Assignment TwoFinding Your Scientific Voice

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

Assigned: January 27, 2009

Due: February 3, 2009

Submission: Blackboard

Format: Electronic - One File Upload

General Introduction

This week’s course curriculum is focused upon objectives surrounding scientific literature.

Each of the skills covered are key to any of the many paths a scientific career may take: research, medicine, teaching, industry, or some combination thereof. Your ability to search for and evaluate literature of interest is how other researchers selectively speak to you. Conversely, your ability to pen and present your writing is how you address your colleagues. It quickly becomes one of the most important methods by which you advertise both your accomplishments and your potential to peers, future employers, and the public at large.

This section of the course curriculum also offers the opportunity to begin to explore the background behind the research this stream will pursue. What are the biological fundamentals of our work? What has been known for the past decade or two? What knowledge is more recent? What candidate research is possible? Each of these questions will be addressed by both this week’s work and the efforts of the weeks to come.

Section A - The Eukaryotic Cell Cycle

The eukaryotic cell cycle is a regulated temporal set of events that controls cellular division. There are distinct phases and points of control implemented such that progress from one phase to another is both controlled and internally checked. If successful, a eukaryotic cell will increase in size, divide its nuclear DNA, and perform cytokinesis to divide from one cell into two daughter cells.

Section A of this assignment entails you researching the eukaryotic cell cycle and presenting a short synopsis of the biological concepts. You are encouraged to use and cite any materials at your disposal: your textbook(s) from other courses, Google, Wikipedia, and one of many online tutorials on the subject. You can use PubMed to locate review articles on the subject but I would not recommend it for this section of the assignment. This section of the assignment is focused upon an understanding of the cell cycle, its phases, and the general requirements a cell must fulfill therein. Both research and review articles in journals will be focused on the mechanistic details of how cells implement these controls - which genes are involved and which other genes they might regulate, for example. For this section of the assignment this would be too much detail.

Your goal will be to describe the steps in Figure I. A good example would be the Phases section of the Wikipedia page on the subject.

You will write two drafts of the synopsis. Each will be approximately a page in length and will be turned in. Include an introductory sentence or two, a main paragraph on the cell cycle phases, and then a closing or concluding set of sentences that states why the cell cycle is studied.

You can decide which to write first; do you write a perfect version and then purposefully introduce flaws to produce the second or do you write an imperfect version first and revise it to perfection for the second? Your decision to make - both must be handed in, however.

Figure I: The Cell Cycle

Synopsis Draft I: Scientific Version

The first will be in the voice of scientific writing as presented and discussed in lecture this week. Pay close attention to each and every one of the requirements discussed. This version will be graded for your attention to these issues. You should consider this to be the version you would want published in a text or other formalized setting. A very short example is provided below.

MicroRNAs are members of a family of non-coding RNAs that regulate gene expression in a post-transcriptional, sequence-specific manner [1]. Originally believed to be few in number, limited in biological function, and phylogentically non-conserved, microRNAs have now been identified within nearly all metazoan genomes, including D. melanogaster, C. elegans, A. thaliana, and H. sapiens.

1. Bartel, D.P., MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 2004.

Synopsis II: Non-Scientific Version

This version will essentially be the same text as the Scientific Version. This version will include flaws that demonstrate inattention to the details and requirements of scientific writing. In this version you are required to call out the mistakes or flaws that make the sentence or word choice not appropriate for scientific writing. Use the technique demonstrated in the small example below.

MicroRNAs is (1) members of a family of a really large number (2) of non-coding RNAs that control the process of how many genes are either turned on or turned off or finely tuned (3) in a post-transcriptional, sequence-specific manner. MicroRNAs (7) were a long time ago (4) believed to be small (5), limited in biological function, and phylogentically non-conserved, microRNAs have now been identified within nearly all metazoan genomes, including D. melanogaster, C. elegans, A. thaliana, and H. sapiens.

1 - subject/verb agreement2 - inappropriate adverb3 - sentence length, too many words4 - casual, informal word choice5 - vague word choice, multiple meanings possible6 - no citations?7 - need to vary sentence structure

Plagiarism & References

Please pay close attention to plagiarism - do not copy materials you reference. Digest information from many sources and the present the process in your own words. You must also provide your references. This can be done informally - you will not be evaluated on correct formatting of references. Simply provide the name of each source as well as publication date and pages numbers if each is relevant.

Submission

Both drafts will be labeled on two separate pages and included in the file submitted on the due date.

Section B - The Eukaryotic Cell Cycle: Research Knowledge

This section of the assignment will build upon the knowledge you learned in Section A. In Section A you explored two main topics: the eukaryotic cell cycle and the differences between scientific and informal writing. Section B now assumes that you are comfortable with each of these topics and ready to take matters one step further.

In this section you will be exercising your ability to use PubMed to perform literature search. What are you searching for? Well, let’s take Section A one step further. In Section A you came to understand the generic concept of the eukaryotic cell cycle - its phases and overall purpose. Let’s get more detailed.

Our research will be focused upon further characterization of the eukaryotic cell cycle in the model organism Saccharomyces cerevisiae. In particular, we will use next-generation sequencing (also called “high-throughput”, also called “short-read”) to characterize whole-genome regulation and control of cell cycle progression. Whole genome means we are not just interested in what one or two genes are doing at each stage of the cell cycle - we are interested in what all the genes in the Saccharomyces cerevisiae genome are doing. This gives us a complete picture as to how control and regulation truly operates.

We will be particularly focused upon the regulation of transcription factors - proteins that bind genomic DNA and affect the expression of nearby genes. This regulation can be either transcriptional activation or repression of a gene. These types of studies have been done before using DNA microarrays. You might be interested in a 1998 research article published in Mol Biol Cell in which Dr. Vishy (Vishwanath) Iyer (IYER, VR) played a role in characterizing a complete catalog of yeast genes that vary periodically as a cell progress through the cell cycle. We will build upon these DNA microarray studies by using next-generation sequencing to provide unprecedented resolution.

The passage above has a lot of words that were intentionally bolded. These bolded word might be good search terms and might assist you in the completion of this section of the assignment.

You will address each of the following questions using PubMed searching techniques that were presented in lecture. You are expected to answer each of these questions in the form of complete sentences or paragraphs for questions that call for longer answers.

Questions To Be Answered

Question 1: What is the name of the 1998 paper that Dr. Iyer co-authored?

The best way to present a paper is in the format found on PubMed itself.

Correspondence analysis applied to microarray data.Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10781-6. Epub 2001

(this is not the answer, just an example)

Question 2: Has Dr. Iyer co-authored other papers that have to do with cell-cycle control? If so, please list one or more of those papers in the PubMed format shown above. If you believe the answer to be no, say so and list one other paper by Dr. Iyer that was published after 2006 (on any subject).

Question 3: Has one of the other authors of the 1998 paper co-authored other papers that have to do with either Saccharomyces cerevisiae or cell-cycle control?

Again, if so, please list one or more of those papers in the PubMed format shown above. If you believe the answer to be no, say so and list one other paper by any of the co-authors that was published after 2006 (on any subject).

Question 4: Provide a paragraph summation of the 1998 paper (from Question 1).

Do not worry if you do not understand some or most of it. You likely do not need to read the paper to address this question; simply read the abstract and do your best to provide a translation of it in language that is comfortable to you.

Effort and adherence to the standards of scientific writing counts most here.

Question 5: What is the most recent research article that seems relevant to this passage?

No one answer is correct.

You must defend your choice, however, by providing four reasons for its relevance (in paragraph form). Does the paper use similar technologies? Does the paper focus upon Saccharomyces cerevisiae as a model for cell cycle control? Does the paper perhaps reference the 1998 paper that was previously mentioned? Is the paper focused upon the action of one or two genes or is it whole-genome in nature? Does the paper study the action of transcription factors? Does the paper study some other form of regulation (the cell has a lot of ways to turn things on and off)?

State your choice of paper and defend it in complete sentences (in the form of a scientific paragraph). You do not need to be guided by the sample defenses I provided - please feel encouraged to state your own.

Question 6: What is the most recent review article that seems relevant to this passage?

You must defend your choice, however, by providing four reasons for its relevance. The same standards apply here as stated in question 5.

Question 7: Is the gene Mcm1 required for any part of the cell-cycle in Saccharomyces cerevisiae?

PubMed should guide you to the answer to this question. If the answer is yes please provide a reference to a paper and summarize the work of the research article (brief paragraph).

Question 8: What is the most recent review article to focus on the use of next-generation sequencing to study transcription factors?

The terms chromatin immunoprecipitation and ChIP-seq may help you here (PubMed).

Please provide a reference to a paper and briefly (again, short paragraph) summarize the work of the research article.

Question 9: What is the most recent research article focusing upon next-generation sequencing and the transcription factor STAT1?

Please provide a reference to a paper and briefly (again, short paragraph) summarize the work of the research article.

Section C - Online Component I, Posting

Post your Section A text for “Synopsis Draft I: Scientific Version” in the course Discussion Board on Blackboard. This means you will be posting your good version - not your version with flaws.

Please perform your post by replying to “Assignment Two (Online Component)” in the Discussion Board. Thus, you will not be posting a new thread, you will be replying to the thread indicated above. You will post the complete text and any references. Formatting is not of incredible importance so do not spend a lot of time trying to get italics right or bolding of section titles. Do your best to make it look clean and readable.

Section D - Online Component II, Peer Review

In this section you will be performing the role of peer reviewer. You will do this many times in your scientific career. It is very common for friends and colleagues to send each other drafts of manuscripts asking for a review before submission.

You are encouraged to read all of your peer replies to the “Assignment Two (Online Component)” thread. This will give you a good feeling for the many personal styles that can still encompass good scientific writing. You are required to respond to four peer posts. In your reply you need to identify some portion of their text that could be improved in terms of the standards of scientific writing. You should suggest a change of wording or sentence structure.

This process should not be taken personally. It is important to begin to be able to accept such review as a professional courtesy and not a personal statement on your individual writing or writing potential. All reviews are expected to be polite and courteous (aka, professional).

I understand that many students may not post (Section A) until near the deadline for this assignment. This might make it challenging to review posts and fulfill Section D’s requirements. I will not be looking for your Section D reply post until February 4 so you will have time after Assignment Two is handed in to return to the Discussion Board and post peer reviews. Worry not.

Assignment Submission

This assignment is due on February 3, 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 Two.doc (or docx, or pdf)”. I will accept only doc, docx, or pdf formatted files.

Complete Section A with each draft synopsis labeled on its own separate page. Complete Section B, making sure that each question response is clearly labeled. Complete Section C by posting your complete text for Section A (scientific version) as instructed above (Blackboard). Complete Section D by responding to four of your peer’s posts as instructed above. This step will be evaluated on or after February 4 in order to ensure that everyone completes Section C.

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.