User:Z3407326

From CellBiology

Lab 12

1. Identify a current technique used in gene sequencing.

A technique that is current being used in the field of gene sequencing is next generation sequencing (NGS).

Adriano Jiménez-Escrig, Isabel Gobernado, Antonio Sánchez-Herranz [Whole genome sequencing: a qualitative leap forward in genetic studies]. [Secuenciación de genoma completo: un salto cualitativo en los estudios genéticos.] Rev Neurol: 2012, 54(11);692-8 PubMed 22627750


2. Identify a recent cell biology research paper that has used microarray technology.

The following article used microarray technology to detect the proteins responsible for the tolerance of milk: F Wulfert, G Sanyasi, L Tongen, L A Watanabe, X Wang, N K Renault, F H Falcone, C M A Jacob, M J C Alcocer Prediction of tolerance in children with IgE mediated cow's milk allergy by microarray profiling and chemometric approach. J. Immunol. Methods: 2012, 382(1-2);48-57 PubMed 22580759


3. What aspect of the research findings were contributed by the microarray technique.

The protein microarray technique was required to examine four immunoglobulin isotypes (IgA, IgG, IgM, and IgE)which would allow for the prediction of the onset of tolerance of specific milk proteins.


Lab 9

Peer Assessment

Group 1

The introduction is well-explained but much too short - you may need to expand on it. The history seems well-researched. Great idea to include a colorful table as it is visually pleasing. I like how you broke down the biosynthesis, as well as included an image to make it easier to understand. In addition, the sections on regulation and signaling pathways are detailed and easy to read. The general formatting of normal functioning, abnormal functioning, and clinical uses is fine, but you might want to include more pictures in this section, as it is a little bit difficult to read such a large chunk of text. The section on current and ongoing research needs some improvement. It would be helpful to have a short paragraph before you go into the numbered list. For the glossary, just ensure that you keep the formatting the same for all terms. That is, some words have colons and others do not - choose one. Overall it seems to be a good project, however, you still need to include a student drawing, use less Wikipedia images, include copyright information on your images, and correct some grammatical and spelling errors.

Group 2

The introduction is a good overview of the project, but it is too short. You may want to consider elaborating on it. I like the inclusion of a table for the history section, which seems to be well-researched. The section on normal functioning is well-divided, however, the part on hormones is incomplete (you wrote "steroids?"). In the signaling pathway component, you have two sub-headings in a row. Try to combine these or just use one to make it more visually pleasing. The table is a nice summary of the information below it. However, when you say "induces other factors", try to be more specific, and perhaps elaborate on VEGFR-3. I really like the table for abnormal function. It is a great addition, especially with the pictures, and is well-researched and well-explained. The remaining section (therapeutic applications) is good, but consider including other diseases (such as the ones you mentioned in abnormal functioning). Also, it may be better to have your glossary before your references. Lastly, you still need to include a student image, but the rest of your pictures seem to be well-referenced and the copyright information is included. There is a good inclusion of external links. The project still needs some touching up, but it is fairly decent overall.

Group 3

This is the group I am in, therefore, I cannot do a peer assessment of this project.

Group 4

The introduction seems to be a little bit short, thus I recommend you elaborate a bit more on the overall topic. You might also want to include the title of the pathway you are doing so that it is more obvious to readers what you will be discussing. The history section lacks variety in terms of referencing, and could include a few more important dates, but the table is visually pleasing. The pathway is detailed, however, it could be coupled with an image so that it is a little clearer to readers. Actually, the nice image you have included for your section on proteins and receptors (which was a good overview but could be a bit more detailed) should be in the pathway section. However, the image is lacking copyright information. The section on normal function is well-explained, and I like how it is formatted because it makes it easier to read. The addition of the picture makes things easier to visualize. The further research section is definitely incomplete, but I am certain you are aware of this. The glossary seems fine, but it will probably be longer once the project is finished. Overall, this project requires more work, as well as a student image. Lastly, having additional links in one section is fine, but if the links are mentioned earlier in the project, it is best to include them in that section, rather than write "See video under external link for further understanding".

Group 5

The introduction is a nice overview of the project, but the writing style is a little bit choppy. I recommend looking this over to make it more cohesive. The history is very detailed and seems to be well-researched. Although the image is nice and is correctly referenced and includes the copyright information, I'm not to sure that it is relevant to the section on history. I like the subheadings for the mechanism of action, but this section is a little bit difficult to read. The image helps, and is a good student drawing, however, this section should be simplified and made easier to understand. The disease section is great, and visually pleasing, but the images need copyright information. The table involving the key proteins is very detailed, well-researched, and visually pleasing. All the images are correctly referenced and include the copyright information - well done! My only comment is that this section should be placed before diseases, just so that the flow is a little bit better. The addition of the embryonic development section is good, but you may want to change the title to be a little more descriptive (ex: The role of...in embryonic development). For the section on future directions, it would be best to summarize the future directions, and perhaps include examples of research that is currently underway, or even recent findings involving this signaling pathway. The glossary is well-done and the list of external links is a nice addition.

Group 6

The introduction is nicely detailed, however, given that your topic is insulin, it should have a bigger heading. It also should include more references. I like the inclusion of an image for the structure of insulin, but it is not properly referenced and the there is no copyright information. The history is well-researched and detailed. It was a nice idea to include external links, and the image has the proper reference and copyright information. The sections on the insulin receptor and signaling pathway are nicely explained. Great student drawing, but again, the image in the signaling pathway section needs copyright information. The section on normal functioning needs to be elaborated and include more references and details. The section on abnormal function is well-researched, detailed, and clear. Overall, the current research is good, but perhaps include external links for the different research institutes. Also, the glossary could include a few more terms. Lastly, a couple of more pictures in the last few sections of the project would be great too, just to make it more visually pleasing.

Group 7

I really like the introduction. It is clear, and nicely explained. Great student drawings as well. However, it needs to be proof-read, and include more in-text citations. One word of advice - please remove all the signatures from the project page as this is not visually pleasing. The history is comprehensive, and I like the fact that it includes external links. The genes description is basic, but good, however, it could use an image to make it more visually pleasing. I'm not too sure if the section on receptor agonists is complete. If there are no specific beta-blockers, then do not include this in your table. In fact, given that each subtype has the same information associated with it, I don't think it is necessary to include a table. Try to incorporate this information in another section. The part on receptor structure is well-formatted, and the images are nice, but unfortunately they cannot both be from Wikipedia. The section on pathway and normal functioning is nicely explained and detailed, and it includes more student images - which is great! Abnormal function, disease, and treatments includes a lot of information and is well-referenced, and the images include the necessary reference and copyright information, but the formatting needs some work as it is not visually pleasing (what to put in bold, location of pictures, etc.). Finally, the glossary is great, but the names of things should be in bold, simply so that it is easier to read.

Group 8

The introduction is quite short, and thus you may want to consider making it longer. I like that pathway has been simplified so that it is easier to understand, however, I cannot tell whether the image associated with this section is a student drawn image or not, thus I cannot comment on referencing and copyright information. This being said, more details about this can be provided in the details section of the picture. I am assuming you are aware that you have not completed the history section, and so I cannot comment on that either. The section on normal functioning lacks images to make it more visually pleasing. In addition, in certain cases it is explained in ways that may be too basic, and in other instances, more complicated ideas are being expressed without any referencing. The section on abnormal functioning is well-referenced and detailed. But once again, there lacks images to make the project more visually pleasing. Also, I recommend deleting the extra spaces in this section (especially before and after "other"). The section on proteins is also detailed and clear, but in certain paragraphs, I believe there are references missing. However, I like the images, which have been properly referenced and include copyright information. The glossary of terms is fine, but I assume it will be longer once the project is complete, and includes the missing sections (namely history and current/future research).

Group 9

Overall, I do not believe that it is necessary for me to tell you that I cannot comment on parts of the project that are obviously incomplete, or have not been started at all - namely the sections on receptors, proteins, current research, and abnormal function. The two images you have included are properly referenced and include copyright information - which is good, however, you are still lacking a student-drawn image. Also, please remove all signatures as this is not visually pleasing. The introduction is simple, but clear, and although the section on the pathway is well-explained, it lacks referencing. The history section is really well done. The table is visually pleasing and it is well-researched and referenced properly. The first part of normal functioning could use some more references, and the entire section requires more work in terms of structure and format, but it is a decent start. Don't forget to include external links. Good luck finishing the project! --Mark Hill 13:25, 17 May 2012 (EST) You have not completed the peer assessment process yet. If you have made comments on each project page they need also to be pasted here today for me to include in your individual assessment.

Lab 8

  1. Identify a mammalian cell line in the ATCC catalogue (and add a link)
  2. Identify the original tissue of origin of that cell line.
  3. Identify the original paper that characterised the properties of that cell line. 


293 [HEK-293] is a mammalian cell line from Homo Sapiens, whose tissue of origin is the embryonic kidney. ATCC Catalog

The original paper characterizing the cell line's properties can be found at: F L Graham, J Smiley, W C Russell, R Nairn Characteristics of a human cell line transformed by DNA from human adenovirus type 5. J. Gen. Virol.: 1977, 36(1);59-74 PubMed 886304


Lab 7

Many diseases are a result of the dysregulation of the apoptotic pathway. More specifically, ischemia, autoimmune diseases such as AIDS, and various neurodegenerative conditions such as Parkinson's, Huntington's and Alzheimer's disease are caused by excessive apoptosis - an increase in the amount of programmed cell death. In other cases, such as cancer, there is insufficient apoptosis; thus, there is an increase in the number of cells, and/or a decrease in the programmed death of dysfunctional cells. Given the plethora of diseases that arise from malfunctions of this pathway, there has been a surge in current research in this particular field. Researchers are attempting to fully understand the molecular mechanisms of the critical proteins that underlie apoptosis. With this knowledge, there is hope that therapeutic interventions for the aforementioned diseases can be improved, and result in increased survival rates for afflicted patients.

Susan Elmore Apoptosis: a review of programmed cell death. Toxicol Pathol: 2007, 35(4);495-516 PMID:17562483


One example of current research is Ovadje, Hamm, and Pandey's work on induced extrinsic apoptosis in human Chronic Myelomonocytic Leukemia (CMML) cells through the use of dandelion root extract (DRE). CMML is an agressive type of leukemia that is, unfortunately, difficult to diagnose Ovadje, Hamm, & Pandey; 2012). To make matters worse, patients with this disease do not have a high survival rate (Ovadje, Hamm, & Pandey;2012). Those who do go through tretment, such as chemotherapy, experience severe side effects, and cancer cells quickly develop resistance during the course of treatment (Ovadje, Hamm, & Pandey; 2012). However, this group of researchers studied the effects of DRE on CMML cells, and found that DRE's capacity to induce extrinsic apoptosis may lead to a more natural and safe way to treat this disease (2012). They suggest that DRE speeds the activation of caspase-8, an initiator that plays a critical role in extrinsic apoptosis, followed by the activation of caspase-3 (2012). In addition, the researchers found that certain death resceptors, such as the Fas-Associated Death Domain (FADD) were required for DRE to efficiently induce extrinsic apoptosis in CMML cells (2012). Furthermore, extrinsic cell death was not observed in non-cancerous peripheral blood mononuclear cells (ncPBMcs) (2012). DRE's ability to selectively induce extrinsic apoptosis in CMML cells and to not do so in ncPMBcs demonstrates that DRE may possibly be a more natural alternative to other forms of cancer treatment that exist today.


Pamela Ovadje, Caroline Hamm, Siyaram Pandey Efficient Induction of Extrinsic Cell Death by Dandelion Root Extract in Human Chronic Myelomonocytic Leukemia (CMML) Cells. PLoS ONE: 2012, 7(2);e30604 PMID:22363452

Lab 6

Gif Cell bio lab 19.GIF


1) Do you see a difference in phenotype (morphology) between Tm4 overexpressing and control cells?

2) If so, how could Tm4 overexpression lead to this difference? Answer questions for each section.

As shown in the graph, there was a difference in expressed phenotypes between Tm4 overexpressing B35 cells (Group A) and control B35 cells (Group B). In Tm4 overexpressing cells, a higher number of branching processes, thus a greater amount of the pronged and stringed phenotypes, and a smaller amount of the broken fan and stumped phenotypes, was found. As seen in class, the development of particular cell structures is regulated by the various isoforms of tropomyosin. The results of this experiment suggest that Tm4 plays a critical role in the growth of neurites, leading to an increase in the pronged and stringed phenotypic stages. This would explain the differences observed between these cells and the control cells.

In the second section, the group of Tm4 overexpressing B35 cells that was induced for differentiation using db cAMP (Group A) showed a greater amount of cells, in addition to shorter processes, thus less pronged and stringed phenotypes in comparison to the control group (Group B). This suggests that db cAMP inhibits the ability of Tm4 to regulate the development of neurites in B35 cells.

Lab 4

Musashi1 (Msi1)is an RNA-binding protein that is expressed in both fetal and adult neural stem/progenitor cells. Msi1 plays a role in the self renewal of these neural stem/progenitor cells. Shinsuke Shibata, Masahiko Umei, Hironori Kawahara, Masato Yano, Shinji Makino, Hideyuki Okano Characterization of the RNA-binding protein Musashi1 in zebrafish. Brain Res.: 2012, 1462;162-73 PubMed 22429745


Anti-Musashi 1 / Msi1 antibody [EP1302] is rabbit monoclonal [EP1302] to Musashi 1 / Msi1. It has cross-reactivity with humans, mice, quails, chickens, and rats. It has been used successfully in IHC-P, IHC-Fr, WB, IP, ICC, and Flow Cyt.

ABCAM Antibody Supplier Website

The green-fluorescent Alexa Fluor 488 goat anti—rabbit IgG can be used as a secondary antibody for Anti-Musashi 1 / Msi1 antibody [EP1302]. Dilution: 1/200

Life Technologies Secondary Antibody Supplier Website

Lab 3

Formaldehyde (Aldehyde Cross-Linked Fixative)

Properties

1) Appearance and Odour: Clear and colorless liquid with a pungent odour

2) Specific Gravity: 1.08 g/ml

3) Bulk Density: 1.08 kg/L

4) Solubility: Infinite

5) Vapor Pressure: 40 mm Hg

6) Boiling Point: approximately 100 degrees Celcius

7) pH: between 3.5 and 4.5

8) Percent Volatile (by volume): Unknown

9) Evaporation Rate: Similar to that of water

10) Flash Point: 78 degrees Celcius

11) Upper Flammable Limit: 73%

12) Lower Flammable Limit: 7%


Hazards

1)When storing this product, always ensure that lids are tightly closed, to prevent any formaldehyde from escaping.

2)Formaldehyde is poisonous, and thus can cause irritation to the nose, throat, eyes, and ears. Prolonged exposure can lead to edema or tracheobronchitis. Seek medical attention if any contact with the product occurs (ex: splashed in eyes, dropped on skin, inhaled, or swallowed).

3)Formaldehyde is a moderately hazardous combustion product. Avoid exposure to heat or flame.

4) Avoid spilling or pouring product down a drain. This runs the risk of contaminating water supplies.

5) Do not store near food or plant products. Store below 15 degrees Celcius.

6) When using this product, use all necessary equipment. These include the following: protective clothing (including long-sleeved shirts and pants); chemical-resistant rubber boots and socks; chemical splash goggles; an approved respirator (to prevent inhalation); chemical-resistant or rubber gloves. Work in a well-ventilated area. Once you are finished using the product, wash gloves thoroughly before removing them. Wash and change into clean clothes as soon as possible, and make sure to wash all garments used in the lab prior to re-wearing them.

7) Be careful to avoid exposure of formaldehyde with the air. Air can oxidize this product, changing it into formic acid, which is corrosive.

Reference: Formalin MSDS


Articles

1) Pamela Ovadje, Caroline Hamm, Siyaram Pandey Efficient induction of extrinsic cell death by dandelion root extract in human chronic myelomonocytic leukemia (CMML) cells. PLoS ONE: 2012, 7(2);e30604 PubMed 22363452


This article discusses how natural products, more specifically Dandelion Root Extract, can be used to induce extrinsic apoptosis in Human Chronic Myelomonocytic Leukemia (CMML) Cells. This pertains to both current research, and the section on diseases in our project.


2) Hakan Kültürsay, Meral Kayikçioğlu [Apoptosis and cardiovascular disease]. [Apoptozis ve Kardiyovasküler Hastaliklar.] Anadolu Kardiyol Derg: 2002, 2(4);323-9 PubMed 12460831


In this article, the authors discuss the relationship between cardiovascular disease and apoptosis. This can also be used in the disease section of our project. Cardiovascular diease is very prevalent in today's society, and therefore I think it would be important to discuss.


3) B R Gastman Apoptosis and its clinical impact. Head Neck: 2001, 23(5);409-25 PubMed 11295816


This article provides a summary of the pathways involved in extrinsic apoptosis, as well as how the accumulated knowledge of this pathway has led to important developments in the medical field.


4) Cristina Muñoz-Pinedo Signaling pathways that regulate life and cell death: evolution of apoptosis in the context of self-defense. Adv. Exp. Med. Biol.: 2012, 738;124-43 PubMed 22399377


In this article, a detailed description of the pathway of extrinsic apoptosis is given. It also sheds light as to how humans may have developed this mechanism, thus, it discusses the possible origins of this pathway.



Lab 2

Filamentous Network.jpg

G Blobel, B Dobberstein Transfer of proteins across membranes. I. Presence of proteolytically processed and unprocessed nascent immunoglobulin light chains on membrane-bound ribosomes of murine myeloma. J. Cell Biol.: 1975, 67(3);835-51 PubMed 811671


Assessment:

Hans Blom, Daniel Rönnlund, Lena Scott, Zuzana Spicarova, Jerker Widengren, Alexander Bondar, Anita Aperia, Hjalmar Brismar Spatial distribution of Na+-K+-ATPase in dendritic spines dissected by nanoscale superresolution STED microscopy. BMC Neurosci: 2011, 12;16 PubMed 21272290


In this article, superresolution microscopy techniques were used to determine the distribution of alpha subunits in the structural form of Na+-K+-ATPase in dendritic spines of neurons. Other techniques that have been used in previous studies have shed light on the localization and dispersal of alpha-isoforms in Na+-K+-ATPase. However, given the nanoscale resolution of superresolution microscopy, alpha-subunits at the subcellular level have been located as well. These findings are crucial for understanding the Na+-K+-ATPase, which is needed for the active transportation of Na+ and K+ ions across nearly all animal cell plasma membranes, and is critical to brain functioning.


Lab Attendance

--Z3407326 14:19, 31 May 2012 (EST) --Z3407326 14:15, 24 May 2012 (EST) --Z3407326 16:00, 17 May 2012 (EST) --Z3407326 14:59, 10 May 2012 (EST) --Z3407326 14:14, 3 May 2012 (EST) --Z3407326 16:03, 26 April 2012 (EST) --Z3407326 14:13, 19 April 2012 (EST) --Z3407326 14:15, 5 April 2012 (EST) --Z3407326 14:09, 29 March 2012 (EST) --Z3407326 14:12, 22 March 2012 (EST) --Z3407326 14:26, 15 March 2012 (EST) --Z3407326 15:13, 8 March 2012 (EST)


Lab 1

Hello,

This is my first lab in Cell Biology!

Lecture 1

ASCB website