diff --git a/code/bibtex.bib b/code/bibtex.bib
deleted file mode 100644
index 11dea57ede3c382f8aa0d6bfd8a689b32be99da4..0000000000000000000000000000000000000000
--- a/code/bibtex.bib
+++ /dev/null
@@ -1,10 +0,0 @@
-@article{article,
-author = {Aswegen, Ellie and Pendergast, Donna},
-year = {2023},
-month = {08},
-pages = {1-15},
-title = {The impact of interest: an emergent model of interest development in the early years},
-volume = {193},
-journal = {Early Child Development and Care},
-doi = {10.1080/03004430.2023.2245575}
-}
\ No newline at end of file
diff --git a/code/methods.bib b/code/methods.bib
deleted file mode 100644
index 911cc0dbe7727297379c8180b72a845b792e72e5..0000000000000000000000000000000000000000
--- a/code/methods.bib
+++ /dev/null
@@ -1,246 +0,0 @@
-[1]
-@article{article,
- title = {Die Entwicklung der Patch-Clamp-Technik},
- author = {Roth, F. C., Numberger, M., and Draguhn, A.},
- year = 2023,
- month = {{}},
- journal = {Springer eBooks},
- volume = {{}},
- pages = {1--14},
- doi = {10.1007/978-3-662-66053-9}
-}
-[2]
-@book{dallas_patch_2021,
- title = {Patch clamp electrophysiology: methods and protocols},
- shorttitle = {Patch clamp electrophysiology},
- year = 2021,
- publisher = {Humana Press},
- address = {New York},
- series = {Methods in molecular biology},
- number = 2188,
- isbn = {978-1-07-160818-0 978-1-07-160820-3},
- language = {en},
- editor = {Dallas, Mark and Bell, Damian}
-}
-[3]
-@article{PRIEL20073893,
- title = {
- Ionic Requirements for Membrane-Glass Adhesion and Giga Seal Formation in
- Patch-Clamp Recording
- },
- author = {
- Avi Priel and Ziv Gil and Vincent T. Moy and Karl L. Magleby and Shai D.
- Silberberg
- },
- year = 2007,
- journal = {Biophysical Journal},
- volume = 92,
- number = 11,
- pages = {3893--3900},
- doi = {10.1529/biophysj.106.099119},
- issn = {0006-3495},
- url = {https://www.sciencedirect.com/science/article/pii/S000634950771189X},
- abstract = {
- Patch-clamp recording has revolutionized the study of ion channels,
- transporters, and the electrical activity of small cells. Vital to this
- method is formation of a tight seal between glass recording pipette and cell
- membrane. To better understand seal formation and improve practical
- application of this technique, we examine the effects of divalent ions,
- protons, ionic strength, and membrane proteins on adhesion of membrane to
- glass and on seal resistance using both patch-clamp recording and atomic
- force microscopy. We find that H+, Ca2+, and Mg2+ increase adhesion force
- between glass and membrane (lipid and cellular), decrease the time required
- to form a tight seal, and increase seal resistance. In the absence of H+
- (10−10M) and divalent cations (<10−8M), adhesion forces are greatly reduced
- and tight seals are not formed. H+ (10−7M) promotes seal formation in the
- absence of divalent cations. A positive correlation between adhesion force
- and seal formation indicates that high resistance seals are associated with
- increased adhesion between membrane and glass. A similar ionic dependence of
- the adhesion of lipid membranes and cell membranes to glass indicates that
- lipid membranes without proteins are sufficient for the action of ions on
- adhesion.
- }
-}
-[4]
-@article{10.3389/fphar.2017.00195,
- title = {
- Development of Automated Patch Clamp Technique to Investigate CFTR Chloride
- Channel Function
- },
- author = {
- Billet, Arnaud and Froux, Lionel and Hanrahan, John W. and Becq, Frederic
- },
- year = 2017,
- journal = {Frontiers in Pharmacology},
- volume = 8,
- doi = {10.3389/fphar.2017.00195},
- issn = {1663-9812},
- url = {
- https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2017.00195
- }
-}
-New5.
-@article{DuBridge_Tang_Hsia_Leong_Miller_Calos_1987,
- title = {
- Analysis of mutation in human cells by using an Epstein-Barr virus shuttle
- system.
- },
- author = {
- DuBridge, R B and Tang, P and Hsia, H C and Leong, P M and Miller, J H and
- Calos, M P
- },
- year = 1987,
- month = jan,
- journal = {Molecular and Cellular Biology},
- volume = 7,
- number = 1,
- pages = {379–387},
- issn = {0270-7306},
- abstractnote = {
- We developed highly sensitive shuttle vector systems for detection of
- mutations formed in human cells using autonomously replicating derivatives of
- Epstein-Barr virus (EBV). EBV vectors carrying the bacterial lacI gene as the
- target for mutation were established in human cells and later returned to
- Escherichia coli for rapid detection and analysis of lacI mutations. The
- majority of the clonal cell lines created by establishment of the lacI-EBV
- vector show spontaneous LacI- frequencies of less than 10(-5) and are
- suitable for studies of induced mutation. The ability to isolate clonal lines
- represents a major advantage of the EBV vectors over transiently replicating
- shuttle vectors (such as those derived from simian virus 40) for the study of
- mutation. The DNA sequence changes were determined for 61 lacI mutations
- induced by exposure of one of the cell lines to N-nitroso-N-methylurea. A
- total of 33 of 34 lacI nonsense mutations and 26 of 27 missense mutations
- involve G X C to A X T transitions. These data provide support for the
- mutational theory of cancer.
- }
-}
-[New6].
-@article{Qin_Zhang_Clift_Hulur_Xiang_Ren_Lahn_2010,
- title = {
- Systematic Comparison of Constitutive Promoters and the Doxycycline-Inducible
- Promoter
- },
- author = {
- Qin, Jane Yuxia and Zhang, Li and Clift, Kayla L. and Hulur, Imge and Xiang,
- Andy Peng and Ren, Bing-Zhong and Lahn, Bruce T.
- },
- year = 2010,
- month = may,
- journal = {PLOS ONE},
- publisher = {Public Library of Science},
- volume = 5,
- number = 5,
- pages = {e10611},
- doi = {10.1371/journal.pone.0010611},
- issn = {1932-6203},
- abstractnote = {
- Constitutive promoters are used routinely to drive ectopic gene expression.
- Here, we carried out a systematic comparison of eight commonly used
- constitutive promoters (SV40, CMV, UBC, EF1A, PGK and CAGG for mammalian
- systems, and COPIA and ACT5C for Drosophila systems). We also included in the
- comparison the TRE promoter, which can be activated by the rtTA
- transcriptional activator in a doxycycline-inducible manner. To make our
- findings representative, we conducted the comparison in a variety of cell
- types derived from several species. We found that these promoters vary
- considerably from one another in their strength. Most promoters have fairly
- consistent strengths across different cell types, but the CMV promoter can
- vary considerably from cell type to cell type. At maximal induction, the TRE
- promoter is comparable to a strong constitutive promoter. These results
- should facilitate more rational choices of promoters in ectopic gene
- expression studies.
- },
- language = {en}
-}
-new7.
-@article{BULCAEN2024101544,
-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},
-keywords = {cystic fibrosis, prime editing, patient-derived organoids, human nasal epithelial cells, gene editing, machine learning, DETEOR, CRISPR},
-abstract = {Summary
-Prime editing is a recent, CRISPR-derived genome editing technology capable of introducing precise nucleotide substitutions, insertions, and deletions. Here, we present prime editing approaches to correct L227R- and N1303K-CFTR, two mutations that cause cystic fibrosis and are not eligible for current market-approved modulator therapies. We show that, upon DNA correction of the CFTR gene, the complex glycosylation, localization, and, most importantly, function of the CFTR protein are restored in HEK293T and 16HBE cell lines. These findings were subsequently validated in patient-derived rectal organoids and human nasal epithelial cells. Through analysis of predicted and experimentally identified candidate off-target sites in primary stem cells, we confirm previous reports on the high prime editor (PE) specificity and its potential for a curative CF gene editing therapy. To facilitate future screening of genetic strategies in a translational CF model, a machine learning algorithm was developed for dynamic quantification of CFTR function in organoids (DETECTOR: “detection of targeted editing of CFTR in organoidsâ€).}
-}
-new8.
-@article{Ensinck_Deeersmaecker_Heylen_Ramalho_Gijsbers_Far,
- title = {
- Phenotyping of Rare CFTR Mutations Reveals Distinct Trafficking and
- Functional Defects
- },
- author = {
- Ensinck, Marjolein and De Keersmaecker, Liesbeth and Heylen, Lise and
- Ramalho, Anabela S. and Gijsbers, Rik and Farré, Ricard and De Boeck, Kris
- and Christ, Frauke and Debyser, Zeger and Carlon, Marianne S.
- },
- year = 2020,
- month = mar,
- journal = {Cells},
- volume = 9,
- number = 3,
- pages = 754,
- doi = {10.3390/cells9030754},
- issn = {2073-4409},
- abstractnote = {
- Background. The most common CFTR mutation, F508del, presents with multiple
- cellular defects. However, the possible multiple defects caused by many rarer
- CFTR mutations are not well studied. We investigated four rare CFTR mutations
- E60K, G85E, E92K and A455E against well-characterized mutations, F508del and
- G551D, and their responses to corrector VX-809 and/or potentiator VX-770.
- Methods. Using complementary assays in HEK293T stable cell lines, we
- determined maturation by Western blotting, trafficking by flow cytometry
- using extracellular 3HA-tagged CFTR, and function by halide-sensitive YFP
- quenching. In the forskolin-induced swelling assay in intestinal organoids,
- we validated the effect of tagged versus endogenous CFTR. Results. Treatment
- with VX-809 significantly restored maturation, PM localization and function
- of both E60K and E92K. Mechanistically, VX-809 not only raised the total
- amount of CFTR, but significantly increased the traffic efficiency, which was
- not the case for A455E. G85E was refractory to VX-809 and VX-770 treatment.
- Conclusions. Since no single model or assay allows deciphering all defects at
- once, we propose a combination of phenotypic assays to collect rapid and
- early insights into the multiple defects of CFTR variants.
- },
- language = {eng}
-}
-[new9]
-@misc{ignatova2023,
- author = {Zoya Ignatova},
- title = {Research Group Ignatova at the Institute of Biochemistry and Molecular Biology},
- year = {2023},
- howpublished = {\url{https://www.chemie.uni-hamburg.de/institute/bc/arbeitsgruppen/ignatova.html}},
- note = {Accessed: 28 September 2024},
- institution = {University of Hamburg},
-}
-
-new10.
-@book{Mennella_2024,
- title = {Cilia: methods and protocols},
- year = 2024,
- author = {Mennella, Vito},
- publisher = {Humana Press},
- address = {New York, NY},
- isbn = {978-1-07-163507-0},
- abstractnote = {
- This volume covers the latest advancements in the study of ciliary
- complexity. Protocols cover genomic, proteomic, imaging, and functional
- analysis of different ciliated tissues and their wide applicability in cilia
- biology. Chapters in this book primarily focus on methods to study
- multiciliated cells, and discuss topics such as SARS-CoV-2 infections of
- human primary nasal multiciliated epithelial cells; expansion microscopy of
- ciliary proteins; live-imaging centriole amplification in mouse brain
- multiciliated cells; biophysical properties of cilia motility; and
- mucociliary transport device construction. Written in the highly successful
- Methods in Molecular Biology series format, chapters include introductions to
- their respective topics, lists of the necessary materials and reagents,
- step-by-step, readily reproducible laboratory protocols, and tips on
- troubleshooting and avoiding known pitfalls. Cutting-edge and thorough,
- Cilia: Methods and Protocols is a valuable resource for researchers who are
- interested in learning more about this developing field.
- },
- language = {eng}
-}
diff --git a/code/neurship.bib b/code/neurship.bib
deleted file mode 100644
index 24264760187d02f328aade65fc3a58b524156d12..0000000000000000000000000000000000000000
--- a/code/neurship.bib
+++ /dev/null
@@ -1,217 +0,0 @@
-1
-@article{frontiers_cystic_fibrosis,
- title = {Cystic Fibrosis: A Comprehensive Review},
- year = 2023,
- journal = {Frontiers},
- url = {https://www.frontiersin.org/articles/10.3389/fimmu.2023.123456/full}
-}
-2
-@article{cystic_fibrosis_news_today,
- title = {Cystic Fibrosis: Latest Developments and Research},
- year = 2023,
- journal = {Cystic Fibrosis News Today},
- url = {
- https://cysticfibrosisnewstoday.com/2023/06/10/latest-research-on-f508del-mutation/
- }
-}
-3
-@misc{expertmarketresearch_cystic_fibrosis_market,
- title = {Cystic Fibrosis Treatment Market Report},
- year = 2023,
- url = {
- https://www.expertmarketresearch.com/reports/cystic-fibrosis-treatment-market
- },
- note = {Accessed: 2024-09-27}
-}
-4
-@misc{cystic_fibrosis_news_kaftrio,
- title = {Kaftrio Open to Patients 12 and Up in Europe with One F508del Mutation},
- year = 2023,
- url = {
- https://cysticfibrosisnewstoday.com/news/kaftrio-open-patients-12-and-up-europe-one-f508del-mutation/
- },
- note = {Accessed: 2024-09-27}
-}
-5
-@misc{expert_market_research_cf_market_size,
- title = {Cystic Fibrosis Treatment Market Report},
- year = 2023,
- url = {
- https://www.expertmarketresearch.com/reports/cystic-fibrosis-treatment-market
- },
- note = {Accessed: 2024-09-27}
-}
-6
-@misc{cystic_fibrosis_news_today_gene_therapy,
- title = {Gene Therapy for F508del Mutation: A Growing Opportunity in CF Treatment},
- year = 2023,
- url = {
- https://cysticfibrosisnewstoday.com/2023/09/01/gene-therapy-opportunities-in-f508del-mutation-treatment/
- },
- note = {Accessed: 2024-09-27}
-}
-7
-@misc{expert_market_research_growth_drivers,
- title = {Cystic Fibrosis Treatment Market Report},
- year = 2023,
- url = {
- https://www.expertmarketresearch.com/reports/cystic-fibrosis-treatment-market
- },
- note = {Accessed: 2024-09-27}
-}
-8
-@article{frontiers_growth_drivers_cf,
- title = {Cystic Fibrosis: A Comprehensive Review of Current and Emerging Therapies},
- year = 2023,
- journal = {Frontiers},
- url = {https://www.frontiersin.org/articles/10.3389/fimmu.2023.123456/full}
-}
-9
-@misc{cystic_fibrosis_news_today_rna_therapy,
- title = {CFTR Modulators and the Unmet Need for 10% of Cystic Fibrosis Patients},
- year = 2023,
- url = {
- https://cysticfibrosisnewstoday.com/news/kaftrio-open-patients-12-and-up-europe-one-f508del-mutation/
- },
- note = {Accessed: 2024-09-27}
-}
-10
-@misc{cystic_fibrosis_news_today_cftr_modulators,
- title = {
- Vertex Pharmaceuticals and CFTR Modulators: The Gold Standard in Cystic
- Fibrosis Treatment
- },
- year = 2023,
- url = {
- https://cysticfibrosisnewstoday.com/2023/06/10/kaftrio-trikafta-f508del-mutation-treatment/
- },
- note = {Accessed: 2024-09-27}
-}
-11
-@misc{expert_market_research_cf_competitors,
- title = {Cystic Fibrosis Treatment Market Report},
- year = 2023,
- url = {
- https://www.expertmarketresearch.com/reports/cystic-fibrosis-treatment-market
- },
- note = {Accessed: 2024-09-27}
-}
-12
-@article{frontiers_gene_therapy_competitors,
- title = {
- Advancements in Gene Therapy for Cystic Fibrosis: Overcoming Early Challenges
- },
- year = 2023,
- journal = {Frontiers},
- url = {https://www.frontiersin.org/articles/10.3389/fimmu.2023.123456/full}
-}
-13
-@article{frontiers_regulatory_hurdles,
- title = {Regulatory Challenges in Gene Therapy: A Focus on Cystic Fibrosis},
- year = 2023,
- journal = {Frontiers},
- url = {https://www.frontiersin.org/articles/10.3389/fimmu.2023.123456/full}
-}
-14
-@misc{cystic_fibrosis_news_today_regulatory_approval,
- title = {Regulatory Pathways for RNA-Based Gene Therapies in Cystic Fibrosis},
- year = 2023,
- url = {
- https://cysticfibrosisnewstoday.com/2023/05/20/rna-gene-therapy-regulatory-hurdles/
- },
- note = {Accessed: 2024-09-27}
-}
-15
-@misc{expert_market_research_rnd_costs,
- title = {Cystic Fibrosis Treatment Market Report},
- year = 2023,
- url = {
- https://www.expertmarketresearch.com/reports/cystic-fibrosis-treatment-market
- },
- note = {Accessed: 2024-09-27}
-}
-16
-@article{frontiers_delivery_challenges,
- title = {
- Challenges in RNA-Based Therapy Delivery: Focus on Lipid Nanoparticles for
- Lung Targeting
- },
- year = 2023,
- journal = {Frontiers},
- url = {https://www.frontiersin.org/articles/10.3389/fimmu.2023.123456/full}
-}
-17
-@misc{cystic_fibrosis_news_today_market_saturation,
- title = {
- Vertex Pharmaceuticals Dominates the CF Treatment Market: Challenges for New
- Entrants
- },
- year = 2023,
- url = {
- https://cysticfibrosisnewstoday.com/2023/06/10/kaftrio-trikafta-f508del-mutation-treatment/
- },
- note = {Accessed: 2024-09-27}
-}
-18
-@article{frontiers_clinical_partnerships,
- title = {
- The Role of Clinical Partnerships in Advancing RNA-Based Gene Therapies for
- Cystic Fibrosis
- },
- year = 2023,
- journal = {Frontiers},
- url = {https://www.frontiersin.org/articles/10.3389/fimmu.2023.123456/full}
-}
-19
-@misc{cystic_fibrosis_news_today_clinical_partnerships,
- title = {
- Building Clinical Partnerships for RNA-Based Gene Therapies in Cystic
- Fibrosis
- },
- year = 2023,
- url = {
- https://cysticfibrosisnewstoday.com/2023/05/25/collaborations-in-cf-gene-therapy-research/
- },
- note = {Accessed: 2024-09-27}
-}
-20
-@article{frontiers_early_adopters,
- title = {
- Targeting Early Adopters in Cystic Fibrosis Gene Therapy: A Focus on
- Specialized Clinics
- },
- year = 2023,
- journal = {Frontiers},
- url = {https://www.frontiersin.org/articles/10.3389/fimmu.2023.123456/full}
-}
-21
-@misc{expert_market_research_biotech_partnerships,
- title = {Cystic Fibrosis Treatment Market Report},
- year = 2023,
- url = {
- https://www.expertmarketresearch.com/reports/cystic-fibrosis-treatment-market
- },
- note = {Accessed: 2024-09-27}
-}
-22
-@misc{cystic_fibrosis_news_today_regulatory_strategy,
- title = {
- Regulatory Strategy for RNA-Based Gene Therapies: Focus on Orphan Drug
- Designation and Fast-Track Approvals
- },
- year = 2023,
- url = {
- https://cysticfibrosisnewstoday.com/2023/06/15/fda-fast-track-approval-cystic-fibrosis-therapies/
- },
- note = {Accessed: 2024-09-27}
-}
-23
-@article{frontiers_long_term_vision,
- title = {
- Expanding RNA-Based Gene Therapies Beyond Cystic Fibrosis: A Modular Approach
- to Treating Genetic Disorders
- },
- year = 2023,
- journal = {Frontiers},
- url = {https://www.frontiersin.org/articles/10.3389/fimmu.2023.123456/full}
-}
diff --git a/code/output.txt b/code/output.txt
deleted file mode 100644
index ae0a151d5ea71a41d595f98bb233f926e133b429..0000000000000000000000000000000000000000
--- a/code/output.txt
+++ /dev/null
@@ -1,167 +0,0 @@
-{/*<!-- 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"> Roth, F. C.</span>
- <span property="schema:Name"> Draguhn, A.</span>
- </span>
- <span property="schema:name"> Die Entwicklung der Patch-Clamp-Technik</span>.
- <i property="schema:publisher" typeof="schema:Organization"> Springer eBooks</i>
- <b property="issueNumber" typeof="PublicationIssue"> </b>
- , <span property="schema:pageBegin"> 1</span>-<span property="schema:pageEnd">14</span>
- (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2023">2023</time>).
- <a className="doi" href="https://doi.org/10.1007/978-3-662-66053-9"> doi: 10.1007/978-3-662-66053-9</a>
-</li>
-
-{/*<!-- Citation num 2--> */}
-<li typeof="schema:Book" role="doc-biblioentry" property="schema:citation" id="desc-2">
- <span property="schema:author" typeof="schema:Person">
- <span property="schema:Name"> Dallas, M.</span>
- <span property="schema:Name"> Bell, D.</span>
- </span>
- <span property="schema:name"> Patch clamp electrophysiology: methods and protocols.</span>
- <i property="schema:publisher" typeof="schema:Organization"> Humana Press</i>
- (<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2021">2021</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"> Priel, A.</span>
- <span property="schema:Name"> Gil, Z.</span>
- <span property="schema:Name"> Moy, V. T.</span>
- <span property="schema:Name"> Magleby, K. L.</span>
- <span property="schema:Name"> Silberberg, S. D.</span>
- </span>
- <span property="schema:name">
-Ionic Requirements for Membrane-Glass Adhesion and Giga Seal Formation in
-Patch-Clamp Recording
-</span>.
- <i property="schema:publisher" typeof="schema:Organization"> Biophysical Journal</i>
- <b property="issueNumber" typeof="PublicationIssue"> 92</b>
- , <span property="schema:pageBegin"> 3893</span>-<span property="schema:pageEnd">3900</span>
- (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2007">2007</time>).
- <a className="doi" href="https://doi.org/10.1529/biophysj.106.099119"> doi: 10.1529/biophysj.106.099119</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"> Billet, A.</span>
- <span property="schema:Name"> Froux, L.</span>
- <span property="schema:Name"> Hanrahan, J. W.</span>
- <span property="schema:Name"> Becq, F.</span>
- </span>
- <span property="schema:name">
-Development of Automated Patch Clamp Technique to Investigate CFTR Chloride
-Channel Function
-</span>.
- <i property="schema:publisher" typeof="schema:Organization"> Frontiers in Pharmacology</i>
- <b property="issueNumber" typeof="PublicationIssue"> 8</b>
- (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2017">2017</time>).
- <a className="doi" href="https://doi.org/10.3389/fphar.2017.00195"> doi: 10.3389/fphar.2017.00195</a>
-</li>
-
-{/*<!-- Citation num 5--> */}
-<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-5">
- <span property="schema:author" typeof="schema:Person">
- <span property="schema:Name"> DuBridge, R. B.</span>
- <span property="schema:Name"> Tang, P.</span>
- <span property="schema:Name"> Hsia, H. C.</span>
- <span property="schema:Name"> Leong, P. M.</span>
- <span property="schema:Name"> Miller, J. H.</span>
- <span property="schema:Name"> Calos, M. P.</span>
- </span>
- <span property="schema:name">
-Analysis of mutation in human cells by using an Epstein-Barr virus shuttle
-system.
-</span>.
- <i property="schema:publisher" typeof="schema:Organization"> Molecular and Cellular Biology</i>
- <b property="issueNumber" typeof="PublicationIssue"> 7</b>
- , <span property="schema:pageBegin"> 379</span>-<span property="schema:pageEnd">387</span>
- (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 1987">1987</time>).
-</li>
-
-{/*<!-- Citation num 6--> */}
-<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-6">
- <span property="schema:author" typeof="schema:Person">
- <span property="schema:Name"> Qin, J. Y.</span>
- <span property="schema:Name"> Zhang, L.</span>
- <span property="schema:Name"> Clift, K. L.</span>
- <span property="schema:Name"> Hulur, I.</span>
- <span property="schema:Name"> Xiang, A. P.</span>
- <span property="schema:Name"> Ren, B.</span>
- <span property="schema:Name"> Lahn, B. T.</span>
- </span>
- <span property="schema:name">
-Systematic Comparison of Constitutive Promoters and the Doxycycline-Inducible
-Promoter
-</span>.
- <i property="schema:publisher" typeof="schema:Organization"> PLOS ONE</i>
- <b property="issueNumber" typeof="PublicationIssue"> 5</b>
- (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2010">2010</time>).
- <a className="doi" href="https://doi.org/10.1371/journal.pone.0010611"> doi: 10.1371/journal.pone.0010611</a>
-</li>
-
-{/*<!-- Citation num 7--> */}
-<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-7">
- <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"> et al.</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 8--> */}
-<li typeof="schema:ScolarlyArticle" role="doc-biblioentry" property="schema:citation" id="desc-8">
- <span property="schema:author" typeof="schema:Person">
- <span property="schema:Name"> Ensinck, M.</span>
- <span property="schema:Name"> De Keersmaecker, L.</span>
- <span property="schema:Name"> Heylen, L.</span>
- <span property="schema:Name"> Ramalho, A. S.</span>
- <span property="schema:Name"> Gijsbers, R.</span>
- <span property="schema:Name"> Farré, R.</span>
- <span property="schema:Name"> De Boeck, K.</span>
- <span property="schema:Name"> et al.</span>
- </span>
- <span property="schema:name">
-Phenotyping of Rare CFTR Mutations Reveals Distinct Trafficking and
-Functional Defects
-</span>.
- <i property="schema:publisher" typeof="schema:Organization"> Cells</i>
- <b property="issueNumber" typeof="PublicationIssue"> 9</b>
- <span property="schema:pageBegin">754</span>
- (<time property="schema:datePublished" datatype="xsd:gYear" dateTime=" 2020">2020</time>).
- <a className="doi" href="https://doi.org/10.3390/cells9030754"> doi: 10.3390/cells9030754</a>
-</li>
-
-{/*<!-- Citation num 9--> */}
-<li typeof="schema:WebPage" role="doc-biblioentry" property="schema:citation" id="desc-9">
- <span property="schema:author" typeof="schema:Organisation">
- <span property="schema:Name"> Zoya Ignatova</span>.
- </span>
- <span property="schema:name">Research Group Ignatova at the Institute of Biochemistry and Molecular Biology.</span>
- <i property="schema:publisher" typeof="schema:Organization">\url{https://www.chemie.uni-hamburg.de/institute/bc/arbeitsgruppen/ignatova.html}</i>
- (<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2023">2023</time>).
-</li>
-
-{/*<!-- Citation num 10--> */}
-<li typeof="schema:Book" role="doc-biblioentry" property="schema:citation" id="desc-10">
- <span property="schema:author" typeof="schema:Person">
- <span property="schema:Name"> Mennella, V.</span>
- </span>
- <span property="schema:name"> Cilia: methods and protocols.</span>
- <i property="schema:publisher" typeof="schema:Organization"> Humana Press</i>
- (<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2024">2024</time>).
-</li>
-
diff --git a/code/safety-bibtex.bib b/code/safety-bibtex.bib
deleted file mode 100644
index b5a4e9c5d4f8e43068d91c4d39be65b118c02223..0000000000000000000000000000000000000000
--- a/code/safety-bibtex.bib
+++ /dev/null
@@ -1,645 +0,0 @@
-@article{Cloarec-Ung_Beaulieu_Suthananthan_Lehnertz_Sauvageau_Sheppard_Knapp_2024,
- title = {
- Near-perfect precise on-target editing of human hematopoietic stem and
- progenitor cells
- },
- author = {
- Cloarec-Ung, Fanny-Mei and Beaulieu, Jamie and Suthananthan, Arunan and
- Lehnertz, Bernhard and Sauvageau, Guy and Sheppard, Hilary M. and Knapp,
- David J. H. F.
- },
- year = 2024,
- month = jun,
- journal = {eLife},
- volume = 12,
- pages = {RP91288},
- doi = {10.7554/eLife.91288},
- issn = {2050-084X},
- abstractnote = {
- Precision gene editing in primary hematopoietic stem and progenitor cells
- (HSPCs) would facilitate both curative treatments for monogenic disorders as
- well as disease modelling. Precise efficiencies even with the CRISPR/Cas
- system, however, remain limited. Through an optimization of guide RNA
- delivery, donor design, and additives, we have now obtained mean precise
- editing efficiencies >90% on primary cord blood HSCPs with minimal toxicity
- and without observed off-target editing. The main protocol modifications
- needed to achieve such high efficiencies were the addition of the DNA-PK
- inhibitor AZD7648, and the inclusion of spacer-breaking silent mutations in
- the donor in addition to mutations disrupting the PAM sequence. Critically,
- editing was even across the progenitor hierarchy, did not substantially
- distort the hierarchy or affect lineage outputs in colony-forming cell assays
- or the frequency of high self-renewal potential long-term culture initiating
- cells. As modelling of many diseases requires heterozygosity, we also
- demonstrated that the overall editing and zygosity can be tuned by adding in
- defined mixtures of mutant and wild-type donors. With these optimizations,
- editing at near-perfect efficiency can now be accomplished directly in human
- HSPCs. This will open new avenues in both therapeutic strategies and disease
- modelling.
- },
- language = {eng}
-}
-@article{Nelson_Randolph_Shen_Everette_Chen_Anzalone_An_Newby_Chen_Hsu_et,
- title = {Engineered pegRNAs improve prime editing efficiency},
- author = {
- Nelson, James W. and Randolph, Peyton B. and Shen, Simon P. and Everette,
- Kelcee A. and Chen, Peter J. and Anzalone, Andrew V. and An, Meirui and
- Newby, Gregory A. and Chen, Jonathan C. and Hsu, Alvin and Liu, David R.
- },
- year = 2022,
- month = mar,
- journal = {Nature Biotechnology},
- publisher = {Nature Publishing Group},
- volume = 40,
- number = 3,
- pages = {402–410},
- doi = {10.1038/s41587-021-01039-7},
- issn = {1546-1696},
- rights = {
- 2021 The Author(s), under exclusive licence to Springer Nature America, Inc.
- },
- abstractnote = {
- Prime editing enables the installation of virtually any combination of point
- mutations, small insertions or small deletions in the DNA of living cells. A
- prime editing guide RNA (pegRNA) directs the prime editor protein to the
- targeted locus and also encodes the desired edit. Here we show that
- degradation of the 3′ region of the pegRNA that contains the reverse
- transcriptase template and the primer binding site can poison the activity of
- prime editing systems, impeding editing efficiency. We incorporated
- structured RNA motifs to the 3′ terminus of pegRNAs that enhance their
- stability and prevent degradation of the 3′ extension. The resulting
- engineered pegRNAs (epegRNAs) improve prime editing efficiency 3–4-fold in
- HeLa, U2OS and K562 cells and in primary human fibroblasts without increasing
- off-target editing activity. We optimized the choice of 3′ structural motif
- and developed pegLIT, a computational tool to identify non-interfering
- nucleotide linkers between pegRNAs and 3′ motifs. Finally, we showed that
- epegRNAs enhance the efficiency of the installation or correction of
- disease-relevant mutations.
- },
- language = {en}
-}
-@article{Doench_Fusi_Sullender_Hegde_Vaimberg_Donovan_Smith_Tothova_Wilen_Orchard_et,
- title = {
- Optimized sgRNA design to maximize activity and minimize off-target effects
- of CRISPR-Cas9
- },
- author = {
- Doench, John G. and Fusi, Nicolo and Sullender, Meagan and Hegde, Mudra and
- Vaimberg, Emma W. and Donovan, Katherine F. and Smith, Ian and Tothova,
- Zuzana and Wilen, Craig and Orchard, Robert and Virgin, Herbert W. and
- Listgarten, Jennifer and Root, David E.
- },
- year = 2016,
- month = feb,
- journal = {Nature Biotechnology},
- publisher = {Nature Publishing Group},
- volume = 34,
- number = 2,
- pages = {184–191},
- doi = {10.1038/nbt.3437},
- issn = {1546-1696},
- rights = {2015 Springer Nature America, Inc.},
- abstractnote = {
- Genome-wide sgRNA libraries based on rules for on-target activity improve
- results of Cas9-based screens and facilitate a further refinement of on- and
- off-target prediction algorithms.
- },
- language = {en}
-}
-@article{White_Sadeeshkumar_Sun_Sudarsan_Breaker_2022,
- title = {
- Na+ riboswitches regulate genes for diverse physiological processes in
- bacteria
- },
- author = {
- White, Neil and Sadeeshkumar, Harini and Sun, Anna and Sudarsan, Narasimhan
- and Breaker, Ronald R.
- },
- year = 2022,
- month = aug,
- journal = {Nature Chemical Biology},
- publisher = {Nature Publishing Group},
- volume = 18,
- number = 88,
- pages = {878–885},
- doi = {10.1038/s41589-022-01086-4},
- issn = {1552-4469},
- rights = {2022 The Author(s)},
- abstractnote = {
- Only one protein factor is known that senses Na+ and controls gene
- expression. The Breaker Laboratory describes a bacterial riboswitch class
- selective for Na+ that regulates genes important for Na+ homeostasis, pH
- maintenance, osmotic stress response and ATP synthesis.
- },
- language = {en}
-}
-@article{Iwawaki_Akai_2006,
- title = {
- Analysis of the XBP1 splicing mechanism using endoplasmic reticulum
- stress-indicators
- },
- author = {Iwawaki, Takao and Akai, Ryoko},
- year = 2006,
- month = nov,
- journal = {Biochemical and Biophysical Research Communications},
- volume = 350,
- number = 3,
- pages = {709–715},
- doi = {10.1016/j.bbrc.2006.09.100},
- issn = {0006-291X},
- abstractnote = {
- Under endoplasmic reticulum (ER) stress conditions, XBP1 mRNA is processed by
- unconventional splicing and translated into a functional transcription
- factor. ER stress-specific XBP1 splicing is also known to be activated by
- IRE1. However, many aspects of the molecular mechanism of XBP1 splicing
- remain to be elucidated. We previously developed an indicator system that
- enabled detection of XBP1 splicing using fluorescent proteins as the reporter
- signals. Here, we use a modification of this method that employs modified ER
- stress-indicators and mutant IRE1 in vivo and in vitro to analyze XBP1
- splicing mechanisms. Our analyses suggest that the 506–579nt region of the
- XBP1 mRNA is necessary and sufficient for XBP1 splicing, that XBP1 splicing
- can occur in the cytoplasm, and that cleavage and ligation of XBP1 mRNA
- during splicing may occur as a coupled reaction.
- }
-}
-@article{Zhang_Lin_Yao_Cai_Chen_Aierken_Wang_Song_2023,
- title = {
- XBP1 splicing contributes to endoplasmic reticulum stress-induced human islet
- amyloid polypeptide up-regulation
- },
- author = {
- Zhang, Yun and Lin, Susan and Yao, Jing and Cai, Wantong and Chen, Huaqiu and
- Aierken, Ailikemu and Wang, Zhe and Song, Weihong
- },
- year = 2023,
- month = oct,
- journal = {Genes & Diseases},
- volume = 11,
- number = 5,
- pages = 101148,
- doi = {10.1016/j.gendis.2023.101148},
- issn = {2352-4820},
- abstractnote = {
- As a pathological hallmark of type 2 diabetes mellitus (T2DM), islet amyloid
- is formed by the aggregation of islet amyloid polypeptide (IAPP). Endoplasmic
- reticulum (ER) stress interacts with IAPP aggregates and has been implicated
- in the pathogenesis of T2DM. To examine the role of ER stress in T2DM, we
- cloned the hIAPP promoter and analyzed its promoter activity in human
- β-cells. We found that ER stress significantly enhanced hIAPP promoter
- activity and expression in human β-cells via triggering X-box binding protein
- 1 (XBP1) splicing. We identified a binding site of XBP1 in the hIAPP
- promoter. Disruption of this binding site by substitution or deletion
- mutagenesis significantly diminished the effects of ER stress on hIAPP
- promoter activity. Blockade of XBP splicing by MKC3946 treatment inhibited ER
- stress-induced hIAPP up-regulation and improved human β-cell survival and
- function. Our study uncovers a link between ER stress and IAPP at the
- transcriptional level and may provide novel insights into the role of ER
- stress in IAPP cytotoxicity and the pathogenesis of T2DM.
- }
-}
-@article{wei_lung_2023,
- title = {
- Lung {SORT} {LNPs} enable precise homology-directed repair mediated
- {CRISPR}/{Cas} genome correction in cystic fibrosis models
- },
- author = {
- Wei, Tuo and Sun, Yehui and Cheng, Qiang and Chatterjee, Sumanta and Traylor,
- Zachary and Johnson, Lindsay T. and Coquelin, Melissa L. and Wang, Jialu and
- Torres, Michael J. and Lian, Xizhen and Wang, Xu and Xiao, Yufen and Hodges,
- Craig A. and Siegwart, Daniel J.
- },
- year = 2023,
- month = nov,
- journal = {Nature Communications},
- volume = 14,
- number = 1,
- pages = 7322,
- doi = {10.1038/s41467-023-42948-2},
- issn = {2041-1723},
- url = {https://www.nature.com/articles/s41467-023-42948-2},
- urldate = {2024-04-16},
- copyright = {2023 The Author(s)},
- note = {Publisher: Nature Publishing Group},
- abstract = {
- Approximately 10\% of Cystic Fibrosis (CF) patients, particularly those with
- CF transmembrane conductance regulator (CFTR) gene nonsense mutations, lack
- effective treatments. The potential of gene correction therapy through
- delivery of the CRISPR/Cas system to CF-relevant organs/cells is hindered by
- the lack of efficient genome editor delivery carriers. Herein, we report
- improved Lung Selective Organ Targeting Lipid Nanoparticles (SORT LNPs) for
- efficient delivery of Cas9 mRNA, sgRNA, and donor ssDNA templates, enabling
- precise homology-directed repair-mediated gene correction in CF models.
- Optimized Lung SORT LNPs deliver mRNA to lung basal cells in Ai9 reporter
- mice. SORT LNP treatment successfully corrected the CFTR mutations in
- homozygous G542X mice and in patient-derived human bronchial epithelial cells
- with homozygous F508del mutations, leading to the restoration of CFTR protein
- expression and chloride transport function. This proof-of-concept study will
- contribute to accelerating the clinical development of mRNA LNPs for CF
- treatment through CRISPR/Cas gene correction.
- },
- language = {en},
- keywords = {Biomedical engineering, CRISPR-Cas9 genome editing, Gene delivery}
-}
-8:
-@article{IBRAHIM2022215,
- title = {
- Polyethylene glycol (PEG): The nature, immunogenicity, and role in the
- hypersensitivity of PEGylated products
- },
- author = {
- Mohamed Ibrahim and Eslam Ramadan and Nehal E. Elsadek and Sherif E. Emam and
- Taro Shimizu and Hidenori Ando and Yu Ishima and Omar Helmy Elgarhy and Hatem
- A. Sarhan and Amal K. Hussein and Tatsuhiro Ishida
- },
- year = 2022,
- journal = {Journal of Controlled Release},
- volume = 351,
- pages = {215--230},
- doi = {https://doi.org/10.1016/j.jconrel.2022.09.031},
- issn = {0168-3659},
- url = {https://www.sciencedirect.com/science/article/pii/S0168365922006265},
- keywords = {
- Polyethylene glycol (PEG), anti-PEG antibodies, Hypersensitivity, COVID-19
- mRNA vaccines, complement activation-related pseudoallergy (CARPA)
- },
- abstract = {
- Polyethylene glycol (PEG) is a versatile polymer that is widely used as an
- additive in foods and cosmetics, and as a carrier in PEGylated therapeutics.
- Even though PEG is thought to be less immunogenic, or perhaps even
- non-immunogenic, with a variety of physicochemical properties, there is
- mounting evidence that PEG causes immunogenic responses when conjugated with
- other materials such as proteins and nanocarriers. Under these conditions,
- PEG with other materials can result in the production of anti-PEG antibodies
- after administration. The antibodies that are induced seem to have a
- deleterious impact on the therapeutic efficacy of subsequently administered
- PEGylated formulations. In addition, hypersensitivity to PEGylated
- formulations could be a significant barrier to the utility of PEGylated
- products. Several reports have linked the presence of anti-PEG antibodies to
- incidences of complement activation-related pseudoallergy (CARPA) following
- the administration of PEGylated formulations. The use of COVID-19 mRNA
- vaccines, which are composed mainly of PEGylated lipid nanoparticles (LNPs),
- has recently gained wide acceptance, although many cases of post-vaccination
- hypersensitivity have been documented. Therefore, our review focuses not only
- on the importance of PEGs and its great role in improving the therapeutic
- efficacy of various medications, but also on the hypersensitivity reactions
- attributed to the use of PEGylated products that include PEG-based mRNA
- COVID-19 vaccines.
- }
-}
-9:
-@article{jiang_combinatorial_2024,
- title = {
- Combinatorial development of nebulized {mRNA} delivery formulations for the
- lungs
- },
- author = {
- Jiang, Allen Y. and Witten, Jacob and Raji, Idris O. and Eweje, Feyisayo and
- MacIsaac, Corina and Meng, Sabrina and Oladimeji, Favour A. and Hu, Yizong
- and Manan, Rajith S. and Langer, Robert and Anderson, Daniel G.
- },
- year = 2024,
- month = mar,
- journal = {Nature Nanotechnology},
- volume = 19,
- number = 3,
- pages = {364--375},
- doi = {10.1038/s41565-023-01548-3},
- issn = {1748-3387, 1748-3395},
- url = {https://www.nature.com/articles/s41565-023-01548-3},
- urldate = {2024-09-10},
- language = {en}
-}
-10:
-@article{vila-gonzalez_vitro_2024,
- title = {
- In vitro platform to model the function of ionocytes in the human airway
- epithelium
- },
- author = {
- Vilà -González, Marta and Pinte, Laetitia and Fradique, Ricardo and Causa,
- Erika and Kool, Heleen and Rodrat, Mayuree and Morell, Carola Maria and
- Al-Thani, Maha and Porter, Linsey and Guo, Wenrui and Maeshima, Ruhina and
- Hart, Stephen L. and McCaughan, Frank and Granata, Alessandra and Sheppard,
- David N. and Floto, R. Andres and Rawlins, Emma L. and Cicuta, Pietro and
- Vallier, Ludovic
- },
- year = 2024,
- month = apr,
- journal = {Respiratory Research},
- volume = 25,
- number = 1,
- pages = 180,
- doi = {10.1186/s12931-024-02800-7},
- issn = {1465-993X},
- url = {
- https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-024-02800-7
- },
- urldate = {2024-09-10},
- abstract = {
- Background  Pulmonary ionocytes have been identified in the airway epithelium
- as a small population of ion transporting cells expressing high levels of
- CFTR (cystic fibrosis transmembrane conductance regulator), the gene mutated
- in cystic fibrosis. By providing an infinite source of airway epithelial
- cells (AECs), the use of human induced pluripotent stem cells (hiPSCs) could
- overcome some challenges of studying ionocytes. However, the production of
- AEC epithelia containing ionocytes from hiPSCs has proven difficult. Here, we
- present a platform to produce hiPSCderived AECs (hiPSC-AECs) including
- ionocytes and investigate their role in the airway epithelium.
-
- Methods  hiPSCs were differentiated into lung progenitors, which were
- expanded as 3D organoids and matured by air-liquid interface culture as
- polarised hiPSC-AEC epithelia. Using CRISPR/Cas9 technology, we generated a
- hiPSCs knockout (KO) for FOXI1, a transcription factor that is essential for
- ionocyte specification. Differences between FOXI1 KO hiPSC-AECs and their
- wild-type (WT) isogenic controls were investigated by assessing gene and
- protein expression, epithelial composition, cilia coverage and motility, pH
- and transepithelial barrier properties.
-
- Results  Mature hiPSC-AEC epithelia contained basal cells, secretory cells,
- ciliated cells with motile cilia, pulmonary neuroendocrine cells (PNECs) and
- ionocytes. There was no difference between FOXI1 WT and KO hiPSCs in terms of
- their capacity to differentiate into airway progenitors. However, FOXI1 KO
- led to mature hiPSC-AEC epithelia without ionocytes with reduced capacity to
- produce ciliated cells.
-
- Conclusion  Our results suggest that ionocytes could have role beyond
- transepithelial ion transport by regulating epithelial properties and
- homeostasis in the airway epithelium.
- },
- language = {en}
-}
-11:
-
-@book{book,
- title = {Genome Editing and Biological Weapons: Assessing the Risk of Misuse},
- author = {Paris, Katherine},
- year = 2023,
- month = {01},
- publisher = {Springer Nature Switzerland AG},
- pages = {},
- doi = {10.1007/978-3-031-21820-0},
- isbn = {978-3-031-21819-4}
-}
-12:
-@article{wickiser2020biosecurity,
- title = {
- The democratization of biology: how CRISPR and synthetic biology usher in new
- biosecurity threats
- },
- author = {Wickiser, Jason K., et al.},
- year = 2020,
- journal = {Defense Horizons},
- volume = 85,
- pages = {1--16},
- url = {
- https://ndupress.ndu.edu/Media/News/News-Article-View/Article/2386026/democratization-of-biology-crispr-synthetic-biology-new-biosecurity-threats/
- }
-}
-13:
-@article{cohen2019security,
- title = {
- Security implications of CRISPR-enabled genome editing: New weapons of mass
- disruption?
- },
- author = {Cohen, Jon and Desai, Tej},
- year = 2019,
- journal = {Journal of Bioethical Inquiry},
- publisher = {Springer},
- volume = 16,
- number = 2,
- pages = {219--228},
- doi = {10.1007/s11673-019-09914-5},
- url = {https://doi.org/10.1007/s11673-019-09914-5}
-}
-14:
-@article{doudna2020synthetic,
- title = {
- The rise of synthetic biology: New biosecurity risks and regulatory
- challenges
- },
- author = {Doudna, Jennifer A. and Charpentier, Emmanuelle},
- year = 2020,
- journal = {Nature Reviews Genetics},
- publisher = {Nature},
- volume = 21,
- number = 3,
- pages = {144--156},
- doi = {10.1038/s41576-019-0182-7},
- url = {https://www.nature.com/articles/s41576-019-0182-7}
-}
-15:
-@article{shwartz2019public,
- title = {
- Public perception of CRISPR and genome editing: Misconceptions and media
- portrayal
- },
- author = {Shwartz, Mark and Conklin, Brian},
- year = 2019,
- journal = {Journal of Science Communication},
- volume = 18,
- number = 4,
- pages = {A02},
- doi = {10.22323/2.18040202},
- url = {https://jcom.sissa.it/archive/18/04/JCOM_1804_2019_A02}
-}
-16:
-@book{Chadwick_2012,
- title = {Encyclopedia of applied ethics},
- author = {Chadwick, Ruth F.},
- year = 2012,
- publisher = {Academic Press},
- address = {London},
- isbn = {978-0-12-373932-2},
- edition = {2nd ed},
- language = {eng}
-}
-17:
-@article{Rubeis_Steger_2018,
- title = {Risks and benefits of human germline genome editing: An ethical analysis},
- author = {Rubeis, Giovanni and Steger, Florian},
- year = 2018,
- month = jul,
- journal = {Asian Bioethics Review},
- volume = 10,
- number = 2,
- pages = {133–141},
- doi = {10.1007/s41649-018-0056-x},
- issn = {1793-8759, 1793-9453},
- language = {en}
-}
-18:
-@article{Ansah_2022,
- title = {
- Ethical Challenges and Controversies in the Practice and Advancement of Gene
- Therapy
- },
- author = {Ansah, Emmanuel Owusu},
- year = 2022,
- month = aug,
- journal = {Advances in Cell and Gene Therapy},
- volume = 2022,
- pages = {1–5},
- doi = {10.1155/2022/1015996},
- issn = {2573-8461},
- rights = {https://creativecommons.org/licenses/by/4.0/},
- abstractnote = {
- One of the most important technologies in modern medicine is gene therapy,
- which allows therapeutic genes to be introduced into cells of the body. The
- approach involves genetics and recombinant DNA techniques that allow
- manipulating vectors for delivery of exogenous material to target cells. The
- efficacy and safety of the delivery system are a key step towards the success
- of gene therapy. Somatic cell gene therapy is the easiest in terms of
- technology and the least problematic in terms of ethics. Although genetic
- manipulation of germline cells at the gene level has the potential to
- permanently eradicate certain hereditary disorders, major ethical issues such
- as eugenics, enhancement, mosaicism, and the transmission of undesirable
- traits or side effects to patients’ descendants currently stymie its
- development, leaving only somatic gene therapy in the works. However, moral,
- social, and ethical arguments do not imply that germline gene therapy should
- be banned forever. This review discusses in detail the current challenges
- surrounding the practice of gene therapy, focusing on the moral arguments and
- scientific claims that affect the advancement of the technology. The review
- also suggests precautionary principles as a means to navigate ethical
- uncertainties.
- },
- editor = {Miao, Carol H.},
- language = {en}
-}
-19:
-@book{Pugh_2020,
- title = {Autonomy, Rationality, and Contemporary Bioethics},
- author = {Pugh, Jonathan},
- year = 2020,
- month = apr,
- publisher = {Oxford University PressOxford},
- doi = {10.1093/oso/9780198858584.001.0001},
- isbn = {978-0-19-885858-4},
- url = {https://academic.oup.com/book/33778},
- edition = 1,
- rights = {https://creativecommons.org/licenses/by-nc-nd/4.0/},
- abstractnote = {
- Abstract Personal autonomy is often lauded as a key value in
- contemporary Western bioethics, and the claim that there is an important
- relationship between autonomy and rationality is often treated as an
- uncontroversial claim in this sphere. Yet, there is also considerable
- disagreement about how we should cash out the relationship between
- rationality and autonomy. In particular, it is unclear whether a rationalist
- view of autonomy can be compatible with legal judgments that enshrine a
- patient’s right to refuse medical treatment, regardless of whether ‘… the
- reasons for making the choice are rational, irrational, unknown or even
- non-existent’. This book brings recent philosophical work on the nature of
- rationality to bear on the question of how we should understand autonomy in
- contemporary bioethics. In doing so, the author develops a new framework for
- thinking about the concept, one that is grounded in an understanding of the
- different roles that rational beliefs and rational desires have to play in
- personal autonomy. Furthermore, the account outlined here allows for a deeper
- understanding of different forms of controlling influence, and the
- relationship between our freedom to act, and our capacity to decide
- autonomously. The author contrasts his rationalist account with other
- prominent accounts of autonomy in bioethics, and outlines the revisionary
- implications it has for various practical questions in bioethics in which
- autonomy is a salient concern, including questions about the nature of
- informed consent and decision-making capacity.
- },
- language = {en}
-}
-20:
-@inbook{Gstraunthaler_Lindl_2013,
- title = {Allgemeine Aspekte der Primärkultur},
- author = {Gstraunthaler, Gerhard and Lindl, Toni},
- year = 2013,
- booktitle = {Zell- und Gewebekultur: Allgemeine Grundlagen und spezielle Anwendungen},
- publisher = {Springer},
- address = {Berlin, Heidelberg},
- pages = {151–162},
- doi = {10.1007/978-3-642-35997-2_16},
- isbn = {978-3-642-35997-2},
- url = {https://doi.org/10.1007/978-3-642-35997-2_16},
- abstractnote = {
- Definitionsgemäß versteht man unter Primärkultur alle In-vitro-Züchtungen von
- Zellen, Geweben und Organen, die direkt aus dem Organismus entnommen wurden.
- Wird diese Erstkultur weiter subkultiviert, spricht man von einer
- Sekundärkultur und in weiterer Folge bereits von einer Zelllinie (Schaeffer,
- 1990) (Abb. 16-1). In den meisten Fällen kann eine Primärkultur nicht mehr
- weitergezüchtet werden (Abschn. 16.2). Während eine Organkultur nicht in
- ihrer Struktur- und Organisationseinheit zerstört werden soll (Kap. 23), ist
- die Gewebekultur von einer mehr oder minder starken Desintegration aus einem
- Organismus abhängig. Für die Gewinnung einer Zellkultur ist eine vollständige
- Dissoziation des Gewebes bzw. des Organs in Einzelzellen notwendig.
- },
- editor = {Gstraunthaler, Gerhard and Lindl, Toni},
- language = {de}
-}
-21:
-@book{book1,
- author = {Thiele, F.},
- year = 2001,
- booktitle = {International Encyclopedia of the Social & Behavioral Sciences},
- publisher = {Elsevier},
- pages = {13224–13227},
- doi = {10.1016/B0-08-043076-7/00191-1},
- isbn = {978-0-08-043076-8},
- url = {https://linkinghub.elsevier.com/retrieve/pii/B0080430767001911},
- rights = {https://www.elsevier.com/tdm/userlicense/1.0/},
- language = {en}
-}
-22:
-@inbook{Gethmann_2001,
- title = {Research: Ethical Aspects of Long-term Responsibilities},
- author = {Gethmann, C.F.},
- year = 2001,
- booktitle = {International Encyclopedia of the Social & Behavioral Sciences},
- publisher = {Elsevier},
- pages = {13227–13231},
- doi = {10.1016/B0-08-043076-7/00159-5},
- isbn = {978-0-08-043076-8},
- url = {https://linkinghub.elsevier.com/retrieve/pii/B0080430767001595},
- rights = {https://www.elsevier.com/tdm/userlicense/1.0/},
- language = {en}
-}
-23:
-@article{Kiani_Pheby_Henehan_Brown_Sieving_Sykora_Marks_Falsini_Capodicasa_Miertus_et,
- title = {Ethical considerations regarding animal experimentation},
- author = {
- Kiani, Aysha Karim and Pheby, Derek and Henehan, Gary and Brown, Richard and
- Sieving, Paul and Sykora, Peter and Marks, Robert and Falsini, Benedetto and
- Capodicasa, Natale and Miertus, Stanislav and Lorusso, Lorenzo and
- Dondossola, Daniele and Tartaglia, Gianluca Martino and Ergoren, Mahmut
- Cerkez and Dundar, Munis and Michelini, Sandro and Malacarne, Daniele and
- Bonetti, Gabriele and Dautaj, Astrit and Donato, Kevin and Medori, Maria
- Chiara and Beccari, Tommaso and Samaja, Michele and Connelly, Stephen
- Thaddeus and Martin, Donald and Morresi, Assunta and Bacu, Ariola and Herbst,
- Karen L. and Kapustin, Mykhaylo and Stuppia, Liborio and Lumer, Ludovica and
- Farronato, Giampietro and Bertelli, Matteo and INTERNATIONAL BIOETHICS STUDY
- GROUP
- },
- year = 2022,
- month = jun,
- journal = {Journal of Preventive Medicine and Hygiene},
- volume = 63,
- number = {2 Suppl 3},
- pages = {E255–E266},
- doi = {10.15167/2421-4248/jpmh2022.63.2S3.2768},
- issn = {2421-4248},
- abstractnote = {
- Animal experimentation is widely used around the world for the identification
- of the root causes of various diseases in humans and animals and for
- exploring treatment options. Among the several animal species, rats, mice and
- purpose-bred birds comprise almost 90% of the animals that are used for
- research purpose. However, growing awareness of the sentience of animals and
- their experience of pain and suffering has led to strong opposition to animal
- research among many scientists and the general public. In addition, the
- usefulness of extrapolating animal data to humans has been questioned. This
- has led to Ethical Committees’ adoption of the “four Rs†principles
- (Reduction, Refinement, Replacement and Responsibility) as a guide when
- making decisions regarding animal experimentation. Some of the essential
- considerations for humane animal experimentation are presented in this review
- along with the requirement for investigator training. Due to the ethical
- issues surrounding the use of animals in experimentation, their use is
- declining in those research areas where alternative in vitro or in silico
- methods are available. However, so far it has not been possible to dispense
- with experimental animals completely and further research is needed to
- provide a road map to robust alternatives before their use can be fully
- discontinued.
- },
- language = {eng}
-}
diff --git a/src/contents/Human Practices/Introduction.tsx b/src/contents/Human Practices/Introduction.tsx
index 36a07cb909016ea8062d965c6dcc05bf8de5b5c6..8a4b62611a4c5edc2a987f1956c7f9af78dabb17 100644
--- a/src/contents/Human Practices/Introduction.tsx
+++ b/src/contents/Human Practices/Introduction.tsx
@@ -1,6 +1,5 @@
import { ButtonOne } from "../../components/Buttons";
import { H5 } from "../../components/Headings";
-import { LoremMedium } from "../../components/Loremipsum";
import PreCyse from "../../components/precyse";
import { BlockQuoteB } from "../../components/Quotes";
import { Section } from "../../components/sections";
diff --git a/src/contents/description.tsx b/src/contents/description.tsx
index e475dc463c569b35f35cdc595afde251ce694b4f..41eb8948e3d0bfb8cf236011cd0886a8e6d0de49 100644
--- a/src/contents/description.tsx
+++ b/src/contents/description.tsx
@@ -3,7 +3,7 @@ import { TabButtonRow } from "../components/Buttons";
import Collapsible from "../components/Collapsible";
import { SupScrollLink } from "../components/ScrollLink";
import { H2, H4} from "../components/Headings";
-import { LoremMedium, LoremShort } from "../components/Loremipsum";
+import { LoremMedium } from "../components/Loremipsum";
import { Circle } from "../components/Shapes";
import { ButtonRowTabs } from "../components/Tabs";
import PieChart from "../components/Graph";
@@ -185,14 +185,14 @@ export function Description() {
<img src="https://static.igem.wiki/teams/5247/delivery/sort-lnp-ohne-beschriftung.webp"/>
</div>
<div className='col'>
- <p>We optimized lipid nanoparticles (LNPs) as a robust delivery system to transport larger therapeutic cargo, such as Prime Editing mRNA, to lung epithelial cells via inhalation. LNPs were chosen over other delivery systems, like Adeno-associated viruses (AAVs), due to their superior cargo capacity and reduced immunogenicity. Our goal was to create a spray-dried lung-specific LNP named</p>
+ <p>We optimized LNPs as a robust delivery system to transport larger therapeutic cargo, such as Prime Editing mRNA, to lung epithelial cells via inhalation. LNPs were chosen over other delivery systems, like Adeno-associated viruses (AAVs), due to their superior cargo capacity and reduced immunogenicity. Our goal was to create a spray-dried lung-specific LNP named</p>
<img src="https://static.igem.wiki/teams/5247/delivery/airbuddy.webp" style={{maxHeight: "80pt"}}/>
<p>capable of efficiently delivering of our Prime Editing components, referred to as PrimeGuide, to lung tissues through inhalation. This approach is designed to advance precision medicine by ensuring targeted delivery with minimal off-target effects.</p>
</div>
</div>
<Collapsible id="Col1" open={false} title="LNPs explained">
<H4 text="LNPs and their impact on modern medicine" id="text" />
- <p>Lipid nanoparticles (LNPs) are an advanced delivery system designed to transport therapeutic molecules like RNA, DNA or proteins into the cells. These nanoparticles are tiny spheres made of lipids that form a protective shell around the cargo. The size of LNs typically ranges from 50 to 200 nm in diameter, making them incredibly small - about 1,000 times thinner than a human hair [1]. </p>
+ <p>LNPs are an advanced delivery system designed to transport therapeutic molecules like RNA, DNA or proteins into the cells. These nanoparticles are tiny spheres made of lipids that form a protective shell around the cargo. The size of LNs typically ranges from 50 to 200 nm in diameter, making them incredibly small - about 1,000 times thinner than a human hair [1]. </p>
<p>Overall, LNPs represent a significant advancement in drug delivery technology. LNPs offer exceptionally high drug-loading capacities, making them highly effective for delivering substantial amounts of therapeutic agents in a single dose. Their advanced design allows for the encapsulation of a large payload, which enhances the efficacy of treatments and reduces the frequency of administration [3]. By encapsulating and protecting therapeutic agents like mRNA, LNPs enhance the stability, targeted delivery, and effectiveness of treatments. Their ability to be tailored for specific delivery needs, such as targeting particular organs or overcoming physiological barriers, makes them a powerful tool in modern medicine [9].</p>
<H4 text="Protection of cargo" id="text" />
<p> The primary function of LNPs is to shield the therapeutic agents they carry, such as mRNA, from degradation and facilitate their delivery into cells. mRNA is a critical component in many modern vaccines and therapies, but it is highly susceptible to breaking down before it can reach its target within cells. LNPs address this challenge by encapsulating the mRNA, thus protecting it from harmful enzymes, like RNases and environmental conditions [2]. </p>
@@ -220,12 +220,19 @@ export function Description() {
<p>Moreover, the surface of LNPs can be customized to improve targeting. For instance, incorporating specific lipids or modifying the surface with charged groups can direct the delivery of mRNA to targeted organs like the lungs or spleen [6]. Additionally, LNPs can be engineered with targeting ligands or antibodies to precisely direct their payload to specific cell types, further enhancing their therapeutic efficacy [7]. Another approach can be chitosan-based nanoparticles have been explored for their ability to adhere to mucus and enhance drug delivery through the respiratory tract. These nanoparticles can penetrate through the mucus layer to reach the lung tissues more effectively [8]. This versatility in design is essential for optimizing the delivery and effectiveness of LNP-based therapies.</p>
</Collapsible>
<Collapsible id="Col2" open={false} title="Challenges of working with LNPs">
- texthere
-
+ <p>Maintaining the stability of LNPs throughout formulation, storage, and delivery is critical, as factors like temperature changes, pH shifts, or mechanical stress can affect their integrity [1] [2]. Equally important is ensuring efficient encapsulation of the genetic material, as any inefficiency can lead to degradation of the therapeutic cargo or inadequate delivery to the target cells. Once inside the body, LNPs face the challenge of cellular uptake and successful endosomal escape [3] [4]. If they cannot escape the endosome after entering the cells, there is a risk that the genetic material will be degraded in the lysosomes, limiting the efficacy of the treatment. In addition, the formulation must minimize immunogenicity and toxicity, particularly with repeated dosing, which is often necessary for chronic diseases [2] [3]. Achieving this sensitive balance is crucial for maximizing the therapeutic potential of LNPs in gene delivery.</p>
+ <p>While these are general difficulties in the use of LNPs for gene therapy, further challenges arise when administering the LNPs via inhalation into the lungs, due to the unique environment and anatomy of the respiratory system.</p>
+ <H4 text="Challenges of inhalated lung-specific LNPs" id="chall2" />
+ <p>These challenges range from formulation and particle size to overcoming biological barriers and maintaining consistent dosing, all of which impact the overall efficacy of the therapy. </p>
+ <p>When transforming LNP formulations into inhalable particles, even greater attention must be paid to stability than is already the case. During processes like nebulization or spray-drying, LNPs are exposed to strong <strong>mechanical stress</strong> such as shear forces during aerosolization that can damage the LNP and thus their ability to protect and deliver genetic material effectively [5]. Ensuring that the LNPs maintain their structure throughout this transformation while remaining suitable for aerosol delivery is critical to the success of the therapy.</p>
+ <p>The <strong>size</strong> of the nanoparticles is another important factor. For successful lung delivery, LNPs should be smaller than 2 µm [6]. If the particles are too large, there is a risk that they will get stuck in the upper airways not able to reach the target cells; if they are too small, they may be exhaled before reaching the deeper lung tissue. The right particle size is crucial for the LNPs to reach the alveoli, where they can provide the greatest therapeutic impact.</p>
+ <p>Another major challenge is overcoming the lungs' natural <strong>protective barriers</strong>. The airways are lined with mucus and surfactants, which help to defend against pathogens, but also make it difficult for LNPs to be transported. In diseases such as cystic fibrosis, the thickened mucus presents an even greater obstacle, making it more difficult for the LNPs to reach the target cells [5]. The development of LNPs that can penetrate these barriers is essential for the success of gene therapy. </p>
+ <p>Finally, inhaled administration leads to fluctuations in the consistency of the <strong>dosage</strong>. Unlike intravenous administration, where dosing can be strictly controlled, the results of inhalation are influenced by factors such as the patient's breathing pattern, lung capacity and inhalation technique. These variables can affect how much of the LNP formulation actually reaches the lungs, complicating efforts to maintain a consistent therapeutic dose over time, which is a reasonable price to pay when you consider that inhalation is a non-invasive form of therapy compared to systemic therapy via injections into the bloodstream</p>
+ <p>All these challenges complicate the work with LNPs and present scientists with a great challenge, which makes working with LNPs even more important to find solutions.</p>
</Collapsible>
<br/>
<div className='row align-items-center'>
- <p>To optimize AirBuddy for pulmonary delivery, we collaborated extensively with several experts, including <a onClick={() => goToPagesAndOpenTab('weber', '/human-practices')}>Prof. Weber, Dr. Große-Onnebrink</a> and <a onClick={() => goToPagesAndOpenTab('tabid', '/human-practices')}>Dr. Kolonko</a> as medical experts, <a onClick={() => goToPagesAndOpenTab('kristian', '/human-practices')}>Prof. Dr. Müller</a>, <a onClick={() => goToPagesAndOpenTab('radukic', '/human-practices')}>Dr. Radukic</a>, Benjamin Moorlach and the Physical and Biophysical Chemistry working group as academic experts form Bielefeld University and FH Bielefeld as well as <a onClick={() => goToPagesAndOpenTab('corden', '/human-practices')}>Corden Pharma</a> and <a onClick={() => goToPagesAndOpenTab('rnhale', '/human-practices')}>RNhale</a> as industrial experts. Throughout the <a onClick={() => goToPagesAndOpenTab('delivery head', '/engineering')}>development process</a>, we tested two commercially available kits: the <strong>Cayman Chemical LNP Exploration Kit (LNP-102)</strong> and the <strong>Corden Pharma LNP Starter Kit #2</strong>. While the Cayman kit demonstrated limited transfection efficiency, the Corden Pharma formulation significantly enhanced cellular uptake in lung tissues. Building on this, we integrated the <strong>SORT LNP</strong> method based on Wang's research [1], making our nanoparticles lung-specific. Additionally, we employed the <strong>spray-drying technique</strong> in cooperation with RNhale [2] to improve the stability of our LNP, ensuring that it withstands the inhalation process without degradation. This stability is crucial for the efficient delivery of mRNA into lung epithelial cells, where PrimeGuide can effectively perform genome editing.</p>
+ <p>To optimize AirBuddy for pulmonary delivery, we collaborated extensively with several experts, including <a onClick={() => goToPagesAndOpenTab('weber', '/human-practices')}>Prof. Weber, Dr. Große-Onnebrink</a> and <a onClick={() => goToPagesAndOpenTab('tabid', '/human-practices')}>Dr. Kolonko</a> as medical experts, <a onClick={() => goToPagesAndOpenTab('kristian', '/human-practices')}>Prof. Dr. Müller</a>, <a onClick={() => goToPagesAndOpenTab('radukic', '/human-practices')}>Dr. Radukic</a>, <a onClick={() => goToPagesAndOpenTab('moorlach', '/human-practices')}>Benjamin Moorlach</a> and the <a onClick={() => goToPagesAndOpenTab('biophysik', '/human-practices')}>Physical and Biophysical Chemistry working group</a> as academic experts form Bielefeld University and FH Bielefeld as well as <a onClick={() => goToPagesAndOpenTab('corden', '/human-practices')}>Corden Pharma</a> and <a onClick={() => goToPagesAndOpenTab('rnhale', '/human-practices')}>RNhale</a> as industrial experts. Throughout the <a onClick={() => goToPagesAndOpenTab('delivery head', '/engineering')}>development process</a>, we tested two commercially available kits: the <strong>Cayman Chemical LNP Exploration Kit (LNP-102)</strong> and the <strong>Corden Pharma LNP Starter Kit #2</strong>. While the Cayman kit demonstrated limited transfection efficiency, the Corden Pharma formulation significantly enhanced cellular uptake in lung tissues. Building on this, we integrated the <strong>SORT LNP</strong> method based on Wang's research [1], making our nanoparticles lung-specific. Additionally, we employed the <strong>spray-drying technique</strong> in cooperation with RNhale [2] to improve the stability of our LNP, ensuring that it withstands the inhalation process without degradation. This stability is crucial for the efficient delivery of mRNA into lung epithelial cells, where PrimeGuide can effectively perform genome editing.</p>
<img src="https://static.igem.wiki/teams/5247/delivery/big-plan-inhalation-teil-del.webp"/>
</div>
<p>To evaluate the <strong>delivery efficiency</strong>, we transfected HEK293 and CFBE41o- cells using fluorescent cargo and quantified the results through FACS analysis. We also ensured that AirBuddy meets the necessary standards for safety and efficacy since we conducted extensive <a onClick={() => goToPageAndScroll ('In-Depth Characterization of LNPsH', '/materials-methods')}> characterization of the LNPs </a>using techniques such as Zeta potential analysis, Dynamic Light Scattering (DLS), Scanning Electron Microscopy (SEM), and Cryogenic Electron Microscopy (cryo-EM). These methods confirmed the uniformity, stability, and optimal size distribution of the nanoparticles. Furthermore, <strong>cytotoxicity assessments</strong> including MTT and proliferation assays demonstrated that our LNPs are biocompatible and do not impede cell growth or function by the incorporation of <a onClick={() => goToPagesAndOpenTab('it4', '/engineering')}>PEG</a> and other ambivalent components. These findings reinforce AirBuddy's potential as a safe and effective tool for pulmonary delivery, with broad implications for gene therapies targeting lung diseases.</p>
diff --git a/src/contents/safety.tsx b/src/contents/safety.tsx
index e757278a666dadec37608d3d8254ee424062d82c..367be6539c31a5d8e5dc8f375343e455850f81ee 100644
--- a/src/contents/safety.tsx
+++ b/src/contents/safety.tsx
@@ -100,14 +100,16 @@ export const Safety: React.FC = () =>{
<strong>HEK293 cell line: </strong>HEK 293 (Human Embryonic Kidney 293) cells are an immortal cell line originally derived from the kidney cells of a human embryo. They are characterized by their fast division rate and high transfection efficiency, which makes them a popular model in biomedical research. For our studies, the basic HEK293 cells were provided to us by the Cellular and Molecular Biotechnology Group at Bielefeld University, headed by Prof. Dr. Kristian Müller. Prof. Dr. Müller is also one of the Principal Investigators of our team. We use this cell line in our proof-of-concept studies and for testing the Prime Editing Guide pegRNA (pegRNA) to evaluate the efficiency and functionality of our constructs.
</p>
<p>
- <strong>HEK293T-3HA-CFTR cell line: </strong>The HEK293T-3HA-CFTR cell line is based on HEK293T cells expressing an additional tsA1609 allele of the SV40 large T antigen. This allele enables the replication of vectors containing the SV40 origin of replication. In addition to the native CFTR gene, which is not expressed in HEK cells, the HEK293T-3HA-CFTR cell line from Leuven carries another copy of the CFTR gene embedded in an expression cassette. This cassette contains a CMV promoter, which is derived from the human cytomegalovirus and is frequently used for the overexpression of genes in human cells. In addition, the cassette contains a puromycin resistance gene that is co-expressed with CFTR, allowing continuous selection of CFTR-expressing cells.
+ <strong>HEK293T-3HA-CFTR cell line: </strong>The HEK293T-3HA-CFTR cell line is based on HEK293T cells expressing an additional tsA1609 allele of the SV40 large T antigen. This allele enables the replication of vectors containing the SV40 origin of replication. In addition to the native CFTR gene, which is not expressed in HEK cells, the HEK293T-3HA-CFTR cell line carries another copy of the CFTR gene embedded in an expression cassette. This cassette contains a CMV promoter, which is derived from the human cytomegalovirus and is frequently used for the overexpression of genes in human cells. In addition, the cassette contains a puromycin resistance gene that is co-expressed with CFTR, allowing continuous selection of CFTR-expressing cells.
</p>
<p>
<strong>HEK293T-3HA-F508del-CFTR cell line:</strong> The HEK293T-3HA-F508del-CFTR cell line is a modified HEK293T cell line that carries the F508del mutation in the CFTR gene, which is responsible for the most common mutation in cystic fibrosis. This mutation leads to a defective CFTR protein that impairs the normal function of the chloride channel. The cell line is therefore ideal for studying the effects of this mutation and for evaluating potential therapies for cystic fibrosis.
</p>
<p>
<strong>CFBE41o- cell line:</strong> The CFBE41o- cell line, derived from the bronchial epithelial cells of a cystic fibrosis patient, is homozygous for the F508del-CFTR mutation and was essential for our cystic fibrosis research. A reduced CFTR expression level is present. The cell line carries the CFTR defect and can therefore represent a patient with CF. The cell line is used to test our mechanism. These cells were immortalized with a replication-defective plasmid that retains their physiological properties.
- When working with the HEK293T and CFBE41o- cell lines, it’s important to consider the minimal risks associated with their use. While not harmful on their own, the genetic modifications in HEK293T cells require careful handling to prevent accidental release or exposure. These cells, engineered to overexpress CFTR, including the F508del mutation, necessitate strict safety measures like regular monitoring and proper waste disposal to comply with S1 laboratory standards. Similarly, CFBE41o- cells, due to their genetic modifications and disease relevance, require careful handling to avoid cross-contamination and ensure biosafety.
+ <p>
+ When working with the HEK293T and CFBE41o- cell lines, it’s important to consider the minimal risks associated with their use. While not harmful on their own, the genetic modifications in HEK293T cells require careful handling to prevent accidental release or exposure. These cells, engineered to overexpress CFTR, including the F508del mutation, necessitate strict safety measures like regular monitoring and proper waste disposal to comply with S1 laboratory standards. Similarly, CFBE41o- cells, due to their genetic modifications and disease relevance, require careful handling to avoid cross-contamination and ensure biosafety.
+ </p>
</p>
<p>
<strong>Human nasal epithelial cells (hNECs):</strong> Human nasal epithelial cells (hNECs) were harvested using a nasal brush, a minimally invasive procedure, and cultured in air-liquid interface (ALI) cultures to model the airway epithelium. Human nasal epithelial cells (hNECs) were obtained using a nasal brush, a minimally invasive technique, and then cultured in air-liquid interface (ALI) cultures to model the airway epithelium. Using these primary cultures, derived from donors with airway diseases such as cystic fibrosis, we were able to simulate the in vivo conditions of such diseases.
diff --git a/src/utils/TabNavigation.tsx b/src/utils/TabNavigation.tsx
index e4197b49bb05536dba36af7794e53f999d8ac978..6b2c3017daac668357272d2f0160dd6b558c8af9 100644
--- a/src/utils/TabNavigation.tsx
+++ b/src/utils/TabNavigation.tsx
@@ -1,7 +1,6 @@
import { useEffect, useState } from 'react';
import { useNavigate, useLocation } from 'react-router-dom';
import { openFromOtherPage } from './openFromOtherpAge';
-import { useNavigation } from '.';
import { useLoading } from './LoadingContext';
// Funktion, um den Haupttab zu öffnen