diff --git a/.gitignore b/.gitignore
index ddbfb3f0fe2cc6c99985597df523c64d3be36c55..505e472c3b54b001f47267be029506ee5e59edb8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -16,3 +16,4 @@ dist
src/components/resources
code/test.bib
.DS_Store
+code/test file gitignore.txt
diff --git a/src/App/Timelines.css b/src/App/Timelines.css
index c14380430da3e9d637f5566f5e898fbc7c863bb3..f0080f05163fc01b2b02e4d2e421fccd43eb743f 100644
--- a/src/App/Timelines.css
+++ b/src/App/Timelines.css
@@ -178,8 +178,8 @@ button.tabbutton:nth-child(1), button.tabbutton:nth-child(6){
.Industry, button.tabbutton:nth-child(5){
background-color: var(--mediumpurple);
}
-.Activist{
- background-color: var(--igemlightgreen);
+.Activist, .Milestone{
+ background-color: var(--igemlightgreen) !important;
}
.Ethics{
diff --git a/src/components/HP-timeline.tsx b/src/components/HP-timeline.tsx
index c2cf859f891c0dc4bf13f52c5ec48fb45a10c192..f8b2a64586ee5b6c12cd33d5cd147cf60726c8dd 100644
--- a/src/components/HP-timeline.tsx
+++ b/src/components/HP-timeline.tsx
@@ -41,6 +41,11 @@ export function HPTimeline(){
node: <TimeHori tab="Industry" ></TimeHori>,
buttonname: "Industry",
cssname: "Industry"
+ },
+ {
+ node: <TimeHori tab="Milestone" ></TimeHori>,
+ buttonname: "Milestones",
+ cssname: "Milestone"
}
]
diff --git a/src/components/Tabs.tsx b/src/components/Tabs.tsx
index 0e1123d97abe6766e59d348666069eabbf85d328..4b8662848198a867b99fcc75c4f98c5e93d5c856 100644
--- a/src/components/Tabs.tsx
+++ b/src/components/Tabs.tsx
@@ -67,10 +67,10 @@ import { stringToSlug } from "../utils";
quoted = data[i].vorname + " " + data[i].nachnname;
}
}
- else{
+ /* else{
problem = true;
problem_desc.push("quote missing");
- }
+ } */
/* textparts */
let aiM: JSX.Element = <></>
@@ -151,12 +151,12 @@ import { stringToSlug } from "../utils";
problem_desc.push(" job missing" );
}
}
- if(data[i].type === "meta"){
+ /* if(data[i].type === "meta"){
if(data[i].quoteVorname === undefined || data[i].quoteVorname === ""){
problem = true;
problem_desc.push(" who is the quote from?" );
}
- }
+ } */
/* References */
var refs: React.ReactNode = <></>;
@@ -236,7 +236,7 @@ import { stringToSlug } from "../utils";
<div className="row align-items-stretch">
<div className="col d-flex flex-column">
<div className="row flex-grow-1 mitte">
- <p style={{paddingTop: "50px", fontSize: "large"}}>Summary:</p>
+ <h4 style={{paddingTop: "50px"}}>Summary:</h4>
<p>{data[i].summary}</p>
</div>
<div className="row unten" style={{fontSize: "large"}}>
diff --git a/src/contents/Human Practices/Conclisuin.tsx b/src/contents/Human Practices/Conclisuin.tsx
index 27335a16746e99106239bc632a524c2aa31b4793..aa545564c2357c351f8c37733bbb43c14f82753b 100644
--- a/src/contents/Human Practices/Conclisuin.tsx
+++ b/src/contents/Human Practices/Conclisuin.tsx
@@ -282,7 +282,7 @@ function AnalyseBharti(){
function AnalyseIgnatova(){
return(
<Collapsible title="Prof. Dr. Ignatova – CF Expert & Researcher" id="ignatovaanalyseC">
- <p>Through our collaboration with iGEM Hamburg[Link], we were introduced to Prof. Ignatova, a leading expert in cystic fibrosis (CF) research. Initially, we consulted her to gain a deeper understanding of CF. Later, when the HEK cells from Leuven proved unsuitable for our tests, we reached out again to explore alternative cell models. </p>
+ <p>Through our collaboration with <a href="https://2024.igem.wiki/hamburg/" title="iGEM Hamburg" > iGEM Hamburg</a>, we were introduced to Prof. Ignatova, a leading expert in cystic fibrosis (CF) research. Initially, we consulted her to gain a deeper understanding of CF. Later, when the HEK cells from Leuven proved unsuitable for our tests, we reached out again to explore alternative cell models. </p>
<p>Prof. Ignatova provided access to the CFBE41o- cell line, immortalized CF cells derived from a CF patient, which we obtained with permission from Prof. Karl Kunzelmann at the University of Regensburg. This cell line offered us a new, reliable testing system, and we successfully cultivated the cells in our lab, although they required significant time to acclimate and grow. </p>
<p>Looking forward, we plan to conduct patch-clamp experiments with these cells to validate our prime editing approach. Our discussions with Prof. Ignatova also broadened our perspective on gene therapy. She shared her work on recoding tRNAs to address defective mutations, which introduced us to alternative therapeutic strategies. This was an eye-opening experience that added depth to our approach. </p>
<figure>
diff --git a/src/contents/methods.tsx b/src/contents/methods.tsx
index 7b63f4ad2581d9fa66c43539b1a834e73d94a325..52a31ec859a2407518455431cf870c9f0770924d 100644
--- a/src/contents/methods.tsx
+++ b/src/contents/methods.tsx
@@ -73,25 +73,46 @@ export function Methods() {
<H4 text="Assessing the Safety of Our LNPs "></H4>
<p>Ensuring the safety and thorough characterization of our lipid nanoparticles (LNPs) was a central part of our project, as these particles are intended for use in biological systems. We implemented a comprehensive range of assays and techniques to assess their biosafety and physical properties, ensuring their suitability for applications such as drug delivery and gene therapy. Below is an overview of the key steps we took in our assessment.</p>
<H4 text="MTT Assay"></H4>
+ <div className='row align-items-center'>
+ <div className='col'>
+ <figure>
+ <img src="https://static.igem.wiki/teams/5247/integrated-human-practices/mttassay.webp" alt="PC1" style={{maxHeight: "200pt"}}/>
+ <figcaption>
+ <b>Figure 6. </b>
+ MTT Assay: formation of purple formazan crystals by living cells.
+ </figcaption>
+ </figure>
+ </div>
+ <div className='col'>
<p>To evaluate the cytotoxicity of our LNPs, we conducted an MTT assay, which measures the metabolic activity of cells. This assay is based on the ability of living cells to reduce MTT, a yellow tetrazolium salt, into purple formazan crystals through NAD(P)H-dependent enzymes. Cells were treated with various concentrations of LNPs, and after dissolving the formazan crystals with DMSO, we measured absorbance. Higher absorbance values indicate greater cell viability. Our results showed no significant reduction in cell viability across all LNP concentrations, demonstrating that the LNPs did not induce cytotoxic effects. This finding is crucial for ensuring that the LNPs are safe for biological use, supporting their potential in clinical applications such as drug delivery and gene therapy. Overall, the MTT assay provided strong evidence of the biocompatibility of our LNPs. </p>
+ </div>
+ </div>
<H4 text="Proliferation Assay to Monitor Long-Term Safety"></H4>
<p>In addition to assessing immediate cytotoxicity, we also evaluated the long-term safety of the LNPs by conducting a proliferation assay. This assay tracked cell division and growth over time to determine whether the LNPs impacted cellular function. Our results showed that LNP-treated cells had similar growth rates to untreated controls, indicating that the LNPs do not interfere with normal cell processes. This further confirms their biocompatibility and suitability for use in biological systems.</p>
</Subesction>
- <Subesction title="Transfection Efficiency" id="Transfection Efficiency">
- <p></p>
- <H4 text="Fluorescence-Activated Cell Sorting (FACS)"></H4>
+ <Subesction title="Fluorescence-Activated Cell Sorting (FACS)" id="FACS">
<p>To assess the transfection efficiency of our LNPs, we used fluorescence-activated cell sorting (FACS). This method involved tagging the LNPs with fluorescent markers and measuring their ability to deliver genetic material into target cells. FACS provided quantitative insights into how effectively the LNPs transfected cells, helping us optimize their design for gene therapy applications. </p>
</Subesction>
<Subesction title="In-Depth Characterization of LNPs" id="In-Depth Characterization of LNPs">
- <H4 text="Dynamic Light Scattering (DLS) and Zeta Potential"></H4>
- <p>We used dynamic light scattering (DLS) to measure the size distribution and polydispersity index (PDI) of our LNPs. This technique allowed us to confirm that the LNPs had a consistent size distribution with minimal aggregation, which is essential for their stability. Additionally, we measured the zeta potential of the LNPs to assess their surface charge. A high zeta potential confirmed that the LNPs were stable in suspension, which is critical for their effectiveness in biological environments. </p>
- <H4 text="SEM and Cryo-EM for Structural Analysis"></H4>
+ <H4 text="Dynamic Light Scattering (DLS) and Zeta Potential"></H4>
+ <p>We used dynamic light scattering (DLS) to measure the size distribution and polydispersity index (PDI) of our LNPs. This technique allowed us to confirm that the LNPs had a consistent size distribution with minimal aggregation, which is essential for their stability. Additionally, we measured the zeta potential of the LNPs to assess their surface charge. A high zeta potential confirmed that the LNPs were stable in suspension, which is critical for their effectiveness in biological environments. </p>
+ <H4 text="SEM and Cryo-EM for Structural Analysis"></H4>
+ <div className='row align-items-center'>
+ <div className='col'>
<p>To further characterize the morphology and surface structure of the LNPs, we employed scanning electron microscopy (SEM). SEM provided high-resolution images that confirmed the spherical shape and uniformity of the LNPs. Additionally, cryo-electron microscopy (cryo-EM) allowed us to investigate the internal structure of the LNPs, revealing the presence of lipid layers and encapsulated materials, which are crucial for understanding their function in drug delivery. </p>
- {/* <H4 text="DNase Assay for Stability of Encapsulated Material "></H4>
- <p>Finally, we conducted a DNase assay to evaluate whether the LNPs could protect encapsulated nucleic acids, such as mRNA, from enzymatic degradation. This assay demonstrated that the LNPs successfully shielded the genetic material, ensuring its stability until it reaches target cells. </p> */}
+ </div>
+ <div className='col'>
+ <figure>
+ <img src="https://static.igem.wiki/teams/5247/delivery/plasmatem.webp" alt="PC1" style={{maxHeight: "200pt"}}/>
+ <figcaption>
+ <b>Figure 7. </b>
+ Sample preparation for SEM: sputtering in Argon plasma.
+ </figcaption>
+ </figure>
+ </div>
+ </div>
</Subesction>
-
<Subesction title="Conclusion" id="Conclusion">
<H4 text="Importance of Safety in LNP Development"></H4>
<p>Testing the safety of our LNPs was a critical step in their development. LNPs are increasingly being used in cutting-edge therapies, such as mRNA vaccines and targeted drug delivery systems. For these technologies to be viable, the nanoparticles must not harm the cells they are intended to interact with. The MTT and proliferation assays provided robust data, confirming the biocompatibility of our LNPs and reinforcing their potential for safe use in further research and clinical applications. </p>
diff --git a/src/data/hptimelinedata.tsx b/src/data/hptimelinedata.tsx
index e9f3a2982c1d01126995e6c13836ecfbafdd925d..24411455a35411388227850433d4ceece76dbf5a 100644
--- a/src/data/hptimelinedata.tsx
+++ b/src/data/hptimelinedata.tsx
@@ -21,6 +21,19 @@ function HPgoToPageAndScroll({id, text, path}:{id: string, text: string, path: s
)
}
+function HPgoToPageAndOpenTab({id, text, path}:{id: string, text: string, path: string}){
+ const {goToPagesAndOpenTab} = useNavigation();
+ return(
+ <a onClick={() => goToPagesAndOpenTab(id, path)}> {text} </a>
+ )
+}
+function HPgoToPageAndOpenTabAndScroll({tab, text, path, scrollId}:{tab: string, text: string, path: string, scrollId: string}){
+ const {goToPageWithTabAndScroll} = useNavigation();
+ return(
+ <a onClick={() => goToPageWithTabAndScroll({tabId: tab, path: path, scrollToId: scrollId})}> {text} </a>
+ )
+}
+
export interface TimelineDatenpunkt {
title?: string; /* Prof. , Dr., ... */
vorname: string;
@@ -766,7 +779,6 @@ export const timelinedata: Array<TimelineDatenpunkt> = [
aimofcontact: "",
insights: "",
implementation: "",
- type: "meta",
summary: "",
months: "june"
},
@@ -1143,7 +1155,7 @@ export const timelinedata: Array<TimelineDatenpunkt> = [
language: "de",
cardtext: "",
quote: "x",
- aimofcontact: [<p>When we realized that the creation of a nickase from the endonucleases in use was a desired outcome, it became necessary to talk to an expert in the field of enzyme engineering. Our first contact was Kai Schülke, a former iGEMer and PhD student under the guidance of Prof. Dr. Hammer[Link Hammer], who is the leader of the working group organic chemistry and bioanalytics at Bielefeld University.</p>],
+ aimofcontact: [<p>When we realized that the creation of a nickase from the endonucleases in use was a desired outcome, it became necessary to talk to an expert in the field of enzyme engineering. Our first contact was Kai Schülke, a former iGEMer and PhD student under the guidance of <HPLinktoOtherHPTab tab="hammer" text="Prof. Dr. Hammer"/>, who is the leader of the working group organic chemistry and bioanalytics at Bielefeld University.</p>],
insights: [<p>In the process of our interaction with Kai, we learned about the various methods employed in enzyme engineering. He demonstrated the complexity of this field of research and emphasized the importance of choosing the right approach. As a former iGEMer, Kai, inspired by his past experiences, is highly motivated and determined to develop an outstanding project. He pointed out that we cannot rely on classical methods such as directed evolution, but instead should use a rational approach to select mutation candidates. His insights and enthusiasm have encouraged us to think critically and pursue innovative solutions in our work. </p>],
implementation: [<p>We incorporated Kai's insights into our project by shifting our approach to enzyme engineering. By focusing on a more targeted approach, we were able to refine our enzyme optimization process, ensuring that the modifications we made were based on informed, calculated decisions. This not only streamlined our research but also improved the chances of success by reducing the trial-and-error inherent in traditional methods. </p>],
summary: "The team reached out to Kai Schülke, a former iGEM participant and enzyme engineering expert, for guidance on developing a nickase from the endonucleases in use. Kai emphasized the need for a rational, targeted approach rather than traditional methods like directed evolution. His insights helped the team refine their enzyme optimization process, making it more strategic and efficient. This shift reduced trial-and-error efforts and improved the chances of success, driving innovation in their project.",
@@ -1162,7 +1174,7 @@ export const timelinedata: Array<TimelineDatenpunkt> = [
interviewtabid: "nberelsmann",
cardtext: "",
quote: "X",
- aimofcontact: [<p>During our interview with Makoto Saito[Linkinterview] 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[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>],
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.",
@@ -1387,7 +1399,6 @@ export const timelinedata: Array<TimelineDatenpunkt> = [
This knowledge is crucial as we think about the future of our project, particularly if we aim to move our gene therapy approach for cystic fibrosis closer to clinical trials and real-world applications. My participation in the GXP training has equipped me with the necessary tools to potentially guide our team through the complex regulatory landscape, ensuring our work remains aligned with industry standards and ready for the next steps in development.
One of the key speakers during the GXP course was Dr. Marcus Berger [LINK INtreview Beerger], whose expertise was invaluable to me and the entire team. After the course, I had the opportunity to ask Dr. Berger some questions, further deepening my understanding of the practical applications of GXP in research. The connection with Dr. Berger has been highly beneficial, as his insights helped shape key aspects of our project’s development and compliance with industry standards. His guidance will continue to be a valuable resource for our team moving forward.
Through this training, I feel better positioned to contribute to the team’s efforts, ensuring our project adheres to global safety and ethical guidelines. This experience has strengthened our approach and set a solid foundation for future progress, ensuring that our research, public engagement, and potential clinical applications continue to meet the highest regulatory standards. </p>],
- type: "meta",
summary: "Kaya, a member of the iGEM Bielefeld 2024 team, completed an intensive one-week GXP (Good Practice) training, which covered Good Laboratory Practice (GLP), Good Clinical Practice (GCP), and Good Manufacturing Practice (GMP). The training provided valuable insights into maintaining high standards of quality, safety, and ethics throughout the research process. Kaya learned crucial skills, such as documenting research processes for reproducibility, creating standard operating procedures (SOPs), and conducting risk assessments using techniques like Failure Mode and Effects Analysis (FMEA). This knowledge is essential for advancing their cystic fibrosis gene therapy project toward clinical trials and ensuring compliance with regulatory standards. Dr. Marcus Berger, a key speaker in the course, provided additional guidance, offering valuable insights that will continue to benefit the team.",
months: "august",
pictureurl_implementation: "https://static.igem.wiki/teams/5247/photos/for-wiki-texts/gxp/gxp-course-kaya.webp",
@@ -1676,7 +1687,7 @@ export const timelinedata: Array<TimelineDatenpunkt> = [
interviewtabid: "gxpexpert",
cardtext: "",
quote: "Minimum requirement: Acute toxicity study on animals - important for calculating the starting dose for humans. In addition, pharmacological studies, genotoxic studies and immunotoxic studies. In your case also chronic toxicity studies.",
- aimofcontact: [<p>The aim of our contact with GxP expert Dr. Marcus Berger [Link https://gxpexpert.de/] was to gather insights and ask questions about how to proceed with the Precyse project, clarifying the next steps required for its continued development, particularly concerning regulatory strategy, quality management, and clinical development. GxP, which stands for ‘Good Practice’ guidelines, encompasses various regulations and standards intended to ensure quality and compliance in the development and manufacturing of pharmaceutical and biopharmaceutical products. </p>],
+ aimofcontact: [<p>The aim of our contact with GxP expert <a href="https://gxpexpert.de/">Dr. Marcus Berger</a> was to gather insights and ask questions about how to proceed with the Precyse project, clarifying the next steps required for its continued development, particularly concerning regulatory strategy, quality management, and clinical development. GxP, which stands for ‘Good Practice’ guidelines, encompasses various regulations and standards intended to ensure quality and compliance in the development and manufacturing of pharmaceutical and biopharmaceutical products. </p>],
insights: [<p>From the discussion with Dr. Berger expert, we gained several key insights into how to proceed with the Precyse project. First, it became clear that obtaining a Scientific Advice from the Paul-Ehrlich-Institut (PEI) [Link https://www.pei.de/DE/home/home-node.html] is essential to get qualified feedback on our development project and align our regulatory strategy. The expert emphasized the need to collect and document preclinical data, including acute and chronic toxicity studies, genotoxicity, immunotoxicity, and carcinogenicity studies, as well as conducting safety pharmacology and biodistribution studies to ensure a thorough understanding of the substance's mechanism of action.
The expert also provided guidance on how to establish a GxP-compliant quality management system (QMS), stressing the importance of setting up a robust SOP system for manufacturing, preclinical, and clinical development. This system must adhere to ICH Q10 guidelines, ensuring that the quality control processes are in line with regulatory expectations. Furthermore, we learned about the critical initial steps for validating and verifying the manufacturing process, including defining the physical and chemical properties of the active substance and excipients, developing the pharmaceutical formulation, and identifying critical quality attributes (CQAs) and critical material attributes (CMAs).
The ICH-GCP guidelines, which apply to all clinical trials, are essential for ensuring the integrity and safety of clinical development. These guidelines include E2A-E2F, which cover topics like clinical safety data management and adverse event reporting, E3 for clinical study reports, E5 for handling ethnic factors, and E9 for statistical principles. Additionally, E14 is crucial for managing cardiovascular risks, an especially important consideration for gene therapies, where monitoring for heart-related side effects is critical. Guidelines like E15 and E16 address biomarkers and pharmacogenomics, helping tailor clinical development to the specifics of the treatment being tested. Implementing these GCP requirements ensures compliance, patient safety, and data integrity throughout the trial process.