Difference between revisions of "User:Z3418837"

From CellBiology
Line 10: Line 10:
--[[User:Z3418837|Z3418837]] ([[User talk:Z3418837|talk]]) 15:11, 3 April 2014 (EST)
--[[User:Z3418837|Z3418837]] ([[User talk:Z3418837|talk]]) 15:11, 3 April 2014 (EST)
--[[User:Z3418837|Z3418837]] ([[User talk:Z3418837|talk]]) 15:25, 10 April 2014 (EST)
==Add a sub-heading.==
==Add a sub-heading.==

Revision as of 15:25, 10 April 2014

Add your own student page to the site.

Add your signature for Lab attendance.

--Z3418837 (talk) 15:45, 13 March 2014 (EST)

--Z3418837 (talk) 15:07, 20 March 2014 (EST)

--Z3418837 (talk) 15:13, 27 March 2014 (EST)

--Z3418837 (talk) 15:11, 3 April 2014 (EST)

--Z3418837 (talk) 15:25, 10 April 2014 (EST)

Add a sub-heading.

Add an external Link.


Add an internal Link.

Mickey Mouse

This is a wonderful picture of two cells.



This is about Prokaryotes.[1]

<pubmed limit=5>Prokaryote</pubmed>

  1. <pubmed>24603758</pubmed>

Individual Assessments

Lab 1

Chloroplast present in Eukaryotes and not in Prokaryotes.png

Chloroplast present in Eukaryotes and not in Prokaryotes [1]

  1. <pubmed>17710148</pubmed>| PLoS One.

Copyright: © 2007 Henderson et al. 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.

--Z3418837 (talk) 21:05, 18 March 2014 (EST)

Lab 2

1. On your own student page upload an image with the reference using the Pubmed formatting shown in the practical class tutorial last week.

Plant Nucleus.png

Plant Nucleus [1]

  1. <pubmed>23155403</pubmed>| PLoS One.

Copyright © 2012 Gao et al. 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.

--Z3418837 (talk) 21:42, 23 March 2014 (EST)

2. Identify a recent research article (not review) that uses either confocal microscopy or super-resolution microscopy as one of the study's techniques. Explain briefly (1 paragraph) how the microscopy technique specifically contributed to the article's findings.

In Vivo Determination of Organellar pH Using a Universal Wavelength-Based Confocal Microscopy Approach.

The purpose of the study was to measure the intracellular pH of organelles in situ using the physics behind confocal microscopy. This was achieved by extracting the colonies of Saccharomyces cerevisiae which were associated at various developmental stages. Confocal fluorescence microscopy was then used to monitor the variation in intracellular pH by targeting fusion proteins to subcellular compartments and then quantifying the fluctuations in the emission wavelengths obtained. The use of confocal microscopy imaging enabled researchers to distinguish between the various fluorescent fractions that were present in single cells. It also provided enhanced readings of emissions by the decreased photobleaching and amplified signal-to-noise ratios which detected a wide range of fusion proteins and intracellular pKa levels leading to precise quantifications of organellar pH. Ultimately, the use of confocal microscopy imaging has advanced to such a high level that determining intracellular level of pH is simple and efficient compared to the previous methods of microscopy and spectrofluorometry used. Confocal microscopy also promises much greater result as research proceeds.[1]

  1. <pubmed>22470445</pubmed>

--Z3418837 (talk) 23:45, 23 March 2014 (EST)


1.Select 4 reference papers related to your selected topic sub-section. Read these papers and write a brief description of their findings and relevance to the selected topic sub-section. The reference along with your description should then be pasted on both your group discussion page and your own personal page.

Article 1 - Charge as a Selection Criterion for Translocation through the Nuclear Pore Complex.

Nuclear pore complexes (NPCs) are porous structures that selectively control the components that pass through the nucleus to the cytoplasm and vice versa. A common understanding on the selective aspect of NPCs comes from the various diameter sizes that NPCs can occupy, however scientists have been focusing on another governing principle of translocation that they believe is related to charge. It is known that proteins that undergo rapid translocation are highly negatively charged, whereas proteins that are blocked from this translocation process are positively charged. Analysis has shown that, proteins that occupy the inside of the pore channel are net positively charged and transport receptors are negatively charged. This indicates that translocation rates within NPS are dependent on the electrostatic interactions between transport receptors and NPC due to an immense gain in energy. Overall, the investigation suggests that the negative charge plays a significant role in determining which components pass through the NPC.[1]

Article 2 - Role of Molecular Charge in Nucleocytoplasmic Transport.

Similarly to article one, this study focuses on the role of charge in the selectivity of Nucleocytoplasmic transport. It highlights the significance of phenylalanine-glycine (FG) nucleoporins (Nups) in creating a selective barrier with net positive charges in the nuclear pore complex. It is known that the positive charge accounts for the passive diffusion of small molecules and transport-receptor facilitated diffusion of cargo molecules. However, it was recently hypothesized that a negative surface charge plays a significant role in determining which components pass through the NPC. This study aims to unpack how these charge interactions may impact transport kinetics and spatial transport routes for both passive diffusion and facilitated translocation. By using high-speed fluorescence microscopy, scientists were able to determine that the electrostatic interactions between the negatively charged surface receptors and positively charged FG-Nups although increased the likelihood of NPC binding, did not reveal the nuclear transport mode or spatial transport routes. Instead, Nucleocytoplasmic transport was found to be dependent on molecular size, signal and surface charge and not one or the other.[2]

Article 3 - Higher Nucleoporin-Importin β Affinity at the Nuclear Basket Increases Nucleocytoplasmic Import.

For many years scientists have debated on whether the presence of an affinity gradient in NPCs for the import receptor Importin β increased or decreased Nucleocytoplasmic Import. However the answer to this postulation remained obscure. This study aimed to understand how this affinity gradient may have enhanced Nucleocytoplasmic Import by using agent based modelling (ABM) that looked at the association between rate constants and molecular binding. By employing different values of the affinity gradient, they have found that the rate of transport had increased by 10% compared to the pores lacking an affinity gradient. They also found that this effect was maximised at 200 µM for Importin β. Overall, this study highlighted the significance of Importin β Affinity in Increasing Nucleocytoplasmic Import rate.[3]

Article 4 - Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating.

Our current understanding suggests that the central transport channel which is a part of the NPC is formed by repeating subunits of FG-nups and serves as the selective barrier for incoming material. By analysing the spatial arrangements of nups, scientists can understand how NPC serves as a filter for macromolecules and allows for diffusion of small molecules below 40kDA. In this study, scientists used molecular dynamics to model the possible variations of Nsp1 (Nsp1-FG). They have discovered brush-like structures that consist of bundles that have been cross-linked to various nups. They have also found that transport factors are tightly associated with multiple FGS in cross-linking zones and also dissociate the bundles to widen the pores and allow molecules to enter. Overall, the model of the nuclear pore complex gating shows that the periphery of the NPC central channel consists of a few brushes with many cross-linked bundles due to the tethering of nups. However, the central regions shows a sieve-like structure of bundles with repeated cross-links as tethering of nups is less prominent.[4]

  1. <pubmed>20421988</pubmed>
  2. <pubmed>24558427</pubmed>
  3. <pubmed>24282617</pubmed>
  4. <pubmed>24626154</pubmed>

2.Select an image related to your selected topic sub-section (this can be from one of the 4 above or from elsewhere). The image should be uploaded (with all the required information: description, reference, copyright and student template) and pasted onto the project page sub-section and onto your own personal page.

Charge as a selection criterion for nuclear transport.png

Charge as a selection criterion for nuclear transport [1]

  1. <pubmed>20421988</pubmed>|PLoS One.

© 2010 Colwell et al. 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.

--Z3418837 (talk) 05:36, 3 April 2014 (EST)

Lab 4

1. Identify an antibody that can been used in your group's transport project.

Anti-Nuclear Pore Complex Proteins [Mab414] antibody - ChIP Grade (ab24609)

2. Identify the species deriving the antibody.

Mouse and it is monoclonal

3.Species reactivity

Reacts with: Mouse, Rat, Cat, Human, Saccharomyces cerevisiae, Xenopus laevis, Caenorhabditis elegans, Zebrafish, Vertebrates, Yeast.

4. IsoType


5. Epitope and use.

ab24609 recognizes the conserved domain FXFG repeats in nucleaporins such as the p62, p152, p90 and this NPC family is used to study the morphology and composition of the nucleus and nuclear envelope.

6. Identify the working concentration for the antibody.

100 µl at 1 mg/ml

7. Applications:

WB: 1:5,000, IF: 1:5,000, IHC: 1:500, IP: 1:5,000, IEM: 1:5,000, ChIP: use at an assay dependent dilution.

8. Identify a paper that has used this antibody.

Yeast nuclear envelope proteins cross react with an antibody against mammalian pore complex proteins.[1]

  1. <pubmed>2661560</pubmed>

--Z3418837 (talk) 23:24, 9 April 2014 (EST)