User:Z3372830

From CellBiology

--Z3372830 (talk) 15:45, 13 March 2014 (EST)Welcome this is my first cell biology lab :) Trying bold

--Z3372830 (talk) 16:01, 20 March 2014 (EST)

Was also here on the 27th. Was unaware that signing was the form of roll call

--Z3372830 (talk) 15:11, 3 April 2014 (EST)

--Z3372830 (talk) 15:04, 10 April 2014 (EST)

--Z3372830 (talk) 15:17, 17 April 2014 (EST)

--Z3372830 (talk) 16:02, 1 May 2014 (EST)

--Z3372830 (talk) 15:06, 15 May 2014 (EST)

--Z3372830 (talk) 15:20, 22 May 2014 (EST)

--Z3372830 (talk) 15:08, 29 May 2014 (EST)

This is a sub heading

pubmed

Lab1 internal link

This is a wonderful picture of two cells





LAB 2 WORK

Viral particle with plasma membrane.png


LAB2 Individual Assessment

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

Scs2 Regulates the Function of Opi1 on the Nuclear Membrane.png Nuclear membrane

--Mark Hill (talk) 14:58, 3 April 2014 (EST) Still just missing the student template with the image.

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.

Erika B Westcott, Steven S Segal Ageing alters perivascular nerve function of mouse mesenteric arteries in vivo. J. Physiol. (Lond.): 2013, 591(Pt 5);1251-63 PubMed 23247111


Westcott and Segal use intravital confocal microscopy in their study Ageing alters perivascular nerve function of mouse mesenteric arteries in vivo (2013). Intravital microscopy is a technique used to observe biological systems in vivo at high resolution on a two photon microscope and through an optimised attached window preparation. (Westcott & Segal 2013) The confocal microscopy was used as a comparison between the two images obtained from two photon and single photon confocal microscope.

--Mark Hill (talk) 14:59, 3 April 2014 (EST) Very brief explanation here.

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 a prokaryote. [1]


Lars Witting The natural selection of metabolism and mass selects lifeforms from viruses to multicellular animals. Ecol Evol: 2017, 7(21);9098-9118 PubMed 29152201

Conte Antonella, Papale Maria, Amalfitano Stefano, Mikkonen Anu, Rizzo Carmen, De Domenico Emilio, Michaud Luigi, Lo Giudice Angelina Bacterial community structure along the subtidal sandy sediment belt of a high Arctic fjord (Kongsfjorden, Svalbard Islands). Sci. Total Environ.: 2017, 619-620;203-211 PubMed 29149744

Messaouda Khallef, Süleyman Cenkci, Dilek Akyil, Arzu Özkara, Muhsin Konuk, Djamel Eddine Benouareth Ames and random amplified polymorphic DNA tests for the validation of the mutagenic and/or genotoxic potential of the drinking water disinfection by-products chloroform and bromoform. J Environ Sci Health A Tox Hazard Subst Environ Eng: 2017;1-6 PubMed 29148923

Ulrich Omasits, Adithi R Varadarajan, Michael Schmid, Sandra Goetze, Damianos Melidis, Marc Bourqui, Olga Nikolayeva, Maxime Québatte, Andrea Patrignani, Christoph Dehio, Juerg E Frey, Mark D Robinson, Bernd Wollscheid, Christian H Ahrens An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. Genome Res.: 2017; PubMed 29141959

Esti Singer, Yardena Bh Silas, Sigal Ben-Yehuda, Ophry Pines Bacterial fumarase and L-malic acid are evolutionary ancient components of the DNA damage response. Elife: 2017, 6; PubMed 29140245


  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

Lab 3 Individual Assessment

--Mark Hill (talk) 14:48, 1 May 2014 (EST) Very good, would have been good if you had identified your actual project section.

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.

1. Article 1 - Sharpness of Spike Initiation in Neurons Explained by Compartmentalization, Romain Brette (2013) This first article discusses spike initiation in the axons initial segment. The results support the researcher’s theory that high frequency signals from cortical neurons can be explained by a compartmentalisation of spike initiation. I however used this article as it provides a fantastic description of action potentials, Na channels and provides a great understanding of the initial neuron soma to axon process.

Romain Brette Sharpness of spike initiation in neurons explained by compartmentalization. PLoS Comput. Biol.: 2013, 9(12);e1003338 PubMed 24339755


2. Article 2 - Laser-Based Single-Axon Transection for High-Content Axon Injury and Regeneration Studies. Kunik et al, (2011) The second article investigates regenerative responses of neurons to axonal injury. The results showed cells that were capable of repair or regrowth of damaged axons migrated more slowly than cells that could not. Moreover, cells with long axons could not recover their injured axons, and such cells were much more motile. [1] I have used this article as it provides an understanding of future studies into potential cures for neuronal dysfunction disorders such as Alzheimers diseases, multiple sclerosis, trauma, glaucoma and peripheral neuropathies.

Darío Kunik, Carolyne Dion, Tsuneyuki Ozaki, Leonard A Levin, Santiago Costantino Laser-based single-axon transection for high-content axon injury and regeneration studies. PLoS ONE: 2011, 6(11);e26832 PubMed 22073205


3. Impaired Function of HDAC6 Slows Down Axonal Growth and Interferes with Axon Initial Segment Development. Tapia et al, (2010) My third article examines the effects of HDAC6 on tubulin deacetylase in the distal region of the axon and it’s effects in reducing axonal length. This article provides an understanding of the development of morphological neuronal polarity starts by the formation and elongation of an axon. Furthers the study of structural and functional proteins which contribute the neuronal action potential.

Mónica Tapia, Francisco Wandosell, Juan José Garrido Impaired function of HDAC6 slows down axonal growth and interferes with axon initial segment development. PLoS ONE: 2010, 5(9);e12908 PubMed 20886111


4. Automated and Accurate Detection of Soma Location and Surface Morphology in Large-Scale 3D Neuron Images. Yan et al, (2013) My final article observes automated and accurate localization and morphometry of somas in 3D neuron images which are essential for quantitative studies of neural networks in the brain. The researcher’s method for locating the neuron somas reveal the soma distributions in large-scale neural networks more efficiently. This is an extremely useful study as this method for soma surface detection will serve as a valuable tool for systematic studies of neuron types based on neuron structure. The study also provides a greater understanding of previous, current and future techniques that are used to image neuron somas.

Cheng Yan, Anan Li, Bin Zhang, Wenxiang Ding, Qingming Luo, Hui Gong Automated and accurate detection of soma location and surface morphology in large-scale 3D neuron images. PLoS ONE: 2013, 8(4);e62579 PubMed 23638117


  1. Darío Kunik, Carolyne Dion, Tsuneyuki Ozaki, Leonard A Levin, Santiago Costantino Laser-based single-axon transection for high-content axon injury and regeneration studies. PLoS ONE: 2011, 6(11);e26832 PubMed 22073205


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.

The deblocking strategy used for soma detection in a large-scale image stack.png

LAB 4 EXERCISE

Identify an antibody that can been used in your group's transport project. Identify the species deriving the antibody. Identify the working concentration for the antibody.

- A mouse monoclonal anti-βIII tubulin antibody (1:2000; Promega UK, Southampton, UK

Identify a secondary antibody that could be used with this antibody.

- Alexa Fluor-488 conjugated goat anti-mouse secondary antibody (1:1000, Invitrogen Inc.

Identify a paper that has used this antibody.

Natalie D Bull, Alessandra Guidi, Michel Goedert, Keith R Martin, Maria Grazia Spillantini Reduced axonal transport and increased excitotoxic retinal ganglion cell degeneration in mice transgenic for human mutant P301S tau. PLoS ONE: 2012, 7(4);e34724 PubMed 22496848


--Mark Hill (talk) 14:46, 1 May 2014 (EST) All fine here.

LAB 6 EXERCISE

TM4 Over expressors vs. Wild type expression in cells Lab 6 exercise.jpg

LAB 9 INDIVIDUAL ASSESSMENT

1. Aim: To investigate the mechanism by which brain cells undergo apoptosis in vascular dementia.

2. Hypothesis: The apoptosis mechanism that will be observed as the primary mechanism of cell death in these cells will be of an intrinsic mitochondrial nature.

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

- In-gel tryptic digestion and isobaric labelling (iTRAQ analysis) – are a non-gel-based technique used to quantify proteins from different sources in a single experiment. It uses isotope-coded covalent tags. iTRAQ is used in proteomics to study quantitative changes in the proteome.

- Electrostatic repulsion and hydrophilic interaction chromatography (ERLIC) - uses hydrophilic stationary phases with reversed-phase type eluents

- Western blotting – analytical technique used to detect specific proteins in a sample of tissue homogenate or extract. It uses gel electrophoresis to separate native proteins by 3-D structure or denatured proteins by the length of the polypeptide. The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are stained with antibodies specific to the target protein.


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

[1]


5. Now prepare a flow diagram of how the experiment will be carried out and analysed. Patient selection

- Age matching

- Post-mortem interval matching

- Location matching

Post mortem sample collection

Two Phases

Discovery phase

Proteomic SAMPLE Preparation

1. Protein extraction

2. In-gel Trypic Digestion, Peptide Extraction

Shot-Gun Proteomics & bioinformatics

1. iTRAQ Labelling

2. ERLIC

3. RP-LC-MS MS

Western blotting

Post –proteomic Validation Phase

1. Biological replicate

Densitometric Analysis

Data Interpretation

Generation of Hypothesis

6. What will different experimental results (outcomes) mean. This process results in apoptosis of an intrinsic nature it involves mitochondrial pathways in cell death. Difference in results would mean that an external pathway of caspase 3 is triggering death of the cells


Peer assessment of projects

Group 1

Well thought out and executed introduction. Summarises succinctly the main aspects of the topic. Thus far the assignment seems to have a good flow. When I was reading the introduction I noticed the two divisions of phagocytes. “Phagocytes can be divided into two groups; Professional Phagocytes (usually referring to Polymorphonucleocytes - PMNs), and Non-professional Phagocytes.” There seems to be no elaboration of these two types, perhaps this has yet to be added would be beneficial for the reader.

Appropriate use of headers, separate topics well and allow for greater ease when navigating through the page. However under mechanical mechanisms there is quite a bit of content that is clustered together. To alleviate this I would either consider listing the information, tabulating it, or even further sub dividing the headings. Such as ‘trigger model’ or ‘zipper model’. The diagrams provided are easily comprehendible. Also in the contents everything seems to be under one point “1. Phagocytosis”, changing it to something along the lines of “2.Mechanisms of Phagocytosis”, “3. Diseases”, “4. Current and future studies” etc. Although this a small cosmetic issue it would be easier to navigate through assignment.

Need for images sub heading, as an index of diagrams and figure that have been used. An addition of a glossary page would be a good idea. Wide range of references however the set out need to be consistent. It is a little distracting although I’m sure this will be resolved before submission. Otherwise this wiki page assignment seems to be on the right track.

Group 2

Introduction which covers mitochondria structure, yet it is a little long. I also didn’t really see until the protein what was going to be covered on the page. I would reposition certain details to be small introductions. Perhaps just create a sub heading of mitochondria structure under the introduction would be sufficient.

The assignment makes great use of headings separates information clearly and succinctly. However everything seems to just be covered under the one point “1. Transport from the Cytoplasm to the Mitochondria”, changing it to something along the lines of “2. Transport to the Mitochondria”, “3.What can go wrong with transport… ”, “4. Current and future studies” etc. Although this a small cosmetic issue it would be easier to navigate through assignment.

Images provided are good, however the one provided under diseases need information as to what it is and what is being conveyed. Need for images sub heading, as an index of diagrams and figure that have been used. Reference are from a myriad of sources. Glossary is a fantastic addition, provides further information for the reader with terms they may not necessarily know. Overall this wiki page seems to heading in the right direction.


Group 3

Thus far, the page seems to be on the right track. Contents and headers are well thought and set out. Further information under certain headers is missing yet the assignment is not complete. Contents already covered is well set out, appropriate use of list and tables assist in understanding of the topic. Images that are used as figures are well thought out and relevant. Images sub heading is clever as it provide an index of all figures. Also maybe an addition of a glossary sub heading between the future research and images would be beneficial.

References need to be structured a little better. Yet I’m sure this will be sorted before submission. Generally this assignment is well-structured, easy to comprehend, interesting and appears to be on the right track.

LAB 11 INDIVIDUAL ASSESSMENT

1. How many Gbases (Gb) would you require to sequence the human genome to 40x coverage?

3O times

2. Describe an advantage of using next-generation sequencing technology over microarrays to study gene expression?

The primary advantage of using next-generation sequencing instead of microarrays would be to study the gene expression of an unknown gene. Microarrays are limited in that they can only express sequencing patterns of known genes.