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From CellBiology

Lab Attendance

--Michael Orenstein 10:42, 10 March 2011 (EST)

--Michael Orenstein 10:35, 17 March 2011 (EST)

--Michael Orenstein 09:15, 24 March 2011 (EST)

--Michael Orenstein 09:17, 31 March 2011 (EST)

--Michael Orenstein 09:33, 7 April 2011 (EST)

--Michael Orenstein 09:06, 14 April 2011 (EST)

--Michael Orenstein 09:39, 21 April 2011 (EST)

--Michael Orenstein 09:39, 5 May 2011 (EST)

--Michael Orenstein 10:10, 12 May 2011 (EST)

--Michael Orenstein 10:18, 19 May 2011 (EST)

--Michael Orenstein 10:42, 26 May 2011 (EST)

--Michael Orenstein 09:39, 2 June 2011 (EST)

Individual Assessments

Lab 1

1. What are the key cell biology journals?

Journal of Cell Science

Cell

Nature Cell Biology

Journal of Cell Biology

BMC Cell Biology

Public Library of Science

2. Which journals allow reuse of their published content?

BMC Cell Biology

Journal of Cell Biology

Public Library of Science

Lab 2

1. Which chromosomes contribute to the nucleolus?

In humans, chromosomes 13, 14, 15, 21, and 22 contribute to the nucleolus.

2. Identify and add a link to your page of a recent cell biology article using confocal microscopy from the Pubmed database.

Pigmented Nodular Basal Cell Carcinomas in Differential Diagnosis with Nodular Melanomas: Confocal Microscopy as a Reliable Tool for In Vivo Histologic Diagnosis

Lab 3

1.Find the SDS information for chloroform and identify the hazards associated with this chemical.

SDS Choloroform Information

The hazards associated with chloroform are that it causes cancer in lab animals and is a possible carcinogen for humans. Inhaling or ingesting chloroform is extremely harmful and can be fatal. Chloroform may cause reproductive damage. Exposure of chloroform to alcohol may cause toxic effects. Chloroform is also an irritant and repeated or prolonged contact to skin may cause dermatitis.

2.You will need to upload an image and add it to your page, with the reference and copyright information with the image.

Validation of ultrasound dimension measurements by light microscopy.jpg

Validation of ultrasound dimension measurements by light microscopy[1]


Image Reference

  1. Junwu Mu, John C Slevin, Dawei Qu, Sarah McCormick, S Lee Adamson In vivo quantification of embryonic and placental growth during gestation in mice using micro-ultrasound. Reprod. Biol. Endocrinol.: 2008, 6;34 PubMed 18700008

Lab 4

1. Identify a commercial supplier of an antibody that relates to your group project topic.

GenScript is a commercial supplier of antibodies. Our group project is gap junctions and GenScript makes a connexin 30 antibody that can react with connexin 30 in rabbits, mice, human, and bovine due to sequence homology. Here is a link to the connexin 30 antibody available from GenScript: GenScript Connexin 30 Antibody

2. In mitochondria, where is the gene located that encode Cytochrome C and what keeps this protein trapped within the mitochondria? (Hint - Watch Part 2: Factors Involved in the Intrinsic Pathway of Apoptosis

The CYCS gene, which encodes for Cytochrome C, is located on chromosome 7. Therefore, it is located in the nucleus. Its cytogenetic location is 7p15.3. Cytochrome C is a key part of the electron transport chain. It is a highly soluble protein that normally remains trapped within the mitochondrial intermembrane space and is associated with the inner mitochondrial membrane. During apoptosis, the outer mitochondrial membrane becomes permeable, and factors such as Cyctochrome C are released into the cytosol. This finding tells us that it is the outer mitochondrial membrane which is responsible for keeping the Cytochrome C protein trapped within the mitochondria.

Lab 6

Percentage of Morphological Phenotypes in Groups A and B.JPG

1. A) What are the changes in phenotypes that you observe between Group A and Group B?

The majority of phenotypes for both Group A and Group B were phenotypes D and E (Pronged and Stringed respectively) . However, there was 10% more of phenotype D observed in Group A as well as nearly 15% more of phenotype E observed in Group A. Phenotypes A and F (Fan and Pygnotic respectively) were present at nearly the same rate, with Group B having 1-2% more for both phenotypes A and F. Finally, for phenotypes B and C (Broken Fan and Stumped respectively), there was slightly over 10% more of these phenotypes found in Group B as opposed to Group A. Overall, we found that the pronged and stringed phenotypes, which display more and longer neurites, were found more often in Group A (Tm4).

B) How does Tm4 mediate these changes?

Tm4, which is over expressed in Group A, clearly is mediating phenotypic changes observed since there is a clear difference in the percentage of phenotypes observed in Group A and opposed to Group B (Control Group). Tm4 is causing longer processes to form and more of these processes, thus resulting in a greater percentage of pronged and stringed phenotypes. Without over expression of Tm4, less cells will grow these processes, thus resulting in a greater number of cells that lack long and multiple processes, such as fan, broken fan, stumped, and pygnotic. This is clearly observed in Group B, which is the control group.

2. A) What are the changes in phenotypes that you observe between Group A and Group B?

In genotype A, we overexpressed Tm4. This caused lots of branching and processes to form. This increase in branch formation led to more touching and therefore interactions between cells. It was also noticed that the cells in group A were more brightly stained, since they are expressing more Tm4. In Genotype B, the control group, we simply noticed the opposite of genotype A. There was lass branching and less processes formed. There was less interaction between cells and overall the cells were less brightly stained.

B) How does Tm4 mediate these changes?

There are multiple types of actin binding proteins that are present in the nervous system. These proteins regulate the assembly and spatial organization of the microfilaments. One of these actin binding proteins is Tropomyosin, which stabilizes actin filaments. Although there are many isoforms of tropomyosin, the one that is of interest to us is Tm4. Tm4 is present in high concentrations in young animals, such as rats, which is a period where there is lots of neurite growth. This suggests that Tm4 plays a role in neurite growth.[1] This finding is continuous with what we observed when contrasting the phenotypes of group A and B, since Group A, which overexpressed Tm4, was found to have many more neurites growing from the cell body. Tm4 is very important for a developing brain since it is involved in neurite growth, thus allowing more connections to be formed.[2] This is consistent with our finding that group A had many more cells touching and interacting. overall, Tm4 is clearly mediating the phenotypic changes that we see by enhancing neurite growth and increasing the number of interactions between cells.

Lab 9

1. Identify from one of the cell line repositories: a neural cell line and a muscle cell line.

ATCC: The Global Bioresource Center supplies cell lines and hybridomas.

Neural Cell Line: Neuroblastoma

Muscle Cell Line: Muscle Myoblast

2. Identify the species and growth conditions for these cell lines.

Neuroblastoma

Species: Mus musculus (mouse)

ATCC complete growth medium: The base medium for this cell line is ATCC-formulated Eagle's Minimum Essential Medium, Catalog No. 30-2003. To make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 10%.

Atmosphere: air, 95%; carbon dioxide (CO2), 5%

Temperature: 37.0°C

Muscle Myoblast

Species: Mus musculus (mouse)

ATCC complete growth medium: The base medium for this cell line is ATCC-formulated Dulbecco's Modified Eagle's Medium, Catalog No. 30-2002. To make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 10%.

Temperature: 37.0°C

Lab 10

Peer Review of Five Other Group Projects (Posted also on each Discussion Board

Synaptic Junction (Group 1)

While I thought it was smart of this group to start with a brief understanding of the CNS, They wrote a full paragraph on the CNS without using a single reference. It shouldn’t be assumed that information about the CNS is common knowledge. Also, I may be wrong but I don’t think that synaptic junction should be capitalized every time it is written in the introduction. The groups’ history of synaptic junction ends in 1981. I’m sure that there have been important points on synaptic junctions that have came about in the last 30 years. The first sentence of “What is a Synaptic Junction” is very unclear and ahs grammar mistakes (to should be two). I would advise that this whole paragraph be re read to make clearer as there are a few sentences where the word “is” is used instead of “are”. Also, all 3 references for this section are placed at the end of the paragraph but I think that if a person looking at this page wanted specific information on one of their points, it would be easier for that person to access if they referenced immediately after the specific point. This is a thing that I noticed in the section “Types of Synaptic Junctions” as well. I liked the use of the schematic sketch (in the “What is a Synaptic Junction” section) to illustrate the synaptic junction. I found it made the paragraph easier to understand. The electrical and chemical synapse pictures that the student drew are really great and creative. I find it really cool that someone was able to draw these so well. One suggestion that I have that may make the page clearer is to possibly bold some important parts of the text. For example when the page mentions that the synapse has two key parts, I would then say to maybe make axon terminal and receptive region in bold to make them stand out more. In their table, I believe that gap junctions carry more than just ion current. There is no copyright information for the picture labelled “Steps of Transmission in Neural Networks”. I like the use of tables by this group. It helps summarize many paragraphs. There is no copyright information for the picture labelled “Proposed Model for the voltage dependent calcium channels”. I found the section on synaptic integration and modulation very well done and easy to understand. The image “Neurotransmitters” is missing reference information. Also, most of the section “Neurotransmitters” has no references whatsoever. It is a bit confusing in the disease section when it switches from Parkinson’s to Myasthenia Gravis. I know this is a formatting issue but I figured I would mention that they should make it clearer that they are addressing a new disease. Overall this was a clear project but there are certain grammar issues as well as referencing issues that need to be addressed.

Tight Junctions (Group 3)

The introduction is simple and clear. However, the picture “Schematic of the various cell-cell junctions” is lacking copyright and reference information. The history is clear and concise but seems to be lacking any important discoveries from the 1950s and 1970s. Perhaps there were none made during this time period but that gap jumped out at me. In the Structure section, there seems to be a lack of referencing at the beginning of the section. The picture titled “Schematic model of the basic structural transmembrane components of tight junctions” is lacking copyright and referencing information. The group may mean that this picture was made by them but I can’t tell so perhaps they should make it clearer if that is the case. I found the use of bullet points to display the roles of occludins, claudins and other proteins very helpful and clear. This makes for an easy read for the reader. The structure section was extremely informative and easy to read. The Barrier Function section is missing some content. It says “If the tight junction were not present then solutes from could…” Solutes from what? For the “Transcellular and Paracellular Transport section, I would say to maybe put the first use of those 2 words in bold so that the reader can easily find their definition. The picture with the legend “Circuit Model for the Measure of TER” is missing copyright information. Under the section “Classification of Epithelia Using Tight Junctions”, when the paragraph starts to talk about TER and circuit models I find that it becomes a bit confusing. There are a couple of run on sentences there that, if fixed, would make it way easier to comprehend the information. I liked how the “Disease” section provides a brief introduction into how tight junctions can malfunction followed by a table which provides a brief summary on many of the diseases affiliated with abnormal tight junctions.

Desmosomes (Group 4)

I think the introduction should have a basic picture of a desmosome just so while reading the following sections we have a basic idea of structure. I also think it would be more appealing to the reader if the history section had 1 or 2 pictures of some of the findings that are stated in the history. The intro to the structure of desmosomes did a great job of clearly defining what the rest of the section would be talking about. I also thought that the use of a picture or diagram in each structure subsection was great for helping me visualize what it is I just read. The function section is a bit confusing. There are some run on sentences which make the content somewhat difficult to understand. For example: “Electron microscopy (EM) and specialised freeze fracture histological techniques viewing these electron dense structures make it possible to suggest the manner in which these extracellular core domain (ECD) transmembrane homophillic cell-cell adhesion glycoprotein cadherins, namely desmocollin and desmoglein, bind to each other, zipper like, in the midline between two cells.” I thought that the discussion of KO mice to investigate function was a really smart idea to discuss in this group project. The brief discussion of hemidesmosomes was a useful addition to this page. The picture in the calcium section lacks copyright and referencing. The picture in the desmoplakin section lacks referencing. The Arrhythmogenic Right Ventricular Cardiomyopathy section does not really say how desmosomes are affected in this disease. I am unsure if they mean that all cell adhesions are affected or if it is just desmosomes. The pictures “Presence of Desmoplakin in Cells”, “ECM of Desmosomes”, and “Desmoplakin” (pictures 1, 2, and 4 in the Images and Videos Section lack referencing information.

Adherens Junctions (Group 5)

I think the introduction section would be more interesting and educational if it had a basic picture of an adherens junction just so the reader can have a basic idea of structure as he continues to read through the following sections. The History section has a 120 year gap from 1839-1961. I don’t know if any research was done during this time period but if there was it should be mentioned to complete the content. The section on cadherin structure was very well done. It is straight to the point and easy to understand. Also, the use of bolding key words was helpful in emphasizing what are the key structural components. The video link was also helpful. The first paragraph in Function section is lacking referencing. I liked how the function section discussed particular experiments that were done to help show adherens junction function. The function section does not have any images so that part of the page is a bit boring to look at. It would be great if there were pictures of the adherens junctions performing their function. The first image in the Importance and Regulation section is lacking referencing information. The final points in the importance and regulation section states that if it is controlled correctly it can be a huge step in medical fields but it says nothing about how this is so. Finally, I thought that the use of a table to give a brief description of the different types of junctions was a really smart way to give the reader an idea of how all these junctions function. Furthermore, each of the Junctions associated with a 2011 group project link out to that project page. The gap junction picture is missing copyright information.

Neuromuscular Junction (Group 6)

The 1914 history note has a typo (warded should be awarded). The use of point form throughout the text is really good because it allows each important point to stick out. The History section is pretty informative but it ends in the year 2000. I think the addition of one or two recent history points would be a good addition to the page. The whole first paragraph in the Mechanism of Action section is missing referencing. The first sentence of the mechanism of action section is also confusing. The first paragraph under the Acetylcholine section is missing referencing. The YouTube videos throughout the project don’t have any copyright information so perhaps this group should post whatever it is YouTube says about its content. The “Acetylcholine Nicotine” image in the AChR’s section is missing referencing information. The use of a table in the Important Structural Component was a smart idea because it presents relevant information about the different components in a clear, organized manner. The image in the synaptic vesicles part of the table is lacking referencing information. The Ion gated channels and receptors part of the table has no referencing in it. The images in the postsynaptic membrane, Schwann cell, and Mitochondria parts of the table do not have referencing information. There is also no referencing information for any of the content written about Schwann Cells. I like how the group numbered the 3 principle ways in which muscle fibres form ATP. Beginning with the second sentence of the Embryonic Development of the NMJ section to the end of that paragraph there is no reference information. Although the content there is very informative, there should definitely be some referencing information to back it up. The “Human Embryo” picture lacks referencing information. The two pictures in the “Innervation of individual endplates” subsection lack copyright information. The two pictures in the “Presence of Multiple Endplates” subsection also lack copyright information. Furthermore, the text written in this subsection does not have any referencing. It isn’t common knowledge that multiple endplates are present. The picture accompanying the Myasthenia Gravis disorder lacks referencing information. The image accompanying the Botulism disease has copyright information that does not necessarily allow the group to use the image. It says to ask for permission. The current associated research section was very well done because it had many pictures that related to the actual research that this section of the project discussed. For many of the referencing done for images throughout this project, the group simply lists the website. I am not sure if that is ok or not. This occurs for all images in the Current Associated Research section. Both the C elegans and the synaptic vesicle images in the Future Research section lack referencing.


References

  1. L Had, C Faivre-Sarrailh, C Legrand, J Méry, J Brugidou, A Rabié Tropomyosin isoforms in rat neurons: the different developmental profiles and distributions of TM-4 and TMBr-3 are consistent with different functions. J. Cell. Sci.: 1994, 107 ( Pt 10);2961-73 PubMed 7876361
  2. L Had, C Faivre-Sarrailh, C Legrand, J Méry, J Brugidou, A Rabié Tropomyosin isoforms in rat neurons: the different developmental profiles and distributions of TM-4 and TMBr-3 are consistent with different functions. J. Cell. Sci.: 1994, 107 ( Pt 10);2961-73 PubMed 7876361

Work Area

Lab 1

Here is some bold text

Here is some italic text

Lab 1 2011

J of Cell Biology Homepage

Lab 2

Pubmed

Lab 3

copy thing + pmid on pubmed

reference --> Clifford P Brangwynne, Timothy J Mitchison, Anthony A Hyman Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes. Proc. Natl. Acad. Sci. U.S.A.: 2011, 108(11);4334-9 PubMed 21368180


This is about frog nucleoli shape changes.[1]

Reference List

  1. Clifford P Brangwynne, Timothy J Mitchison, Anthony A Hyman Active liquid-like behavior of nucleoli determines their size and shape in Xenopus laevis oocytes. Proc. Natl. Acad. Sci. U.S.A.: 2011, 108(11);4334-9 PubMed 21368180