BISC219/F13: Assignment Series2 Classical Genetics Paper

Grading Rubric & Information for Scientific Paper on Forward (Classical) Genetics Project: Locating and Characterizing the Gene Responsible for an Aberrant Phenotype – 50 points

Title, Abstract, Introduction, Results, Discussion, References
See wiki Calendar for Due Date for your lab section

The Guidelines for Scientific Writing section on the Resources page of the Wiki goes into exhaustive detail about the general requirements and expectation for each section of your paper. You should spend significant time digesting all of that information and putting it to use in the drafts of your paper. Included below is additional advice (dos and don’ts) for writing this paper on your classical (forward) project.

Remember that your audience for this paper is not your lab instructor or a classmate who knows all about these experiments; rather, the audience is a group of scientifically literate strangers who don’t necessarily know anything about your project and its goals or about genetic tools, laws, or worms. The Introduction is the place to spell out your overall topic (a forward genetics project to characterize the gene responsible for a dumpy phenotype in C. elegans), your experimental goals: locating and characterizing a functionally significant gene mutation in C. elegans, in order to tie and gene to its function. The introduction should end with a brief, general summary of your experimental design.

Your Introduction, first, must attempt to develop the audience’s interest in the topic by showing prospective readers (who aren’t students in this course) that your project’s goal is important. This is not so easy. Your readers are pretty sure they can live quite full and productive lives without knowing anything about dumpy worms--- unless you convince them otherwise. So why do geneticists spend so much time hunting for functionally significant (those that cause a phenotype change) mutations and then sleuthing out the location and gene sequence change compared to the wild type sequence? This is, basically, about elucidating structure/function relationships. Now that the entire genome of C. elegans has been sequenced, geneticists have to annotate the sequence (eg. find out which parts are coding regions and what the products of those coding regions do in this model organism and in other organisms--us for example). Your forward genetics project is modeling that type of annotating investigation. It is crucial to keep in mind that the big picture here is not to learn exclusively about the mutation in a lowly soil worm, but also, to learn as much as we can about a normal gene and, even more importantly, about its functional product (usually a protein), particularly if that gene and its functional product are relevant to many other eukaryotes.

A forward genetics study accomplishes those goals in a series of experiments that stem from the finding of an interesting abnormal phenotype to study. That aberrant phenotype is assumed to be caused by an defective gene product (usually a protein) that comes from a mutation in a gene encoding that product. If you discover a change from wild type in a DNA sequence and discover if or how it changes a polypeptide, you can often predict the severity of the change in the folded protein or in a regulatory product. You can also predict if or how that gene product change is likely to cause the functional aberration seen as an abnormal phenotype. Noting what a mutant can't do, does differently, or does better than when it possesses the wild type form of the gene product, then you have learned a lot about the role of the normal gene.

After you located (mapped) your mutation to a particular position on a chromosome, you used a variety of classical and modern genetic tools to characterize this phenotypically significant gene mutation. Specifically, you wanted to find out if the mutation had been previously characterized. Once you know the exact location of the gene you can find out a previously characterized gene's name. If that location has no previously characterized gene, you may have found a new gene. DNA sequence analysis of the mutant gene sequence compared to wild type structurally characterizes the extent and nature of the gene change and allows you to find functionally significant regions of the gene product. Even if your gene has been previously characterized, you may have helped annotated the genome of C. elegans by characterizing a new functionally significant region by finding a previously unstudied mutation in that gene. (There can be many functionally significant mutations in the same gene, not just one.) You will need to do research on public databases to find out if this gene and mutation you studied is new or previously characterized. You will also need to do some bioinformatics investigation to see what is known about similar genes and gene products in other species. Because C. elegans homology with humans (and with most other eukaryotic organisms) is astonishingly high, genetic researchers, like you, can apply, quite often, aspects of worm genes' structure and function to other organisms, including Homo sapiens.

Do not assume that your reader understands what you did and why you did it. Remember that it is not intuitive to those who didn’t hear lectures on laws of inheritance that certain ratios of progeny from certain crosses means that genes are linked or that assortment should follow Mendel's laws of independent segregation. In your Results section, you do not need to repeat the overall summary of the experimental design because you did that at the end of your introduction. You should structure your results section logically so that each section proceeds in our basic structure: In order to find out____..... The goals described for each section should be incremental goals in a sequence that helps the reader follow the entire project. This order is not necessarily a chronological description of your experiments. Note that you will have to BRIEFLY summarize each of your experiments, including the rationale for your crosses, in order to help the reader understands how the resulting progeny of particular parents allowed you to figure out your conclusions: where your particular dumpy mutation is located in the C. elegans genome, the name and nature of the gene of interest and the change in the gene product that is likely responsible for the aberrant phenotype. DO NOT include the complete diagrams of crosses that you did for homework assignments!

Concise "explaining" in a logical and progressive sequence is the most difficult and important part of a scientific research report . Just because you are allowed to omit the Materials and Methods section of this paper, does not mean that your reader does not need to understand the genotype of the parents in your crosses and the rational for these crosses to be able to see how you made conclusions from the scoring of those crosses. You need not be specific in the Results narrative about media recipes, incubation times, etc. However, future investigators, who are also working in this field, need for you to be specific about strain names and genotypes and phenotypes of parents and progeny of crosses. You must use established nomenclature and you must make sure that any acronyms (Dpy for dumpy, for example) are clearly defined at first use and wherever ambiguous.

Remember to italicize genes and references to mutants (organisms with mutations in their genes) but don't italicize phenotype or protein references. Our phenotypes are abbreviated Dpy or Unc Avoid non-specific words like “plates”. Plates are just pieces of plastic. It is the culture conditions (medium, worm strain, bacterial food) or the type of worms on the plates that need to be named because that's what's important--not the plastic.

Students are often confused about what goes into results and what should be saved for discussion. In the Results section, you should make and include conclusions when your data allow them. If you can answer the main question or any part of it from your experimental data, do so in Results! You should be able to use the data to conclude the location of your unique dumpy mutation in the C. elegans genome, to explain exactly what the gene and protein change is from wild type. Don’t just describe your data in Results and leave your reader scratching her head, thinking, “ok, why does this number of this kind of offspring mean that”?

When organizing the narrative part of the data analysis in results, do so logically rather than in a chronological way. Yes, it's is true that we completed the complementation testing before we start the mapping work, but consider whether or not it a good idea to interrupt to explain complementation testing in the middle of linkage testing and mapping the mutation. That's a lab time course organization. Would it be better to explain linkage analysis and mapping from start to finish, including giving the conclusion to the exact location of the gene before you start explaining the complementation analysis? It's best to organize by experimental goals: linkage and mapping are under the goal of locating the gene associated with the Dpy phenotype while complementation analysis determines whether or not the gene associated with the phenotype has been previously characterized or not and, if so, allows you to confirm the location?

When should you introduce your findings from DNA sequencing analysis? You must know either the name of the gene of interest (if previously characterized) or it's location (if not previously characterized) before you could determine which part (ORF) of the C. elegans genome to sequence because sequencing requires investigator designed primers with bases that are complementary in sequence to a specific part of the genome. Therefore, you should not introduce the sequencing analysis until AFTER you have explained how you know the name and/or location of the gene of interest. The goal of sequencing analysis is to characterize the nature and extent of the mutation in order to, if possible, identify a functional significant area of the gene product and to introduce, our overall goal, to figure out what the normal gene product does that's important in C. elegans and in other species. Since we didn't do any experimental work with the normal gene product (we looked at phenotype in the mutant), the section of proposing normal function and significance must be saved for discussion because you don't have any experimental findings that directly address that.

Your discussion should briefly reiterate your main findings WITH SPECIFIC REFERENCES TO DATA BY FIGURE NUMBER and then propose potential relevance, significance, or broader application of your findings. You should use other researchers work (citing those sources correctly!) to strength or weaken your argument; however, the discussion is centered around YOUR thoughts about your findings in relation to others or as it paves new ground. Previous research by others is integral to the discussion, but NOT it's focus. Your bioinformatics work to find homologs and the larger potential significance of this gene in other species are discussion material.

Your Discussion will include some conjectures about this mutation's functional significance in the worm and in other eukaryotes and about whether or not this is a new or previously characterized gene and mutation. Deciding if your mutation is a new mutation or a previously characterized one is a conclusion that came from your complementation analysis and your mapping work so that conclusion should be in results; however, since you need to bring in outside information from the original paper published about that gene, some discussion of how your work complements previous work on this gene or mutation should be in your discussion, too.

Your references should be formatted according to the journal "Genetics". The Wellesley College Library allows electronic access to this journal; therefore, you should download a few recent articles in pdf format and use them as models for how to structure your references, both in-text and in the reference page. Attention to detail is expected and required, so please make note of exactly where commas and periods are located. Note that Genetics uses hanging formatting in its Literature Cited page. (In this journal, the references section is called Literature Cited rather than References.) This structure is far from universal so you must pay attention to getting it right ---or use a reference manger system like EndNote that automatically formats everything correctly when you tell it which journal to mimic.

More Resources for Writing Help:
Resources section of the WIKI
Your lab instructor! and the materials posted in the Science Writing folder of your lab Sakai site.
Science Writing Peer-Mentors- The Writing Program provides free help from Writing mentors. The student writing advisers have scheduled hours in Sage Lounge and elsewhere on campus. Appointments can be made through an on-line appointment scheduler at: www.rich65.com/wellesley. Don't forget that your instructor is a good source of help! Come see us to discuss your struggles. We like working with students.

Grading Rubric for Forward Genetics Project Paper – 50 points

	At or Above Standard	Below Standard	Points Earned
Title/ Abstract	5.5-7.5 pts. Title reflects paper’s main message. Concisely summarizes in appropriate format: topic, experimental questions, general summary of methods, major findings (specific!), conclusions & implications of the findings in relation to what is known or expected. Information is brief but intelligible to any scientifically literate reader.	0-5 pts. Title stresses techniques or general goals rather than conclusions. Abstract omits topic, experimental goals, or a concise description of the experimental design with key results. Does not include conclusions or significance of those conclusions. Information unintelligible to novice reader. Includes tangential information or too much detail; misinterprets information and/or implications.	__/7.5
Introduction	8.5-10 pts. Identifies central topic, includes appropriate background information (brief history of the topic) from primary sources, & ends with a synopsis of the overall experimental design. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise. Reference citations in proper format (Genetics style) in the body of the paper for all information not common knowledge.	0-8 pts. Does not correctly identify central topic; does not include appropriate background information, or a synopsis of the experimental design; does not explain relevance of the experiments; does not use primary sources or give properly formatted reference citations for information not common knowledge. Includes background info. unrelated to topic; related background info is in too much detail or too tangential to topic. Writing style is not clear or concise and/or uses incorrect vocabulary, grammar, spelling, or punctuation.	__/10
Results/ Conclusions	17.5-20 pts. Each experiment explained in the format, In order to find out_____, we did_______. We found_______. It means_____ because_____.Includes sufficient appropriate figures and tables designed for maximum clarity and ease of interpretation of evidence. All figures & tables are numbered & have correctly formatted titles & legends; The narrative is structured to avoid if…then hypothesis (out of context) emphasis. Instead it describes accurately, clearly, and succinctly the evidence for stated conclusions that are made from the evidence presented and THEN uses theory to explain why those conclusions are appropriate using the context of these data. Includes specific references to figures/tables that are designed to allow new reader to easily interpret data & understand main message. All major findings are evaluated appropriately for meaning and importance in answering experimental questions and explained for a reader who does not know the topic or research methods well. Appropriate conclusions are drawn from evidence presented. Writing style uses correct vocabulary, grammar, spelling, punctuation; is clear and concise.	0-17 pts. Key figures and/or tables omitted. Unprocessed data included. Figures &/or tables difficult to read or to interpret due to missing information and/or poor design. The narrative omits research goals, experimental design synopsis, key findings, describes the data inaccurately or unclearly, includes irrelevant information, or is repetitive. Data analysis emphasizes theory or hypothesis without using data. Not all major findings are evaluated for meaning & importance, or are incorrectly interpreted. Conclusion omitted, or, if present, conclusions are incorrectly drawn, unexplained and/or not related to experimental data. Writing style is not clear or concise and/or uses incorrect grammar, spelling, punctuation & vocabulary.	__/20
Discussion	8.5-10 pts. Discussion begins with restatement of topic and experimental goals and then gives a summary of the main findings in results with specific figure and title numbers. Importance of findings, broader significance & context are adequately explained. Connections are made among experimental findings, background information & relevant research from outside sources. Appropriate conclusions are drawn and related to larger context. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise	0-8 pts. Not all major findings evaluated for meaning & importance, or are incorrectly interpreted. Connections among experimental findings missing or incorrectly applied. Relationship between experimental findings, background information & relevant research missing or incorrectly interpreted. Conclusions incorrectly drawn, and/or not related to larger significance. Writing style is not clear or concise and/or uses incorrect grammar, spelling, punctuation & vocabulary.	__/10
References	2-2.5 pts. Includes complete, properly formatted citation for each work cited in body of report modeled after style of journal Genetics. Includes an appropriately formatted Literature Cited page at end of paper in Genetics style. Includes a citation for all info that is not common knowledge. Uses an adequate number of reliable, appropriate sources.	0-2 pts. Does not use reliable or sufficient appropriate sources. Citations are incomplete, improperly formatted (not in Genetics style in body of paper and/or in Literature Cited page; lists works not cited in body of paper, or fails to give reference citation for information not common knowledge.	__/2.5
Total			__/50