Skip to content
Snippets Groups Projects
Commit 21f35d0a authored by Philip Mundt's avatar Philip Mundt
Browse files

Merge branch 'main' of ssh://gitlab.igem.org/2024/bielefeld-cebitec

parents 7e8b1248 7f4fc8f7
No related branches found
No related tags found
No related merge requests found
Pipeline #473547 failed
Stage: build
Expand all Hide whitespace changes
Inline Side-by-side
code/bibtex.bib deleted 100644 → 0
+ 0
− 10
View file @ 7e8b1248
@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
code/methods.bib deleted 100644 → 0
+ 0
− 246
View file @ 7e8b1248
[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 organoids”).}
}
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}
}
code/neurship.bib deleted 100644 → 0
+ 0
− 217
View file @ 7e8b1248
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}
}
code/output.txt deleted 100644 → 0
+ 0
− 167
View file @ 7e8b1248
{/*<!-- 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">&nbsp;Die Entwicklung der Patch-Clamp-Technik</span>.
<i property="schema:publisher" typeof="schema:Organization"> Springer eBooks</i>
<b property="issueNumber" typeof="PublicationIssue"> </b>
,&nbsp;<span property="schema:pageBegin"> 1</span>-<span property="schema:pageEnd">14</span>&nbsp;
(<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">&nbsp;Patch clamp electrophysiology: methods and protocols.</span>
<i property="schema:publisher" typeof="schema:Organization">&nbsp;Humana Press</i>
&nbsp;(<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">&nbsp;
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>
,&nbsp;<span property="schema:pageBegin"> 3893</span>-<span property="schema:pageEnd">3900</span>&nbsp;
(<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">&nbsp;
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">&nbsp;
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>
,&nbsp;<span property="schema:pageBegin"> 379</span>-<span property="schema:pageEnd">387</span>&nbsp;
(<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">&nbsp;
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">&nbsp;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>&nbsp;
(<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">&nbsp;
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>&nbsp;
(<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>
&nbsp;(<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">&nbsp;Cilia: methods and protocols.</span>
<i property="schema:publisher" typeof="schema:Organization">&nbsp;Humana Press</i>
&nbsp;(<time property="schema:datePublished" datatype="xsd:gYear" dateTime="2024">2024</time>).
</li>
code/safety-bibtex.bib deleted 100644 → 0
+ 0
− 645
View file @ 7e8b1248
This diff is collapsed.
src/contents/Human Practices/Introduction.tsx
+ 0
− 1
View file @ 21f35d0a
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";
......
src/contents/description.tsx
+ 13
− 6
View file @ 21f35d0a
......@@ -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>
......
src/contents/safety.tsx
+ 4
− 2
View file @ 21f35d0a
......@@ -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.
......
src/utils/TabNavigation.tsx
+ 0
− 1
View file @ 21f35d0a
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
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment