The Multiple Loci VNTR (variable nucleotide tandem repeat) analysis (MLVA) technique is used to identify strains of organisms.
Because the database is quite large for S. aureus and publicly available, we’re going to focus this second assignment on an analysis of this method. Go to the website http://mlva.u-psud.fr/mlvav4/genotyping/index.php, which contains a link to a number of databases. On the left menu, click on the Staphylococcus_aureus database under the Collaborative databases option. First click the “View” button. You’ll then see appear a large list of different isolates of this strain. Click on the “Panels” button on the right to reveal different MLVA data.
1. Under the MLVA section to the right, there are a series of mostly tags: “Sa0122, Sa0266”, …. Below that are mostly integers. Explain what these tags mean and what the numbers stand for, based on your readings in other sections this week.
2. Describe the difference between MLVA and MLST.
3. Why are some of the MLVA numbers blank?
Now go back to the left menu and select “Staphyloccus_aureus” and choose the “Query” button instead.
4. There is a button that says “select a panel”, or you can select using checkboxes the ones you want to use. Describe the difference between the two.
Select the MLVA14Orsay option and click “Submit”. (make sure it is the MLVA option on the left, not the MLSA on the right).
Now you see a MLVA box listing the different loci that you are going to query. Each site is a different MLVA marker. Below is an option where you can enter your MLVA set with a space between each number. Notice that there are 14 numbers, matching the MLVA14Orsay option. Type in the sample sequence exactly as listed to see what the sample output would look like. “10 6 3 4 3 7 7 5 4 4 5 2 3 3”
You get a direct hit (of course), and it shows you the those fingerprints most closely related to the one you chose. To which strains was this hit most similar?
5. Does this mean the strains themselves came from these locations?
Notice how the red boxes indicate differences from the sequences that you entered.
6. Click on “Tree” using the “Tools” pullout menu, and select the Newick tree. Download the tree as a text file. Upload it here (http://etetoolkit.org/treeview/) and download the graph that you get from it, placing it into this assignment.
Now we’re going to switch over to doing analysis of Yersinia pestis using MLVA typing. Go back to the main page and select “Yersinia pestis2004”. Again, click “View” so you have an idea of what you are looking at.
7. The nomenclature is slightly different, as are the markers. Why?
8. Why doesn’t it make sense to use 50 markers for MLVA analysis, to increase specificity? Here’s a paper that discusses the addition of more VNTRs the current Anthrax MLVA analysis for ideas. http://www.ncbi.nlm.nih.gov/pubmed/19469279
9. Open the Y. pestis MLVA7 database and choose one of them. (For example, I chose (10 9 9 8 7.5 9 6).) Make a tree using the instructions on the website. Purposely make a mismatch and see what happens when you generate a second tree. What changes? Describe the major difference between the two “trees”.
10. Go back to the main menu. Select “Geographic View”. Notice how it takes you to a world map that shows you where the isolates were found.
11. Access the matrix of distances. What does this do?
12. Find at least one other MLVA site that does sequence analysis and post it in the conference area. In one or more sentences, briefly say what the site is, what it focuses on, and what nation it is from.
13. Complete your assignment by summarizing what you’ve learned in one paragraph. It should be a rather detailed paragraph that reflects on the various issues that this assignment has shown you.
Here are a few more sites that talk about some issues with this database.
http://mlva.u-psud.fr/MLVAnet/spip.php?article90
APA format, in-text citation, references include, 3 pages to answer all 13 questions.
Try it now!
How it works?
Follow these simple steps to get your paper done
Place your order
Fill in the order form and provide all details of your assignment.
Proceed with the payment
Choose the payment system that suits you most.
Receive the final file
Once your paper is ready, we will email it to you.
Our Services
Custom Writings Help is a Quality-Oriented Company in Online Writing as a result of hiring exceptional professionals to execute clients' tasks.
Essays
At Custom Writings Help,We understand the struggle of research paper writing, and that is why at Custom WritingS Help, we are all out to help you. We pride ourselves on having a team of clinical writers. The stringent and rigorous vetting process ensures that only the 'BEST' Writers are chosen for the job. We have highly qualified Ph.D. and MA writers working with us; we equally offer these experienced writers specific bonuses and incentives to make them deliver highly original, unique, and informative content at reasonably low prices.
Admissions
Thesis Writing Service
Worlwide, Many Masters Students are struggling with Thesis Completion. A thesis is likely to be the longest and most challenging piece of work a student has ever completed. However, unlike essays and other assignments, a student can pick a particular interest topic and work on their initiative. Fortunately, we are there for you. At Custom Writings Help, you are assured of an authentic, imaginative, informative, linguistically great, and advantageous thesis that adheres to all your needs. So, why continue considering different writers when you have discovered the best in the field?
Editing
Custom Papers
Not a single student can avoid writing custom papers. However, a total lack of experience, skills, and time makes it very hard to produce a superb writing piece. Therefore, if you are seeking professional help, turn to us. Our specialized and experienced writers compose a variety of model papers, including custom essays, college term papers, research papers, book reports, MBA essays, executive summaries, dissertations, Ph.D. theses, admission essays, and research proposals for college and university students at any level.
Coursework
Essay Writing
Most of the students disregard the critical principles of essay writing and compose papers below sensible guidelines. Therefore, with Custom Writings Help, one should not worry about his/her essay. Our Writers compose informative and engaging content on all complexities and topics. We write meaningful and smart essays while prioritizing all aspects that bring about a good grade, such as impeccable grammar, proper structure, zero-plagiarism, and conformance to guidelines.
Coursework
Coourse Work Writing
Don't let the seemingly never-ending onslaught of writing assignments get you down. If you are looking where to get course work assistance online, the writers at Custom Writings Help are here to assist you with all of your writing needs. We undertake to unique delivery of papers that meet the professor's requirements. The content is proofread, edited, and checked plagiarism before submission to customers. No matter how big or small your work is, we will deliver on time. Try US Now! !
Coursework
Dissertation Writing Service
High-Quality Dissertation Writing Services are rare. They require Ph.D. academicians – not easily found. However, are an exception. The years, time, and resources we have invested in the dissertation world has given us a competitive advantage over others. Choose to come to Custom Writings Help; You will find perfect Ph.D. consultants who have written hundreds of dissertations theses ready to help you. Let our dissertation-writing services help you craft your dissertation, for you are assured we will give you the results.