From c1425bad670bf403977cf7ded3d0f92443847eb9 Mon Sep 17 00:00:00 2001
From: txj <21307110035@m.fudan.edu.cn>
Date: Wed, 4 Dec 2024 09:24:35 +0800
Subject: [PATCH] fix 3
---
src/description.md | 4 ++--
src/inclusivity.md | 6 +++---
src/notebook.md | 2 +-
src/safety.md | 8 ++++----
written-by.md | 1 +
5 files changed, 11 insertions(+), 10 deletions(-)
diff --git a/src/description.md b/src/description.md
index 7b0f67d..a5b347f 100644
--- a/src/description.md
+++ b/src/description.md
@@ -54,7 +54,7 @@ Nickel can be sourced from either mining or recycling. Today, nickel recycling m
Despite the environmental damage caused by mining, it remains the more cost-effective option compared to recycling. As a result, there is little economic incentive to prioritize recycling. Currently, only 1% of the global nickel supply comes from recycling[^4].
<div style="text-align: center;" id="fig3">
- <img src="https://static.igem.wiki/teams/5115/description/description-fig3-1.png" style="width:100%">
+ <img src="https://gitlab.igem.org/2024/fudan/-/raw/main/img-should-be-compressed/description-fig3-1.png" style="width:100%">
<div>
<span style="color:gray">Figure 3: Current nickel recycling methods</span>
<br><br>
@@ -115,7 +115,7 @@ Addressing these four challenges is crucial for our project's success.
We present four interrelated modules to tackle the problems identified in the previous section: Nickel Enrichment, Survival, Nickel Microparticle, and Hydrogen Supply Module. These systems work together to enable efficient and low-impact nickel absorption, then processed into reusable nickel microparticles.
<div style="text-align: center;" id="fig5">
- <img src="https://static.igem.wiki/teams/5115/description/description-fig5.png" style="width:100%">
+ <img src="https://gitlab.igem.org/2024/fudan/-/raw/main/img-should-be-compressed/description-fig5.png" style="width:100%">
<div>
<span style="color:gray">Figure 5: Four modules of MINERAL</span>
<br><br>
diff --git a/src/inclusivity.md b/src/inclusivity.md
index 9ff8e98..f7b949f 100644
--- a/src/inclusivity.md
+++ b/src/inclusivity.md
@@ -40,14 +40,14 @@ Unfortunately, **real barriers still exist**. Through literature reviews, interv
3. **Low public awareness:** Attention and inclusiveness of public towards the ASD population are insufficient, and the importance of scientific outreach for the ASD community is often overlooked.
4. **Economical Burden on ASD families:** Families find it difficult to bear the financial burden of education.
-Our interviewees, including parents of ASD individuals, experts in special education and public welfare, as well as staff from rehabilitation centers and special schools, have all expressed **a shared desire to** **remove these barriers**. This is exactly the vision we have gathered here for.
+Our interviewees, including parents of ASD individuals, experts in special education and public welfare, as well as staff from rehabilitation centers and special schools, all expressed **a shared desire to** **remove these barriers**. This is exactly the vision we have gathered here for.
The following figure shows our overall strategy for addressing barriers.
<div style="text-align: center;" id="fig2">
<img src="https://static.igem.wiki/teams/5115/inclusivity/barriers-new-new.png" style='width:100%'>
<div>
- <span style="color: gray">The barriers and the solutions.</span>
+ <span style="color: gray">The barriers that ASD individuals face and the solutions we propose.</span>
<br><br>
</div>
</div>
@@ -336,7 +336,7 @@ After thorough validation and discussion, we carefully launched the STEAMed cour
**Practical Skills:** We designed a "Gene Editing" game to enhance their physical coordination during the activity and deepen their understanding of scientific concepts.
<div style="text-align: center;" id="fig16">
- <img src="https://static.igem.wiki/teams/5115/inclusivity/course-2-game.png" style="width:100%">
+ <img src="https://static.igem.wiki/teams/5115/collaborations-final/course-2-3.webp" style="width:100%">
<div>
<span style="color: gray">Course 2.3</span>
<br><br>
diff --git a/src/notebook.md b/src/notebook.md
index df6ac2c..16820af 100644
--- a/src/notebook.md
+++ b/src/notebook.md
@@ -58,7 +58,7 @@ On April 5th, team members visited an [art exhibit](/fudan/inclusivity/#_2-2-did
## May
-In a weekly meeting on May 2nd, everyone of us confirmed the roles, and we discussed various project aspects, such as nickel ion binding, transport, and coexistence with nitrifying bacteria. On May 4th, discussions with other universities revealed a similarity with [BIT](https://2024.igem.wiki/bit/), we quickly evaluated our project and emphasized our unique strength ([ribozyme parts from 2022](https://2022.igem.wiki/fudan/parts) and [survival modules from 2023](https://2023.igem.wiki/fudan/results/)). On May 10th, we discussed gas vesicles in *E. coli*, nickel ion conversion, and the potential for nitrification and denitrification. On May 19th, further discussions focused on [the symbiotic system from 2023](https://2023.igem.wiki/fudan/part-collection/#symbiotic-system), metal-binding proteins, and potential application directions, refining our project's educational outreach. On May 24th, we participated in the [Stargazing Cultural and Art Festival](/fudan/education/#education-for-university-students) and promoted our project during the event (as shown [below](#fig5)).
+In a weekly meeting on May 2nd, everyone of us confirmed the roles, and we discussed various project aspects, such as nickel ion binding, transport, and coexistence with nitrifying bacteria. On May 4th, discussions with other universities revealed a similarity with [BIT](https://2024.igem.wiki/bit/), we quickly evaluated our project and emphasized our unique strength ([ribozyme parts from 2022](https://2022.igem.wiki/fudan/parts) and [survival modules from 2023](https://2023.igem.wiki/fudan/results/)). On May 10th, we discussed gas vesicles in *E. coli*, nickel ion conversion, and the potential for nitrification and denitrification. On May 19th, further discussions focused on [the symbiotic system from 2023](https://2023.igem.wiki/fudan/part-collection/#symbiotic-system), metal-binding proteins, and potential application directions, refining our project's educational outreach. On May 24th, we participated in the [Starry Cultural and Art Festival](/fudan/education/#education-for-university-students) and promoted our project during the event (as shown [below](#fig5)).
<div style="text-align: center;" id="fig5">
<img src="https://static.igem.wiki/teams/5115/notebook/may-1.jpg" style="width:100%">
diff --git a/src/safety.md b/src/safety.md
index dd628ff..435099e 100644
--- a/src/safety.md
+++ b/src/safety.md
@@ -17,7 +17,7 @@ However, this project comes with significant challenges in terms of biosafety ma
### Application risk management
-We incorporated environmental risk management into our considerations from the project design stage. Firstly, we addressed the issue of the biotoxicity of metal microparticles. After consulting with [Professor Wei Feng](/fudan/human-practices/#c3-3-discuss-with-professor-feng-wei) from the Department of Chemistry at our university, we were gald to know that our product, micro-nickel particles, likely have low chemical toxicity due to its small environmental concentration and inert chemical nature. The main concern lies in the size effect rather than chemical toxicity. Microparticles exhibit minimal biotoxicity when they are either too large or too small. However, when their size is less than 100 nm, they could be absorbed into bodily fluids, leading to strong biotoxicity[^1]. To mitigate this, we introduced [carboxysomes](/fudan/description/#_3-nickel-microparticle-module) as reaction hubs in the system, which concentrates nickle particles to reduce their biological toxicity, while simultaneously increasing local enzyme concentrations to increase the reaction efficiency.
+We incorporated environmental risk management into our considerations from the project design stage. Firstly, we addressed the issue of the biotoxicity of metal microparticles. After consulting with [Professor Wei Feng](/fudan/human-practices/#c3-3-discuss-with-professor-feng-wei) from the Department of Chemistry at our university, we were gald to know that our product, micro-nickel particles, likely have low chemical toxicity due to its small environmental concentration and inert chemical nature. The main concern lies in the size effect rather than chemical toxicity. Microparticles exhibit minimal biotoxicity when they are either too large or too small. However, when their size is less than 100 nm, they could be absorbed into bodily fluids, leading to strong biotoxicity[^1]. To mitigate this, we introduced [carboxysomes](/fudan/description/#_3-nickel-microparticle-module) as reaction hubs in the system, which concentrates nickle particles to reduce their biological toxicity, while increasing local enzyme concentrations to increase the reaction efficiency.
Moreover, we are fully aware that any product, especially synthetic biology product, should be carefully tested before releasing into open environments. Please refer to our [Implementation](/fudan/implementation/) page about how our project could be implementated. Please note that we have designed [Hardware](/fudan/hardware/), where we immobilized the engineered bacteria onto carbon fiber threads coated with agarose, effectively preventing the unwanted spread of the engineered bacteria into varied environment.
@@ -43,7 +43,7 @@ This year we utilized *Caenorhabditis elegans* in assessing the outcome of relea
<img src="https://static.igem.wiki/teams/5115/txj/safety-u.gif" style="width:80%; height: auto;"><br>
<div>
<span style="color: gray">Figure 1-3: Representative images of <em>Caenorhabditis elegans</em> swimming, fed with <em>E. coli</em> strain OP50, <em>E. coli</em> expressing <a href='https://parts.igem.org/Part:BBa_K5115067'>module F</a>, and <em>E. coli</em> expressing <a href='https://parts.igem.org/Part:BBa_K5115068'>module U</a>.<br>
- <small>For the later two, bacteria has been cultured at 37°C for 30 hours in 100 mg/L NiCl~2~ solution with bubbled hydrogen gas, assuming massive nickel microparticles formed inside bacteria. After 30-hour culture, bacteria were collected by 3000 rpm 10-min centrifugation, briefly washed with 2x YT media, plated directly onto the NGM plate, briefly dried before seeding worm. Dark brown balls in the fields are bacteria aggregates. These videos were captured using a household <a href='https://en.wikipedia.org/wiki/Digital_single-lens_reflex_camera'>DSLR</a> camera, and are displayed at 6x the real speed.</small>
+ <small>For the later two, bacteria has been cultured at 37°C for 30 hours in 100 mg/L NiCl<sub>2</sub> solution with bubbled hydrogen gas, assuming massive nickel microparticles formed inside bacteria. After 30-hour culture, bacteria were collected by 3000 rpm 10-min centrifugation, briefly washed with 2x YT media, plated directly onto the NGM plate, briefly dried before seeding worm. Dark brown balls in the fields are bacteria aggregates. These videos were captured using a household <a href='https://en.wikipedia.org/wiki/Digital_single-lens_reflex_camera'>DSLR</a> camera, and are displayed at 6x the real speed.</small>
</span>
<br><br>
</div>
@@ -61,7 +61,7 @@ This year we utilized *Caenorhabditis elegans* in assessing the outcome of relea
</div>
<div style="text-align: center; margin-top: 10px;">
<span style="color: gray">Figure 4 & 5: Comparison of the average distance moved per minute and the average turning angle per turn of <em>Caenorhabditis elegans</em>, 18 hours after seeding.<br>
- <small>The nematodes were fed with <em>E. coli</em> strain OP50, <em>E. coli</em> expressing <a href='https://parts.igem.org/Part:BBa_K5115067'>module F</a>, and <em>E. coli</em> expressing <a href='https://parts.igem.org/Part:BBa_K5115068'>module U</a>. For the later two, bacteria has been cultured at 37°C for 30 hours in 100 mg/L NiCl~2~ solution with bubbled hydrogen gas, assuming massive nickel microparticles formed inside bacteria. After 30-hour culture, bacteria were collected by 3000 rpm 10-min centrifugation, briefly washed with 2x YT media, plated directly onto the NGM plate, briefly dried before seeding worm. Five L2-stage nematodes were picked for each plate and cultured at 20°C for 18 hours. For each dataset, images from at least three nematode were collected, and at least 1-minute worm movement was recorded at 1080p 30fps, yielding at least 1900 data points, analyzed by ImageJ Plugins Animal Tracker, and graphed in GraphPad Prism.</small></span>
+ <small>The nematodes were fed with <em>E. coli</em> strain OP50, <em>E. coli</em> expressing <a href='https://parts.igem.org/Part:BBa_K5115067'>module F</a>, and <em>E. coli</em> expressing <a href='https://parts.igem.org/Part:BBa_K5115068'>module U</a>. For the later two, bacteria has been cultured at 37°C for 30 hours in 100 mg/L NiCl<sub>2</sub> solution with bubbled hydrogen gas, assuming massive nickel microparticles formed inside bacteria. After 30-hour culture, bacteria were collected by 3000 rpm 10-min centrifugation, briefly washed with 2x YT media, plated directly onto the NGM plate, briefly dried before seeding worm. Five L2-stage nematodes were picked for each plate and cultured at 20°C for 18 hours. For each dataset, images from at least three nematode were collected, and at least 1-minute worm movement was recorded at 1080p 30fps, yielding at least 1900 data points, analyzed by ImageJ Plugins Animal Tracker, and graphed in GraphPad Prism.</small></span>
</div>
By feeding nematodes with engineered bacteria [containing nickel microparticles](/fudan/results/#fig7), and comparing their locomotion behavior, we found no significant difference in worm motion between the control group and the experimental group. This indicates that our product is harmless to nematodes, likely to be environmentally and biologically friendly.
@@ -82,7 +82,7 @@ Although our project is currently applied in a controlled environment, it has th
### Dual risk identification
-In the laboratory setting, our engineered bacteria exhibit a growth disadvantage compared to wild-type *E. coli*, suggesting they face significant competitive pressure and potentially fade out in natural environments. However, their [high tolerance](/fudan/description/#_2-survival-module) to heavy metal conditions and resistance to bacteriophages could grant them a survival advantage in special environments. For instance, in densely populated and heavily polluted urban areas, our engineered bacteria could theoretically be maliciously exploited to carry pathogenic factors and released into these regions. Nonetheless, we believe that every project has its bright and dark sides, and we must not forsake promising solutions due to potential risks. Our commitment to a brighter future compels us to navigate challenges with optimism and resilience.
+In the laboratory setting, our engineered bacteria exhibit a growth disadvantage compared to wild-type *E. coli*, suggesting they face significant competitive pressure and potentially fade out in natural environments. However, their [high tolerance](/fudan/description/#_2-survival-module) to heavy metal conditions and resistance to bacteriophages could grant them a survival advantage in special environments. For instance, in densely populated and heavily polluted urban areas, our engineered bacteria could be maliciously exploited to carry pathogenic factors and released into these regions. Nonetheless, we believe that every project has its bright and dark sides, and we must not forsake promising solutions due to potential risks. Our commitment to a brighter future compels us to navigate challenges with optimism and resilience.
## Conclusion
diff --git a/written-by.md b/written-by.md
index 45a32a2..391533b 100644
--- a/written-by.md
+++ b/written-by.md
@@ -22,6 +22,7 @@
| Part Collection | Yi Shi, Liyue Chen |
| Parts | Liyue Chen, Yi Shi |
| Plant | none |
+| Presentation Video | all |
| Promotion Video | Yuhan Li, Yuhan Wang |
| Proof of Concept | -- |
| Results | Xujie Tan, Ruiwen Ma, Yi Shi |
--
GitLab