User:Z3377769

From CellBiology

Lab Attendence

Lab 1 --Z3377769 (talk) 15:54, 14 March 2013 (EST)

Lab 2 --Z3377769 (talk) 16:19, 21 March 2013 (EST)

Lab 3 --Z3377769 (talk) 15:11, 28 March 2013 (EST)

Lab 4 ----

lab 5 --Z3377769 (talk) 15:12, 18 April 2013 (EST)

Lab 6 --Z3377769 (talk) 15:08, 2 May 2013 (EST)

Lab 7 --Z3377769 (talk) 16:16, 9 May 2013 (EST)

Lab 8 --Z3377769 (talk) 15:07, 16 May 2013 (EST)

Cells

Blood Cell Variations

External Link

[1]


Individual Assessments

Lab 1

Schema of Bi genomic prokaryote.png

Schema of Bi Genomic Prokaryote

Gross L (2006) The More the Merrier: Multiple Genomes in a Parasitic Prokaryote. PLoS Biol 4(6): e212. doi:10.1371/journal.pbio.0040212

© 2006 Public Library of Science. 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.

Lab 2

[1]


Article Using Confocal Microscopy

The Role of Siglec-1 and SR-BI Interaction in the Phagocytosis of Oxidized Low Density Lipoprotein by Macrophages

This article was attempting to find the role of Siglec-1 in atherosclerosis because of its highly expressed levels in the plaques of atherosclerosis patients. One of the techniques used in this study was laser scanning confocal microscopy (LSCM). This technique allowed researchers to investigate how uptake of Low Density Lipid (LDL) was affected by Siglec-1, by analyzing the effect of Siglec-1 treated cultures.


[2]

[2]

--Mark Hill (talk) 10:35, 11 April 2013 (EST) This recent research article uses CLSM for localisation, your explanation could have been clearer as to "how" it contributes to the findings. I have also shown below how the reference should be located, as in research articles and your group project.


This article[3] was attempting to find the role of Siglec-1 in atherosclerosis because of its highly expressed levels in the plaques of atherosclerosis patients. One of the techniques used in this study was laser scanning confocal microscopy (LSCM). This technique allowed researchers to investigate how uptake of Low Density Lipid (LDL) was affected by Siglec-1, by analyzing the effect of Siglec-1 treated cultures.

Lab 3

Article 1

A new model for nuclear envelope breakdown[4]

This article used fluorescent 70-kDa dextran dye in order to investigate their hypothesis. While this technique has been used previously this new report postulated that in the second phase of nuclear breakdown the permeability of the neuron pores changed. Immediately before the germinal vesicle (nuclear) breakdown (GVDB). The magnitude of permeability increased from .04 micro m/s to .15 micro m/s. This increase of magnitude allowed the 70-kDa dextran to enter the nuclear pore which it would not normally be able to do. This discovery indicates that disassembly of the nuclear pore happens further before breakdown that previously understood. At the end of the paper they propose a new model for nuclear envelope breakdown in three stages as opposed to the previous model of two. This article related mainly to breakdown of the nuclear envelope but also to current and future research.



Article 2

Structural organization of the human gene encoding nuclear lamin A and nuclear lamin C[5]

The researchers have discovered the section of the human genome that encodes for nuclear lamin proteins. These proteins are being increasingly studied in order to understand their role in nuclear replication and their links to diseases like cancer. Also referencing another reviewed work these lamins have been linked with nuclear spindle defects during the mitotic cycle. The lamins are then linked to specific cell proteins and functions because of the way they are alternatively spliced, indicating they can be modified to achieve specific needs of the nuclear envelope or cell. There is also evidence to suggest that all lamins have a common ancestor as their structures were found to be very similar in other species


Article 3

Diseases of the Nuclear Envelope[6]

This review paper outlines diseases that effect the nuclear envelope (NE). A major topic of this paper are mutations of the LMNA gene which codes for the type A nuclear lamins. These are filament proteins of the nuclear envelope. Dysfunctional version of these proteins or mutations of the gene have been linked to a wide variety of diseases from dilated cardio-myopathy to muscular dystrophy. Collectively these diseases are known as Laminopathies or Nuclear Envelopathies. While the exact role of these proteins in Laminopathies is not known the article collates strong evidence that the filament proteins have more of a role than just structural support. Abnormalities in the lamina proteins could perhaps affect cytoskeleton structure according to Crisp et al 2006 [1]. This paper related well to abnormalities in nuclear breakdown as it discusses the potential role of lamin proteins in the pathogenesis of multiple diseases.

[1.] Crisp M, Liu Q, Roux K, Rattner JB, Shanahan C, Burke B, Stahl PD, Hodzic D 2006. Coupling of the nucleus and cytoplasm: Role of the LINC complex. J Cell Biol 172:41–53.

Article 4

The Nuclear Envelope[7]

This review article discusses the nuclear envelope (NE) and its components. Specifically for our research page it has good depth concerning the mitotic functions of nuclear envelope components. Research compiled over the years has provided strong evidence for the NE being “absorbed” into the endoplasmic reticulum (ER) [Ellenberg et al. 1997[1]; Anderson and Hetzer 2007[2]; Anderson and Hetzer 2008a[3]; Anderson et al. 2009a[4]; Lu et al. 2009[5]]. In fact data discussed in this paper has postulated that reshaping the ER could be critical in NEBD (nuclear envelope breakdown) (Voeltz et al 2006)[6]. The idea that NE components have a role in mitosis is still an idea being investigated but the article mentions research where this idea is becoming increasingly likely. This article briefly touched on lamins, these are “intermediate-filament proteins” and are a part of the nuclear lamina.

[1]Ellenberg J, Siggia ED, Moreira JE, Smith CL, Presley JF, Worman HJ, Lippincott-Schwartz J 1997. Nuclear membrane dynamics and reassembly in living cells: Targeting of an inner nuclear membrane protein in interphase and mitosis. J Cell Biology 138:1193–1206.

[2]Anderson DJ, Hetzer MW 2007. Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum. Nat Cell Biol 9:1160–1166

[3]Anderson DJ, Hetzer MW 2008a. Reshaping of the endoplasmic reticulum limits the rate for nuclear envelope formation. J Cell Biol 182:911–924

[4]Anderson DJ, Vargas J, Hisao J, Hetzer MW 2009a. Recruitment of functionally distinct membrane proteins to chromatin mediates nuclear envelope formation in vivo. J Cell Biol 186:183–191

[5]Lu L, Ladinsky MS, Kirchhausen T 2009. Cisternal organization of the endoplasmic reticulum during mitosis. Mol Biol Cell 15:3471–3480

[6]Voeltz GK, Prinz WA, Shibata Y, Rist JM, Rapoport TA 2006. A class of membrane proteins shaping the tubular endoplasmic reticulum. Cell 124:573–586

Image

300px

--Mark Hill (talk) 16:25, 13 June 2013 (EST) You do not have permission to reuse this image. It has been deleted. I spent some time in the practical tutorial and 0nline Copyright Tutorial covering copyright issues.


This ref listing was fine, but it is not what was asked. You needed to use the pubmed ref format, as I have added below.

M Terasaki, P Campagnola, M M Rolls, P A Stein, J Ellenberg, B Hinkle, B Slepchenko A new model for nuclear envelope breakdown. Mol. Biol. Cell: 2001, 12(2);503-10 PubMed 11179431


Lab 7 Assessment

Untitled.png

1)Do you see any change in phenotype between Group A (Tm4 over-expression) and Group B (control)?


The above graph shows there is a difference in the phenotypes expressed between group A and B. Over 40% of group A (cell had Tm$ over-expression) cell were in the C (stumped). This contrasts with group B which contained less than 50% in this phenotype. Furthermore only 7% of the group A sample displayed a broken fan phenotype. In group B cells (not containing over expression) this percentage jumped to 28% a four-fold increase. Phenotype A, (fan shape) E (stringed) and C (stumped) stayed relatively similar in both phenotypes.


2)If you see a difference, speculate about a potential molecular mechanism that has led to the change. If you don’t see a change speculate why that could be. Tm4 is an isoform of the tropomyosin family, which is a family of actin-binding proteins. Tm4 is natural cells is found in higher concentrations is neuron growth sites (neurites). It stands to reason therefore that over-expressing the Tm4 will increase the branching and neuritic growth of these cells which we observed and tabulated in the graph. Interestingly there was no increase (in fact there was a slight decrease) in the number of stringed cells. These cells have the largest projections so one would assume that increasing the expression of Tm4 would increase the number of this phenotype. However what is clear is that the increased expression of Tm4 greatly increases the expression of D (pronged) phenotype which nearly doubled between conditions. Another marked difference between conditions was the number of B phenotypes (broken fan) expressed. In the control (group B) more than 25% displayed the broken fan phenotype. While in group A (over-expression) only 7% were classified with this phenotype.


References

--Mark Hill (talk) 10:25, 11 April 2013 (EST) I have added this sub-heading for your references to display correctly.

  1. Liza Gross The more the merrier: multiple genomes in a parasitic prokaryote. PLoS Biol.: 2006, 4(6);e212 PubMed 20076595
  2. Yi-song Xiong, Juan Yu, Chang Li, Lin Zhu, Li-juan Wu, Ren-qian Zhong The role of Siglec-1 and SR-BI interaction in the phagocytosis of oxidized low density lipoprotein by macrophages. PLoS ONE: 2013, 8(3);e58831 PubMed 23520536
  3. Yi-song Xiong, Juan Yu, Chang Li, Lin Zhu, Li-juan Wu, Ren-qian Zhong The role of Siglec-1 and SR-BI interaction in the phagocytosis of oxidized low density lipoprotein by macrophages. PLoS ONE: 2013, 8(3);e58831 PubMed 23520536
  4. M Terasaki, P Campagnola, M M Rolls, P A Stein, J Ellenberg, B Hinkle, B Slepchenko A new model for nuclear envelope breakdown. Mol. Biol. Cell: 2001, 12(2);503-10 PubMed 11179431
  5. F Lin, H J Worman Structural organization of the human gene encoding nuclear lamin A and nuclear lamin C. J. Biol. Chem.: 1993, 268(22);16321-6 PubMed 8344919
  6. Howard J Worman, Cecilia Ostlund, Yuexia Wang Diseases of the nuclear envelope. Cold Spring Harb Perspect Biol: 2010, 2(2);a000760 PubMed 20182615
  7. Martin W Hetzer The nuclear envelope. Cold Spring Harb Perspect Biol: 2010, 2(3);a000539 PubMed 20300205


Lab 4

Z3377769 (talk) ANK-1 Antibody (8G6): sc-81550. [3]

"This is a monoclonal (NCAM) rat antibody raised against affinity-purified brain ANK-1 of mouse origin."

"Each vial contains 200 μg IgM in 1.0 ml of PBS with < 0.1% sodium azide and 0.1% gelatin. Available as phycoerythrin (sc-81550 PE) or fluorescein (sc-81550 FITC) conjugates for flow cytometry, 100 tests"

ANK-1(8G6) is used for detecting ANK-1 carbohydrate epitope present on most NCAMS. It is expressed on on NK (natural killer) human and mouse cells.

techniques used in: WB, IP, IF, IHC(P) and FCM

used in: [4]

all quotes taken from antibody data sheet data sheet. [5]


--Mark Hill (talk) 17:02, 13 June 2013 (EST) Where are all your Project peer reviews? They were supposed to be pasted here and on each project discussion page.