From 72b418882fb50b5fdaa73e43108b809ee8999b67 Mon Sep 17 00:00:00 2001 From: Liliana Sanfilippo <liliana.sanfilippo@uni-bielefeld.de> Date: Wed, 25 Sep 2024 22:01:19 +0200 Subject: [PATCH] hp --- code/bibtex.bib | 89 ++++++++++++++++++++++++++---- code/output.txt | 79 ++++++++++++++++++++++++--- src/components/Link.tsx | 8 +++ src/data/hptimelinedata.tsx | 105 +++++++++++++++++++++++++++++++++++- 4 files changed, 262 insertions(+), 19 deletions(-) create mode 100644 src/components/Link.tsx diff --git a/code/bibtex.bib b/code/bibtex.bib index 4691c076..a3a5f33b 100644 --- a/code/bibtex.bib +++ b/code/bibtex.bib @@ -1,10 +1,79 @@ -@article{article, -author = {Bulcaen, Mattijs and Kortleven, Phéline and Liu, Ronald and Maule, Giulia and Dreano, Elise and Aubert, Mairead and Ensinck, Marjolein and Thierie, Sam and Smits, Maxime and Ciciani, Matteo and Hatton, Aurélie and Chevalier, Benoit and Ramalho, Anabela and Casadevall i Solvas, Xavier and Debyser, Zeger and Vermeulen, François and Gijsbers, Rik and Sermet-Gaudelus, Isabelle and Cereseto, Anna and Carlon, Marianne}, -year = {2024}, -month = {05}, -pages = {101544}, -title = {Prime editing functionally corrects cystic fibrosis-causing CFTR mutations in human organoids and airway epithelial cells}, -volume = {5}, -journal = {Cell Reports Medicine}, -doi = {10.1016/j.xcrm.2024.101544} -} \ No newline at end of file +@article{[1], + +title = {Prime editing functionally corrects cystic fibrosis-causing CFTR mutations in human organoids and airway epithelial cells}, + +journal = {Cell Reports Medicine}, + +volume = {5}, + +number = {5}, + +pages = {101544}, + +year = {2024}, + +issn = {2666-3791}, + +doi = {https://doi.org/10.1016/j.xcrm.2024.101544}, + +url = {https://www.sciencedirect.com/science/article/pii/S2666379124002349}, + +author = {Mattijs Bulcaen and Phéline Kortleven and Ronald B. Liu and Giulia Maule and Elise Dreano and Mairead Kelly and Marjolein M. Ensinck and Sam Thierie and Maxime Smits and Matteo Ciciani and Aurelie Hatton and Benoit Chevalier and Anabela S. Ramalho and Xavier {Casadevall i Solvas} and Zeger Debyser and François Vermeulen and Rik Gijsbers and Isabelle Sermet-Gaudelus and Anna Cereseto and Marianne S. Carlon},} + +@article{2, + +author = {Teeratakulpisarn, Jamaree and Kosuwon, Pensri and Srinakarin, Jiraporn and Panthongviriyakul, Charnchai and Sutra, Sumitr}, + +year = {2006}, + +month = {11}, + +pages = {1756-61}, + +title = {Cystic fibrosis in three northeast Thai infants is CF really a rare disease in the Thai population?}, + +volume = {89}, + +journal = {Journal of the Medical Association of Thailand = Chotmaihet thangphaet} + +} + +@article{3, + +author = {Ahmed, Shakil and Cheok, Gary and Goh, AnneE and Han, Aye and Hong, SJ and Indawati, Wahyuni and Kabir, AR and Kabra, Sushil and Kamalaporn, Harutai and Kim, HyungYoung and Kunling, Shen and Lochindarat, Sorasak and Moslehi, MohammadAshkan and Nathan, AnnaMarie and Ng, Daniel and Phung, NguyenNg and Singh, V and Takase, Masato and Triasih, Rina and Dai, Zen-Kong}, + +year = {2020}, + +month = {01}, + +pages = {8}, + +title = {Cystic fibrosis in asia}, + +volume = {4}, + +journal = {Pediatric Respirology and Critical Care Medicine}, + +doi = {10.4103/prcm.prcm_5_20} + +} + +@article{4, + +author = {Bobbo, Khadijatabubakar and Ahmad, Umar and Chau, De-Ming and Nordin, Norshariza and Abdullah, Syahril}, + +year = {2023}, + +month = {05}, + +pages = {103685}, + +title = {A comprehensive review of Cystic Fibrosis in Africa and Asia}, + +volume = {30}, + +journal = {Saudi Journal of Biological Sciences}, + +doi = {10.1016/j.sjbs.2023.103685} + +} \ No newline at end of file diff --git a/code/output.txt b/code/output.txt index 15db0d49..28d6c5e5 100644 --- a/code/output.txt +++ b/code/output.txt @@ -3,30 +3,95 @@ <span property="schema:author" typeof="schema:Person"> <span property="schema:Name"> Bulcaen, M.</span>; <span property="schema:Name"> Kortleven, P.</span>; - <span property="schema:Name"> Liu, R.</span>; + <span property="schema:Name"> Liu, R.B.</span>; <span property="schema:Name"> Maule, G.</span>; <span property="schema:Name"> Dreano, E.</span>; - <span property="schema:Name"> Aubert, M.</span>; - <span property="schema:Name"> Ensinck, M.</span>; + <span property="schema:Name"> Kelly, M.</span>; + <span property="schema:Name"> Ensinck, M.M.</span>; <span property="schema:Name"> Thierie, S.</span>; <span property="schema:Name"> Smits, M.</span>; <span property="schema:Name"> Ciciani, M.</span>; <span property="schema:Name"> Hatton, A.</span>; <span property="schema:Name"> Chevalier, B.</span>; - <span property="schema:Name"> Ramalho, A.</span>; - <span property="schema:Name"> Casadevall i Solvas, X.</span>; + <span property="schema:Name"> Ramalho, A.S.</span>; + <span property="schema:Name"> Solvas, X.</span>; <span property="schema:Name"> Debyser, Z.</span>; <span property="schema:Name"> Vermeulen, F.</span>; <span property="schema:Name"> Gijsbers, R.</span>; <span property="schema:Name"> Sermet-Gaudelus, I.</span>; <span property="schema:Name"> Cereseto, A.</span>; - <span property="schema:Name"> Carlon, M.</span> + <span property="schema:Name"> Carlon, M.S.</span> </span> <span property="schema:name"> Prime editing functionally corrects cystic fibrosis-causing CFTR mutations in human organoids and airway epithelial cells. </span> <i property="schema:publisher" typeof="schema:Organization"> Cell Reports Medicine</i> <b property="issueNumber" typeof="PublicationIssue"> 5</b>, <span property="schema:pageBegin">101544</span> (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2024">2024</time>). - <a className="doi" href="https://doi.org/10.1016/j.xcrm.2024.101544"> doi: 10.1016/j.xcrm.2024.101544</a> + <a className="doi" href="https://doi.org/https://doi.org/10.1016/j.xcrm.2024.101544"> doi: https://doi.org/10.1016/j.xcrm.2024.101544</a> +</li> + +{/*<!-- Citation num 2--> */} +<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-2"> + <span property="schema:author" typeof="schema:Person"> + <span property="schema:Name"> Teeratakulpisarn, J.</span>; + <span property="schema:Name"> Kosuwon, P.</span>; + <span property="schema:Name"> Srinakarin, J.</span>; + <span property="schema:Name"> Panthongviriyakul, C.</span>; + <span property="schema:Name"> Sutra, S.</span> + </span> + <span property="schema:name"> Cystic fibrosis in three northeast Thai infants is CF really a rare disease in the Thai population?. </span> + <i property="schema:publisher" typeof="schema:Organization"> Journal of the Medical Association of Thailand = Chotmaihet thangphaet</i> + <b property="issueNumber" typeof="PublicationIssue"> 89</b>, + <span property="schema:pageBegin"> 1756</span>-<span property="schema:pageEnd">61</span> + (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2006">2006</time>). +</li> + +{/*<!-- Citation num 3--> */} +<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-3"> + <span property="schema:author" typeof="schema:Person"> + <span property="schema:Name"> Ahmed, S.</span>; + <span property="schema:Name"> Cheok, G.</span>; + <span property="schema:Name"> Goh, A.</span>; + <span property="schema:Name"> Han, A.</span>; + <span property="schema:Name"> Hong, S.</span>; + <span property="schema:Name"> Indawati, W.</span>; + <span property="schema:Name"> Kabir, A.</span>; + <span property="schema:Name"> Kabra, S.</span>; + <span property="schema:Name"> Kamalaporn, H.</span>; + <span property="schema:Name"> Kim, H.</span>; + <span property="schema:Name"> Kunling, S.</span>; + <span property="schema:Name"> Lochindarat, S.</span>; + <span property="schema:Name"> Moslehi, M.</span>; + <span property="schema:Name"> Nathan, A.</span>; + <span property="schema:Name"> Ng, D.</span>; + <span property="schema:Name"> Phung, N.</span>; + <span property="schema:Name"> Singh, V.</span>; + <span property="schema:Name"> Takase, M.</span>; + <span property="schema:Name"> Triasih, R.</span>; + <span property="schema:Name"> Dai, Z.</span> + </span> + <span property="schema:name"> Cystic fibrosis in asia. </span> + <i property="schema:publisher" typeof="schema:Organization"> Pediatric Respirology and Critical Care Medicine</i> + <b property="issueNumber" typeof="PublicationIssue"> 4</b>, + <span property="schema:pageBegin">8</span> + (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2020">2020</time>). + <a className="doi" href="https://doi.org/10.4103/prcm.prcm_5_20"> doi: 10.4103/prcm.prcm_5_20</a> +</li> + +{/*<!-- Citation num 4--> */} +<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-4"> + <span property="schema:author" typeof="schema:Person"> + <span property="schema:Name"> Bobbo, K.</span>; + <span property="schema:Name"> Ahmad, U.</span>; + <span property="schema:Name"> Chau, D.</span>; + <span property="schema:Name"> Nordin, N.</span>; + <span property="schema:Name"> Abdullah, S.</span> + </span> + <span property="schema:name"> A comprehensive review of Cystic Fibrosis in Africa and Asia. </span> + <i property="schema:publisher" typeof="schema:Organization"> Saudi Journal of Biological Sciences</i> + <b property="issueNumber" typeof="PublicationIssue"> 30</b>, + <span property="schema:pageBegin">103685</span> + (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2023">2023</time>). + <a className="doi" href="https://doi.org/10.1016/j.sjbs.2023.103685"> doi: 10.1016/j.sjbs.2023.103685</a> </li> diff --git a/src/components/Link.tsx b/src/components/Link.tsx new file mode 100644 index 00000000..a45c8e48 --- /dev/null +++ b/src/components/Link.tsx @@ -0,0 +1,8 @@ +import { useNavigation } from "../utils" + +export function TabScrollLink({tab, scrollId, num}:{tab: string, scrollId: string, num: string}){ + const {goToPageWithTabAndScroll} = useNavigation(); + return( + <sup><a onClick={() => goToPageWithTabAndScroll({path: "", tabId: tab, scrollToId: scrollId})}>{num}</a></sup> + ) +} \ No newline at end of file diff --git a/src/data/hptimelinedata.tsx b/src/data/hptimelinedata.tsx index 42035ba2..d04e5999 100644 --- a/src/data/hptimelinedata.tsx +++ b/src/data/hptimelinedata.tsx @@ -1,4 +1,5 @@ import { QaBox } from "../components/Boxes"; +import { TabScrollLink } from "../components/Link"; import { ScrollLinkWithChild } from "../components/ScrollLink"; export interface TimelineDatenpunkt { @@ -34,6 +35,8 @@ type StakeholderTag = 'Industry' | 'Academia' | 'Patient' | 'Medical Professiona type TypeTag = 'meta' | 'kaya' ; type Language = 'en' | 'de'; + + const pics: { [key: string]: string } = { placeholder: "https://static.igem.wiki/teams/5247/placeholders/placehilderperson.jpeg", max: "https://static.igem.wiki/teams/5247/photos/hp/hp-max-portrait.jpg", @@ -426,7 +429,7 @@ export const timelinedata: Array<TimelineDatenpunkt> = [ cardtext: "", language: "en", quote: "[…] Prime Editing system is more complex than the canonical CRISPR systems, with more variables that can influence success or failure.", - aimofcontact: "Shortly after we decided to use prime editing as the gene editing method for our cystic fibrosis therapy, Mattijs Bulcaen from the Laboratory of Molecular Virology and Gene Therapy at KU Leuven and his colleagues published a paper directly related to our research[1]. In contrast to our approach, Bulcaen et al. 2024 targeted other, less common but drug-refractory CFTR-specific mutations (L227R- and N1303K).  ", + aimofcontact: [<p>Shortly after we decided to use prime editing as the gene editing method for our cystic fibrosis therapy, Mattijs Bulcaen from the Laboratory of Molecular Virology and Gene Therapy at KU Leuven and his colleagues published a paper directly related to our research <TabScrollLink tab="mattijsinv" scrollId="desc-1" num="1" />. In contrast to our approach, Bulcaen et al. 2024 targeted other, less common but drug-refractory CFTR-specific mutations (L227R- and N1303K).  </p>], insights: "The interview with Mattijs was valuable for us in a lot of ways. At that point in the project we were starting to design the components of our prime editor, but we were lacking a broader overview over the state of the field. Mattijs gave us this insight, mentioning techniques like PE3b systems, dsgRNAs and a talk given by David Liu,[Link] the principal investigator behind prime editing that helped us to consider further novel advancements in in Prime Editing and include them into our project. He discussed with us the difficulties that might await us when targeting the CFTR F508del deletion and mentioned that insertions of all the edits possible with prime editing are the hardest to make, the recognition of edits in the region might attract mismatch repair systems and the chromatin organization might negatively impact prime editing efficiency. Also, we learned a lot about how to design our pegRNAs, with important inputs being the 3’ stem loop motif trevopreQ1 used by Mattijs in his publication and the suggestion to use prediction tools to evaluate sgRNA spacer cutting efficiency. We reviewed our approach of testing pegRNAs using the PEAR reporter system and Mattjis recommended to use HEK cell lines for screening because of their easy handling and naturally impaired mismatch repair system. ", implementation: "The inputs given by Mattijs directly impacted our design choices for multiple parts of the project. For the pegRNA design, we decided to use the same 3’ motif as Mattijs had used and also, like he suggested, checked our spacer candidates for predicted cleavage efficiency. Also we used HEK cells for screening our pegRNAs. We looked further into PE systems that influence cellular mismatch repair (such as PE4) and tried to include these into our design. ", interview:<> @@ -597,7 +600,105 @@ export const timelinedata: Array<TimelineDatenpunkt> = [ aimofcontact: "We contacted the organization CF vests worldwide [Link] with the aim to hear more diverse perspectives beyond Germany. After the founder Rod connected us with Joshua, Joshua was so kind to conduct an interview with us not only about the perspectives and stories he heard but also about his personal experiences with his daughter and living in a country where CF care is very hard to get. Joshua (from the USA) and his family live in Thailand where he and his wife run a children’s home. Their daughter is the only child with CF.", insights: "Joshua showed us just how dire the situation is for CF patients is in some regions. It was shocking to hear there is only one doctor knowledgeable about CF in Thailand and that many doctors dismiss the possibility of CF due to racial bias and misinformation. Additionally, we confirmed how much the accessibility of care depends on the healthcare system, as we already touched on during the interview with Nicole Friedlein [link]. On the parenting level, Joshua brought in many perspectives contrary to what we previously heard. In the interview with Max [Link], we learned he vehemently avoids ponding water while Joshua’s daughter is allowed to roam around with no such restrictions. Neither have chronic infections. ", implementation: "The interview with Josh made us realize we too needed to look at the reason why we chose F508del. Did we, too, fall for bias? Despite a change of target not being feasible anymore, we looked into it and traced back our steps that led to our decision. We did not find as much information about other mutations when first researching cystic fibrosis, especially in the context of prime editing. Mattijs Bulceans's paper on targeting the mutations L227R and N1303K [1] was one of few papers. After explicitly searching for cystic fibrosis records for specific countries and regions, we uncovered a moderate number of papers examining CF in Asia and other regions we previously did not know much about. The very first article supported Joshua's hypotheses and painted a sad picture: Among other things, it describes the case of a four-month-old boy who was diagnosed with cystic fibrosis. Nothing unusual in itself, but the circumstances are depressing. Two of the three siblings born before him died within months of birth and had previously presented with symptoms of cystic fibrosis. He was the first to be diagnosed. A sweat test aimed at cystic fibrosis was not available at the hospital, so one was improvised. Later on, a genetic test revealed the presence of 508del. [2] We found ourselves and our lack of knowledge in good company as we found papers as new as from 2020 (14 years after the previously mentioned paper) containing statements such as “recent reports suggest that CF does occur in Asia†[3]. Fortunately, there is a rising number of cystic fibrosis experts for Asia and other previously overlooked regions such as Africa. [4] We chose to not only look at the scientific data but also into anecdotal evidence. To find the latter, we searched official and private websites and chatrooms for information and experiences of patients. In the end, we found narratives from most ethnic backgrounds about being dismissed and often misdiagnosed. Of course, this is not an occurrence unique to cystic fibrosis. Our conclusion is that yes, we did fall for bias. But regardless of ethnicity, 508del occurs and is overall the most prevalent mutation as was confirmed in our interview with CF expert Sriram .... This experience was uncomfortable as we felt the pressure to be thorough and deliver a perfect project. What would have been more devastating than realizing we made a wrong choice at the very core? We made the conscious decision to invest our resources into figuring out if we indeed made a mistake and we want to encourage other teams to do the same. iGem stands for innovation – but also for growth. Especially in the context of Integrated Human Practices, it is important to examine both the positive and the negative to create a project with a future. ", - pictureurl_interview: "", + pictureurl_interview: "", + references: [<ol>{/*<!-- Citation num 1--> */} + <li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-1"> + <span property="schema:author" typeof="schema:Person"> + <span property="schema:Name"> Bulcaen, M.</span>; + <span property="schema:Name"> Kortleven, P.</span>; + <span property="schema:Name"> Liu, R.B.</span>; + <span property="schema:Name"> Maule, G.</span>; + <span property="schema:Name"> Dreano, E.</span>; + <span property="schema:Name"> Kelly, M.</span>; + <span property="schema:Name"> Ensinck, M.M.</span>; + <span property="schema:Name"> Thierie, S.</span>; + <span property="schema:Name"> Smits, M.</span>; + <span property="schema:Name"> Ciciani, M.</span>; + <span property="schema:Name"> Hatton, A.</span>; + <span property="schema:Name"> Chevalier, B.</span>; + <span property="schema:Name"> Ramalho, A.S.</span>; + <span property="schema:Name"> Solvas, X.</span>; + <span property="schema:Name"> Debyser, Z.</span>; + <span property="schema:Name"> Vermeulen, F.</span>; + <span property="schema:Name"> Gijsbers, R.</span>; + <span property="schema:Name"> Sermet-Gaudelus, I.</span>; + <span property="schema:Name"> Cereseto, A.</span>; + <span property="schema:Name"> Carlon, M.S.</span> + </span> + <span property="schema:name"> Prime editing functionally corrects cystic fibrosis-causing CFTR mutations in human organoids and airway epithelial cells. </span> + <i property="schema:publisher" typeof="schema:Organization"> Cell Reports Medicine</i> + <b property="issueNumber" typeof="PublicationIssue"> 5</b>, + <span property="schema:pageBegin">101544</span> + (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2024">2024</time>). + <a className="doi" href="https://doi.org/https://doi.org/10.1016/j.xcrm.2024.101544"> doi: https://doi.org/10.1016/j.xcrm.2024.101544</a> + </li> + + {/*<!-- Citation num 2--> */} + <li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-2"> + <span property="schema:author" typeof="schema:Person"> + <span property="schema:Name"> Teeratakulpisarn, J.</span>; + <span property="schema:Name"> Kosuwon, P.</span>; + <span property="schema:Name"> Srinakarin, J.</span>; + <span property="schema:Name"> Panthongviriyakul, C.</span>; + <span property="schema:Name"> Sutra, S.</span> + </span> + <span property="schema:name"> Cystic fibrosis in three northeast Thai infants is CF really a rare disease in the Thai population?. </span> + <i property="schema:publisher" typeof="schema:Organization"> Journal of the Medical Association of Thailand = Chotmaihet thangphaet</i> + <b property="issueNumber" typeof="PublicationIssue"> 89</b>, + <span property="schema:pageBegin"> 1756</span>-<span property="schema:pageEnd">61</span> + (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2006">2006</time>). + </li> + + {/*<!-- Citation num 3--> */} + <li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-3"> + <span property="schema:author" typeof="schema:Person"> + <span property="schema:Name"> Ahmed, S.</span>; + <span property="schema:Name"> Cheok, G.</span>; + <span property="schema:Name"> Goh, A.</span>; + <span property="schema:Name"> Han, A.</span>; + <span property="schema:Name"> Hong, S.</span>; + <span property="schema:Name"> Indawati, W.</span>; + <span property="schema:Name"> Kabir, A.</span>; + <span property="schema:Name"> Kabra, S.</span>; + <span property="schema:Name"> Kamalaporn, H.</span>; + <span property="schema:Name"> Kim, H.</span>; + <span property="schema:Name"> Kunling, S.</span>; + <span property="schema:Name"> Lochindarat, S.</span>; + <span property="schema:Name"> Moslehi, M.</span>; + <span property="schema:Name"> Nathan, A.</span>; + <span property="schema:Name"> Ng, D.</span>; + <span property="schema:Name"> Phung, N.</span>; + <span property="schema:Name"> Singh, V.</span>; + <span property="schema:Name"> Takase, M.</span>; + <span property="schema:Name"> Triasih, R.</span>; + <span property="schema:Name"> Dai, Z.</span> + </span> + <span property="schema:name"> Cystic fibrosis in asia. </span> + <i property="schema:publisher" typeof="schema:Organization"> Pediatric Respirology and Critical Care Medicine</i> + <b property="issueNumber" typeof="PublicationIssue"> 4</b>, + <span property="schema:pageBegin">8</span> + (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2020">2020</time>). + <a className="doi" href="https://doi.org/10.4103/prcm.prcm_5_20"> doi: 10.4103/prcm.prcm_5_20</a> + </li> + + {/*<!-- Citation num 4--> */} + <li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-4"> + <span property="schema:author" typeof="schema:Person"> + <span property="schema:Name"> Bobbo, K.</span>; + <span property="schema:Name"> Ahmad, U.</span>; + <span property="schema:Name"> Chau, D.</span>; + <span property="schema:Name"> Nordin, N.</span>; + <span property="schema:Name"> Abdullah, S.</span> + </span> + <span property="schema:name"> A comprehensive review of Cystic Fibrosis in Africa and Asia. </span> + <i property="schema:publisher" typeof="schema:Organization"> Saudi Journal of Biological Sciences</i> + <b property="issueNumber" typeof="PublicationIssue"> 30</b>, + <span property="schema:pageBegin">103685</span> + (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2023">2023</time>). + <a className="doi" href="https://doi.org/10.1016/j.sjbs.2023.103685"> doi: 10.1016/j.sjbs.2023.103685</a> + </li> + + </ol>] }, { title: "Prof. Dr.", -- GitLab