From 758dbfe389412097546e67133b8d8e26ce4bf9d5 Mon Sep 17 00:00:00 2001
From: Kaya <kaya.lange@uni-bielefeld.de>
Date: Wed, 2 Oct 2024 15:56:34 +0200
Subject: [PATCH] changes hp
---
src/data/hptimelinedata.tsx | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/src/data/hptimelinedata.tsx b/src/data/hptimelinedata.tsx
index 328d0441..9e8742e4 100644
--- a/src/data/hptimelinedata.tsx
+++ b/src/data/hptimelinedata.tsx
@@ -1050,8 +1050,8 @@ export const timelinedata: Array<TimelineDatenpunkt> = [
the measurement of the membrane potential above and below a monolayer of confluent cells<ScrollLinkWithChild targetId="desc-3"><sup>3</sup></ScrollLinkWithChild>. Consequently,
it enables precise measurement of conductivity dependent on CFTR expression. </p>
</>],
- implementation: [<p>We decided to use HEK293T[Link] cells lines which do overexpress the
- correct CFTR and those which express CFTR with F508del mutation for the Patch-Clamp measurements[LINK Methodspatchclamp]. To conduct the
+ implementation: [<p>We decided to use HEK293T{/*[Link]*/} cells lines which do overexpress the
+ correct CFTR and those which express CFTR with F508del mutation for the Patch-Clamp measurements{/*LINK Methodspatchclamp*/}. To conduct the
Patch-Clamp experiments, we contacted the Cellular Neurophysiology group to perform the necessary
measurements. It was a pleasure to work together with, who is working as a post-doc for
the Cellular Neurophysiology working group at Bielefeld University. He taught us about the Patch-Clamp
@@ -1192,7 +1192,7 @@ export const timelinedata: Array<TimelineDatenpunkt> = [
<li>Using Ala or Gly for substitution</li>
<li>Development of a nickase assay</li>
</ul>,
- <p>We developed our mutation candidates on this basis [link zum Cycle oder New Part ?]</p>
+ <p>We developed our mutation candidates on this basis. {/*[link zum Cycle oder New Part ?]*/}</p>
],
summary: "In our discussion with Prof. Dr. Hammer, we explored several theoretical approaches in enzyme engineering, including PAM engineering, chimeric proteins, Phage-Assisted Continuous Evolution (PACE), and rational design involving zinc-finger mutations. We evaluated the potential of using structural simulations with AlphaFold 3 and the construction of chimeric proteins. The conversation highlighted the importance of analyzing homologous mechanisms through sequence alignments to identify structural similarities in catalytic centers. We also discussed targeted mutations, such as substitutions to alanine, and the development of a nickase assay. Overall, we concluded that transferring mutations to homologous proteins is a promising rational approach for optimizing enzyme function.",
months: "July"
@@ -1251,7 +1251,7 @@ export const timelinedata: Array<TimelineDatenpunkt> = [
quoteNachname: "Lange, Teammember",
quoteVorname: "Kaya",
quote: "It was amazing to see how exciting the conversations were with future STEM scientists and to hear the fresh perspectives from young minds. The entire experience was both inspiring and energizing.",
- summary: [<p>MINT Sommer 2024 [Link Mint Sommer unten] is a program for high school graduates interested in STEM fields, and iGEM Bielefeld participated to raise awareness about CF and promote their gene therapy research. The team engaged future scientists, explaining the iGEM competition and their synthetic biology approach to address CF. Using insights from previous workshops, they designed interactive activities to make the complexities of CF accessible to attendees. Over two weeks, they formed meaningful connections with professors, students, and STEM professionals, enriching their research discussions. Overall, the event helped improve their science communication skills and fostered valuable professional growth.</p>],
+ summary: [<p>MINT Sommer 2024 is a program for high school graduates interested in STEM fields, and iGEM Bielefeld participated to raise awareness about CF and promote their gene therapy research. The team engaged future scientists, explaining the iGEM competition and their synthetic biology approach to address CF. Using insights from previous workshops, they designed interactive activities to make the complexities of CF accessible to attendees. Over two weeks, they formed meaningful connections with professors, students, and STEM professionals, enriching their research discussions. Overall, the event helped improve their science communication skills and fostered valuable professional growth.</p>],
months: "July"
},
{
@@ -1270,7 +1270,7 @@ export const timelinedata: Array<TimelineDatenpunkt> = [
quoteNachname: "Vinke ,Member of the Safety and Security Committee at iGEM HQ ",
quoteVorname: "Dr. Svenja",
aimofcontact: [<p>We contacted Svenja Vinke, a former iGEMer from Bielefeld and Member of the Safety and Security Committee at iGEM HQ , to get her insight and her opinion regarding the use of phage assisted continuous evoluWe contacted Svenja Vinke, a former iGEMer from Bielefeld, to get her insight and her opinion regarding the use of phage assisted continuous evolution
- (PACE, see engineering cycle 1[Link]) for our prime editing optimizations. Svenja works at the iGEM Safety and Security Committee. Additionally, she was part of the Biosafety and Security Award Team of Bielefeld University in 2016.</p>],
+ (PACE, see engineering cycle 1) for our prime editing optimizations. Svenja works at the iGEM Safety and Security Committee. Additionally, she was part of the Biosafety and Security Award Team of Bielefeld University in 2016.</p>],
insights: [<p>Svenja explained, that a PACE approach is not feasible to use for optimization of our nickase candidates because of several reasons:</p>,
<ul>
<li>Implementing a PACE system takes way too much time to use for our project.</li>
@@ -1319,7 +1319,7 @@ export const timelinedata: Array<TimelineDatenpunkt> = [
quoteNachname: "Mundt, Teammember",
quoteVorname: "Philip",
aimofcontact: [<p>After our first interview with Mattijs Bulcaen we stayed in contact via email and eventually visited him in Leuven at his laboratory. Here we wanted to gain further information about the CFTR F508del models and editing confirmation.</p>],
- insights: [<p>We spoke about approaches for testing CFTR F508del correction in models and methods of confirmation. In this context we talked about HEK293T cell lines[Link] established in his laboratory that stably overexpress CFTR wild-type and F508del. We also discussed how to handle these cell lines. He explained, that the CFTR is fused with a 3HA tag, that in wild-type CFTR would be exposed to the extracellular space and therefore can be used for immunohistochemical staining of the protein, showing correct protein processing and channelling. Also, this allows for a western blot to be made using 3HA antibodies. Functional recovery of CFTR can also be visualized using halide sensitive eYFP or organoid assay, the ladder Mattijs had established an automated readout. Furthermore, we talked about how to handle Sanger sequencing data to analyse edits and discussed the possibility to avoid the weaknesses of Sanger sequencing by using Nanopore sequencing instead. We asked about the applicability of patch clamp analysis in the context of CFTR and Mattijs said that, to his knowledge, it has not been used to test for successful editing in CFTR.
+ insights: [<p>We spoke about approaches for testing CFTR F508del correction in models and methods of confirmation. In this context we talked about HEK293T cell lines established in his laboratory that stably overexpress CFTR wild-type and F508del. We also discussed how to handle these cell lines. He explained, that the CFTR is fused with a 3HA tag, that in wild-type CFTR would be exposed to the extracellular space and therefore can be used for immunohistochemical staining of the protein, showing correct protein processing and channelling. Also, this allows for a western blot to be made using 3HA antibodies. Functional recovery of CFTR can also be visualized using halide sensitive eYFP or organoid assay, the ladder Mattijs had established an automated readout. Furthermore, we talked about how to handle Sanger sequencing data to analyse edits and discussed the possibility to avoid the weaknesses of Sanger sequencing by using Nanopore sequencing instead. We asked about the applicability of patch clamp analysis in the context of CFTR and Mattijs said that, to his knowledge, it has not been used to test for successful editing in CFTR.
Lastly Mattijs explained how he plans to deliver the prime editing complex to the patient, and we evaluated the advantages and disadvantages of delivery strategies, including our very own LNP approach.</p>],
implementation: [<p>When planning how to test and confirm editing by our own constructs, we were largely inspired by the information given to us by Mattijs. For example, we tested prime editing in the HEK293 cell lines we spoke about with Mattijs and used halide sensitive eYFP to check for CFTR function. Also, we tried differentiating wild-type and F508del cells using patch clamp. Unfortunately, a lot of the methods mentioned were not usable for us because of time constraints, but are still valuable for future projects and research built upon PreCyse. </p>],
summary: "We visited Mattijs Bulcaen in Leuven to enhance our understanding of CFTR F508del models and editing confirmation. During the visit, we examined HEK293T cell lines that stably overexpress wild-type CFTR and the F508del variant. Mattijs demonstrated how to use a 3HA tag for visualizing protein processing and discussed methods for assessing CFTR functional recovery. We also compared Sanger and Nanopore sequencing techniques and evaluated delivery strategies for our prime editing complex. The insights from this visit guided our project, leading us to test prime editing in HEK293T cells using halide-sensitive eYFP. While some methods were not feasible due to time constraints, they laid the groundwork for future research in the PreCyse project.",
@@ -1349,7 +1349,7 @@ export const timelinedata: Array<TimelineDatenpunkt> = [
</ul>
],
implementation: [<p>The collaboration expanded our understanding of what's possible, inspiring us to consider new ideas for how we might integrate advanced techniques into our nanoparticle systems in future projects. The collaborative process also encouraged us to document our work more thoroughly, ensuring that future iGEM teams could benefit from both our successes and the challenges we encountered along the way. Beyond the technical improvements, the experience taught us the value of teamwork across borders and disciplines. Each team brought a unique perspective, and by working together, we were able to develop a resource that was far greater than the sum of its parts</p>],
- summary: "This collaboration with Linköping and the other iGEM teams was an incredibly enriching experience. Together, we developed a “Delivery-Based Handbookâ€[link Handbook] that will serve as a valuable resource for future teams working with LNPs and liposomes. The knowledge we gained not only enhanced our project but also strengthened our sense of community within iGEM. We are excited to present the handbook at the Grand Jamboree, where we will finally meet our collaborators in person and celebrate the culmination of our collective efforts. This partnership has shown us the immense power of collaboration, and we are proud to have been part of such a meaningful initiative.",
+ summary: "This collaboration with Linköping and the other iGEM teams was an incredibly enriching experience. Together, we developed a “Delivery-Based Handbook†that will serve as a valuable resource for future teams working with LNPs and liposomes. The knowledge we gained not only enhanced our project but also strengthened our sense of community within iGEM. We are excited to present the handbook at the Grand Jamboree, where we will finally meet our collaborators in person and celebrate the culmination of our collective efforts. This partnership has shown us the immense power of collaboration, and we are proud to have been part of such a meaningful initiative.",
months: "several times",
pictureurl_aim: "https://static.igem.wiki/teams/5247/photos/hp/linkoping-handbook-lnp.webp",
pictureurl_implementation: "https://static.igem.wiki/teams/5247/photos/hp/linkoping-cooperation-photo.png",
@@ -1390,7 +1390,7 @@ export const timelinedata: Array<TimelineDatenpunkt> = [
quote: "Selection for multiple plasmid integrations is the easiest way to optimize protein expression in the yeast strain",
quoteNachname:"Berelsmann, Specilist of yeast culturvation",
quoteVorname: "Nils",
- aimofcontact: [<p>During our interview with <HPLinktoOtherHPTab tab="saito" text="Makoto Saito"/> about fanzor[link fanzor], it became evident that the expression of our fanzor nickases in yeast is very promising. We then refined our expression strategy for the nickases and approached Nils Berelsmann, who is currently working on his PhD thesis with the yeast strain Pichia pastoris (SMD1163). This particular strain could be ideal for expressing the SpuFz1 nickase variants. Our main aim in contacting Nils was to gain insight and advice on yeast expression and he generously shared his expertise with us. Not only did he give us valuable advice, but he also provided us with the yeast strain itself, along with a corresponding expression vector for possible experiments. He also provided us with detailed protocols and the plasmid map of the vector and gave us practical tips on how to optimize the expression process. His support was invaluable in moving our work forward. </p>],
+ aimofcontact: [<p>During our interview with <HPLinktoOtherHPTab tab="saito" text="Makoto Saito"/> about fanzor, it became evident that the expression of our fanzor nickases in yeast is very promising. We then refined our expression strategy for the nickases and approached Nils Berelsmann, who is currently working on his PhD thesis with the yeast strain Pichia pastoris (SMD1163). This particular strain could be ideal for expressing the SpuFz1 nickase variants. Our main aim in contacting Nils was to gain insight and advice on yeast expression and he generously shared his expertise with us. Not only did he give us valuable advice, but he also provided us with the yeast strain itself, along with a corresponding expression vector for possible experiments. He also provided us with detailed protocols and the plasmid map of the vector and gave us practical tips on how to optimize the expression process. His support was invaluable in moving our work forward. </p>],
insights: [<p>Pichia pastoris (SMD1163) is a promising option for expressing SpuFz1 nickase variants. Refining expression strategies based on expert insights is crucil for success. Nils provided practical tips on yeast expression, including optimizing growth conditions and fine-tuning induction protocols.</p>],
implementation: [<p>We adapted our expression strategy for Fanzor nickases in yeast by incorporating the Pichia pastoris strain (SMD1163) and the provided expression vector into our experiments. Following Nils' detailed protocols and plasmid map, we optimized key steps, enhancing expression efficiency and protein yield.</p>],
summary: "The team sought expert advice from Nils to optimize yeast expression for Fanzor nickases. Nils provided invaluable guidance on addressing potential challenges and troubleshooting the process. He supplied the Pichia pastoris (SMD1163) strain along with a suitable expression vector, crucial for expressing SpuFz1 nickase variants. Additionally, he shared detailed protocols for yeast transformation and growth optimization, enabling the team to replicate his methods effectively for their experiments.",
@@ -1458,7 +1458,7 @@ export const timelinedata: Array<TimelineDatenpunkt> = [
quoteVorname: "Kaya",
quoteNachname: "Lange, Teamm",
quote: "It was wonderful to be part of the Student Academy and to experience how much we learned while teaching. Sharing our knowledge and seeing the students' enthusiasm was incredibly rewarding, even though we couldn't convey everything in just one session.",
- summary: [<p>The CeBiTec Student Academy[Link unten Schüler akademie] at Bielefeld University provides high school students with hands-on experience in biotechnology and molecular biology, supported by the Osthushenrich Foundation and Detmold district government. iGEM Bielefeld participated by guiding students through a nanopore sequencing experiment, teaching them about lab work, experiment preparation, and safety protocols. The team also presented their iGEM project, PreCyse, giving students insight into real-world research projects and synthetic biology. Many students were excited by the iGEM concept and expressed interest in joining during their future studies. Overall, the academy helped inspire students to explore STEM fields and gain practical scientific skills.</p>],
+ summary: [<p>The CeBiTec Student Academy at Bielefeld University provides high school students with hands-on experience in biotechnology and molecular biology, supported by the Osthushenrich Foundation and Detmold district government. iGEM Bielefeld participated by guiding students through a nanopore sequencing experiment, teaching them about lab work, experiment preparation, and safety protocols. The team also presented their iGEM project, PreCyse, giving students insight into real-world research projects and synthetic biology. Many students were excited by the iGEM concept and expressed interest in joining during their future studies. Overall, the academy helped inspire students to explore STEM fields and gain practical scientific skills.</p>],
months: "August"
},
{
--
GitLab