1. Shiva Mozaffarian
The effect of silencing genes pdl-1 and F26A10.1 on the chemosensory function of the
organism Caenorhabditis elegans.
Abstract
The ability of the Caenorhabditis elegans to respond to chemicals in the surrounding
environment is an indispensible asset to its survival. In this experiment, the chemosensory
implications of suppressing the genes pdl-1 and F26A10.1 in the C. elegans’ neural sensory
pathway were tested. The hypothesis was tested by performing an RNAi experiment over the
course of one week during which gene specific dsRNA was incorporated into the DNA of C.
elegans progeny through ingestion of Escherichia coli. A subsequent chemotaxis assay
revealed inconclusive evidence that the pdl-1 gene may play a role in inhibition of
chemosensory processes. The results also indicated that the F26A10.1 gene was not involved
in the chemosensory ability of C. elegans.
Introduction
The purpose of this experiment was to determine what physiological factors are
involved in the ability of the organism Caenorhabditis elegans to recognize and respond to
odors in its environment. Specifically, this experiment addresses the role of “transcription
factors and signaling molecules” on the nervous system function of chemotaxis (Bush, et al.,
2012).
The affect of physiological factors on the function of the nervous system can be
observed effectively due to the many physiognomies that make the C. elegans an optimal
model organism. In 1963, Sydney Brenner discovered that the organism was particularly
suitable for genetic and physiological studies (Chao and Hart, 2009). The 1-millimeter,
transparent nematode is an ideal specimen to be observed and maintained in the laboratory.
Many features of the C. elegans’ cellular anatomy can be seen using an inverted fluorescent
microscope (Figure 1). Its short life cycle and large number of offspring also allow for the
organisms rapid growth and reproduction on agar plates in the laboratory (Bush, et al., 2012).
Figure 1. On the left is a
fluorescent image of the
C. elegans,on the right
is a bright field image
of the C. elegans. These
still images were taken
from an inverted
fluorescent microscope
(Bush, et al., 2012).

2. Shiva Mozaffarian
The model organism is comprised of only 959 somatic cells. This simplicity in the
structure of the C. elegans in comparison to the complex functionality of its systems and
internal processes is quite advantageous in research. The nervous system is the most complex
organ of the C. elegans, consisting of 302 neurons and 56 glial cells (Brenner, 1986). Among
these neurons, 32 are chemosensory neurons that control the complex behavior of chemo-
perception. Each of these neurons expresses certain G proteins and transmembrane receptors
that detect and respond to different odorants (Bargmann, 2006). The chemosensory neurons
AWC and AWA are involved in chemo-attraction, and the chemosensory neuron AWB is
involved in chemo-repulsion. The ciliated endings of the chemosensory cells (shown in Figure
2) recognize odorant molecules, which transduce the signal to motor neurons and ultimately to
muscles that move animal towards or away from stimuli (Bush, et al., 2012).
Chemosensation is fundamental to the survival of the C. elegans and it is a component
of their biology to which over 5% of its genome is devoted. The entire genome of the
organism, consisting of 100 million base pairs, was completely sequenced, which allowed us
to study the function of specific genes in the organism (Bargmann, 2006). The affect of
specific genes on the chemosensory function of C. elegans can be tested using the ribonucleic
acid interference (RNAi) technique. In 1998, Andrew Fire and Craig Mello discovered a way
to inhibit specific genes in the organism C. elegans. The technique of RNAi utilizes specific
gene sequences of double stranded RNA (dsRNA) for post-transcriptional gene silencing
(Driver, 1998). A larval C. elegans can ingest double stranded bacterial plasmid dsRNA from
its food source, Escherichia coli, and incorporate the dsRNA into the next generation’s
genome. The interfering RNA represses a specific gene and therefore allows genes of interest
to be studied independently (Bush, et al., 2012).
Figure 2. The structure of a
chemosensory organ. A
sensory cell with its ciliated
endings exposed to the
outside environment.
Specific chemosensory
neurons AWA, AWB,and
AWC are shown. These
neurons are involved in
chemosensation (Bargmann,
2006).

3. Shiva Mozaffarian
A chemotactic assay reveals whether the removal of the specific gene affects the
chemo-perception of the C. elegans by blocking translation of proteins they encode. The
ODR-10 gene is known to code for a G-protein-coupled receptor involved in chemotaxis. It
was used as a positive control in the experiment to ensure that when the silencing of a gene
results in a malfunction of chemotaxis, the gene is involved in chemoreception. L4440 is a
non-nematode gene used as the negative control in the experiment to ensure that the methods
of the experiment did not have any effect on the chemotaxis ability of C. elegans (Bush, et al.,
2012). The experimental genes pdl-1 and F26A10.1 will be statistically tested against this
negative control.
No previous testing had been done on the F26A10.1 gene. Therefore, the gene
sequence, genetic position, and its coding protein are unknown (Worm base: Gene F26A10.1).
In 1995, pdl-1 in C. elegans was discovered to encode for a
phosphodiesterase protein, PDE6D, responsible for cGMP
breakdown (Maduro and Pilgrim, 1995). In 2006, mutations in pdl-
1 were tested to identify its role in the gustatory plasticity of C.
elegans. The worms containing mutated pdl-1 were pre-exposed to
NaCl and a subsequent chemotaxis assay to NaCl revealed, with
99% confidence, that the gene “regulates the gustatory adaptability
of an organism to changes in its environment or differences
between its various habitats”. These results are graphed in Figure 3
(Burghoorn, et al., 2006).
After the results of the experiment were collected, the experimenters presented a
plausible pathway in which PDE6D could affect gustatory plasticity (Figure 4). They
proposed that once odorant molecules bind to the G protein-coupled receptors (GPCRs), the
signal transduces into the cell where it activates G proteins. As a result, PDE6D is activated
and hydrolyzes cGMP to GMP (Burghoorn, et al., 2006).
Figure 3. A graphical
representation of the
experimental results. The
mutation of pdl-1 (P<0.01)
affected gustatory plasticity.
(Burghoorn, et al., 2006).
Figure 4. Pathway of
phosphodiesterase in
regulating gustatory
plasticity. The protein
signals cGMP molecules
which can then be involved
in many functions
(Burghoorn, et al., 2006).

4. Shiva Mozaffarian
Many neurons involved in chemotaxis, such as AWC and AWB, utilize cGMPs to
open cGMP-gated channels required for the function of chemotaxis (Maduro and Pilgrim
1995). As such, a protein responsible for the breakdown of cGMP could potentially affect the
function of chemotaxis. Although this experiment did not offer conclusive evidence for the
role of the pdl-1 gene in the chemosensation of diacetyl, the experiment offers a plausible
cascade of signaling events that could interfere in the chemotactic processes of the C. elegans.
All aforementioned factors of both the experimental genes and the model organism
propelled us to investigate and discover the function of the genes pdl-1 and F26A10.1 in the
chemosensory system of the C. elegans.
Methods
The RNAi experiment was conducted by setting up four agar plates corresponding to
the four genes being tested. The plates contain the bacteria, E.coli, transformed with gene-
specific RNAi constructs. A 4l suspension of C. elegans’ larvae was placed at the edge of
the bacterial lawn in the middle of the agar plate. The plates were then sealed and incubated at
15℃for 7 days, during which the worms were able to reproduce in the presence of the RNAi
construct. After one week, a chemotaxis assay was conducted by setting up four large agar
plates shown in Figure 5.
Sodium azide (2l) was dispensed in the circles on both the “DA” and “O” sides in
order to paralyze the worms once they reached either side. While the sodium azide absorbed
into the plates for 10 minutes, the RNAi treated worms were harvested from the plates using
0.75 ml water. The worm suspension was then pipetted onto a filter screen with kimwipe
underneath. The filters were rinsed with 200l of water and subsequently pressed into the
center of the chemotaxis plates. The diacetyl (2l) was dispensed in the circle to the right,
Figure 5. An example of a
completed chemotaxis assay plate.
A line is drawn down the middle of
the plates. Three circles are drawn:
one on the centerline and two
smaller ones on the left and right
hand sides of the plate. The left
side is labeled “DA” and the right
side is labeled “O” (Bush, et al.,
2012).

5. Shiva Mozaffarian
labeled “DA”. Once chemical attractant was added to the plates, they were sealed for a 60-
minute time period. After the hour, each plate was counted for worms present on the diacetyl
side (designated ‘A’) and the sodium azide side (designated ‘B’) not including the worms still
left inside the middle circle of the chemotaxis plate. A chemotaxis index for each plate and
corresponding gene was then calculated using the equation: (A)/(A+B) (Bush, et al., 2012).
Results
The chemotaxis indices were calculated for each of the four plates and presented in
Table 1. The ODR-10 positive control plate had a chemotaxis index of 0.48, while the L4440
negative control plate had a chemotaxis index of 0.67. The experimental genes, pdl-1 and
F26A10.1 yielded a chemotaxis index of 0.44 and 0.63, respectively.
Plate Number
of worms
on RNAi
plate
Number
of worms
on “DA”
side (A)
Number of
worms on
“O”side
(B)
Chemotaxis
index, P,
(A)/(A+B)
Class Average
Chemotaxis
Index
% Error
compared
to class
average
ODR10 4 26 28 .48 .52 8%
L4440 3 16 8 .67 .65 3%
pdl-1 5 19 24 .44 .66 33%
F26A10.1 3 20 12 .63 .66 5%
Table 1. A comparison of my individual and class average chemotaxis values which were determined from the
number of worms on the “DA” side of the chemotaxis plate divided by the number of worms on the “DA” side
of the plate plus the number of worms on the “O” side of the plate.
The class average chemotaxis indices were utilized to assess the precision of my own
data (Figure 6).
Figure 6. A graph comparing my chemotaxis indices to that of the class averages.
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
Odr-10 L4440 pdl-1 F26A10.1
ChemotaxisIndex
The Effect of RNAi on Chemotaxis in C. elegans
My Data
Average Data

6. Shiva Mozaffarian
The average chemotaxis index for the positive control of a sample of 513 students was
0.52. The average chemotaxis index for the negative control of a sample of 519 students was
0.65. The chemotaxis index average for the pdl-1 gene of a sample of 30 students was 0.66,
excluding outliers. The average chemotaxis index for the F26A10.1 gene of a sample of 29
students was 0.66, excluding outliers. The method of comparison between my data and the
data of my colleagues was to calculate percent error. My data for the chemotaxis index of the
ODR-10, L4440, pdl-1, and F26A10.1 yielded an 8%, 3%, 33%, and 3% error compared to
that of the class average.
A statistical approach using a Z-score was then applied to a normal curve, which is
used to determine the statistical significance of our data, enough to make a confident
conclusion as to whether or not the experimental genes play a role in chemosensory ability.
The statistical analysis tests the “null hypothesis”, the hypothesis that the difference between
the chemotaxis indices of the experimental and controls are due to sampling error (Pcontrol =
Pexperimental) bycalculating the Z-scores of the two experimental genes using the equation:
(Pexperimental – Pcontrol) / [Pexperimental(1-Pexperimental)/n]. Where ‘P’ is the chemotaxis index and ‘n’
is the standard deviation of the negative control (Bush, et al., 2012). The Z-score of the pdl-1
gene was calculated to be -1.84 with a P value of 0.0329 (Table 2). Since the corresponding P
value is lower than 0.05, there is 95% confidence that the difference between the chemotaxis
index of the pdl-1 gene and the control are significant, therefore, we reject the null hypothesis
for the gene. The Z-score of the F26A10.1 gene was calculated to be -0.02 with a P value of
0.4920 (Table 2). Since the corresponding P value is higher than 0.05, there is low statistical
confidence that the difference between the chemotaxis index of the F26A10.1 gene and the
control are significant, therefore, we accept the null hypothesis for the gene.
Z-score Probability
Pdl-1 -1.84 0.0329
F26A10.1 -0.02 0.4920
Table 2. The Z-scores and corresponding P-values of the experimental genes.
We accept the null hypothesis for F26A10.1 and reject the null hypothesis for
pdl-1.
Discussion
Our experiment was designed to investigate effect of removing certain proteins on the
chemosensory function of C. elegans.

7. Shiva Mozaffarian
First we determine whether the silencing of the unknown gene, F26A10.1, has any
effect on chemo-perception. As graphed in Figure 6, our results show that F26A10.1 has a
chemotaxis index of 0.63, which is lower than that of the negative control (0.65). In order to
gauge the precision of my data, it was compared to the class average data (Figure 6) and
yielded a 3% error (Table 1). This low percent error affirms the precision of my data.
Statistical analysis of the data lead us to accept the null hypothesis with low confidence (Table
2). In other words, the statistical procedure did not provide us with enough confidence to
accept that the removal of F26A10.1 had a significant effect on the chemo-attraction of the
worm to diacetyl. We conclude that the unknown gene F26A10.1 does not play a role in
chemotactic function.
Subsequently, we determined whether the silencing of the gene, pdl-1, has any effect
on chemosensation. As graphed in Figure 6, our results show that pdl-1 has a chemotaxis
index of 0.44, which is lower than that of the negative control (0.65). Statistical analysis of
this data lead us to reject the null hypothesis with 95% confidence (Table 2). In other words,
the statistical procedure supplied us with enough confidence to accept that the removal of the
pdl-1 gene had a significant effect on the chemo-attraction of the worms to diacetyl. The pdl-1
gene encodes for PDE6D, the phosphodiesterase responsible for hydrolyzing cGMP into
GMP. The use of cGMP to open cGMP-gated channels plays a crucial role in the function of
chemosensory neurons. As such, it is not surprising that blocking the translation of PDE6D
altered chemosensory function in C. elegans (Burghoorn, et al., 2006).
My results confirmed the hypothesis that silencing network proteins responsible for
chemotaxis alter the organisms’ functionality. Although my datum is conclusive of this, the
class average leads to a different conclusion. A calculated 33% error to the class average
undermined the precision of my data. The class averages do not support my data or
conclusions based on my data, however, there are many factors that destabilize the reliability
of the class average chemotaxis index for the pdl-1 gene such as small sample size and a wide
range of chemotaxis values. The pdl-1 gene was silenced in only 30 experiments that
contributed to the class average, and the values of chemotaxis indices for pdl-1 ranged from
0.27-1.00.
Although statistical analysis of my data confirms that pdl-1 affects chemo-perception,
the overall data is inconclusive because of discrepancies when compared to the data of my
peers. In future experiments, in order to prevent such discrepancies, it may be beneficial to

8. Shiva Mozaffarian
increase the sample size of the experimental genes in order to increase the reliability of the
averages. In order to further ensure that the differences in the chemotaxis indices are
significant, the incubation time of the RNAi plates could be extended. This could help to
increase the number of worms on the chemotaxis plates and decrease the chance that the
distribution of the worms are due to random sampling. Further experimentation of pdl-1 with
these improvements set in place would assist in building a more reliable database that can be
used to conclusively prove this genes role in chemosensory function.
Conclusion
The experiment revealed conclusive evidence that the unknown gene F26A10.1 was
not involved in the chemosensory function of C. elegans. The experiment also revealed
inconclusive evidence to support predictions that pdl-1 is involved in these chemosensory
functions. The class average data did not support the statistical analysis of my results. Further
research of pdl-1 is warranted to settle these discrepancies.
References
Bargmann, C. I. (2006). Chemosensation in C. elegans. Wormbook, 2-16.
Burghoorn, J., Dekkers, M. P., Hukema, R. K., Jansen, G., and Rademakers, S. (2006).
Antagonistic sensory cues generate gustatory plasticity in Caenorhabditis elegans.
EMBO Journal 25, 313-318.
Brenner S., Southgate E., Thomson J.N., and White J. (1986). The structure of the nervous
system of the nematode Caenorhabditis elegans. Philosophical Transactions of the
Royal Society 34, 212–240.
Bush, D., Kaska, D., and Paulsen, K. (2012). Exercise 4: Introduction to Research: The
Nervous System of C. elegans. In Introductory Biology II Laboratory Manual (Santa
Barbara: University of California), pp. 66.
Chao, Y. M., and Hart, C. A. (2009). From Odors to Behaviors in Caenorhabditis elegans.
Neurobiology of Olfaction 1, 4-19.
Driver S.E., Fire A., Kostas S.A., Mello C.C., Montgomery M.K., Xu S. (1998).
Potent and specific genetic interference by double-stranded RNA in Caenorhabditis
elegans. Nature 391, pp. 806-811.
Maduro, M. F., and Pilgrim, D. B. (1995). Identification and cloning of unc-119, a gene
expressed in the Caenorhabditis elegans nervous system. Genetics 141, 980-988.
Wormbase: Gene F26A10.1. (N.d.).Web. Retrieved from
http://www.wormbase.org/db/get?name=WBGene000178;class=Gene