User:Z3223095

From CellBiology

Lab 10

--Z3223095 (talk) 15:01, 22 May 2014 (EST)

Lab 9

--Z3223095 (talk) 15:05, 15 May 2014 (EST)

Hypothesis:

Isolated cells grown in optimal tissue culture conditions will most likely undergo apoptosis once placed in a foreign environment.

Aim:

To determine whether the cell undergoes an intrinsic or extrinsic apoptotic pathway by observing the amount of caspase 8 activated.

Method:

Human adherent cells are used for the tissue culture. They are washed carefully and loose cells are isolated. Adherent cells are gently spun and labelled with FAM green fluorescence from the FLICATM kit before trypsinization. Cells are incubated with the FLICA at 37oC for roughly 60 minutes before washing. After the addition of apoptosis wash buffer, cells are placed on ice and protected from light. Observations are made by the analysis of cells with a flow cytometer.

Click ‘Protocol’ tab in the following link for more detailed instructions.

http://www.immunochemistry.com/products/apoptosis-assays/caspase-assay-kits/green-flica-caspase-8-assay-kit.html

Suppliers: Immunochemistry Technologies

Resource: Green FLICA™ Caspase 8 Assay Kit

Flow Diagram:

50

Results:

If there is a high fluorescence reading observed, that means that there is a high amount of caspase 8 present and therefore, leads to an extrinsic apoptotic pathway. However, if there is a low fluorescence reading observed, there is less caspase 8 and hence, there is no extrinsic pathway activated.

Lab 8

Group 1:

-The Introduction was nice and brief and gave a good overview on phagocytosis.

-The links fitted in nicely, helped outsource information.

-AS I am not a scientist probably better off explaining some of the short hand names.

-Receptors could be expanded upon.

-Nice comparison with the 2 types of models introduced. I think this could be enhanced by a picture of each model (not just one of them), as some people are visual learners and can use the pictures to help understand.

-The mechanism had good information, although some of the sentences didn’t flow.

-In the disease section, the references should be placed after key information and not after.

-I like the fact they had a few diseases to talk about (which gives me ideas for my project), maybe just need to go a little bit more in depth of certain activities and causes.

-With the referencing, I think a lot could be improved and this would help the information and flow of the project be formatted much better.

-Also one reference section at the end rather than 2.

-Some references were used twice, which is fine but doubled up in the reference list for some reason..

-I think overall, this project has good information, it just needs some adjusting in the formatting and referencing departments.

Group 3:

-I think images would be useful in describing pathway the mechanisms involved.

-The names should be stated before the names are written in shorthand, so that the reader can know the full name. The information on them is good though.

-More information needed on the structure and function of the Rans mentioned.

-More headings needed.

-Expand the diseases, go into a bit more detail.

-With the referencing, need to fix up the list a little bit. There are some which appear twice on the list, so a quick edit will do the job.

-I think, overall this project has good information, which needs to be expanded upon and the use of images would really enhance the page.

Group 4:

-The introduction lacked information. The mechanisms are basically the same, so not sure if there is a need to individualise the various transports.

-The transports were well written, just an image/diagram would help visualise the mechanisms involved.

-The table for the proteins were an added benefit for the reader.

-Before the use of short hand names, the name should be introduced so the reader is aware of the actual name of the product.

-More information should be used to explain the headings involved.

-Images need to be spread amongst the project page and not centralised at the bottom. Therefore some of the images actually correlate to above headings but are at the bottom of the page where there is no correlation.

-In the referencing there were a few mistakes with putting in the right format.

-I think overall, this project needs to add a fair amount of information, better format with more headings and subheadings. I think they are on the right track for a good project.

Lab 7

--Z3223095 (talk) 15:13, 1 May 2014 (EST)

Lab 6

--Z3223095 (talk) 15:20, 17 April 2014 (EST)

Phenotype graph.png

Lab 5

--Z3223095 (talk) 15:17, 10 April 2014 (EST)

Lab 4

--Z3223095 (talk) 15:08, 3 April 2014 (EST)

anti-TOMM20 antibody

The Anti-TOMM20 antibody, Product code ab56783, is a monoclonal antibody raised in mouse. The antibody reacts with rat and human. The applications that can be used with this antibody are; western blotting, immunohistochemistry and immunofluorescence.

Zhang B et al. SIRT3 overexpression antagonizes high glucose accelerated cellular senescence in human diploid fibroblasts via the SIRT3-FOXO1 signaling pathway. Age (Dordr) 35:2237-53 (2013). ICC/IF ; Human . Bin Zhang, Shaoyuan Cui, Xueyuan Bai, Li Zhuo, Xuefeng Sun, Quan Hong, Bo Fu, Jianzhong Wang, Xiangmei Chen, Guangyan Cai SIRT3 overexpression antagonizes high glucose accelerated cellular senescence in human diploid fibroblasts via the SIRT3-FOXO1 signaling pathway. Age (Dordr): 2013, 35(6);2237-53 PubMed 23494737

Ramonet D et al. Optic atrophy 1 mediates mitochondria remodeling and dopaminergic neurodegeneration linked to complex I deficiency. Cell Death Differ : (2012). D Ramonet, C Perier, A Recasens, B Dehay, J Bové, V Costa, L Scorrano, M Vila Optic atrophy 1 mediates mitochondria remodeling and dopaminergic neurodegeneration linked to complex I deficiency. Cell Death Differ.: 2013, 20(1);77-85 PubMed 22858546

Steketee MB et al. Mitochondrial dynamics regulate growth cone motility, guidance, and neurite growth rate in perinatal retinal ganglion cells in vitro. Invest Ophthalmol Vis Sci 53:7402-11 (2012). PubMed: 23049086 Verfaillie T et al. PERK is required at the ER-mitochondrial contact sites to convey apoptosis after ROS-based ER stress. Cell Death Differ 19:1880-91 (2012). T Verfaillie, N Rubio, A D Garg, G Bultynck, R Rizzuto, J-P Decuypere, J Piette, C Linehan, S Gupta, A Samali, P Agostinis PERK is required at the ER-mitochondrial contact sites to convey apoptosis after ROS-based ER stress. Cell Death Differ.: 2012, 19(11);1880-91 PubMed 22705852

Munday DC et al. Quantitative proteomic analysis of A549 cells infected with human respiratory syncytial virus. Mol Cell Proteomics 9:2438-59 (2010). ICC/IF ; Human . PubMed: 20647383 Darna M et al. Time of day-dependent sorting of the vesicular glutamate transporter to the plasma membrane. J Biol Chem 284:4300-7 (2009). WB ; Rat . Mahesh Darna, Isabelle Schmutz, Karin Richter, Sowmya V Yelamanchili, Gurudutt Pendyala, Markus Höltje, Urs Albrecht, Gudrun Ahnert-Hilger Time of day-dependent sorting of the vesicular glutamate transporter to the plasma membrane. J. Biol. Chem.: 2009, 284(7);4300-7 PubMed 19103593

Whittaker R et al. Kinetics of the translocation and phosphorylation of alphaB-crystallin in mouse heart mitochondria during ex vivo ischemia. Am J Physiol Heart Circ Physiol 296:H1633-42 (2009).


Lab 3

--Z3223095 (talk) 15:14, 27 March 2014 (EST)

This article talks about how a mitochondrial dysfunction is a common characteristic in parkinson disease. The disease gene PINK1, results in deterioration of the functions of mitochondria. PINK1 is also found in the cytoplasm and when overexpressed enhanced cell motility. [1]


Mutations in PTEN-induced putative kinase 1 (PINK1) are a cause of autosomal recessive familial Parkinson's disease. [2] Attempts in studying the PINK1 pathway have been controversial because of its location in the cell and within the mitochondria. This study shows that this protein has a topology that the kinase domain faces the cytoplasm and the N-terminal tail is in the mitochondria. The results within this study rectify the location of PINK1 in mitochondria and may help in realising the normal and physiological function and normal physiological function and potential pathogenic role in Parkinsons disease. [3]


PINK1 is a serine/threonine kinase in the outer membrane of mitochondria. [4] It is referred to as the gene responsible of Parkinson's disease. In the cytosol is where PINK1's precursor is made and then transported into the mitochondria through the TOM complex. It discusses the fact that the import receptor Tom70 is essential for PINK1 import. It also states that the study observed that PINK1 has predicted mitochondrial targeting signal. Thus, the research results suggest that PINK1 is transported to the mitochondria by a pathway that is independent of the TOM core complex but crucially depends on the import receptor Tom70. [5]


PINK1 mutations are connected to autosomal recessive parkinsonism. PINK1 influences the shape and the function of the mitochondria. this paper describes a mechanism linking the dysfunction of the mitochondria and the changing of the mitochondrial shape that is related to PINK1. [6]

PINK1.png

  1. Hitoshi Murata, Masakiyo Sakaguchi, Yu Jin, Yoshihiko Sakaguchi, Jun-ichiro Futami, Hidenori Yamada, Ken Kataoka, Nam-ho Huh A new cytosolic pathway from a Parkinson disease-associated kinase, BRPK/PINK1: activation of AKT via mTORC2. J. Biol. Chem.: 2011, 286(9);7182-9 PubMed 21177249
  2. Chun Zhou, Yong Huang, Yufang Shao, Jessica May, Delphine Prou, Celine Perier, William Dauer, Eric A Schon, Serge Przedborski The kinase domain of mitochondrial PINK1 faces the cytoplasm. Proc. Natl. Acad. Sci. U.S.A.: 2008, 105(33);12022-7 PubMed 18687899
  3. Chun Zhou, Yong Huang, Yufang Shao, Jessica May, Delphine Prou, Celine Perier, William Dauer, Eric A Schon, Serge Przedborski The kinase domain of mitochondrial PINK1 faces the cytoplasm. Proc. Natl. Acad. Sci. U.S.A.: 2008, 105(33);12022-7 PubMed 18687899
  4. Hiroki Kato, Qiping Lu, Doron Rapaport, Vera Kozjak-Pavlovic Tom70 is essential for PINK1 import into mitochondria. PLoS ONE: 2013, 8(3);e58435 PubMed 23472196
  5. Hiroki Kato, Qiping Lu, Doron Rapaport, Vera Kozjak-Pavlovic Tom70 is essential for PINK1 import into mitochondria. PLoS ONE: 2013, 8(3);e58435 PubMed 23472196
  6. Anna Sandebring, Kelly Jean Thomas, Alexandra Beilina, Marcel van der Brug, Megan M Cleland, Rili Ahmad, David W Miller, Ibardo Zambrano, Richard F Cowburn, Homira Behbahani, Angel Cedazo-Mínguez, Mark R Cookson Mitochondrial alterations in PINK1 deficient cells are influenced by calcineurin-dependent dephosphorylation of dynamin-related protein 1. PLoS ONE: 2009, 4(5);e5701 PubMed 19492085

Lab 2

--Z3223095 (talk) 15:06, 20 March 2014 (EST)

1.

Cell nucleus.png

2.In vivo, confocal microscopy is being used more and more to study corneal abnormalities. Using this, we can find drug deposits in systemic disease. This article talks about a woman diagnosed with fibromyalgia on systemic choloquine who is going for an ophthalmic examination. [1]

--Mark Hill (talk) 14:29, 3 April 2014 (EST) Not a great paper. I was after something more about cell biology and microscopy.

sub heading

cell biology

Pubmed

this is wonderful picture of 2 cells.

Reference

This is about prokaryotes.[2]

Jiahn-Haur Liao, Cheng-Han Tsai, Sanjay G Patel, Jhih-Tian Yang, I-Fan Tu, Matteo Lo Cicero, Magdalena Lipka-Lloyd, Wan-Ling Wu, Wen-Jie Shen, Meng-Ru Ho, Chi-Chi Chou, Garima R Sharma, Hiroki Okanishi, Louis Y P Luk, Yu-Hsuan Tsai, Shih-Hsiung Wu Acetylome of Acinetobacter baumannii SK17 Reveals a Highly-Conserved Modification of Histone-Like Protein HU. Front Mol Biosci: 2017, 4;77 PubMed 29230394

D F R Cleary, A R M Polónia, N J de Voogd Prokaryote Composition and Predicted Metagenomic Content of Two Cinachyrella Morphospecies and Water from West Papuan Marine Lakes. FEMS Microbiol. Ecol.: 2017; PubMed 29228244

Ki Woo Kim Electron microscopic observations of prokaryotic surface appendages. J. Microbiol.: 2017, 55(12);919-926 PubMed 29214488

Zhengna Yin, Mengyun Gao, Sasa Chu, Yiping Su, Chunping Ye, Yiquan Wang, Zhuanqin Pan, Zhuming Wang, Huilin Zhang, Hua Tong, Jin Zhu Antitumor activity of a newly developed monoclonal antibody against ROR1 in ovarian cancer cells. Oncotarget: 2017, 8(55);94210-94222 PubMed 29212222

Leyla Tahrani, Joris Van Loco, Roel Anthonissen, Luc Verschaeve, Hedi Ben Mansour, Tim Reyns Identification and risk assessment of human and veterinary antibiotics in the wastewater treatment plants and the adjacent sea in Tunisia. Water Sci. Technol.: 2017, 76(11);3000-3021 PubMed 29210687


--Z3223095 (talk) 15:45, 13 March 2014 (EST)

this is great

  1. Iacopo Paladini, Ugo Menchini, Rita Mencucci In vivo confocal microscopy in chloroquine-induced keratopathy. Middle East Afr J Ophthalmol: 2013, 20(1);77-9 PubMed 23580857
  2. Tomohiro Shimada, Yukiko Yamazaki, Kan Tanaka, Akira Ishihama The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli. PLoS ONE: 2014, 9(3);e90447 PubMed 24603758