User:Z3377989

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--Z3377989 (talk) 15:46, 13 March 2014 (EST)

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PubMed


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WORLD DOMINATION

cell division

Hitomi Aoki, Akira Hara, Masayuki Niwa, Tsutomu Motohashi, Takashi Suzuki, Takahiro Kunisada Transplantation of cells from eye-like structures differentiated from embryonic stem cells in vitro and in vivo regeneration of retinal ganglion-like cells. Graefes Arch. Clin. Exp. Ophthalmol.: 2008, 246(2);255-65 PubMed 18004585


Reference

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


This is about prokaryotes. [1]

Ahmad S Khazali, Amanda M Clark, Alan Wells Inflammatory cytokine IL-8/CXCL8 promotes tumour escape from hepatocyte-induced dormancy. Br. J. Cancer: 2017; PubMed 29169181

Moe Shiokawa, Sho Yamasaki, Shinobu Saijo C-type lectin receptors in anti-fungal immunity. Curr. Opin. Microbiol.: 2017, 40;123-130 PubMed 29169147

Chunying Zhong, Gang Cao, Kuan Rong, Zhengwu Xia, Ting Peng, Honggao Chen, Jiangang Zhou Characterization of a microbial polysaccharide-based bioflocculant and its anti-inflammatory and pro-coagulant activity. Colloids Surf B Biointerfaces: 2017, 161;636-644 PubMed 29169118

Alexios S Antonopoulos, Evi Papanikolaou, Georgia Vogiatzi, Evangelos Oikonomou, Dimitris Tousoulis Anti-inflammatory agents in peripheral arterial disease. Curr Opin Pharmacol: 2017, 39;1-8 PubMed 29169069

Ying-Hua Li, Jing Wang, Ying Liu, Lie Qiu, Jian-Zhong Li, Hong-Gang Hu, Zhen-Lin Hu, Wen Zhang, Bin Lu, Jun-Ping Zhang Esculentoside A specifically binds to ribosomal protein S3a and impairs LPS-induced signaling in macrophages. Int. Immunopharmacol.: 2017, 54;254-260 PubMed 29169044


  1. 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

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Random Stuff

Hoi Yeung Li, Denis Wirtz, Yixian Zheng A mechanism of coupling RCC1 mobility to RanGTP production on the chromatin in vivo. J. Cell Biol.: 2003, 160(5);635-44 PubMed 12604592


http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2169373/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC65638/

Nuclear Membrane

Hello. Hello--Z3377989 (talk) 15:39, 13 March 2014 (EST)

The Nuclear Pore Complexes (NPCs) cross the nuclear envelope and allow the transport of water-soluble molecules across the nuclear envelope. Proteins transportred through the NPC include RNA and ribosomes moving from nucleus to the cytoplasm as well as DNA polymerase, lamins, carbohydrates, signal molecules, and lipids moving into the nucleus from the cytoplasm.

Individual Assessment Lab 2

--Z3377989 (talk) 12:15, 27 March 2014 (EST)

Part 1

--Mark Hill (talk) 14:50, 3 April 2014 (EST) still not uploaded a larger version of the original image as requested.

dnTRF2 Expression in Cell Nucleus[1]

Part 2

FtsZ is a fundamental protein involved in cell division of prokaryotic cells. Holden et al were investigating the structural composition of the in vivo Z-ring that FtsZ forms during cell division and how it relates to its function. Before the research took place, the Z-ring was initially thought to have either a patchy banded or a lateral interaction model, previously proposed by other researchers. In order to understand whether the z-ring was a patchy band or a continuous lateral interaction; Holden et all used high-throughput 3D super-resolution microscopy and took images to form a 3D structure of the z-ring at different stages of cell division. What they concluded is that FtsZ actually switches from the patchy band model to the lateral interaction and is dependent on the cell cycle. By using super-resolution microscopy they were able to determine that during cytokinesis the z-ring is in lateral interaction form to perform the constriction and division of the prokaryotic cell, and is in it's noninteracting patchy banded state beforehand.[2]


References

  1. Kaitlin M Stimpson, Lori L Sullivan, Molly E Kuo, Beth A Sullivan Nucleolar organization, ribosomal DNA array stability, and acrocentric chromosome integrity are linked to telomere function. PLoS ONE: 2014, 9(3);e92432 PubMed 24662969
  2. Seamus J Holden, Thomas Pengo, Karin L Meibom, Carmen Fernandez Fernandez, Justine Collier, Suliana Manley High throughput 3D super-resolution microscopy reveals Caulobacter crescentus in vivo Z-ring organization. Proc. Natl. Acad. Sci. U.S.A.: 2014, 111(12);4566-71 PubMed 24616530


Individual Assessment Lab 3

Part 1

Nuclear Pore Complexes are formed of many different nucleoporin proteins, roughly estimated to be around 30~ different types. The article focuses on Phenylalanine-Glycine Rich Nucleoporins, otherwise known as FG-nups. FG-nups have what are known as FG motifs, which are repeated sequences of Phenylalanine and Glycine within their Amino Acids. These are most prominent around the central complex and are suggested to contribute to bidirectional transport of large proteins and molecules. By having Transport Factors (TF) attach themselves to these large molecules, the TFs have FG-nup binding sites to allow for transport through the Nuclear Membrane by “widening” the hole to allow for larger structures to pass through. In this article, the researchers were to trying to understand the structure of the nuclear pore complex and how frequent FG-nups can be found within this central zone.[1]

Nuclear Pore[1]

Importin-8 (IPO-8) is part of the Karyopherin β family which govern mostly in nucleocytoplasmic transport of large molecules. One of their major functions is mediation between the nucleoplasm and cytoplasm and the large molecules that reside in either space. In this article, Yao Wei et al focused on IPO-8 and its major function in miRNA transport from the cytoplasm to the nucleus. They found out that during IPO-8 Knockdown, mature miRNAs, although they didn’t decrease in cellular amount, they were not transferred to the nucleoplasm due to IPO-8 being essentially “blocked”. Also, they found out that another complex known as Ago2 was needed to bind with IPO-8 in order to transfer miRNA into the nucleus, although the mechanism is still unclear on how Ago2 binds to miRNA. They used Trypaflavine (TPF) as a variable to disrupt the binding of Ago2 and miRNA, and was shown that IPO-8 still binded to Ago2 and transferred the complex into the nucleoplasm.[2]

FG-nups are assembled in an eight-folded symmetry, also as mentioned above in the previous article, they have repeat motifs of Phenylalanine and Glycine and come in various forms of nucleotide sequencing. Nuclear Localisation Signals may in fact be another form of a transport factor, and is involved in many different models that entail structure of the Nuclear Pore Complex. Mincer and Simon try to create a 3D model depicting the Nuclear Pore Complex without having any connections to any one particular model that has been proposed. FG-nups are single filament that can vary in size, because of this Mincer and Simon try to employ random variations to their model to simulate random FG-FG binding between FG-nups. Another factor involved in nucleocytoplasmic transport is RanGTP which was essentially shown to speed up the transport rate of molecules with Nuclear Localisation Signals. This essentially coincides with the Brownian Ratchet Model, which is the movement of cargo through the NPC through thermal fluctuations. It was previously thought that Transport Factors carrying cargo through the NPC do not get released into the nucleoplasm until it is released by RanGTP. [3]

Transportin molecules were used in this experiment and showed that there was a level of avidity for transport receptors on the Nuclear Transport Receptor- cargo complex to bind with FG-nups on the cytoplasmic side of the NPC and this helped in efficient transportation of the cargo towards the nucleoplasm. It is believed that although NTR helps in membrane permeability, that RanGTP is the factor that releases the cargo into the nucleus and re-use the NTR in the cytoplasm. Each transportin molecule on the bound cargo (M9-βGal‐8C) connects to an FG but is dependent on the availability and density of FG binding sites on the NPC. By understanding structure of FG-nups, they were able to determine that FG-FG binding sites allow for modulation of bidirectional transport and NTR-FG interactions. [4]


References

  1. 1.0 1.1 Ramya Gamini, Wei Han, John E Stone, Klaus Schulten Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating. PLoS Comput. Biol.: 2014, 10(3);e1003488 PubMed 24626154
  2. Yao Wei, Limin Li, Dong Wang, Chen-Yu Zhang, Ke Zen Importin 8 regulates the transport of mature microRNAs into the cell nucleus. J. Biol. Chem.: 2014, 289(15);10270-5 PubMed 24596094
  3. Joshua S Mincer, Sanford M Simon Simulations of nuclear pore transport yield mechanistic insights and quantitative predictions. Proc. Natl. Acad. Sci. U.S.A.: 2011, 108(31);E351-8 PubMed 21690354
  4. Li-Chun Tu, Guo Fu, Anton Zilman, Siegfried M Musser Large cargo transport by nuclear pores: implications for the spatial organization of FG-nucleoporins. EMBO J.: 2013, 32(24);3220-30 PubMed 24213245



Additional Research Articles for Nucleocytoplasmic Transport

Torunn Sletten, Michal Kostas, Joanna Bober, Vigdis Sorensen, Mandana Yadollahi, Sjur Olsnes, Justyna Tomala, Jacek Otlewski, Malgorzata Zakrzewska, Antoni Wiedlocha Nucleolin regulates phosphorylation and nuclear export of fibroblast growth factor 1 (FGF1). PLoS ONE: 2014, 9(3);e90687 PubMed 24595027

Matthew S Stake, Darrin V Bann, Rebecca J Kaddis, Leslie J Parent Nuclear trafficking of retroviral RNAs and Gag proteins during late steps of replication. Viruses: 2013, 5(11);2767-95 PubMed 24253283

Alexander Goryaynov, Weidong Yang Role of molecular charge in nucleocytoplasmic transport. PLoS ONE: 2014, 9(2);e88792 PubMed 24558427

Ramya Gamini, Wei Han, John E Stone, Klaus Schulten Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating. PLoS Comput. Biol.: 2014, 10(3);e1003488 PubMed 24626154

Joshua S Mincer, Sanford M Simon Simulations of nuclear pore transport yield mechanistic insights and quantitative predictions. Proc. Natl. Acad. Sci. U.S.A.: 2011, 108(31);E351-8 PubMed 21690354

Yao Wei, Limin Li, Dong Wang, Chen-Yu Zhang, Ke Zen Importin 8 regulates the transport of mature microRNAs into the cell nucleus. J. Biol. Chem.: 2014, 289(15);10270-5 PubMed 24596094

Alejandra Vásquez-Limeta, Kylie M Wagstaff, Arturo Ortega, Dorothy H Crouch, David A Jans, Bulmaro Cisneros Nuclear import of β-dystroglycan is facilitated by ezrin-mediated cytoskeleton reorganization. PLoS ONE: 2014, 9(3);e90629 PubMed 24599031

Stefanie Hügel, Reinhard Depping, Gunnar Dittmar, Franziska Rother, Ryan Cabot, Matthias D Sury, Enno Hartmann, Michael Bader Identification of importin α 7 specific transport cargoes using a proteomic screening approach. Mol. Cell Proteomics: 2014, 13(5);1286-98 PubMed 24623588


Individual Assessment Lab 4

Part 1

Anti-Nuclear Pore O-Linked Glycoprotein [RL1] antibody (ab2734)

Part 2

Mouse (Monoclonal)

Part 3

100 µl at 1 mg/ml

Part 4

T Guan, S Müller, G Klier, N Panté, J M Blevitt, M Haner, B Paschal, U Aebi, L Gerace Structural analysis of the p62 complex, an assembly of O-linked glycoproteins that localizes near the central gated channel of the nuclear pore complex. Mol. Biol. Cell: 1995, 6(11);1591-603 PubMed 8589458


Individual Assessment Lab 5

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Group Feedbacks

Group 1

Introduction

A well structured and informative introduction into phagocytosis, clearly demonstrates a thorough understanding of the basic structure and mechanisms involved in immune response, but I would suggest talking a little bit more about its relationship to transport. And for clarity, are those references at the bottom of the introduction or external links? If they are external links, there is a way to change their link into a general description i.e. “Phagocytosis” (while still being a hyperlink) within the ‘editing basics’ link under the side bar.

- General Improvements:

o Change the general format of the external links at the bottom of the introduction heading.

o Clathrin? What is it? There is no description of what clathrin is and its function. This can be easily remedied by having a glossary heading at the bottom with its description.

o A little more info into how phagocytosis is IMPORTANT to transport within the cell.


Structure of Plasma Membrane

I don’t think this needs a separate heading and can just be included within the introduction as a sub-heading. Needs to be referenced properly.

- General Improvements:

o Change the positioning of this heading somewhere else within the text. Preferably in the Introduction

o Reference Properly.


Receptors

A great deal of detail and text needs to be added to this part of the heading. I believe this is a crucial part of the project as it refers to the binding and recognition of phagocytes to foreign bodies, and thus for transport in general. Images are needed and this heading has to be fleshed out with more references.

- General Improvements:

o Needs more text

o Needs to more references

o Needs more images


Mechanism of Phagocytosis

This heading has a great deal of detailed text, images and references that explain the mechanisms of phagocytic membrane formation around the targeted foreign body. The only downside is that it is very hard to read as it has no set structure in paragraphing and is separated every sentence. Make them into paragraphs and possibly include sub-sub headings.

- General Improvements:

o Move the references into the correct place

o Make the text into paragraphs

o Glossary is needed to understand terminology


Diseases Related to Phagocytosis

Descriptive and well thought out. Not much more is needed in this heading as it is not that relevant to the project.

- General Improvements:

o Maybe add one more disease related to phagocytosis? My personal opinion.

Current/Future Research

Expand on this topic a little bit further.

- General Improvements:

o More information related to possible future research.


References

All your references are not done properly.

- General Improvements:

o Some of your references are doubled up. Look at the ‘editing basics’ tab to learn how to fix this.

o Put all your references down here, there is too much within the bottom of the headings and needs to be put in properly at the bottom.

Overall

A lot of editing needs to be done on your project, but overall the information you provided has shown a good understanding on Phagocytotic transport. A lot of information on the mechanism of phagocytosis is good, but needs to be supported by the other sub-headings. A lot more images are needed especially in the “receptors” section, and this part can be expanded on immensely. The role and structure of actin, which is covered in “Morphological Mechanisms” can also have it’s own heading as it is an integral motor protein involved in phagocytosis. Overall, good information that just needs to be structured properly.




Group 2

Introduction

A descriptive introduction that links into the parts of the projects, and sets the basis to understanding the mechanisms of transport within the mitochondria and the proteins involved. Maybe a bit too much information is put into the Introduction, but that is my opinion and I still think it is a very good intro. Well referenced, and a related image. Well done.

- General Improvements:

o Possibly remove this sentence and place this in the Current/Future Research section. “It has puzzled researchers for years as to how RNA molecules from the nucleus makes its way through into the mitochondria mainly because the inner membrane is semipermeable and RNA molecules are not as flexible as proteins.”


Protein Transport into Mitochondria

Good text with relevant references. Probably needs to be expanded on slightly more. Images are definitely needed to show structure and possibly mechanisms of binding of TOM and TIM complex.

- General Improvements:

o What do the numbers signify after the TOM annotation? Is that a measure of molecular weight? Please alliterate onto how they are ordered.

o Images are essential here.


Pyruvate transport into Mitochondria

- General improvements

o Needs more information pertaining to pyruvate transport

o Images needed


Diseases

A lot of information is provided with relevant references. The only criticism that I have with this part is the usage of sentences. Try to connect the sentences or elongate them to provide a fluid reading to the audience. There are too many short sentences that can either be expanded or conjoined, and this would greatly increase the readability of this part.

- General improvements

o More images

o Good text, but needs to flow well


Current or Future Research

- General Improvements

o Maybe more future research?

o Images if needed. Otherwise, it is very good.

Overall

The structure is well thought out and the information is very detailed and relevant to the project in terms of mitochondrial transport. The only suggestion I could make is the use of more pictures, as it would help illustrate the text you are writing.



Group 4

Fast and Slow Transport

A good description on fast and slow transport. Can be expanded on immensely on to the mechanisms and possibly the proteins involved with both fast and slow transport.

- General improvements:

o A lot of text is needed in this area.

o Needs to be structured in paragraphs rather than dot points.

o Images are greatly needed.


Kinesin

Informative text that is relevant to the project, although it is severely lacking in images.

- General Improvements:

o Needs images

o A glossary would be handy for all the acronyms used.


Overall

There is not enough information to come to a relevant conclusion on how much I understood on Neuronal transport. I suggest that you start working on the Fast and Slow transport focusing on specific proteins that are needed and the mechanisms for transport, as well as supporting images to the information you provided. A lot of text is missing here to come to a consensus on how good your structure and information are.



Individual Lab Assessment 9

1. Write a hypothesis that you are going to test.

Large quantities of cytochrome C will be detected in the cytoplasm of the cell which can only be released via the intrinsic pathway during apoptosis.

2. Write aims of your experiment.

To measure the amount of cytochrome C within the cytoplasm.

3. Identify key techniques and procedures used in your investigation (Spell these out in some detail).

Centrifugation – To separate the supernatant from the tissue culture.

Western blotting – analytical technique used in this experiment to detect cytochrome C.

4. Identify suppliers that have resources that you will need for your study (create links to the supplier resource pages, kits, antibodies etc).

http://www.abcam.com/cytopainter-mitochondrial-staining-kit-green-fluorescence-ab112143.html

http://www.cellsignal.com/product/productDetail.jsp?productId=4272

http://www.lifetechnologies.com/order/catalog/product/KHO1051

http://www.mblintl.com/products/datasheets/JM-K257.pdf

5. Now prepare a flow diagram of how the experiment will be carried out and analysed. Tissue  Add 1ml of mitochondria Extraction Buffer and 1 ml of Cytosol Extraction Buffer individually  Centrifuge  Wash cells with PBS  Incubate on ice  Homogenize cells in an ice-cold dounce tissue grinder  Collect supernatant as Cytosolic Fraction and Mitochondrial Fraction Load 10 μg of each cytosolic and mitochondrial fraction on a 12% SDS-PAGE  Western blotting and probe with cytochrome c antibody.

6. What will different experimental results (outcomes) mean.

After using the Assay kit we will see a large amount of Cytochrome C within the Cytoplasm, and by analysing the Mitchondria, we will see pores formed on the outer membrane. Thus, proving that Apoptosis occurred due to the Intrinsic Pathway.