In order to
investigate what factors influence the acceptance of Vibrio Natriegens as a chassis organism in
biology-related laboratories, we designed a questionnaire with the expectation that the statistical
results would provide useful suggestions for the overall design of the project.
Firstly, we designed
the questionnaire based on a logical chain of "reliance on and need for the characteristics of
chassis organisms in biology-related laboratories-acceptance of Vibrio Natriegens as a chassis
organism - factors influencing the long-term selection and use of a new chassis organism". During
the design process, we actively communicated with students from the School of Public Administration
of Sichuan University, who gave us advice on the number of questions and the design of the
completion introductions of the questionnaire, which helped us to complete the questionnaire design
section.
Immediately
afterward, we contacted people from biological laboratories in different fields, both nationally and
internationally, to fill out our questionnaire in various ways. Due to the fact that the epidemic
has not yet been fully controlled worldwide, many offline seminars have been canceled. However, the
internet has allowed many teams within the iGEM family to be better connected with each other.
Through email, we got in touch with many iGEM teams in China and abroad. In the meantime, we would
also like to thank Ms. Tong Ying from the School of Life Sciences of Sichuan University. Her
guidance and assistance in translating the questionnaire into English has allowed us to communicate
with foreign teams more accurately. In this kind of communication across geographical distances,
many teams had put forward quantities of unique insights when they were filling the questionnaire,
which had inspired us a lot. For example, The University of Heidelberg mentioned that when choosing
a long-term used new chassis organism, we might put more attention on the safety level and the
protocol difficulty, such as to make Vibrio Natriegens competent and transform, rather than whether
it has a faster growth rate and easier pathways to get. The collision between different thoughts has
benefited us a lot, and it has also prompted us to consider more about the subject design.
In early October, we
finished a three-month questionnaire survey and started to analyze the results of the questionnaire.
We received a total of 113 valid questionnaires from other researchers in different fields. We
analyzed the questionnaire from four aspects:
The analysis
of the questionnaire data showed that biological laboratories have a high level of reliance
on chassis organisms. This suggests that our efforts on this topic could provide support to
many biological laboratories in the future. And this conclusion has given us much more
confidence.
Fig 1. Do you use organisms such as E. coli or yeast in your laboratory?
According to
Pearson correlation analysis, the correlation between the use of chassis organisms such as
E. coli or yeast and the percei+ved importance of the characteristics of the chassis
organisms is 0.69(p<0.05), which demonstrates a strong correlation between them. This
indicates that researchers using chassis organisms such as Saccharomyces cerevisiae place a
high value on the characteristics of the chassis organisms. This also confirms the need to
modify the characteristics of the chassis organisms.
| Project |
Mean |
Standard deviation |
Do you use organisms such as E. coli or yeast in your
study?
|
|
|
| Do you use organisms such as E. coli or
yeast in your study?
|
3.91 |
1.12 |
1 |
|
| What do you think the importance of
biological characteristics of chassis organism in the experiment
is?
|
3.89 |
1.75 |
0.69** |
1 |
| * p<0.05 ** p<0.01 |
Table 1. The correlation between the use of chassis organisms in the biological
laboratory and the importance placed on the characteristics of the chassis organisms.
We cleaned
the data by removing rows containing -3 from the data (i.e. the corresponding questionnaire
for chassis organisms was not applicable at all in the laboratory). After data cleaning, we
used the resulting data in a multiclassification regression to build a mapping model where
the input was the degree of willingness to use the bacterium as a substrate and the output
was the degree of willingness to use it twice afterwards. Since the input is manually
cleared, there are only 3, 4 and 5 three input options. After building a multicategorical
LOGISTICREGREESION and optimising it using stochastic gradient descent, we concluded that
those who were neutral in their thoughts about trying to use Vibrio Natriegens would also be
neutral in their consideration for the next use. And those who were more willing to use our
bacteria would be more likely to choose our modified Vibrio Natriegens next time. However,
it is worth noting that those who were most willing to use our modified Vibrio Natriegens
for the first time would doubt about the chassis organisms at the next time when they need
to choose one to use. We analyse that these laboratories were more willing to experiment
with a new chassis organism. But once they had found another suitable one, they were less
willing to choose the old chassis organism in the long run, which is somewhat of a warning.
Unlike trial use, getting more biological laboratories to accept the long-term use of a new
chassis organism remains a huge challenge.
$$
\left\{ \begin{array}{c}
x\in \left[ 3,4,5 \right]\\
h_{\theta}\left( x \right) g\left( \theta ^Tx \right) =\frac{1}{1}+e^{-\theta ^TX}\\
g\left( Z \right) =\frac{1}{1}+e^{-z}\\
\end{array} \right.
\\
\left\{ \begin{array}{c}
y=h_{\theta}\left( x\mathrm{'} \right)\\
y\in \left[ 1,2,3,4,5 \right]\\
x\mathrm{'}\in \left[ 1,2,3,4,5 \right]\\
\end{array} \right.
$$
| Willing |
1 |
2 |
3 |
4 |
5 |
| Continue |
3 |
3 |
3 |
4 |
2 |
Table 2. The possibility that Vibrio Natriegens will be used again after having been used
with good results.
The data
shows that the convenience of the access, whether the price is affordable, whether it can
overcome the shortcomings of the previously used chassis organisms, and whether our modified
Vibrio Natriegens has unique advantages are the key directions we need to focus on in the
future. It is worth thinking about how modified Vibrio Natriegens can be used on a wider
scale as chassis organisms for long-term use in the biological laboratory. This will also be
explored in more dimensions during our follow-up communication activities.
Fig 2. The factors that affect the long-term selection and use of new chassis
organisms.
