BIO 407 - Molecular Biology

1. Setup of a reference manager [AKA a Citation Manager]

For scientific publishing you will need reference manager software that is a repository of references and allows inserting them into text, formatting according to journal instructions. Reference manager programs include proprietary ones such as Endnote, and free software such as Zotero. I recommend you use Mendeley, which is the one I use. It allows sharing and searching, its basic plan is free, and it can be accessed both
locally and in the cloud.

If you already have a reference manage then you don’t need to install another. If you don’t have one, then install one- I recommend Mendeley (www.mendeley.com). We will go over the details in class. Besides being a reference manager, Mendeley also allows you to search for articles, authors, and groups. To document your setup of the library, you can do either of the following:

1) “interact” with me on Mendeley (share, follow, etc.)

2) post within your blog post a screenshot of your library showing that you have at least 3 articles in it already.

More about Citation Management Software

2. Setup of a library search consultation

NU library has a large number of resources for research. Set up a consultation with the library (see Library website or contact refdesk@nu.edu) to help with your research. Email confirmation is a proof that you have done so. When you contact them please let them know that this is a class assignment for this course.  Remember to include your topic along with the day/time you want to meet with a librarian.

Library Consultation Request Form

3. Blog posting (20p).

Your posting will be at least 750 words and will:

• Recount the process of search for a Drosophila gene you will be working on (includes bibliography, library, and other searches- see below)
• Summarize your ideas so far.
• Give feedback to your peers about their posting, and respond to their feedback (see below).

You do NOT need to make a decision at this point about your gene choice! The idea is to reflect and receive advice from your peers (and me).  In real science life you will be often ask to write a grant, project etc. proposal. At that stage it is critical that you do a thorough background research. I wrote 2 blog postings about it when teaching a similar class but at the graduate level:

• http://barralopolis.wordpress.com/2012/04/13/so-what-2/

• http://barralopolis.wordpress.com/2012/04/17/searching-for-information/

So what are you looking for?  The molecular biology-themed goal of this project is that you work all your way down a gene from function to structure, and apply those concepts we have learned in class to a gene of your interest.

Some of you may have a gene/gene family in mind already. hox, notch, hedgehog are great candidates if you are interested in development. There are also many “classic” Drosophila genes that were important in early molecular genetics.  However, if you are not familiar with Drosophila, one approach could be to search for a gene with a human homologue that is important for human diseases. Here is a good
starting point:

• http://pharmrev.aspetjournals.org/content/63/2/411.long and a great database:

• http://superfly.ucsd.edu/homophila/

Due Sunday 5/25/2014

Need help navigating the world of ciation management software? Take a look at the video overview below then use the tabs across the top of the page to learn a little more about four of the most popular options.

Link to Citation Management Software Guide   http://nu.libguides.com/cms

The following Sample searches are general and not specific to species, genes or related characteristics.  Searches can be modified to locate additional published research.

General Databases:

• Academic Search Complete  (EBSCO)  Sample Search:  drosophila AND gene*  24,806 results / Note: Database strong for scholarly journals, but not specific to science

• JSTOR Arts & Sciences

• ProQuest Central

• Academic OneFile  (Galel)  

• ProQuest Dissertations and Theses-Full Text  Sample Search:  “drosophila melanogaster” AND gene*   320 results / Note:  Dissertations have extensive bibliographies as part of their literature review. These articles will help you track down additional resources.

Subject Databases:

• ProQuest Science Journals  Sample Search:  drosophila AND gene*  4,017 results / Note: all science journal

• Medline (EBSCO)  Sample Search:  drosophila AND gene*  72,372 results /

Peer-reviewed (refereed) articles are certified by experts in the field before they are accepted for publication. 

Brief Glossary:

   Academic:  Refers to the audience of a publication

   Scholarly:   Refers to the audience of a publication

   Refereed:   Articles are monitored before publication

   Peer-Review:  "Blind review" by scholars and experts

Search tips:

• Keep search terms simple and grouped by synonyms.

• Use Advanced Search to help “chunk” your search. Keep one idea or concept in each box.

• Use Asterisk to expand searches for variant endings:  gene* looks for gene or genes or genetic.

• Connector words (and/or) need to be capitalized whether searching in a library database or on Google.

• Use quotation marks to keep phrases together, such as “genetic sequencing.”

• Look at the “subject terms” used on articles that look good in your initial results.  These may suggest alternate ways to phrase your terms.

Example:  Subjects: Drosophila melanogaster genetics; Heterozygote; Sex Chromosome Aberrations; X Chromosome; Female

Need to Find Full Text?  See the Finding Full Text Guide:  http://nu.libguides.com/fulltext or use the Online Journal List,