User:Z3284061

From CellBiology

lab Attendance

--Maqdad Al Saif 10:42, 17 March 2011 (EST) I accidentally deleted the previous attendance which is supposed to be (10th). I have already spoken to Dr.Mark Hill.

Maqdad Al Saif 10:42, 17 March 2011 (EST)

Maqdad Al Saif 9:00, 24 March 2011 (EST)

--Maqdad Al Saif 10:22, 31 March 2011 (EST)

--z3284061 09:38, 7 April 2011 (EST)

--z3284061 09:06, 14 April 2011 (EST)

--z3284061 09:16, 21 April 2011 (EST)

--z3284061 09:29, 5 May 2011 (EST)

--z3284061 10:10, 12 May 2011 (EST)

--z3284061 09:21, 19 May 2011 (EST)

Peer Assessments

Group 2: Gap Junctions:

Overall, a great effort can be seen from the Page.

However, I have some points that might be useful to improve the page:

1) Introduction Section: the photos are not titled, and the second photo with channels is slightly big, it might look better with a smaller version.

2) History shows lots of information, and the group has done more than enough research. It looks long.

3) The em Photos in the History Section could be moved to the Structure.

4) Functional role, location and comparison, I don’t see how it can be improved, because I like the balance between photos and words. Well done.

5) Photos in “ Diseases Associated with Gap junctions could be moved to the right or left so they don’t take too much space

in the page.


Group 3 Tight Junctions:

I like how you manage to use photos in each section, which makes the reader keen to look through the content. History is the

appropriate length of information. As for the Structure: The photo on the left could be resized to smaller. The use of dot points

is a great way and it makes it easier to read.

Maybe for the classification section, It would be alot easier if you make it as a table.

Finally the Table of Diseases is remarkable. Shows good description of all the diseases mentioned.

I think for the Glossary, Having such a deep understanding of the Topic, It be expected to be more than 7 words. References are a

minor issue, it can be fixed later on.

Overall, The page shows a deep research and cooperation between the group members.


Group 4" Desmosomes"

Magnificent effort with the project information and details. You manage to have all the essential subheadings. I do ,however, have some suggestions;

With regards, to the function, you could add some small subheading or bolded.

I loved all the microscopic images.

Make sure the “Changes in adhesive state influence function of epithelia” image is aligned properly.

Finally, spend some time adjusting the reference list.

Group5: Adherens Junction:

Fantastic Job with the visualizations. Drawings are great :)

For the Structure: I reckon it will be easier to read if you add another minor subheadings.

As for the Function, you could number the functions.

I’m not entirely sure if you are allowed to leave the whole article as a reference in “ the Current Research”

I like the variety of references. And So is the table… Well done.

Group 6: Neuromuscular junction.

The page speaks for itself. I love the layout of the whole project. The content is diversified. It was easy for me to see and look

up the required information :) . I would suggest you to minimize the size of images, since some of them are quite big. Great use of table for the component.

I noticed in the Mechanism of Action: I found it a little confusing, because if they all belong to the same structure and in

order, I Would number them. ( i.e. 1) motor neuron, 2) ACh, 3) AChR’s 4) Motor End plate.

It is well referenced and I find it hard to criticise the project page.

Overall, Marvellous piece of work.


Individual Assessments

Lab 1

1. What are the key cell biology journals?

A. The Journal of Cell Biology

B. Public Library of Science

C. Nature Cell Biology

D. Trends in Cell Biology

E. Cell

2. Which Journals allow reuse of their published content?

A. BMC Cell Biology

B. The Journal of Cell Biology

C. Public Library of Science

Lab 2

1. Which chromosomes contribute to the nucleolus?

There are several functions carried out by the nucleolus including; ribosome assembly, processing of ribosomal (rRNA), and trascription. The nucleolus contains clumps of chromatin which include chromosomes containing nuclear organizer regions. In Human cells these chromosomes are mainly; 13, 14, 15, 21 and 22.

Source The nucleolus

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

Reflectance Confocal Microscopy as an aid to Dermoscopy to improve Diagnosis on Equivocal Lesions: Evaluation of Three Bluish Nodules

Lab 3

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

Health hazard information of Chloroform

1. Harmful if Swallowed.

2.Causes Skin Irritation.

3.Causes Eye Irritation.

4.Suspected of causing cancer.

5.Suspected of Damaging the unborn child.

6.May Cause Drowsiness or Dizziness.

7.May Cause Damage to Liver and Kidneys Through Prolonged or Repeated Exposure.


For more details regarding the SDS information, please click on the link. SAFETY DATA SHEET CHLOROFORM


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

Comparison of micrograph and microCT scans in spiders.jpg[1]


Lab 4

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

Synapsin I antibody is supplied by Abcam antibodies in Cambridge,UK. It is a member of the synapsin family. Synapsins are neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles.Family members are characterized by common protein domains, and they are implicated in synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. This member of the synapsin family plays a role in regulation of axonogenesis and synaptogenesis. The protein serves as a substrate for several different protein kinases and phosphorylation may function in the regulation of this protein in the nerve terminal. Mutations of the Synapsin I gene may be associated with X linked disorders with primary neuronal degeneration such as Rett syndrome.

For further reference:

Synapsin I Antibody

# In mitochondria, where is the gene located that encode Cytochrome C and what keeps this protein trapped within the mitochondria?

Cytochrome c is Electron carrier protein, exclusively localized in the mitochondria. Cytochrome c gene is located on chromosome Number 7. It is the only water soluble and trapped inside the mitochondria by Alpha membrane of mitochondria.

The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain.

Plays a role in apoptosis. Suppression of the anti-apoptotic members or activation of the pro-apoptotic members of the Bcl-2 family leads to altered mitochondrial membrane permeability resulting in release of cytochrome c into the cytosol. Binding of cytochrome c to Apaf-1 triggers the activation of caspase-9, which then accelerates apoptosis by activating other caspases.

Lab 6

Graph of Phenotypes.JPG

Write a summary of the Table!

This table illustrates the difference in Phenotype percentage between Group A and B


Q1: What are the changes in phenotypes that you observe between Group A and Group B in your graph?

Write a summary of the Graph

Tm4= group A, Control= Group B Phenotype A: There was no observable presence of Tm4 cells in group A, whereas more than 10% of Group B.

Phenotype B: Group A (Tm4) is less than Group B by more than 10%.

Phenotype C: There is approximately 10% difference between the 2 groups.

Phenotype D: There’s a big difference (>20%) between Group A(Tm4) and group B(control)

Phenotype E: Tm4 is about 5% more than group B.

Phenotype F: The % of Group B has decreased dramatically.


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

Group A ( Tm4) Group B (Control)
Generally Pink in appearance Red in appearance
Yellow in the edges No observable yellow in the edges.
Blue-pink nuclei Purple-Blue nuclei.
More stringed and prolonged phenotypes. More stumped and broken fan phenotypes
Cells are likely to be separated Cells are more fused together


How Does Tm4 mediate these changes?

Background:Tropomyosins are among the most studied structural proteins of the actin cytoskeleton that are implicated in alterations of actin filament organization in transformed cells. Decreased expression of non-muscle tropomysons is commonly associated with transfomed phenotype. The changes in Tm expression appear to correlate well with the rearrangement of microfilament bundles and morphological alterations observed in transformed cells. The decrease in Tm synthesis has been reported to occur in cells transformed by a variety of agents including chemical carcinogens.


It has been hypothesized main role of Tm4 is regulation of the adhesion structures of cells (such as osteoclasts) by stabilizing filamentous actin in podosomes and actin rings and thus affecting migration and function of the cell ( such as bone resorption). Moreover, Tm4 has a strong localization to the actin core of the podosome and in the actin ring. Furthermore, Tm4 is the only product of the delta tropomyosin gene. Finally, Tm4 forms a cap on the actin ring, localizing to the exterior, top, and interior sides of the actin ring denoted by arrows and the yellow merge.

Lab 9

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


Neuron cell Line:

Media: HCN-1A (CRL-10442) DMEM (30-2002) Fetal Bovine Serum (30-2020) Organ: brain Cell Type: cortical neuron; Cellular Products: tubulin; neurofilament protein; somatostatin; cholecystokinin-8 Permits/Forms: In addition to the MTA mentioned above, other ATCC and/or regulatory permits may be required for the transfer of this ATCC material. Anyone purchasing ATCC material is ultimately responsible for obtaining the permits. Please click here for information regarding the specific requirements for shipment to your location. DNA Profile (STR): Amelogenin: X CSF1PO: 10 D13S317: 11,12 D16S539: 12 D5S818: 11,12 D7S820: 11,12 THO1: 9.3 TPOX: 11 vWA: 17 Age: 18 months Gender: female Comments: The cells stain positively for a number of neuronal markers including neurofilament protein, neuron specific enolase (NSE). [48286] They are also positive for tubulin, vimentin, somatostatin (SST), glutamate, gamma aminobutyric acid (GABA), cholecystokinin - 8 (CCK-8) and vasoactive intestinal peptide (VIP). [22022] The cells are negative for glial fibrillary acidic protein (GFAP) and myelin basis protein (MBP). [48286] HCN-1A cells can be induced to differentiate when cultured with a mixture of nerve growth factor (NGF), dibutyryl cyclic adenosine monophosphate (cAMP) and 1-isobutyl-3-methylxanthine (IBMX). [22022] Differentiation is accompanied by mature morphology and slowing of growth (doubling time greater than 120 hours). [22022] Unlike HCN-2 (see ATCC CRL-10742) the growth rate of HCN-1A cells is not affected by phorbol esters. [22022] Propagation: 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 Growth Conditions: The growth medium must be adjusted to pH 7.35 prior to filtration Subculturing: Protocol:

Remove and discard culture medium. Briefly rinse the cell layer with 0.05% (w/v) Trypsin - 0.53 mM EDTA solution to remove all traces of serum which contains trypsin inhibitor. Add 2.0 to 3.0 ml of Trypsin-EDTA solution to flask and observe cells under an inverted microscope until cell layer is dispersed (usually within 5 to 15 minutes). Note: To avoid clumping do not agitate the cells by hitting or shaking the flask while waiting for the cells to detach. Cells that are difficult to detach may be placed at 37C to facilitate dispersal. Add 6.0 to 8.0 ml of complete growth medium and aspirate cells by gently pipetting. To remove trypsin-EDTA solution, transfer cell suspension to centrifuge tube and spin at approximately 125 xg for 5 to 10 minutes. Discard supernatant and resuspend cells in fresh growth medium. Add appropriate aliquots of cell suspension to new culture vessels. Place culture vessels in incubators at 37C.


CRL-10442 has been shown to senesce at approximately passage 17. Current distribution stocks are prepared with a minimum of only 2 passages remaining under recommended culture conditions after cryopreservation. Subcultivation Ratio: A subcultivation ratio of 1:2 to 1:3 is recommended Medium Renewal: 1 to 2 times per week Preservation: Freeze medium: Complete growth medium supplemented with 5% (v/v) DMSO Storage temperature: liquid nitrogen vapor phase Related Products: Recommended medium (without the additional supplements or serum described under ATCC Medium):ATCC 30-2002 recommended serum:ATCC 30-2020 References: 22022: Ronnett GV, et al. Human neuronal cell line. US Patent 5,196,315 dated Mar 23 1993 48286: Ronnett GV, et al. Human cortical neuronal cell line: establishment from a patient with unilateral megalencephaly. Science 248: 603-605, 1990. PubMed: 1692158

Muscle Cell Line:

Media: L6 (CRL-1458) DMEM (30-2002) Fetal Bovine Serum (30-2020)

Tissue: skeletal muscle Cell Type: myoblast myoblast; Cellular Products: myosin Permits/Forms: In addition to the MTA mentioned above, other ATCC and/or regulatory permits may be required for the transfer of this ATCC material. Anyone purchasing ATCC material is ultimately responsible for obtaining the permits. Please click here for information regarding the specific requirements for shipment to your location. Applications: transfection host (Nucleofection technology from Lonza Roche FuGENE® Transfection Reagents) Comments: The L6 myogenic line was isolated originally by Yaffe from primary cultures of rat thigh muscle maintained for the first two passages in the presence of methyl cholanthrene. [22581] L6 cells fuse in culture to form multinucleated myotubes and striated fibers. The extent of cell fusion declines with passage and the cells should be frozen at low passage and periodically recloned with selection for fusion competent cells. Tested and found negative for ectromelia virus (mousepox). Propagation: 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%. Atmosphere: air, 95%; carbon dioxide (CO2), 5% Temperature: 37.0°C Growth Conditions: The myoblastic component of this line will be depleted rapidly if the cells are allowed to become confluent. Subculturing: Protocol: Subculture before the cells become confluent to retard the loss of differentiating ability that is observed as the cells are passaged.

Remove and discard culture medium. Briefly rinse the cell layer with 0.25% (w/v) Trypsin- 0.53 mM EDTA solution to remove all traces of serum that contains trypsin inhibitor. Add 2.0 to 3.0 ml of Trypsin-EDTA solution to flask and observe cells under an inverted microscope until cell layer is dispersed (usually within 5 to 15 minutes). Note: To avoid clumping do not agitate the cells by hitting or shaking the flask while waiting for the cells to detach. Cells that are difficult to detach may be placed at 37°C to facilitate dispersal. Add 6.0 to 8.0 ml of complete growth medium and aspirate cells by gently pipetting. Add appropriate aliquots of the cell suspension to new culture vessels. Incubate cultures at 37°C.


Subcultivation Ratio: A subcultivation ratio of 1:20 to 1:40 is recommended Medium Renewal: 2 to 3 times per week Preservation: Freeze medium: Complete growth medium supplemented with 5% (v/v) DMSO Storage temperature: liquid nitrogen vapor phase Related Products: Recommended medium (without the additional supplements or serum described under ATCC Medium):ATCC 30-2002 recommended serum:ATCC 30-2020 References: 1064: Mandel JL, Pearson ML. Insulin stimulates myogenesis in a rat myoblast line. Nature 251: 618-620, 1974. PubMed: 4421831 22255: Richler C, Yaffe D. The in vitro cultivation and differentiation capacities of myogenic cell lines. Dev. Biol. 23: 1-22, 1970. PubMed: 5481965 22581: Yaffe D. Retention of differentiation potentialities during prolonged cultivation of myogenic cells. Proc. Natl. Acad. Sci. USA 61: 477-483, 1968. PubMed: 5245982 33164: Osawa H, et al. Identification and characterization of basal and cyclic AMP response elements in the promoter of the rat hexokinase II gene. J. Biol. Chem. 271: 17296-17303, 1996. PubMed: 8663388 33165: Osawa H, et al. Analysis of the signaling pathway involved in the regulation of hexokinase II gene transcription by insulin. J. Biol. Chem. 271: 16690-16694, 1996. PubMed: 8663315

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

Neural:

Media: HCN-1A (CRL-10442) DMEM (30-2002) Fetal Bovine Serum (30-2020)

Dulbecco's Modified Eagle's Medium (DMEM) Quantity: 500 ml Storage: 2 to 8 degrees C Biosafety Level: 1 Formulation Permits/Forms: In addition to the MTA mentioned above, other ATCC and/or regulatory permits may be required for the transfer of this ATCC material. Anyone purchasing ATCC material is ultimately responsible for obtaining the permits. Please click here for information regarding the specific requirements for shipment to your location. Comments: Modified to contain 4 mM L-glutamine, 4500 mg/L glucose, 1 mM sodium pyruvate, and 1500 mg/L sodium bicarbonate. NOTE: This reduced level of sodium bicarbonate (NaHCO3, 1.5 g/L) is intended for use in 5% CO2 in air. Additional sodium bicarbonate may be required for use in incubators containing higher percentages of CO2.

Description: Fetal Bovine Serum

Quantity: 500 ml Storage: -20 degrees C Biosafety Level: 1 Permits/Forms: In addition to the MTA mentioned above, other ATCC and/or regulatory permits may be required for the transfer of this ATCC material. Anyone purchasing ATCC material is ultimately responsible for obtaining the permits. Please click here for information regarding the specific requirements for shipment to your location. Comments: Triple filtered through 0.1-um filters. Each lot of fetal bovine serum is tested for sterility and for the ability to support the growth of several different cell lines using both sequential growth curves and plating efficiencies. Fetal bovine serum is manufactured from fetal bovine blood collected in USDA-inspected abattoirs located in the United States.


For Muscle:

Media: L6 (CRL-1458) DMEM (30-2002) Fetal Bovine Serum (30-2020)

Dulbecco's Modified Eagle's Medium (DMEM)

Quantity: 500 ml Storage: 2 to 8 degrees C Biosafety Level: 1 Formulation Permits/Forms: In addition to the MTA mentioned above, other ATCC and/or regulatory permits may be required for the transfer of this ATCC material. Anyone purchasing ATCC material is ultimately responsible for obtaining the permits. Please click here for information regarding the specific requirements for shipment to your location. Comments: Modified to contain 4 mM L-glutamine, 4500 mg/L glucose, 1 mM sodium pyruvate, and 1500 mg/L sodium bicarbonate. NOTE: This reduced level of sodium bicarbonate (NaHCO3, 1.5 g/L) is intended for use in 5% CO2 in air. Additional sodium bicarbonate may be required for use in incubators containing higher percentages of CO2.

Description: Fetal Bovine Serum Quantity: 500 ml Storage: -20 degrees C Biosafety Level: 1 Permits/Forms: In addition to the MTA mentioned above, other ATCC and/or regulatory permits may be required for the transfer of this ATCC material. Anyone purchasing ATCC material is ultimately responsible for obtaining the permits. Please click here for information regarding the specific requirements for shipment to your location. Comments: Triple filtered through 0.1-um filters. Each lot of fetal bovine serum is tested for sterility and for the ability to support the growth of several different cell lines using both sequential growth curves and plating efficiencies. Fetal bovine serum is manufactured from fetal bovine blood collected in USDA-inspected abattoirs located in the United States.

Work Area

Here is some bold text

Here is some italic text

Teaching my favorite students basic stuff

The Journal of Cell Biology Homepage

http://www.ncbi.nlm.nih.gov/pubmed/

Pubmed


References

  1. Lisa M Fenk, Karin Heidlmayr, Philipp Lindner, Axel Schmid Pupil size in spider eyes is linked to post-ecdysal lens growth. PLoS ONE: 2010, 5(12);e15838 PubMed 21209876