specifically analysed the control of Kap121p related cargo molecules into the nucleus. They observed that Kap121p –mediated import is active in interphase but inhibited during mitosis and this was not due to changes in cargo binding to Kap121p. They found that by structurally rearranging the NPC during mitosis, a masked binding site for Kap121p would be revealed on one of its nucleoporins, Nup53p. When Kap121p was bound to this site, movement of Kap121p and its cargo into the nucleus was slowed and it triggered the release of the cargo into the cytoplasm. Hence, Nup53p was considered a transport inhibitory nup (iNUP). They concluded that the regulation of Kap121p-mediated import through the presence of Nup 53p played an important role in the progression through mitosis, showing that increased levels of Nup53p inhibited progression through mitosis.
This research paper is relevant to the subheading “Open vs Closed/semi-closed Mitosis” as it provides a model of closed mitosis and examines a mechanism used to regulate transport of molecules into the nucleus during mitosis which therefore shows the continuous presence of NPCs and hence highlighting the fact that the nuclear envelope stays intact during closed mitosis in lower eukaryotes such as yeast.
This article investigates the translocation of pre-existing nuclear pore complexes (NPC) from mother yeast cell to its bud during cell division and how this contributes to the aging of yeast cells. Shcheprova and peers (2008) used fluorescent tags and photobleaching to track the movement of cellular components including nucleoporins within the nuclear envelope. They observed that NPCs moved freely throughout the nuclear envelope, however, when part of the nucleus penetrated into the bud, NPC movement was restricted to the part of the nuclear envelope within the mother cell as a diffusion barrier was created at the neck of the bud. They established that NPCs are prevented from moving from the mother to the bud during cell division. They also observed that no new NPCs were inserted in the nuclear envelope of the mother and that the pre-existing NPCs remained in the mother, but there was evidence of new NPC (not from the mother) insertion in the bud. They concluded that the division of the yeast nucleus is asymmetric when considering the age of the pores with pre-existing material being preferentially segregated to the mother. 
This article is relevant to the “Open vs. Closed Mitosis” section as it addresses the fate of NPC during closed mitosis and highlights the fact they are not broken up like in open mitosis.
Antibody against Gap Junction Protein Alpha 1 (Connexin 43)
Type of Immunoglobulin: Polyclonal
Species it's raised in: Rabbit
Species it reacts against Human, Mouse and Rat
Application: Western Blot, Immunohistochemistry, Immunofluorescence and ELISA
Reference of use: Staphylococcus aureus-derived peptidoglycan induces Cx43 expression and functional gap junction intercellular communication in microglia
1) Do you see any change in phenotypes between group A and group B?
Yes. The majority of the control group WT undifferentiated B35 cells were of the broken fan and stumped phenotype, with very short lamellum/lamella and neutrite(s). On the other hand the majority of the Tm4 over-expressed undifferentiated B35 cells were of the pronged and stringed phenotype with multiple and longer neutrites and a single lamellum.
2) If you see a difference, speculate about a potential molecular mechanism that has lead to the change
It has been observed that Tm4 is found concentrated in the growth cones of neurons and in growing neutrites being involved in stabilizing the actin filaments and controlling the interactions between actin and actin binding proteins required for the expansion and motility of the growth cone,  hence, the over expression of this tropomyosin isoform would lead to increased actin-actin binding protein interactions that would enhance the motile events needed for neutrite growth. This would account for the increase in neutrite number and length in the Tm4 over-expressed cell group, giving the observed shift from a more broken fan/stumped phenotype to a more pronged/stringed phenotype in B35 cells
Lab 8: Peer Assessments
Group 1: Regulation of Cell Division
- The introduction is sound, highlighting the importance of regulating cell division and listing the topics that will be discussed.
- I feel as though a brief overview of the cell cycle may be helpful either in the intro, as a separate subheading on its own or in the relevant subheadings.
- Could use an image here, perhaps a diagram of the checkpoints
- I see that the timeline isn’t completely finished but so far the discoveries discussed are relevant to the topic and are summarised well (i.e. to the point and of a good length). However, there seems to be quiet big gaps in time, especially 1983-1992, may want to revisit this and add dates in between.
Entry into M-phase:
- May want to discuss what M-phase is briefly (what it stands for and what happens in it etc.)
- The use of subheadings in this section is good
- The phase-contrast photomicrograph image has not been properly formatted in that it’s lacking the info needed for it to be used on the page, i.e. reference, copyright clearance, student image statement, description of the image in own words. Also the thumb on the actual project page could be a little bigger and the caption a little more descriptive
- May want to discuss what exactly cyclin A, B, D and E do, i.e. the CDK’s they activate and when and what. This does this could be done in reference to the accompanying image
- The CDK info has no reference
- The student image statement is missing from the cyclin expression image and it has not been properly referenced
Metaphase to Anaphase Transition:
- Info is succinct and to the point
- Could perhaps add a research study to show the activity of the complex or checkpoint
- Could use an image to break up the text a bit
Mitogens and Cell division:
- I don’t think the word “definition” is necessary, could just go straight into what mitogens are
- Some citations may be missing for some paragraphs?
- Could use another image to break the text up towards the beginning of the section
- Clear and concise explinations
- Good use of subheadings
- Could explain a lot of the jargon in the glossary
- Could some of the history of the PDGF be added to the timeline?
- The schematic could use a legend that summarises the image in your own words, also the student image statement is missing
- I feel this section needs a lot more work, only one disease is briefly touched on
Current and Future Research:
- Good start, maybe consider summarising a few recent research papers and linking to them
- While the image in this section is great, it looks like it can’t be used because you have written “Copyright © 2003, Rights Managed by Nature Publishing Group” which is not a clearance statement. May want to ask about this.
Overall I feel that the project is on its way to being complete, there’s good use of subheadings, info is succinct and easy to understand and there are good images to accompany the text. I feel that some of the sections could be expanded on a little further, maybe add a few more research studies and perhaps you may need more references. You might want to revisit the images to make sure all the info required is there and also a glossary could be very useful.
Group 2: Cytokinesis
- Comprehensive and well summarised explanation of what cytokinesis is, may need to add references used
- May want to briefly summarise what will be discussed on the page
- Good accompanying image which has be properly formatted and referenced
- This section could use a bit more work, so far the summaries of the key discoveries which have been mentioned are relevant and to the point
- May want to stick with one colour for the table
- Good breakdown of this section, good use of subheadings
- Evidence of significant and in depth research
- Might want to refer to specific studies/research papers to enhance section a little further
- Linking to the glossary is very useful
- Could use more images to break-up the text and to help with the visualisation of what is being explained in this section
- Good use of a range of references
- Image is well formatted and referenced; all the necessary requirements for an image on the page are covered. May want to explain the image in own words
- Concise and easy to understand
- This section would be further enhanced with a diagram and/or image of the contractile ring and cleavage furrow
Animal vs Plant Cells:
- There’s a comprehensive explanation of the differences in the mechanisms of cytokinesis in plants and animals
- This section needs referencing
- Another way you could structure this section is in a table
- Good use of subheadings to break-up the section
- May want to explain the difference between stage I and II failure
- Good balance of image and text in this section
- Information is well researched and summarised
- Images look to be properly referenced and all required info is there
- Good summary of a range of current studies
- Could use more info on the direction of future studies
- Good use of links
- May want to add to the reference list
- It would be good if you could include an image from the studies
Overall, the topic appears to have been well researched, a few of the sections need some finishing off and a range of sources have been used but could use more references. Good use of links, external link section is very useful and adds to the page. Glossary is on its way to being completed and can see that it will include abbreviations and technical terms, like the way the text is linked to the glossary. The page could use a few more images to balance out the text.
Group 3: The Golgi Apparatus
- Sound intro, good explanation of what the golgi is and good summary of what will be discussed
- Great image, both schematic and electron microscopy view of the golgi. The student image template is missing and the thumb could be a little bigger so the image can be clearly seen
Structure and Function:
- Structure of the golgi has been summarised well. Function section could be summarised a little more. May be consider putting these two sections together under one subheading as they aren’t the main focus of the project
- Well structured timeline with significant discoveries that are summarised well and no major gaps in time, flows well
Models of Division:
- Interesting info, however, it’s not clear which model the golgi follows, does it follow one of these methods?
Morphology and Molecular Mechanisms:
- Feel as though the first sentence of the section belongs in the structure
- Section is divided up well with appropriate/logical subheadings
- Good balance of text and images
- First image lacks some of the info required (i.e. proper referencing, copyright clearance, student image template)
- Second image has required info but image could be further explained
- Third image has all the info needed but all its parts needs to be explained
- Information is well researched and summarised with good range of references
Current Model for Behaviour during Mitosis and Limitations of Current Models
- Good summary of the different models and their limitations
- Sections are broken up well
- The necessary info needs to be added to the image, like correct referencing and don’t think “Copy Right: Free PMC article Pubmed reference number: PMC2132765” is a copyright clearance statement, might want to double check if you can use this image
- A suggestion could be to present this info in table form, one comparing the two models and another listing the limitations of each
- Could use another image to balance the text
- Some of the info lacks referencing
Areas of Future Research:
- Interesting areas of research discussed
- Are there any current studies being conducted?
Overall, the topic has been well researched; a few structural rearrangements could be considered like the use of tables and the combining of subheadings. Some images also need to be revisited to adjust the referencing and making sure the clearance statements are correct. A few more images could be used.
Group 4: Spindle Apparatus
- I feel as though the actual spindle apparatus should be talked about more. While the definitions of mitosis and meiosis are good, I suggest that maybe these could go in the glossary instead and focus more on the role of the spindles in cell division. Maybe also give a brief overview of what the page will discuss
- Images accompanying text are great, showing the activity of the spindles and breaking up the text
- I think that the large image at the beginning of the page could be used in the body of the project, or made a little smaller if you want to keep it at the top of the page
- Images have all info required but need to fix up the referencing
- This section lacks referencing
- This section is very well researched
- Don’t think that the subheading in this section is necessary
- There are no major gaps in time so it flows well. However, some of the sections could be summarised a little more and may want to reconsider the first few dates and discoveries, could start with the discovery of the spindle
- Some of the discoveries lack referencing
- I like how images have been incorporated into the timeline, however, they should be referenced properly
- May want to include more recent discoveries
- This section contains a substantial amount of information, some of this could be better off in the function section or summarised more
- Good use of images which all contain the necessary information
- This section is very well researched, it does however repeat some of the info previously mentioned (particularly the first paragraph which isn’t referenced)
- This section could use an image or two to break-up the text, perhaps one from a previous section
- Feel as though some more referencing is needed
Mechanism of Formation:
- Good use of subheadings in this section
- Good balance of text and image. Some of the parts of the images could be explained in own words
- There appears to be some repetition of some info in the opening paragraph with the previous sections
- The different research studies have been explained thoroughly and summarised well and the accompanying images contribute to the section well.
- Maybe could provide links to these studies
- Could add some future research topics?
- Interesting section to include, well summarised and broken up
Overall, this topic has been researched well and there’s a good balance of text and images. There appears to be some repetition in the structure, function and mechanism sections particularly in the opening paragraphs and there’s some overlap in the structure and function sections