Bio 4028 - Recently Updated Pages

Final Project Key

ehaswell — Fri, 18 Dec 2009 10:02:58 CST

75 points total:
20 for quality of presentation
15 for screen design
20 for research on genes
20 for future research

average score: 66
high score: 71

12.10.09 Presentations

ehaswell — Thu, 10 Dec 2009 15:39:03 CST

There is no abstract available for this page revision.

12.8.09 Presentations

ehaswell — Wed, 09 Dec 2009 10:21:29 CST

There is no abstract available for this page revision.

Exam #3

ehaswell — Wed, 09 Dec 2009 10:21:06 CST

Average score = 79/100
High score = 91/100

Exam #2

ehaswell — Wed, 09 Dec 2009 10:20:05 CST

Average score = 85

Homework

ehaswell — Mon, 30 Nov 2009 18:20:08 CST

Please scroll down for the Homework and Homework keys.
Homework #1--average score was 22/25 points.
Homework #2--average score was 20/25 points.
Homework #3--average score was 23/25 points.
Homework #4--average score was 24/25 points.

Schedule of Lectures and Reading Assignments

ehaswell — Mon, 23 Nov 2009 08:23:37 CST

Date	#	Topics	Background Readings	Discussion Readings
Thu 8/27	1	Course Overview The evolutionary history of plants Plant Cell Biology: plastids	The Salvation of Doug The Demise of Bill Meyerowitz, 2002 Lopez-Juez, 2007	none
Tue 9/1	2	Plant Cell Biology: the cell wall	Cosgrove, 2005	Jones et al., 2001
Thu 9/3	3	Plant Cell Biology: cytoskeleton	Handbook of Plant Science Chapters	Ishida et al., 2007 Supplementary Information
Tue 9/8	4	Plant Development: introduction, plant life cycle, pollen and ovule development	Yadegari & Drews, 2004 McCormick, 2004	Lee et al., 2007
Thu 9/10	5	Plant Development: pollen tubes, fertilization, embryogenesis	Berleth & Chatfield, 2002	Higashiyama, et al. 2001 Okuda et al., 2009
Tue 9/15	6	Plant Development: embryonic patterning, cell lineage, cell fate	Irish, 1991	Satina et al., 1940
Thu 9/17	7	Plant Development: epidermal patterning	Bergmann & Sack, 2007 Schiefelbein et al., 2009	Savage et al., 2008
Tue 9/22	8	Plant Development: photomorphogenesis, review	Chen et al., 2004	none--review session
Thu 9/24		Exam #1
Tue 9/29	9	Plant Development: meristem establishment and maintenance	Carles & Fletcher, 2003	none
Thu 10/1	10	Plant Development: phase-changes	Turck et al., 2008	none
Tue 10/6	11	Plant Development: flowers	Lohmann & Weigel, 2002	none
Thu 10/8	12	Plant Development: leaves	Bowman et al., 2002	none
Tue 10/13	13	Plant Development: roots	Doerner, 1998	none--review session
Thu 10/15		Exam #2
Tue 10/20	14	Plant genomes, polyploidy	Hegarty & Hiscock, 2008	Dilkes et al., 2008
Thu 10/22	15	Epigenetics, RNAi	Henderson & Jacobsen, 2007	Preuss et al., 2008
Tue 10/27	16	Overview of plant genetic approaches	Meinke et al., 1998	none
Thu 10/29	17	Forward genetics I: mutagenesis and screening/selection	Page & Grossniklaus, 2002	Haughn & Somerville, 1987
Tue 11/3	18	Forward genetics II: processing and analyzing mutants	Hawley & Gilliland, 2006	Vroemen et al., 2003
Thu 11/5	19	Forward genetics III: mapping and cloning mutations	Jander et al., 2002	Krishnakumar & Oppenheimer, 1999
Tue 11/10	20	Genetic screen design, workshop	none	Krishnakumar & Oppenheimer, 1999
Thu 11/12	21	Reverse genetics in Arabidopsis: T-DNA and transposons	Alonso & Ecker, 2006	Thomas et al., 2008 Note: Figs 1-5 only
Tue 11/17	22	Chemical genetics, genomics and high-throughput approaches	Lu & Last, 2008	Lahner et al., 2003
Thu 11/19	23	Natural variation and QTL analysis	Doerge, 2002	Loudet et al, 2007
Tue 11/24	24	Chemical genetics, review session	Blackwell & Zhao, 2003	none--review session
Thu 11/26		No Class--THANKSGIVING
Tue 12/1		Exam #3

Doerge, 2002

ehaswell — Fri, 20 Nov 2009 09:20:33 CST

There is no abstract available for this page revision.

Loudet et al., 2007

ehaswell — Tue, 17 Nov 2009 16:26:17 CST

There is no abstract available for this page revision.

Lahner et al., 2003

ehaswell — Sat, 14 Nov 2009 13:35:14 CST

There is no abstract available for this page revision.

Genetic Screen Workshop

ehaswell — Fri, 13 Nov 2009 09:21:27 CST

Individual Project: Genetic Screen Design Workshop
Bio4028

1. Break into groups of 3-4 (three groups total)

2. Take turns presenting your screen and soliciting feedback from the others in your group.

3. Take time at the end to write down suggestions and new ideas you might have.

Questions to ask yourself and your classmates about the presentation:

Does this experiment address a fundamental biological question?

Is the appropriate plant species being used?

Are the choices of genetic background and mutagen appropriate?

Could a selection scheme be devised?

Is the screen itself reasonably efficient? (For example, can M2s be analyzed in large pools or only
one-by-one? Is special equipment required? How time-consuming is each analysis?)

Is a pool or pedigree approach best?

Could molecular tools like reporter genes be useful for the screen?

What are likely categories of false positives and false negatives?

Can you eliminate some of these categories by careful planning of the screen, or by addition of a
secondary screen?

Individual Project Timeline

ehaswell — Tue, 03 Nov 2009 16:32:53 CST

Individual Project Timeline
Bio 4028: Seeds to Senescence

11/3 – 11/10
1. Narrow your focus to one area, and do background reading.

2. Come up with potential screen/selection strategy. Check Pubmed for originality.
11/10 In-class session to discuss screen ideas in small groups.

11/10-11/24
3. Begin to plan presentation.
11/12 submit 1st and 2nd choices of presentation dates to Liz by email.

4. Flesh out your plan for the screen.
11/24 Homework #4 is due, including a description of your screen:
“Part 2: Design a genetic approach (involving classical forward genetics, genomics, chemical genetics, or natural variation) to identify genes involved in one of the processes you identified in Homework #3. Briefly describe the question you wish to address and your genetic approach below. One or two paragraphs should be sufficient.”

11/24 – 12/10
4. Find out where and when your gene/s are expressed, where the proteins localize, what else has been reported in the literature.
11/12 Lecture 21 will introduce you to several of these useful online tools.
11/27 Receive your gene or genes. If you want them earlier, you are welcome to turn in the homework early, or simply email me with an overview of your plans.

5. Complete your presentation.
See handout for more information.

Thu 12/3, 12/8, or 12/10
6. Give your presentation!
See handout for more information.

Need help?
Check out the course website for an excellent sample presentation (http://seedtosenescence.wetpaint.com/).

Email me at any time to ask questions or set up an appointment (ehaswell@wustl.edu).

You are encouraged to send your homework and your slides early for feedback.

Oral Presentations

ehaswell — Tue, 03 Nov 2009 16:31:34 CST

Individual Project Parts 3 and 4
Bio 4028: Seeds to Senescence

Part 3. You will be assigned one or two genes to “find” in your screen. Using the online tools demonstrated in class, characterize the likely function of the protein encoded by this gene, and propose the role it may play in your process of interest. This part will not be graded separately, but will be included in your presentation in Part 4.

I will assign genes the evening of November 24th, the day that Homework #4 is due. If you would like your assignment earlier, let me know the general nature of your screen by email, and I will send you your results as soon as possible.

Part 4. In a 15-minute presentation, give a brief introduction to your topic, describe your genetic approach and the “results” I assigned you, and present the results of your online investigations. Finally, suggest a few future directions for this research. This will require publication searches and online research, and will be an opportunity for you to practice your communication skills. You will get feedback on your presentation in a questionnaire that is filled out by your fellow students and will be seen only by you.

Email PowerPoint presentations to me by noon on the day of your presentation for loading onto the class computer. If you have a PC presentation, you may wish to bring your own computer; I can also bring a PC to class if requested.

Guidelines for Presenters.
· The fifteen-minute limit will be strictly enforced!
· A good rule of thumb is one slide per minute. This means only 15 slides!
For example:
Slides 1-4 background
Slides 5-7 the screen
Slides 8-13 results
Slides 14-15 future directions
· Practice your talk in advance
· Use animations sparingly
· Use large font

Questions to address in your presentation:
What is the biological question you are addressing in your screen?
What mutagen did you use?
What generation did you screen in?
What tissue and stage of development did you screen in?
What phenotype did you screen for?
How did you identify the mutants of interest (visual, chemical, reporter gene, selection, etc.)
What are the genes you “found”?
What do they encode?
What other information about these genes is relevant to your screen?
How does the identity of these genes answer the question you are asking in your screen?
What experiments will you do next?

Guidelines for the Audience.
· Attendance is mandatory at all talks, even if you are not presenting that day.
· Pay attention, be generous, ask questions.
· You will be asked to fill out a brief evaluation for each talk during class—only constructive criticism is appropriate.

Hawley and Gilliland, 2006

ehaswell — Thu, 29 Oct 2009 07:01:08 CDT

There is no abstract available for this page revision.

Preuss et al., 2008

ehaswell — Thu, 15 Oct 2009 18:49:56 CDT

There is no abstract available for this page revision.

Dilkes et al., 2008

ehaswell — Thu, 15 Oct 2009 18:37:11 CDT

There is no abstract available for this page revision.

Exam #1

ehaswell — Tue, 29 Sep 2009 16:16:44 CDT

Please scroll down for a PDF file of the exam key.

Average grade = 86/100
High grade = 99/100

Discussion of Epistasis

ehaswell — Wed, 16 Sep 2009 13:58:52 CDT

There is no abstract available for this page revision.

Savage et al., 2008

ehaswell — Sat, 12 Sep 2009 16:27:24 CDT

There is no abstract available for this page revision.

Schiefelbein et al., 2009

ehaswell — Sat, 12 Sep 2009 16:26:21 CDT

There is no abstract available for this page revision.