1. Order of progress reports March 11 1.Yamrus/Wirth 2.Terry/Kolansky 3.Hoffert/Sluhocki March 18 1.Pero/Bartlow 2.Janosov/Jescavage/Keiser 3.Ciaston/Suchocki/Yuhas March 25 1.Marx 2.Bird

2. How to make a poster Dina Mandoli, U Washington http://www.aspb.org/education/poster.cfm

3. Characters of good posters 1.Readable: ideas flow easily

4. Characters of good posters 1.Readable: ideas flow easily 2.Legible: can easily read from 10 feet

5. Characters of good posters 1.Readable: ideas flow easily 2.Legible: can easily read from 10 feet 3.Well-organized: elements are arranged logically

6. Characters of good posters 1.Readable: ideas flow easily 2.Legible: can easily read from 10 feet 3.Well-organized: elements are arranged logically 4.Succinct: you have 11 seconds to get your audience’s atention

7. Getting started 1.Choose the main message

8. Getting started 1.Choose the main message 2.Lay out panels crudely to fit space available

9. Getting started 1.Choose the main message 2.Lay out panels crudely to fit space available 3.KISS ( keep it simple, stupid!) Remove all extraneous material

10. Arrangement 1.Humans track vertically from center to top to bottom, and horizontally from left to right. 1 2

11. Arrangement 1.Humans track vertically from center to top to bottom, and horizontally from left to right. 1 23

12. Arrangement 1.Humans track vertically from center to top to bottom, and horizontally from left to right. 1 23 456

13. Arrangement 1.Humans track vertically from center to top to bottom, and horizontally from left to right. Put your best pictures in center, just below title 1 Naked photo at Sydney Opera House highlights openness

14. Arrangement 1.Humans track vertically from center to top to bottom, and horizontally from left to right. Put your best pictures in center, just below title Put your key text elements in upper corners 1 Naked photo at Sydney Opera House highlights openness Abstract:>5,000 people posed naked for a Spencer Tunick photo to show that Australia is a free & equal society

15. Arrangement 1.Humans track vertically from center to top to bottom, and horizontally from left to right. Put your best pictures in center, just below title Put your key text elements in upper corners 1 Naked photo at Sydney Opera House highlights openness Abstract:>5,000 people posed naked for a Spencer Tunick photo to show that Australia is a free & equal society Conclusions 1) Australia is a free & equal society

16. Arrangement 1.Humans track vertically from center to top to bottom, and horizontally from left to right. Put your best pictures in center, just below title Put your key text elements in upper corners 1 Naked photo at Sydney Opera House highlights openness Abstract:>5,000 people posed naked for a Spencer Tunick photo to show that Australia is a free & equal society Conclusions 1) Australia is a free & equal society 2) Many Aussies support gays

17. Arrangement Put your best pictures in center, just below title Put your key text elements in upper corners Put your remaining material down the page in decreasing order of importance 1 Naked photo at Sydney Opera House highlights openness Abstract:>5,000 people posed naked for a Spencer Tunick photo to show that Australia is a free & equal society Conclusions 1) Australia is a free & equal society 2) Many Aussies support gays Introduction: Discussion:

18. Antisense Copies of Light-Regulated Genes in Rice T Mike 1, N Joshi 1, J Bird 1, K Margavage 1,2, Bryant Morocho 1, X-W Deng 2, W Terzaghi 1,2 1 Wilkes University, Wilkes-Barre, PA - 2 YaleUniversity, New Haven, CT P16065 Figure 2: The Os03g07300/ Os03g07310 (ribulose-3-P epimerase/ axi protein) gene pair. A) Low molecular weight Northern showing a 40 nt, root-specific RNA derived from Os03g07310. B) RT-PCR confirming the presence of mRNA of both genes in the leaf tissues. LL: light-grown leaf; DL: dark-grown leaf. Figure 1: Antisense and light regulation. High-throughput techniques identified large numbers of antisense and light- regulated transcripts. This research tested the hypothesis that antisense may play a role in light regulation. Methods Identified antisense transcripts from light-regulated genes in Japonica rice  Query microarray, MPSS, and cDNA databases Treated seedlings to a variety of lighting conditions to determine effect on mRNA and antisense transcription  Plants were grown:  10 days continuous white light or continuous darkness  10 days continuous darkness followed by 4 hours white light  10 days continuous darkness followed by either 1 mmol red light, 1 mmol far red light, or 1 mmol blue, then far red RNA was extracted from roots and leaves using Ambion’s miRvana Total RNA Isolation kit. Detection of mRNA and antisense utilized:  Northern blots to verify presence of RNA  Reverse Transcription using the 5’ or 3’ primer only  Real time PCR to quantify relative expression Introduction Natural Antisense Transcripts (NATs)  RNA molecules complementary to other “sense” RNAs  Present in a variety of organisms, NATs are involved in RNA editing, genomic imprinting, viral defense, etc.  Sense-antisense RNA pairs may reciprocally regulate each other’s production: when production of one transcript increases, production of the other decreases Prevalence of NATs in plants suggests that NATs may help regulate light responses  Light responses are regulated by complex networks of transcripts  Some antisense RNA is involved in circadian rhythms Although NATs have been identified in model plant species, their functions are not clear Conclusions 17 of 21 light-regulated genes examined have NATs, 5 of which are regulated by light Several genes show reciprocal regulation of mRNA and NAT Some NATs were processed into small RNAs which may help regulate sense/ antisense RNA transcription qRT-PCR detected:  ~14-fold more rbcS mRNA than NAT transcripts in shoots grown in continuous darkness  ~5-fold more mRNA than NAT in shoots grown in continuous light  Roots grown 4hr in white light do not increase expression of rbcS mRNA phyA NAT expression greatly increased upon exposure to white light for 4 Hr or to1mmol. m 2 red light. Acknowledgements This research was primarily supported by NSF grant DBI-0421675: Virtual Center for Analysis of Rice Genome Transcription (Xing- Wang Deng, PI). Additional support from Wilkes University, Yale University, and the Howard Hughes Medical Institute is also gratefully acknowledged. Abstract Natural antisense transcripts (NATs) are RNAs complementary to sense RNAs that are known to play roles in gene regulation. We studied 21 genes with NAT that are involved in light-regulated pathways in Nipponbare rice (Oryza sativa japonica). Of these genes, 17 were detected by RT-PCR in shoots and roots of Nipponbare seedlings. RT- PCR of the Os12g17600 rbcS gene detected multiple small antisense fragments rather than one continuous RNA. Quantitative RT-PCR of Os12g17600 identified 5-fold more sense than NAT in shoots of seedlings grown in light, but 14-fold more sense than NAT in dark- grown seedlings. qRT-PCR of the Os03g51030 PHYA gene indicated that all light treatments decreased the ratio of sense to antisense with the exception of far-red light, which increased the ratio. Several genes exhibited reciprocal regulation of NAT and sense RNAs according to light treatment. Low molecular weight RNA blots of the Os03g07300/ Os03g07310 gene pair identified a small RNA (~40 nucleotides) that was only observed in light-treated roots. These small RNAs might be used to down-regulate the expression of genes turned on by light in roots. Discussion Tiling-path microarrays identified thousands of genes with NATs  17 of 21 NATs of light-regulated genes found by microarrays were confirmed, validating this high-throughput approach. Reciprocal light regulation of sense and antisense transcripts was detected for several genes, providing a potential mechanism for regulating the abundance of specific transcripts in response to light. Overlapping NATs initiated from several start sites were identified for Os12g17600  Suggests that antisense is not initiated from a single promoter. Small RNAs derived from several overlapping gene pairs were detected, which may help regulate their expression. NATs are induced in greater magnitudes than sense mRNA in both rbcS and phyA leaves under various light treatments Questions that still need answers:  Which photoreceptors are involved?  Do NATs help modulate light-regulated gene expression?  How is NAT/ mRNA production regulated?  Are NATs polyadenylated?  Sequence of 40nt RNA product of 07300 gene? Figure 3: Reciprocal regulation of Os02g05830 (rbcS2). In tissues expressing higher levels of NAT, the mRNA is found at lower levels, and vice versa, indicating reciprocal regulation. LL: light leaf; DL: dark leaf; LR: light root; DR: dark root; 4hr. WL: 4 hour white light; 4hr. WR: 4 hour white root; RL: red leaf; RR: red root; FRL: far red leaf; FRR: far red root; BL: blue leaf; BR: blue root. Figure 4: Induction of Os03g51030 (phyA) in seedling shoots by various light treatments. A) Graph of level of induction of sense and antisense standardized to the corresponding dark sample. B) Expression levels of sense and antisense RNA in shoots relative to dark shoot antisense along with the ratio of sense to antisense. Figure 5: Induction of Os12g17600 (rbcS) in seedling shoots by various light treatments. A)Graph of level of induction of sense and antisense standardized to the corresponding dark sample. B)Expression levels of sense and antisense RNA in shoots (left) relative to dark shoot antisense and roots (right) relative to dark root antisense along with the ratio of sense to antisense. Table 1: Strength of detected antisense signals. The gene pairs in the red box overlap at their annotated 3’ ends and the snoRNA are transcribed from the opposite strands of RPT2 exons. The antisense strands of the remaining genes have no annotated functions. Os03g07300/ Os03g07310 (ribulose-3-P epimerase/ axi protein)Os02g05830 (rbcS2) Os03g51030 (PHYA)Os12g17600 (rbcS) Expression of Sense and Antisense rbcS Transcripts Relative to DLAS in Shoots AntisenseSenseRatio S:A Blue5.885.314.7 Dark1.013.9 Far Red5.557.410.4 Light100.6527.35.2 Red11.0122.511.2 4 hr White40.2284.07.1 Expression of Sense and Antisense phyA Transcripts Relative to DLAS in Shoots Antisense Sense Ratio S:A Blue1.2156.0130.9 Dark1.0152.1 Far Red0.8132.2172.6 Light2.081.941.8 Red4.9112.323.0 4 hr White2.5186.975.3 B) Expression of Sense and Antisense rbcS Transcripts Relative to DRAS in Roots AntisenseSenseRatio S:A Blue0.45.512.5 Dark1.09.8 Far Red1.215.712.9 Light2418.416842.57.0 Red153.81854.212.1 4 hr White0.12.519.4

19. Appearance (10 pts total) Type, figures large enough to see from 10 feet?1 pts ____________ Figures and tables clear, legible, and nicely presented?2 pts ____________ Good ratio of figures to text?3 pts ____________ Artistic impression4 pts_____________ Effectiveness of presentation (40 pts total) Effective title?1 pt ____________ Readability?3 pts____________ Organization?3 pts_____________ Is abstract concise and prominently displayed? 2 pts_____________ Does abstract have all elements & summarize the poster?4 pts_____________ Do conclusions concisely summarize the major results? 4 pts_____________ Are conclusions supported by data given on the poster?2 pts_____________ Is introduction concise, yet adequate? 3 pts_____________ Do figure and table titles concisely summarize key results?1 pts_____________ Are captions adequate & distinct from figure and table titles?2 pts_____________ Are figures and tables clear and easily understood? 2 pts_____________ Are the various elements effectively arranged? 2 pts_____________ Is discussion concise, yet explain each result? 3 pts_____________ English (spelling, grammar) 3 pts_____________ Overall: did it effectively deliver the key points?5 pts_____________

20. / 10 Team / 1 Organization? / 1 Clarity? / 1 Introduction? / 1 Were the results clearly presented? / 1 Were the conclusions clearly presented? / 1 Discussion? / 1 Understanding? / 1 Future Plans? / 1 Time? / 1 Teamwork? / 10 Individual / 4 Contribution to overall effort / 1 Role in presentation / 1 Level of understanding / 1 Role in question/answer / 1 Quality of answers / 6 Mechanics / 1 Confidence / 1 Diction & volume / 1 Interaction with audience / 1 Pace / 1 poise, mannerisms / 1 use of images

21. Formal Report 1.Title Page: should include the title, name of each author, and the institution at which the work was performed. Text should be centered. DWA3, an Arabidopsis DWD protein, acts as a negative regulator in ABA signal transduction Jae-Hoon Lee, a William Terzaghi, a,b and Xing Wang Deng a,* a Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104, U.S.A. b Department of Biology, Wilkes University, Wilkes-Barre, PA 18766, U.S.A. * Corresponding author, Fax: +1 203 432 3204 E-mail address: xingwang.deng@yale.eduxingwang.deng@yale.edu Keywords: CUL4-based E3 ligase; DWD; ABA; negative regulator; signal transduction pathway; Arabidopsis

22. Formal Report 2. Abstract: summarizes the paper in 250 words or less. DWD proteins have been reported as substrate receptors for cullin– RING ubiquitin ligase 4 (CRL4). Upon screening T-DNA mutants of DWD genes for abscisic acid (ABA) responses we obtained several candidates which exhibited ABA-hypersensitivity and one was named DWA3 (DWD hypersensitive to ABA 3). DWA3 associated with the CRL4 components DDB1 and CUL4, indicating that DWA3 may function as a substrate receptor for CRL4. ABA-inducible transcription factors (ABI5 and AtMYC2) and their downstream genes were hyper- induced by ABA in dwa3. Taken together, we suggest DWA3 is a negative regulator of ABA responses and may be involved in protein degradation mediated by CRL4.

23. Formal Report 2. Abstract: summarizes the paper in 250 words or less. mini-papers that are often published separately DWD proteins have been reported as substrate receptors for cullin– RING ubiquitin ligase 4 (CRL4). Upon screening T-DNA mutants of DWD genes for abscisic acid (ABA) responses we obtained several candidates which exhibited ABA-hypersensitivity and one was named DWA3 (DWD hypersensitive to ABA 3). DWA3 associated with the CRL4 components DDB1 and CUL4, indicating that DWA3 may function as a substrate receptor for CRL4. ABA-inducible transcription factors (ABI5 and AtMYC2) and their downstream genes were hyper- induced by ABA in dwa3. Taken together, we suggest DWA3 is a negative regulator of ABA responses and may be involved in protein degradation mediated by CRL4.

24. Formal Report 2. Abstract: summarizes the paper in 250 words or less. mini-papers that are often published separately should have 1 or 2 sentences of Introduction DWD proteins have been reported as substrate receptors for cullin– RING ubiquitin ligase 4 (CRL4). Upon screening T-DNA mutants of DWD genes for abscisic acid (ABA) responses we obtained several candidates which exhibited ABA-hypersensitivity and one was named DWA3 (DWD hypersensitive to ABA 3). DWA3 associated with the CRL4 components DDB1 and CUL4, indicating that DWA3 may function as a substrate receptor for CRL4. ABA-inducible transcription factors (ABI5 and AtMYC2) and their downstream genes were hyper- induced by ABA in dwa3. Taken together, we suggest DWA3 is a negative regulator of ABA responses and may be involved in protein degradation mediated by CRL4.

25. Formal Report 2. Abstract: summarizes the paper in 250 words or less. mini-papers that are often published separately should have 1 or 2 sentences of Introduction 1- 2 sentences of Materials and Methods DWD proteins have been reported as substrate receptors for cullin– RING ubiquitin ligase 4 (CRL4). Upon screening T-DNA mutants of DWD genes for abscisic acid (ABA) responses we obtained several candidates which exhibited ABA-hypersensitivity and one was named DWA3 (DWD hypersensitive to ABA 3). DWA3 associated with the CRL4 components DDB1 and CUL4, indicating that DWA3 may function as a substrate receptor for CRL4. ABA-inducible transcription factors (ABI5 and AtMYC2) and their downstream genes were hyper- induced by ABA in dwa3. Taken together, we suggest DWA3 is a negative regulator of ABA responses and may be involved in protein degradation mediated by CRL4.

26. Formal Report 2. Abstract: summarizes the paper in 250 words or less. mini-papers that are often published separately should have 1 or 2 sentences of Introduction 1- 2 sentences of Materials and Methods 3-4 sentences of Results, including quantitative data

27. Formal Report 2. Abstract: summarizes the paper in 250 words or less. mini-papers that are often published separately should have 1 or 2 sentences of Introduction 1- 2 sentences of Materials and Methods 3-4 sentences of Results, including quantitative data 1-2 sentences of Discussion

28. Formal Report 2. Abstract: summarizes the paper in 250 words or less. mini-papers that are often published separately should have 1 or 2 sentences of Introduction 1- 2 sentences of Materials and Methods 3-4 sentences of Results, including quantitative data 1-2 sentences of Discussion rarely cite references. If they do, full citation must be included.

29. Formal Report 3. Introduction: explains why the experiment was done.

30. Formal Report 3. Introduction: explains why the experiment was done. provides enough detail about what was previously known to explain what the outstanding questions are

31. Formal Report 3. Introduction: explains why the experiment was done. provides enough detail about what was previously known to explain what the outstanding questions are specifically states the hypothesis that was tested.

32. Formal Report 3. Introduction: explains why the experiment was done. provides enough detail about what was previously known to explain what the outstanding questions are specifically states the hypothesis that was tested. I write it last, to guide readers to my results

33. Formal Report 4. Materials and Methods: provide sufficient detail that another biologist could repeat your experiment.

34. Formal Report 4. Materials and Methods: provide sufficient detail that another biologist could repeat your experiment. list the organisms used (including the latin binomial) the names of the reagents, procedures followed, etc

35. Formal Report 4. Materials and Methods: provide sufficient detail that another biologist could repeat your experiment. list the organisms used (including the latin binomial) the names of the reagents, procedures followed, etc do not give the recipe for each reagent. Instead, cite the reference from which the recipe was obtained.

36. Formal Report 4. Materials and Methods: provide sufficient detail that another biologist could repeat your experiment. list the organisms used (including the latin binomial) the names of the reagents, procedures followed, etc do not give the recipe for each reagent. Do cite the manufacturers of esoteric reagents or equipment

37. Formal Report 4. Materials and Methods: provide sufficient detail that another biologist could repeat your experiment. list the organisms used (including the latin binomial) the names of the reagents, procedures followed, etc do not give the recipe for each reagent. Do cite the manufacturers of esoteric reagents or equipment Both Materials and Methods and Results should be written in the past tense. Routine calculations are not described here, unless they are done in an unusual way.

38. Formal Report 5. Results: devote one paragraph to each figure or table

39. Formal Report 5. Results: devote one paragraph to each figure or table start with a sentence explaining the purpose of the expt

40. Formal Report 5. Results: devote one paragraph to each figure or table start with a sentence explaining the purpose of the expt second sentence should summarize the methods

41. Formal Report 5. Results: devote one paragraph to each figure or table start with a sentence explaining the purpose of the expt second sentence should summarize the methods third sentence states where the results are presented

42. Formal Report 5. Results: devote one paragraph to each figure or table start with a sentence explaining the purpose of the expt second sentence should summarize the methods third sentence states where the results are presented remaining sentences point out the key features.

43. Formal Report 5. Results: devote one paragraph to each figure or table start with a sentence explaining the purpose of the expt second sentence should summarize the methods third sentence states where the results are presented remaining sentences point out the key features. Results can be presented as figures or tables, which should be presented on separate pages attached after the “literature cited”

44. Formal Report 5. Results: devote one paragraph to each figure or table start with a sentence explaining the purpose of the expt second sentence should summarize the methods third sentence states where the results are presented remaining sentences point out the key features. Results can be presented as figures or tables, which should be presented on separate pages attached after the “literature cited” each figure or table should have its own title and caption

45. Formal Report 5. Results: devote one paragraph to each figure or table start with a sentence explaining the purpose of the expt second sentence should summarize the methods third sentence states where the results are presented remaining sentences point out the key features. Results can be presented as figures or tables, which should be presented on separate pages attached after the “literature cited” each figure or table should have its own title and caption caption gives sufficient information that a reader can figure out what it is about without reading the text. i.e. summarizes M&M & identifies panels, symbols, etc

46. Formal Report 6. Discussion: one paragraph per figure or table + a global discussion at end

47. Formal Report 6. Discussion: one paragraph per figure or table + a global discussion at end First sentence summarizes results

48. Formal Report 6. Discussion: one paragraph per figure or table + a global discussion at end First sentence summarizes results Remaining sentences explain them, and may propose ways to test these explanations

49. Formal Report 6. Discussion: one paragraph per figure or table + a global discussion at end First sentence summarizes results Remaining sentences explain them, and may propose ways to test these explanations Last paragraph discusses global implications: now that we know this, how does it change our world?

50. Formal Report 7. Literature cited: all citations listed in the text should be listed at the end of the paper.

51. Formal Report 7. Literature cited: all citations listed in the text should be listed at the end of the paper. Formats for citing and listing references vary among journals.

52. Formal Report 7. Literature cited: all citations listed in the text should be listed at the end of the paper. Formats for citing and listing references vary among journals. For your report use the format (Smith, 2008) in the text

53. Formal Report 7. Literature cited: all citations listed in the text should be listed at the end of the paper. Formats for citing and listing references vary among journals. For your report use the format (Smith, 2008) in the text use this format in the “Literature Cited:” Smith, E.J. (2008) BRF3 encodes a novel ubiquitin ligase. Molecular Plant 3: 345-361

54. Bio 392: Manuscript Draft Grading Checklist 1) Abstract (6 pts) Were all elements (I, M&M, R & D) present? Were all elements adequately explained? Was all information relevant? Was all information clearly and succinctly explained? 2) Introduction (6 pts) Was the hypothesis (or purpose) clearly stated? Was adequate background information provided? Was all information relevant? Was all information clearly explained? 3) Materials and Methods (4 pts) Were all procedures clearly and accurately explained? Was all information relevant?

55. 4) Results (10 pts) Is there a separate paragraph for each expt? Does the first sentence of each para state the purpose? Does the second sentence summarize the methods? Does the third sentence state where the results are? Do the remaining sentences explain the figure/table and point out key results? Do figures and tables do the job? Titles and captions? 5) Discussion (8 pts) Were key results summarized? Were key results discussed? Were further experiments proposed? Were broader implications discussed?

56. 6) Literature cited (2 pts) Were references used correctly in the text? Were all citations made in text listed in correct format? Were any references not cited in the text? 7) Writing (4 pts) Organization Clarity Conciseness Grammar and spelling