Assignment ThreeStream Background Exploration

Functional Genomics Research Stream • Freshman Research Initiative • by Dr. Patrick J. Killion

Assigned: February 3, 2009

Due: February 10, 2009

Submission: Blackboard

Format: Electronic - One File Upload

General Introduction

This is the final week of our research stream’s preparatory material. After this, we are in the laboratory non-stop!

This assignment will fulfill your lab hours for the week of February 2-7. You will be in the laboratory after the next lecture (delivered on February 10, 2009). More details at that time.

Last week’s assignment (Assignment Two) was focused upon you finding and exercising your scientific voice. Additionally, you learned through research and writing about a major focus of our work: the eukaryotic cell cycle. This week we are focused upon a next-step from there: listening, thinking, following-up, and reflecting. These skills are built upon the foundations you have now established in literature search and scientific writing. As with scientific writing and presentation, these skills will be invaluable to you no matter which path you later choose.

Section A - Lecture Thoughts & Questions

At the beginning of lecture you were given a heads-up.

At that time you were told to take some careful notes regarding items, terms, or topics that grabbed your interest. Most importantly, you should have written down a few items that needed clarification, follow-up, or more reading for you to fully understand. This section of the assignment will have you doing just that. I wish for you to pick one - just one - of the topics or question areas you flagged for follow-up and do just that: follow it up.

You will be writing one single-spaced page (minimum) in total for this section (in the form of three paragraphs). The tone of the section will be more casual than the last assignment. The strictures of scientific writing are not needed. This will be in your professional voice; your personality through the filter of clear, grammatically correct writing.

Begin with a paragraph detailing the topic or question that interests you. Give some context. During which part of the lecture did the topic come up? Explain your interest or question.

The next paragraph should describe the process you went through to research the topic or question. What resources did you try? Which ones provided good information? Which ones provided questionable information? What made that information questionable in your mind? Do not include details as to the answer at this point. I simply want details that describes the process you went through to find answers.

Finally, you will write a paragraph detailing answers and conclusions. What did you find out? Did it answer your question? If so, where might you take the topic from here? Can you state one or two interesting questions that come from your discovery or clarity? If you did not find and answer whom do you think you could seek out for guidance? How would you approach them? Can you provide a literal example of the question you might ask if given the chance (write it out)? This question demonstrates that while you might not have the answer, you have done enough work to form a clear, concise, and direct question. Is this form of the question better and more informed than the initial version you jotted down in your notes during lecture?

Summary:

This section of the assignment should have three paragraphs that sum to at least a 1.5 spaced page:

1) introductory statements & context, initial question2) the process by which you sought answers

3) the result: what did you learn and where does that take you?

Not Full Length Example:

The slide on Genomics mentioned that the study of genomic DNA sequence often used conservation as a means by which genomes can be better understood. It is not clear to me what conservation meant in this context. Is it related to the ecological use of the term? Additionally, the figure that was included demonstrated conservation of a gene. I am not sure what the figure displayed or communicated. Is conservation a term that applies to only genes?

Note that I have actually asked several questions here regarding one topic. This is good. I do not understand the term and I am attacking that problem on multiple fronts in the form of multiple questions.

I began the process for clarity where all knowledge begins these days: Google. This approach was stunted at first by an overwhelming set of results focused on the ecological use of the term. Having perused that meaning I am quite certain that it is totally unrelated to the use of the term in the context of genomes and DNA. I continued the search for understanding by simply adding a few of those additional terms to the search “conservation genome DNA”. One of the results was a Wikipedia page for the term “Junk DNA”. This page used the term many times and linked to a page that contained a clear definition (Conservation - genetics). I took the information that was provided there and felt I had a much stronger understanding of the term in the context of genomes. This page also linked to another page (Conserved sequence). There I truly came to understand both the definition, scope, and context of the term as it relates to the study of related genomes of multiple species.

The third paragraph is dedicated to the result in the same tone ..... Be sure to include follow-up questions and where you might go with this new understanding.

Have you chosen a topic or term complex enough for a page of exploration in this manner?

Section B - The Exploration

We are going on a field trip!

I have arranged to take you to several places on campus that are highly relevant to the work of our research stream. They will include several research labs that are a part of the Institute for Cellular & Molecular Biology (ICMB) as well as the Genome Sequencing and Analysis Facility (GSAF). These are labs and facilities rarely seen by undergraduates!

You are required to attend one of these two sessions. I will have a sign-in sheet to document your attendance.

Session assignments are included on the next page.

I have designed these assignments using the availability information you provided me at the beginning of the semester. If you absolutely must attend the other session please feel free to do so - but only if you absolutely must.

I know that you may have a conflict that keeps you from attending the entire duration (estimated from 2:00 to 4:00 PM on Wednesday and Thursday - February 04 and 05). If you need to leave early for a course that is understood. I expect that you will be able to attend at least the first hour.

Session Assignments

Wednesday 2-4 PM (FEB 04) Thursday 2-4 PM (FEB 05)

JOSLIN; ELIZABETH MARY REGO; LAUREN LYNNE

PURCELL; KAYLA DAWN TIEN; MATTHEW

MCKENZIE; ROBERT PIERCE WILLIAMS; MORGAN ROCHA

MUELLER; ANDREW JOSEPH LESSELS; ELISABETH RUTH

NGUYEN; THOMAS DUC ALI; SOPHIA ALTAF

PHAM; CAROLINE AN KOSHY; BRADLEY

SHAH; RONAK VATSAL LIU; HUADAN

SHELTON; ALISSA JANE NGUYEN; CHRISTINE E.

SPEAR; JACQUELYN ABIGAIL SILVA; ABEL ELISEO

WEYN-VANHENTENRY; S. M. SUKAMTOH; EMELINE

WOLFE; LAUREN NICOLE AWAD; JOHN DANIEL

WAGGONER; MADELINE H. FAIRCHILD; LAUREN E.

We will meet in our laboratory, PAI 2.46 (at 2:00 PM). We will proceed from there (walking a short distance to the ICMB and GSAF building MBB).

You will need to bring your laboratory notebook (or something to write in, preferably your lab notebook).

During the trip we will meet several researchers engaged in work very relevant to that of the stream. Some will be using our model organism Saccharomyces cerevisiae to answer dramatically different questions. Some will be using similar technologies to address functional questions in other biological contexts (organism, process in the cell, pathway of interest, etc).

Section C - The Exploration Reflection

In Section A of this assignment you engaged a process to address a term, topic, or question with which you needed clarification of meaning, context, or relevance. This term or topic was derived from the lecture given this week.

In Section C of this assignment you will go through the exact same process (with matching requirements) for a term, topic, or question that arose during your participation in the tour of ICMB and GSAF facilities.

Thus, again, write one page single spaced in the form of three paragraphs. Same expectations as Section A.

Section D - Online Component I, Posting

You should be familiar with posting to our Blackboard “Discussion Board” at this point.

As a reminder: you will be posting by copying the text from your writing - do not upload the file you have been working on. Instead, copy and paste the text of your writing such that it is immediately readable by all students.

You will be performing two posts for this section of the assignment.

Post your Section A text for in the course Discussion Board on Blackboard. Please perform your post by replying to “Assignment Three (Online Component I)” in the Discussion Board. Thus, you will not be posting a new thread, you will be replying to the thread indicated above. Additionally, please reply directly to my initial posting of “Assignment Three (Online Component I)” as opposed to one of your peer’s posts.

Post your Section C text for in the course Discussion Board on Blackboard. Please perform your post by replying to “Assignment Three (Online Component II)” in the Discussion Board. Same guidelines.

Section E - Online Component II, Peer Feedback

In this section you will be adding to or commenting on peer comments.

You will not be critiquing writing as you did in the last assignment. You will simply be reading the writing of your classmates and responding with comments, questions, or additional information. It’s a discussion, really.

Respond to two posts in the thread “Assignment Three (Online Component I)” and two posts in the thread “ Assignment Three (Online Component II)”.

Thus, you will be responding to four posts total.

This section of the assignment will not be evaluated until February 11, 2009.

Assignment Submission

This assignment is due on February 10, 2009. It will be submitted online through Blackboard. If you are unfamiliar with how to do this process please check the following URL for simple instructions:

http://www.utexas.edu/academic/blackboard/tutorials/assigns_u/up.html

You will submit only one file with all sections contained therein. The single file you submit should be named “Assignment Three.doc (or docx, or pdf)”. I will accept only doc, docx, or pdf formatted files.

The due date is the last day the assignment can be submitted through Blackboard. I encourage you to clearly label both section titles and individual sub-parts of sections. There is a direct correlation between clarity of submission and grade.