Writing in the Sciences: Abstracts

1. Writing in the Sciences: Abstracts Kristina Wilson Some slides adapted from Daniel Martinez

2. Science Writing - Logic Readers will often read non-linearly • Read the abstract, scan the references • Read the introduction and conclusion • Scan tables and/or figures • Read the discussion, methods and results last Separable, specialized sections are essential!

3. Abstract • Overview of what you did • Informative • Descriptive • Outline*: • Problem. Key topic. • Method. State your main approach to solving the problem. • Results. Provide one or two key results. • Conclusion. Note your main conclusion. * from Perelman, Paradis, Barrett (1998) The Mayfield Handbook of Scientific Writing. 181.

4. Editing Abstract Content • ID the four parts of an Abstract • Remove unnecessary parts • Add missing information • We’ll address style and grammar in the next section

5. “In the Abstract”: A long-winded (273 word) Abstract from Nature455, 1138-1142 (23 October 2008) • Metals are needed by at least one-quarter of all proteins1, 2. Although metallochaperones3, 4, 5, 6, 7, 8 insert the correct metal into some proteins, they have not been found for the vast majority, and the view is that most metalloproteins acquire their metals directly from cellular pools. However, some metals form more stable complexes with proteins than do others. For instance, as described in the Irving–Williams series9, Cu2+ and Zn2+ typically form more stable complexes than Mn2+. Thus it is unclear what cellular mechanisms manage metal acquisition by most nascent proteins. To investigate this question, we identified the most abundant Cu2+-protein, CucA (Cu2+-cupin A), and the most abundant Mn2+-protein, MncA (Mn2+-cupin A), in the periplasm of the cyanobacterium Synechocystis PCC 6803. Each of these newly identified proteins binds its respective metal via identical ligands within a cupin fold. Consistent with the Irving–Williams series, MncA only binds Mn2+ after folding in solutions containing at least a 104 times molar excess of Mn2+ over Cu2+ or Zn2+. However once MncA has bound Mn2+, the metal does not exchange with Cu2+. MncA and CucA have signal peptides for different export pathways into the periplasm, Tat and Sec respectively. Export by the Tat pathway allows MncA to fold in the cytoplasm, which contains only tightly bound copper or Zn2+ (refs 10–12) but micromolar Mn2+ (ref. 13). In contrast, CucA folds in the periplasm to acquire Cu2+. These results reveal a mechanism whereby the compartment in which a protein folds overrides its binding preference to control its metal content. They explain why the cytoplasm must contain only tightly bound and buffered copper and Zn2+.

6. Abstracts: ID Content 1. PROBLEM • Metals are needed by at least one-quarter of all proteins1, 2. Although metallochaperones3, 4, 5, 6, 7, 8 insert the correct metal into some proteins, they have not been found for the vast majority, and the view is that most metalloproteins acquire their metals directly from cellular pools. However, some metals form more stable complexes with proteins than do others. For instance, as described in the Irving–Williams series9, Cu2+ and Zn2+ typically form more stable complexes than Mn2+. Thus it is unclear what cellular mechanisms manage metal acquisition by most nascent proteins. To investigate this question, we identified the most abundant Cu2+-protein, CucA (Cu2+-cupin A), and the most abundant Mn2+-protein, MncA (Mn2+-cupin A), in the periplasm of the cyanobacterium Synechocystis PCC 6803. Each of these newly identified proteins binds its respective metal via identical ligands within a cupin fold. Consistent with the Irving–Williams series, MncA only binds Mn2+ after folding in solutions containing at least a 104 times molar excess of Mn2+ over Cu2+ or Zn2+. However once MncA has bound Mn2+, the metal does not exchange with Cu2+. MncA and CucA have signal peptides for different export pathways into the periplasm, Tat and Sec respectively. Export by the Tat pathway allows MncA to fold in the cytoplasm, which contains only tightly bound copper or Zn2+ (refs 10–12) but micromolar Mn2+ (ref. 13). In contrast, CucA folds in the periplasm to acquire Cu2+. These results reveal a mechanism whereby the compartment in which a protein folds overrides its binding preference to control its metal content. They explain why the cytoplasm must contain only tightly bound and buffered copper and Zn2+. 2. METHOD 3. RESULTS 4. CONCLUSION

7. Abstracts: Remove excess (158 words) • Cu2+ and Zn2+ typically form more stable complexes than Mn2+. Thus it is unclear what cellular mechanisms manage Mn2+ acquisition by most nascent proteins. To investigate this question, we identified the most abundant Cu2+-protein, CucA (Cu2+-cupin A), and the most abundant Mn2+-protein, MncA (Mn2+-cupin A), in the periplasm of the cyanobacterium Synechocystis PCC 6803. Each of these newly identified proteins binds its respective metal via identical ligands. MncA only binds Mn2+ after folding in solutions containing at least a 104 times molar excess of Mn2+ over Cu2+ or Zn2+. However once MncA has bound Mn2+, the metal does not exchange with Cu2+. Export by the Tat pathway allows MncA to fold in the cytoplasm. In contrast, CucA folds in the periplasm. These results reveal a mechanism whereby the compartment in which a protein folds overrides its binding preference to control its metal content. They explain why the cytoplasm must contain only tightly bound and buffered copper and Zn2+.

8. EXAMPLE 1:

9. EXAMPLE 2:

10. Common Grammatical Problems & SolutionsI • Incomplete sentences • Problem: Sentence is missing a subject or a verb. • Solution: Add the missing element, or merge it with another clause. • Subject-verb disagreement • Problem: The number of the subject does not match the number of the verb • Solution: Test the sentence by leaving out adjectives/adverbs.

11. Common Grammatical Problems & SolutionsII • Tricky, though common, words • Affect is a verb, effect is a noun • it’s (there are no contractions without apostrophes) • and its (possessive) • Correct use of punctuation • Commas • Join an independent with a dependent clause • Separate parts of a list • MUST follow introductory phrases (“As can be seen from the data, you are all going to use commas correctly from now on.”) • Colons • Signify the start of a list • Semi-colons • Join two independent clauses

12. Common Grammatical Problems & SolutionsIII • Past tense • Ask yourself, “Is it still happening?” • Is Ohm’s Law identical to when you learned it? • YES. => “Ohm’s law states…” • “Are you still measuring that voltage?” • NO. => “The voltage was measured…” • Passive Voice • Use only when appropriate • Adelaide and I recorded temperatures at the following time intervals:…” • “Temperatures were recorded at the following time intervals:…” • Can be inefficient • “The column was allowed to operate at 100 C for 5 hours.” • “The column operated at 100 C for 5 hours.”

13. Higher Level Corrections • Word choice • Use a Thesaurus (not online) • Difficult sentences / “Flow” • Identify core phrases • Break up and reassemble thoughts as necessary

14. Problematic Sentences • There have been much advancement in prostheses in recent years. • There is many ideas of how to organize assemblers. • By virtue of their prevalence alone. It is clear that mood disorders do not necessarily breed genius. • Today everybody use cellular phones. • The interagency science community have been issuing technical recommendations about everything from computer modeling to remote sensing in the Everglades.

15. More Problematic Sentences • A mixture of materials were used to withstand high temperatures. • Given the available options; the 100KOHm resistor is ideal for the circuit. • A winglet may cause the introduction of a discontinuity in the lift distribution curve. • It is difficult to monitor the affects of chronic, low level toxicity. • A lion is acutely aware of the scents in it’s surroundings.

16. Strategies • Read aloud • Style Manuals • Ask the librarian or use the library website • A writer’s reference / Diana Hacker LOCATION: Rhees Stacks Internet Link(s): Student companion website Call Number: PE1408 .H118 2003 • Make an appointment at the Writing Center

17. “Writing is thinking on paper. Anyone who thinks clearly can write clearly, about anything at all. Science, demystified, is just another nonfiction subject. Writing, demystified, is just another way for scientists to transmit what they know” On Writing Well William Zinsser