Bio1109A Discussion Handout #1 NAME: _Renata Gonzalez Chong__

Below is some information that will prove helpful as you work your way
through the Palopoli et al. (2008) paper:

(1) Consider the title of the paper. The title is a label that generally tries to
convey the fundamental result of a scientific paper. What does this title
"promise" will be determined by the study reported here?
(2) The copulatory plug polymorphism: Males from some strains of this
species deposit a plug over the vulva after mating. Males from other
strains do not deposit such a plug.
(3) The first paragraph, in bold font, is called the "Abstract". This is an
attempt to summarize the entire paper in a limited number of words.
Reading the abstract is a good way to get a sense of the main question,
approach, results, and interpretations that you will see throughout the rest
of the paper.
(4) The second paragraph (i.e., the first one not in bold font) is the start of
the main text. Letters to the journal Nature do not have separate sections
for the "Introduction", "Results", and "Discussion". Nevertheless, that is
the way the paper is structured—it begins by introducing the problem and
hypothesis being tested, then launches into the experimental results,
generally providing an interpretation of each result.
(5) Note that "Supplementary" material is referred to periodically in the
paper. This material is available online, but does not take up space in the
main paper. Do not worry about looking up the supplementary material
for this or any other papers we will read this semester. Instead, take my
word for it that the supplementary material supports the claim being
made in the paper.
(6) Genetic mapping: Using recombination between known genetic
markers to determine (fairly precisely) where in the genome a particular
gene of interest is located.
(7) Search for PCR product length polymorphism: Using a technique called
the Polymerase Chain Reaction to check whether there are any insertions
or deletions that distinguish plugging vs. non-plugging strains in the
stretch of genome identified via genetic mapping.
(8) Do not worry about the detailed descriptions of the mucin protein at the
end of the second paragraph. Those details are not necessary to get the
main points of the paper.
(9) RT-PCR: (short for "Reverse Transcriptase Polymerase Chain
Reaction"): Technique for looking at whether a particular gene transcript
is present.
Bio1109A Discussion Handout #1 NAME: _Renata Gonzalez Chong__

(10) RNAi (short for "RNA interference") is a technique that allows you to
interfere with gene expression by "convincing" the cell to destroy copies
of the RNA. Basically, this is a way to turn a gene "off" and see what
happens.
(11) Transgene: Copy of a gene that is inserted into the genome of an
organism. Basically, this is a way to add a new gene to an organism and
see what happens.
(12) Staining with a fluorescently tagged lectin: This is a reagent that will
bind to "mucin glycoproteins" (basically mucus), and because it is
fluorescently labelled, we could look at whether it bound to the
copulatory plugs.
(13) Transgenic construct with the plg-1 regulatory region placed in front of
the Green Fluorescent Protein coding region: This allows us to see where
the plg-1 gene is normally expressed. Basically, the cells that glow are
the locations where the plg-1 regulatory region is driving expression.
(14) vas deferens: cells that are part of the male reproductive tract and
secrete stuff…
(15) ability to complement the N2 loss-of-function allele: This is a test
whether each geographic isolate had the ability to deposit copulatory
plugs. If they "failed to complement" then that means that they lacked the
ability to form copulatory plugs. If they "complemented" then that means
they had the ability to form copulatory plugs.
(16) retrotransposon: A type of "selfish" DNA that jumps around in the
genome, making copies of itself and sometimes causing mutations when
it does so. All genomes have them, including humans.
(17) pleiotropy: When a mutation affects more than one thing.
(18) mate-guarding: preventing other males from mating with a female (or
hermaphrodite). This appears to be the function of the copulatory plug.
(19) hermaphrodite: An organism with both male and female reproductive
functions. In the nematode Caenorhabditis elegans, hermaphrodites are
basically females who have gained the ability to produce their own
sperm, so they can fertilize their own eggs (males become unnecessary!).
(20) UTR: "untranslated region"…part of the RNA transcript that never gets
translated into protein…found at the beginning and end of the RNA
transcript.
(21) RACE: technique that allow you to determine the sequence of RNA
molecules…in this case, comparison of the plg-1 genomic DNA
sequence with the resulting RNA sequence allowed the authors to
determine where the introns and exons are located.
Bio1109A Discussion Handout #1 NAME: _Renata Gonzalez Chong__

This week you were asked to read a paper from the primary scientific literature
(Palopoli et al. 2008). We will be discussing this paper in class. Like most
papers from the primary literature, this is a challenging paper to read and
understand fully. To help you prepare for the class discussion, below are three
questions that you must answer. Please turn in this sheet at the beginning of
class.

(1) What is the central hypothesis being tested in Palopoli et al. (2008)? In
other words, what model is being tested?

Plug dimorphism is caused by a derived, loss-of-function mutation.

(2) What result is being depicted in Figure 1a? Note that you can ignore
parts b, c, and d of Figure 1. To help you, you should know that "Cer1"
(which includes the "LTR" sequences) is a retrotransposon.

The retrotransposon Cer1, that is present in the non-plugging strain of

Caenorhabditis elegans, is interrupting a novel, unannotated protein-coding
gene, plg-1, which is predicted to produce a protein-coding gene which codes
for mucins. Because of the retrotransposon Cer1, the non-plugging strain’s plg-
1 gene will not code for mucins.

(3) In Figure 2a, the "Vector" RNAi treatment is called a "negative

control". This is a treatment that is very similar to the experimental
treatment but lacks an essential ingredient, so we do not expect there to
be any effect. Do the results match the expectation for a negative
control?

They do, as this treatment did not have an effect. They still produced plugs and
the mean plug size (around 2.25) was significantly bigger than the ones in
which the plg-1 had been knocked down by RNAi (around 0.2), which
produced fewer and smaller plugs.