BISC219/F11: 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 – due week of Nov 1 at the beginning of lab

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, and include a summary of your general experimental design.

Your Introduction, first, must attempt to develop the audience’s interest in the topic by explaining to prospective readers (who aren’t students in this course) your project’s goal is important. This is, on the surface, 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 others). 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 the normal gene and, even more importantly, about its functional product (usually a protein), particularly if that gene and its functional product are relevant to 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 will have to BRIEFLY summarize your experimental design, including the rationale for your crosses, in order to help the reader understands how the resulting progeny of particular parents allowed you to figure your conclusions: where your particular dumpy mutation is located in the C. elegans genome, the name and nature of the gene and protein change associated with 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 your crosses and the rational for them to be able to see how you made conclusions from the scoring of those crosses. The Results section should begin with a general synopsis of your experiments (but not in anywhere near the level of detail that you would write about what you did in M&M). 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” when you describe your experiment. 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 if 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 function 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.

Note that there are links in the Resources section of this Wiki to a page of instructions for finding sources using the Wellesley College library e-databases. In this paper, you will use the reference format of the journal Genetics. The best way to learn to format your reference citations in this style is to find recent articles in Genetics to use as models; or, (even easier) instruct EndNote&#8482; to format them for this journal.

More Resources for Writing Help: Resources section of the WIKI Your lab instructor! 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.