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src/sidebars/resS.tsx 0 → 100644
View file @ 3fd292fd
import { createSidebar } from "../utils/createSidebar";
export function ResultSidebar(){
let sidebar = createSidebar(tabs);
return(
<div className="col-2 d-none d-lg-block">
{sidebar}
</div>
)
}
const tabs = [
{ tab: "Abstract"},
{tab: "Experimental Design", subtabs: ["Proof of Concept", "PrimeGuide", "LNP Synthesis", "Primary Cell Culture", "Downstream Applications", "PreCyse Results"]},
{tab: "Supplementary Material"}
];
\ No newline at end of file
src/sidebars/safeS.tsx 0 → 100644
View file @ 3fd292fd
import { createSidebar } from "../utils/createSidebar";
export function SafetySidebar(){
let sidebar = createSidebar(tabs);
return(
<div className="col-2 d-none d-lg-block">
{sidebar}
</div>
)}
const tabs = [
{ tab: "Role" },
{ tab: "Biosafety", subtabs: ["Mechanism", "Delivery"] },
{ tab: "Biosecurity", subtabs: ["Our Project", "Risk Assessment", "Managing Risks"] },
{ tab: "Bioethics", subtabs: ["Gene Therapy", "Primary Cells", "Consent and Guidelines"] },
{ tab: "Check-Ins"},
{ tab: "Our Lab" },
];
\ No newline at end of file
src/sources/ScieComWorkshop-Sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function ScoComSources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} />
</div>
);
}
const bibtexSources = [
`@article{
doi:10.1073/pnas.1213273110,
author = {Baruch Fischhoff },
title = {The sciences of science communication},
journal = {Proceedings of the National Academy of Sciences},
volume = {110},
number = {supplement\_3},
pages = {14033-14039},
year = {2013},
doi = {10.1073/pnas.1213273110},
URL = {https://www.pnas.org/doi/abs/10.1073/pnas.1213273110},
eprint = {https://www.pnas.org/doi/pdf/10.1073/pnas.1213273110},
}`
]
src/sources/description-sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function DescSources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} />
</div>
)
}
const bibtexSources = [
`
@article{Rodrigues_2008,
title = {Cystic fibrosis and neonatal screening},
author = {
Rodrigues, Roberta and Gabetta, Carmen S. and Pedro, Karla P. and Valdetaro,
Fabio and Fernandes, Maria I. M. and Magalhães, Patrícia K. R. and Januário,
José N. and Maciel, Léa M. Z.
},
year = 2008,
journal = {Cadernos de Saúde Pública},
publisher = {SciELO},
volume = 24,
number = {suppl 4},
pages = {s592--s602},
doi = {10.1590/S0102-311X2008001600002},
url = {https://doi.org/10.1590/S0102-311X2008001600002}
}`,`
@article{genes11040401,
title = {
The Impact of the CFTR Gene Discovery on Cystic Fibrosis Diagnosis,
Counseling, and Preventive Therapy
},
author = {Farrell, Philip M. and Rock, Michael J. and Baker, Mei W.},
year = 2020,
journal = {Genes},
volume = 11,
number = 4,
doi = {10.3390/genes11040401},
issn = {2073-4425},
url = {https://www.mdpi.com/2073-4425/11/4/401},
article-number = 401,
pubmedid = 32276344
}`,`
@article{zgzugzuzk,
title = {
CFTR Modulators: The Changing Face of Cystic Fibrosis in the Era of Precision
Medicine
},
author = {Lopes-Pacheco, Miquéias},
year = 2020,
journal = {Frontiers in Pharmacology},
volume = 10,
doi = {10.3389/fphar.2019.01662},
issn = {1663-9812},
url = {
https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2019.01662
}
}`,`
@misc{clinicaltrialsarena2024,
title = {Cystic fibrosis: global clinic trials landscape and treatments},
author = {Novotech},
year = 2024,
url = {
https://www.clinicaltrialsarena.com/sponsored/cystic-fibrosis-global-clinical-trials-landscape-and-treatments/
},
note = {Zugriff am 23. September 2024}
}`,`
@misc{MSDmanual2024internet,
title = {Mukoviszidose (zystische Fibrose, CF)},
author = {Gregory Sawicki},
year = 2023,
url = {
https://www.msdmanuals.com/de-de/heim/gesundheitsprobleme-von-kindern/mukoviszidose/mukoviszidose-zystische-fibrose-cf​
},
note = {Zugriff am 23. September 2024}
}`,`
@misc{patient2024internet,
title = {Zahlen, Daten und Fakten für Patienten und Angehörige},
author = {M. Burkhart, L. Nährlich},
year = 2022,
url = {
https://www.muko.info/fileadmin/user_upload/was_wir_tun/register/berichtsbaende/patientenberichtsband.pdf​
},
note = {Zugriff am 23. September 2024}
}`,`
@book{Baird2022,
title = {
Dorothy Hansine Andersen: The Life and Times of the Pioneering
Physician-Scientist Who Identified Cystic Fibrosis
},
author = {Baird, John Scott},
year = 2022,
publisher = {Springer International Publishing},
doi = {10.1007/978-3-030-87484-1},
isbn = 9783030874841,
url = {http://dx.doi.org/10.1007/978-3-030-87484-1}
}`,`
@book{Ballmann2008-bt,
title = {CF-Manual},
author = {Ballmann, Manfred and Smaczny, Christina},
year = 2008,
language = {de}
}`,`
@article{article,
title = {CFTR: folding, misfolding and correcting the ΔF508 conformational defect},
author = {Lukacs, Gergely L.; Verkman, A. S.},
year = 2012,
month = 2,
journal = {Trends in molecular medicine},
volume = {{18(2)}},
pages = {81--91},
doi = {10.1016/j.molmed.2011.10.003}
}`,`
@misc{muko1internet2024,
title = {Was ist Mukoviszidose/ Cystische Fibrose (CF)?},
author = {Mukoviszidose e.V.},
year = 2024,
url = {https://www.muko.info/mukoviszidose/ueber-die-erkrankung​},
note = {Zugriff am 23. September 2024}
}`,`
@misc{muko2internet2024,
title = {Was ist Mukoviszidose/ Cystische Fibrose (CF)?},
author = {Mukoviszidose e.V.},
year = 2024,
url = {https://www.muko.info/mukoviszidose/ueber-die-erkrankung/ursache​},
note = {Zugriff am 23. September 2024}
}`,`
@article{CFTRchannel2013,
title = {The CFTR ion channel: gating, regulation, and anion permeation},
author = {Hwang, Tzyh-Chang and Kirk, Kevin L.},
year = 2013,
journal = {Cold Spring Harbor Perspectives in Medicine},
publisher = {Cold Spring Harbor Laboratory Press},
volume = 3,
number = 1,
pages = {a009498},
doi = {10.1101/cshperspect.a009498}
}`,`
@article{CFTRfunction2008,
title = {CFTR Function and Prospects for Therapy},
author = {Riordan, John R.},
year = 2008,
journal = {Annual Review of Biochemistry},
publisher = {Annual Reviews},
volume = 77,
number = 1,
pages = {701--26},
doi = {10.1146/annurev.biochem.75.103004.142532}
}`,`
@article{ABCprotein2006,
title = {
The ABC protein turned chloride channel whose failure causes cystic fibrosis
},
author = {Gadsby, D.; Vergani, P. & Csanády, L.},
year = 2006,
journal = {Nature},
publisher = {Nature},
volume = 440,
number = 1,
pages = {477--483},
doi = {https://doi.org/10.1038/nature04712}
}`,`
@article{Sheppard1999,
title = {Structure and function of the CFTR chloride channel},
author = {Sheppard, David N. and Welsh, Michael J.},
year = 1999,
journal = {Physiological Reviews},
publisher = {American Physiological Society},
volume = 79,
number = {1 Suppl},
pages = {S23--S45},
doi = {10.1152/physrev.1999.79.1.S23}
}
`,`
@article{article,
title = {
Unravelling the Regions of Mutant F508del-CFTR More Susceptible to the Action
of Four Cystic Fibrosis Correctors
},
author = {Amico, Giulia; Brandas, Chiara; Moran, Oscar; Baroni, Debora},
year = 2019,
month = 1,
journal = {International Journal of Molecular Sciences},
volume = {{20(21)}},
pages = 5463,
doi = {10.3390/ijms20215463}
}`,`
@misc{cff2024digestive,
title = {Managing CF: Digestive Tract},
author = {Cystic Fibrosis Foundation},
year = 2024,
url = {https://www.cff.org/managing-cf/digestive-tract},
note = {Zugriff am 2. Dezember 2024}
}`,`
@misc{mukoleitlinien2024internet,
title = {
Mukoviszidose (Cystische Fibrose): Ernährung und exokrine
Pankreasinsuffizienz
},
author = {M. Stern, H. Ellemunter, B. Palm, H.-G. Posselt, C. Smaczny},
year = 2011,
url = {
https://www.muko.info/fileadmin/user_upload/was_wir_tun/leitlinien/LL_S1_mukoviszidose_ernaehrung_exokrine_pankreasinsuffizienz.pdf​
},
note = {Zugriff am 25. September 2024}
}`,`
@misc{CFF42024internet,
title = {The Digestive Tract},
author = {Cystic Fibrosis Foundation},
year = 2024,
url = {https://www.cff.org/managing-cf/digestive-tract​},
note = {Zugriff am 25. September 2024}
}`,`
@misc{muko2024therapie,
title = {Therapie der Mukoviszidose},
author = {Mukoviszidose e.V.},
year = 2024,
url = {https://www.muko.info/mukoviszidose/therapie-der-mukoviszidose#c1571},
note = {Zugriff am 2. Dezember 2024}
}
`,`
@misc{ncbi2024cf,
title = {Cystic Fibrosis: The Basics},
author = {National Center for Biotechnology Information (NCBI)},
year = 2024,
url = {https://www.ncbi.nlm.nih.gov/books/NBK279303/},
note = {Zugriff am 2. Dezember 2024}
}`,`
@article{DeLisle2013,
title = {The Cystic Fibrosis Intestine},
author = {De Lisle, R. C. and Borowitz, D.},
year = 2013,
month = jun,
journal = {Cold Spring Harbor Perspectives in Medicine},
publisher = {Cold Spring Harbor Laboratory},
volume = 3,
number = 9,
pages = {a009753-a009753},
doi = {10.1101/cshperspect.a009753},
issn = {2157-1422},
url = {http://dx.doi.org/10.1101/cshperspect.a009753}
}`,`
@misc{gesundheit2024leber,
title = {Die Funktionen der Leber},
author = {Gesundheit.gv.at},
year = 2024,
url = {https://www.gesundheit.gv.at/krankheiten/leber/funktion.html},
note = {Zugriff am 2. Dezember 2024}
}`,`
@misc{cfuk2024body,
title = {How Does Cystic Fibrosis Affect the Body?},
author = {Cystic Fibrosis Trust},
year = 2024,
url = {
https://www.cysticfibrosis.org.uk/what-is-cystic-fibrosis/how-does-cystic-fibrosis-affect-the-body
},
note = {Zugriff am 2. Dezember 2024}
}`,`
@misc{ncbi2024glossary,
title = {Glossary of Gene Therapy Terms},
author = {National Center for Biotechnology Information (NCBI)},
year = 2024,
url = {https://www.ncbi.nlm.nih.gov/books/NBK556086/},
note = {Zugriff am 2. Dezember 2024}
}`,`
@misc{CFT2024internet,
title = {Fertility and cystic fibrosis},
author = {Cystic Fibrosis Trust},
year = 2024,
url = {
https://www.cysticfibrosis.org.uk/what-is-cystic-fibrosis/how-does-cystic-fibrosis-affect-the-body/symptoms-of-cystic-fibrosis/fertility
​
},
note = {Zugriff am 25. September 2024}
}`,`
@misc{CFSource2024internet,
title = {Abnehmende Lungenfunktion als Leitsymptom bei CF},
author = {CF Source},
year = 2023,
url = {http://www.cfsource.at/de/cystische-fibrose/symptome/lunge​},
note = {Zugriff am 25. September 2024}
}`,`
@article{Rowe2005,
title = {Cystic Fibrosis},
author = {Rowe, Steven M. and Miller, Stacey and Sorscher, Eric J.},
year = 2005,
month = may,
journal = {New England Journal of Medicine},
publisher = {Massachusetts Medical Society},
volume = 352,
number = 19,
pages = {1992-2001},
doi = {10.1056/nejmra043184},
issn = {1533-4406},
url = {http://dx.doi.org/10.1056/NEJMra043184}
}`,`
@article{OSULLIVAN20091891,
title = {Cystic fibrosis},
author = {O'Sullivan, Brian and Freedman, Steven},
year = 2009,
journal = {The Lancet},
volume = 373,
number = 9678,
pages = {1891--1904},
doi = {https://doi.org/10.1016/S0140-6736(09)60327-5},
issn = {0140-6736},
url = {https://www.sciencedirect.com/science/article/pii/S0140673609603275}
}`,`
@misc{Muko62024internet,
title = {Mukoviszidose: Medikamente und Behandlung},
author = {Lungen Informationsdienst},
year = 2023,
url = {https://www.lungeninformationsdienst.de/krankheiten/mukoviszidose/therapie​},
note = {Zugriff am 25. September 2024}
}`,`
@book{Lambrechts_2023,
title = {Musculoskeletal Abnormalities Caused by Cystic Fibrosis},
author = {Lambrechts, Mark},
year = 2023,
month = mar,
booktitle = {Advances in Skeletal Muscle Health and Disease},
publisher = {IntechOpen},
doi = {10.5772/intechopen.104591},
isbn = 9781803562735,
issn = {2631-8261},
url = {http://dx.doi.org/10.5772/intechopen.104591}
}`,`
@misc{Anatomy2024internet,
title = {Anatomy, Skin (Integument), Epidermis},
author = {Yousef, H., Alhajj, M., Fakoya AO, et al.},
year = 2024,
url = {https://www.ncbi.nlm.nih.gov/books/NBK470464/},
note = {Zugriff am 25. September2024}
}`,`
@article{Wenk_2010,
title = {Cystic Fibrosis Presenting With Dermatitis},
author = {Wenk, Kurt S. and Higgins, Kristen B. and Greer, Kenneth E.},
year = 2010,
month = feb,
journal = {Archives of Dermatology},
publisher = {American Medical Association (AMA)},
volume = 146,
number = 2,
doi = {10.1001/archdermatol.2009.361},
issn = {0003-987X},
url = {http://dx.doi.org/10.1001/archdermatol.2009.361}
}`,`
@article{DAE193172,
title = {Cystic Fibrosis},
author = {Naehrig, Susanne and Chao, Cho-Ming and Naehrlich, Lutz},
year = 2017,
journal = {Dtsch Arztebl International},
volume = 114,
number = {33-34},
pages = {564--574},
doi = {10.3238/arztebl.2017.0564},
url = {https://www.aerzteblatt.de/int/article.asp?id=193172},
eprint = {https://www.aerzteblatt.de/pdf.asp?id=193172}
}`,`
@article{Guta2021,
title = {
Global Burden of Anxiety and Depression among Cystic Fibrosis Patient:
Systematic Review and Meta-Analysis
},
author = {
Guta, Mistire Teshome and Tekalign, Tiwabwork and Awoke, Nefsu and Fite,
Robera Olana and Dendir, Getahun and Lenjebo, Tsegaye Lolaso
},
year = 2021,
month = jul,
journal = {International Journal of Chronic Diseases},
publisher = {Hindawi Limited},
volume = 2021,
pages = {1-9},
doi = {10.1155/2021/6708865},
issn = {2356-6981},
url = {http://dx.doi.org/10.1155/2021/6708865},
editor = {Rao, Kosagi S. Jagannatha}
}`,`
@book{Behrhorst2020,
title = {Mental Health in Cystic Fibrosis},
author = {Behrhorst, Kathryn L. and Everhart, Robin S. and Schechter, Michael S.},
year = 2020,
booktitle = {Cystic Fibrosis},
publisher = {Springer International Publishing},
pages = {429-447},
doi = {10.1007/978-3-030-42382-7_21},
isbn = 9783030423827,
issn = {2197-7380},
url = {http://dx.doi.org/10.1007/978-3-030-42382-7_21}
}`,`
@article{Southern01,
title = {Newborn screening for cystic fibrosis},
author = {Southern, KW, Mérelle, MME, Dankert‐Roelse, JE, and Nagelkerke, A},
year = 2009,
journal = {Cochrane Database of Systematic Reviews},
publisher = {John Wiley & Sons, Ltd},
number = 1,
doi = {10.1002/14651858.CD001402.pub2},
issn = {1465-1858},
url = {https://doi.org//10.1002/14651858.CD001402.pub2},
keywords = {
*Neonatal Screening; Cystic Fibrosis [*diagnosis]; Humans; Infant, Newborn;
Quality of Life; Randomized Controlled Trials as Topic; Survival Analysis
}
}`,`
@book{Paracchini2012,
title = {
Cystic Fibrosis Newborn Screening: Distribution of Blood Immunoreactive
Trypsinogen Concentrations in Hypertrypsinemic Neonates
},
author = {
Paracchini, Valentina and Seia, Manuela and Raimondi, Sara and Costantino,
Lucy and Capasso, Patrizia and Porcaro, Luigi and Colombo, Carla and
Coviello, Domenico A. and Mariani, Tiziana and Manzoni, Emanuela and
Sangiovanni, Monica and Corbetta, Carlo
},
year = 2012,
booktitle = {JIMD Reports - Case and Research Reports, 2012/1},
publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg},
pages = {17--23},
doi = {10.1007/8904_2011_55},
isbn = {978-3-642-25752-0},
url = {https://doi.org/10.1007/8904_2011_55},
abstract = {
The IRT screening test for the use in diagnosing newborns with CF has a high
sensitivity but is not very specific resulting in a large number of screened
positive infants found to have a normal sweat test. The aim of this study was
to analyze the differences in b-IRT levels among different groups of newborns
positive to NBS.
}
}`,`
@article{Barben2006,
title = {A survey of newborn screening for cystic fibrosis in Europe},
author = {
Barben, Jürg and Southern, Kevin W. and Greaves, David A. and Heaf, Annick and
Dodge, Michael J.
},
year = 2006,
journal = {Journal of Cystic Fibrosis},
volume = 5,
number = 3,
pages = {143--148},
doi = {10.1016/j.jcf.2006.05.008},
url = {
https://www.cysticfibrosisjournal.com/article/S1569-1993(06)00073-7/fulltext
}
}`,`
@misc{cff2024newborn,
title = {Newborn Screening for CF},
author = {Cystic Fibrosis Foundation},
year = 2024,
url = {https://www.cff.org/intro-cf/newborn-screening-cf},
note = {Zugriff am 2. Dezember 2024}
}
`,`
@article{genes11040401,
title = {
The Impact of the CFTR Gene Discovery on Cystic Fibrosis Diagnosis,
Counseling, and Preventive Therapy
},
author = {Farrell, Philip M. and Rock, Michael J. and Baker, Mei W.},
year = 2020,
journal = {Genes},
volume = 11,
number = 4,
doi = {10.3390/genes11040401},
issn = {2073-4425},
url = {https://www.mdpi.com/2073-4425/11/4/401},
article-number = 401,
pubmedid = 32276344
}`,`
@article{farrell2020impact,
title = {The impact of the CFTR gene discovery on cystic fibrosis diagnosis, counseling, and preventive therapy},
author = {Farrell, Philip M and Rock, Michael J and Baker, Mei W},
year = 2020,
journal = {Genes},
publisher = {MDPI},
volume = 11,
number = 4,
pages = 401
}`,`
@article{REISMAN1988632,
title = {Role of conventional physiotherapy in cystic fibrosis},
author = {Reisman, John J. and Rivington-Law, Betty and Corey, Mary and Marcotte, Jacques and Wannamaker, Eleanor and Harcourt, Dawn and Levison, Henry},
year = 1988,
journal = {The Journal of Pediatrics},
volume = 113,
number = 4,
pages = {632--636},
doi = {https://doi.org/10.1016/S0022-3476(88)80370-6},
issn = {0022-3476},
url = {https://www.sciencedirect.com/science/article/pii/S0022347688803706}
}`,`
@article{Wainwright2015,
title = {Lumacaftor–ivacaftor in patients with cystic fibrosis homozygous for Phe508del CFTR},
author = {Wainwright, Claire E and Elborn, J Stuart and Ramsey, Bonnie W and Marigowda, Girish and Huang, Xinxin and Cipolli, Marco and Colombo, Carlo and Davies, Jane C and De Boeck, Kris and Flume, Patrick A and others},
year = 2015,
journal = {New England Journal of Medicine},
publisher = {Massachusetts Medical Society},
volume = 373,
number = 3,
pages = {220--231},
doi = {10.1056/NEJMoa1409547}
}`,`
@article{Geller658,
title = {Aerosol Antibiotics in Cystic Fibrosis},
author = {Geller, David E},
year = 2009,
journal = {Respiratory Care},
publisher = {Respiratory Care},
volume = 54,
number = 5,
pages = {658--670},
url = {https://rc.rcjournal.com/content/54/5/658},
ssn = {0020-1324},
eprint = {https://rc.rcjournal.com/content/54/5/658.full.pdf}
}`,`
@article{Tummler2016,
title = {Therapie der Mukoviszidose mit CFTR-Modulatoren},
author = {Tümmler, B.},
year = 2016,
journal = {Pneumologie},
publisher = {Georg Thieme Verlag KG},
volume = 70,
number = 3,
pages = {301--313},
doi = {10.1055/s-0042-100607},
issn = {0934-8387},
url = {https://www.thieme-connect.com/products/ejournals/pdf/10.1055/s-0042-100607.pdf}
}`,`
@misc{MukoTrikafta2024internet,
title = {Kaftrio (Trikafta) – Triple-Therapie für Mukoviszidose (CF)},
author = {Mukoviszidose e.V.},
year = 2024,
url = {https://www.muko.info/mukoviszidose/therapie-der-mukoviszidose/kaftrio-trikafta​},
note = {Zugriff am 07. August 2024}
}
`,`
@misc{muko2024therapie,
title = {Therapie der Mukoviszidose},
author = {Mukoviszidose e.V.},
year = 2024,
url = {https://www.muko.info/mukoviszidose/therapie-der-mukoviszidose},
note = {Zugriff am 7. August 2024}
}`,`
@article{Jia2023,
title = {Cystic Fibrosis Modulator Therapies},
author = {Jia, Shijing and Taylor-Cousar, Jennifer L.},
year = 2023,
journal = {Annual Review of Medicine},
volume = 74,
pages = {413--426},
doi = {10.1146/annurev-med-042921-021447},
url = {https://doi.org/10.1146/annurev-med-042921-021447}
}`,`
@article{Tuemmler2016,
title = {Therapie der Mukoviszidose mit CFTR-Modulatoren},
author = {Tümmler, Burkhard},
year = 2016,
journal = {Pneumologie},
volume = 70,
number = 5,
pages = {301--313},
doi = {10.1055/s-0042-100607},
url = {
https://www.thieme-connect.com/products/ejournals/html/10.1055/s-0042-100607
}
}`,`
@article{doihbjhb,
title = {New drugs in cystic fibrosis: what has changed in the last decade?},
author = {
Roda, Juliana and Pinto-Silva, Catarina and Silva, Iris A.I. and Maia, Carla and
Almeida, Susana and Ferreira, Ricardo and Oliveira, Guiomar
},
year = 2022,
journal = {Therapeutic Advances in Chronic Disease},
volume = 13,
pages = 20406223221098136,
doi = {10.1177/20406223221098136},
url = {https://doi.org/10.1177/20406223221098136},
note = {PMID: 35620188},
eprint = {https://doi.org/10.1177/20406223221098136}
}`,`
@misc{cff2024antibiotics,
title = {Managing CF: Antibiotics},
author = {Cystic Fibrosis Foundation},
year = 2024,
url = {https://www.cff.org/managing-cf/antibiotics},
note = {Zugriff am 7. August 2024}
}`,`
@misc{ema2024tobi,
title = {Tobi Podhaler: EPAR - Summary for the Public},
author = {European Medicines Agency (EMA)},
year = 2024,
url = {https://www.ema.europa.eu/en/medicines/human/EPAR/tobi-podhaler},
note = {Zugriff am 7. August 2024}
}`,`
@misc{muko2024pankreas,
title = {Pankreasinsuffizienz und Enzymsubstitution},
author = {Mukoviszidose e.V.},
year = 2024,
url = {
https://www.muko.info/mitwirken/arbeitskreise-und-arbeitsgemeinschaften/ak-ernaehrung/ernaehrungstherapie-bei-mukoviszidose/pankreasinsuffizienz-und-enzymsubstitution
},
note = {Zugriff am 7. August 2024}
}`,`
@article{hjbhjgj,
title = {Search-and-replace genome editing without double-strand breaks or donor DNA},
author = {Anzalone, Andrew V. and Randolph, Peyton B. and Davis, Jessie R. and Sousa, Alexander A. and Koblan, Luke W. and Levy, Jonathan M. and Chen, Peter J. and Wilson, Christopher and Newby, Gregory A. and Raguram, Aditya and Liu, David R.},
year = 2019,
journal = {Nature},
volume = 576,
number = 7785,
pages = {149--157},
doi = {10.1038/s41586-019-1711-4}
}
`,`
@article{ivpeoamldim2022,
title = {In vivo prime editing of a metabolic liver disease in mice},
author = {
Böck D, Rothgangl T, Villiger L, Schmidheini L, Matsushita M, Mathis N,
Ioannidi E, Rimann N, Grisch-Chan HM, Kreutzer S, Kontarakis Z, Kopf M, Thöny
B, Schwank G
},
year = 2022,
journal = {PupMed},
volume = 14,
number = 1,
pages = {eabl9238},
doi = {10.1126/scitranslmed.abl9238},
url = {https://pmc.ncbi.nlm.nih.gov/articles/PMC7614134/}
}`,`
@article{CasX_enzymes_comprise_a_distinct_family_of_RNA-guided_genome_editors,
title = {CasX enzymes comprise a distinct family of RNA-guided genome editors},
author = {Liu, Jun-Jie and Orlova, Natalia and Oakes, Benjamin L. and Ma, Enbo and Spinner, Hannah B. and Baney, Katherine L. M. and Chuck, Jonathan and Tan, Dan and Knott, Gavin J. and Harrington, Lucas B. and Al-Shayeb, Basem and Wagner, Alexander and Brötzmann, Julian and Staahl, Brett T. and Taylor, Kian L. and Desmarais, John and Nogales, Eva and Doudna, Jennifer A.},
year = 2019,
journal = {Nature},
volume = 566,
number = 7743,
pages = 218,
doi = {10.1038/s41586-019-0908-x}
}`,`
@article{Fanzor_is_a_eukaryotic_programmable_RNA-guided_endonuclease,
title = {Fanzor is a eukaryotic programmable RNA-guided endonuclease},
author = {Saito, Makoto and Xu, Peiyu and Faure, Guilhem and Maguire, Samantha and Kannan, Soumya and Altae-Tran, Han and Vo, Sam and Desimone, AnAn and Macrae, Rhiannon K. and Zhang, Feng},
year = 2023,
journal = {Nature},
volume = 620,
number = 7974,
pages = 660,
doi = {10.1038/s41586-023-06356-2}
}
`,`
@article{Ma2024,
title = {A Perspective of Lipid Nanoparticles for RNA Delivery},
author = {Ma, Yutian and Li, Shiyao and Lin, Xin and Chen, Yupeng},
year = 2024,
journal = {Exploration},
volume = 4,
number = 1,
pages = 20230147,
doi = {10.1002/EXP.20230147},
url = {https://onlinelibrary.wiley.com/doi/10.1002/EXP.20230147}
}`,`
@article{Sahay2021,
title = {Lipid nanoparticles for mRNA delivery},
author = {Sahay, Gaurav and Querbes, Jordan and Gupta, Amit K. and Stanton-Maxey, Benjamin Z. and Davis, Mark E. and Szoka, Frank C. and Anderson, Daniel G.},
year = 2021,
journal = {Nature Reviews Materials},
volume = 6,
pages = {1078--1094},
doi = {10.1038/s41578-021-00358-0},
url = {https://www.nature.com/articles/s41578-021-00358-0}
}
`,`
@article{NEARY2024812,
title = {
Nebulised delivery of RNA formulations to the lungs: From aerosol to cytosol
},
author = {Neary, Michael T. and Mulder, Lianne M. and Kowalski, Piotr S. and MacLoughlin, Ronan and Crean, Abina M. and Ryan, Katie B.},
year = 2024,
journal = {Journal of Controlled Release},
volume = 366,
pages = {812--833},
doi = {https://doi.org/10.1016/j.jconrel.2023.12.012},
issn = {0168-3659},
url = {https://www.sciencedirect.com/science/article/pii/S0168365923007964}
}`,`
@article{WANG2024105547,
title = {
The optimization strategies of LNP-mRNA formulations: Development and
challenges for further application
},
author = {Wang, Sizhen and Guo, Beibei and Wang, Huan and Yang, Feng},
year = 2024,
journal = {Journal of Drug Delivery Science and Technology},
volume = 95,
pages = 105547,
doi = {https://doi.org/10.1016/j.jddst.2024.105547},
issn = {1773-2247},
url = {https://www.sciencedirect.com/science/article/pii/S1773224724002156}
}`,`
@article{TAHA2022345,
title = {
Delivery of CRISPR-Cas tools for in vivo genome editing therapy: Trends and
challenges
},
author = {Taha, Eman A. and Lee, Joseph and Hotta, Akitsu},
year = 2022,
journal = {Journal of Controlled Release},
volume = 342,
pages = {345--361},
doi = {https://doi.org/10.1016/j.jconrel.2022.01.013},
issn = {0168-3659},
url = {https://www.sciencedirect.com/science/article/pii/S016836592200027X}
}`,`
@article{LOPRESTI2022819,
title = {
The replacement of helper lipids with charged alternatives in lipid
nanoparticles facilitates targeted mRNA delivery to the spleen and lungs
},
author = {
LoPresti, Samuel T. and Arral, Mariah L. and Chaudhary, Namit and Whitehead, Kathryn A.
},
year = 2022,
journal = {Journal of Controlled Release},
volume = 345,
pages = {819--831},
doi = {https://doi.org/10.1016/j.jconrel.2022.03.046},
issn = {0168-3659},
url = {https://www.sciencedirect.com/science/article/pii/S0168365922001808}
}`,`
@article{pharmaceutics15030772,
title = {
Recent Progress of Lipid Nanoparticles-Based Lipophilic Drug Delivery: Focus
on Surface Modifications
},
author = {
Seo, Yoseph and Lim, Hayeon and Park, Hyunjun and Yu, Jiyun and An, Jeongyun
and Yoo, Hah Young and Lee, Taek
},
year = 2023,
journal = {Pharmaceutics},
volume = 15,
number = 3,
doi = {10.3390/pharmaceutics15030772},
issn = {1999-4923},
url = {https://www.mdpi.com/1999-4923/15/3/772},
article-number = 772,
pubmedid = 36986633
}`,`
@article{YAMAMOTO2005373,
title = {
Surface-modified PLGA nanosphere with chitosan improved pulmonary delivery of
calcitonin by mucoadhesion and opening of the intercellular tight junctions
},
author = {
Yamamoto, Hiromitsu and Kuno, Yoshio and Sugimoto, Shohei and Takeuchi, Hirofumi and Kawashima, Yoshiaki
},
year = 2005,
journal = {Journal of Controlled Release},
volume = 102,
number = 2,
pages = {373--381},
doi = {https://doi.org/10.1016/j.jconrel.2004.10.010},
issn = {0168-3659},
url = {https://www.sciencedirect.com/science/article/pii/S0168365904004912}
}`,`
@article{Hashiba2024,
title = {
Overcoming thermostability challenges in mRNA-lipid nanoparticle systems with
piperidine-based ionizable lipids
},
author = {
Hashiba, Kazuki and Taguchi, Masamitsu and Sakamoto, Sachiko and Otsu, Ayaka and Maeda, Yoshiki and Ebe, Hirofumi and Okazaki, Arimichi and Harashima, Hideyoshi and Sato, Yusuke
},
year = 2024,
journal = {Communications Biology},
volume = 7,
pages = 556,
doi = {10.1038/s42003-024-06235-0},
url = {https://www.nature.com/articles/s42003-024-06235-0}
}`,`
@article{Schober2024,
title = {
A careful look at lipid nanoparticle characterization: analysis of benchmark
formulations for encapsulation of RNA cargo size gradient
},
author = {Schober, Gretchen B. and Story, Sandra and Arya, Dev P.},
year = 2024,
journal = {Scientific Reports},
volume = 14,
pages = 2403,
doi = {10.1038/s41598-024-52685-1},
url = {https://www.nature.com/articles/s41598-024-52685-1}
}`,`
@article{Cullis2017,
title = {Lipid Nanoparticle Systems for Enabling Gene Therapies},
author = {Cullis, Pieter R. },
year = 2017,
journal = {Molecular Therapy},
volume = 25,
number = 7,
pages = {1463--1466},
doi = {10.1016/j.ymthe.2017.03.027},
url = {
https://www.cell.com/molecular-therapy-family/molecular-therapy/fulltext/S1525-0016(17)30111-9
}
}`,`
@article{Kim2022,
title = {
Engineering Lipid Nanoparticles for Enhanced Intracellular Delivery of mRNA
through Inhalation
},
author = {
Kim, Jeonghwan and Jozic, Antony and Lin, Yuxin and Eygeris, Yulia and Bloom, Elissa and Tan, Xiaochen and Acosta, Christopher and MacDonald, Kelvin D. and Welsher, Kevin D. and Sahay, Gaurav
},
year = 2022,
journal = {Proceedings of the National Academy of Sciences},
volume = 119,
number = 36,
pages = {e2202539119},
doi = {10.1073/pnas.2202539119},
url = {https://www.pnas.org/doi/10.1073/pnas.2202539119}
}`,`
@article{Wang2023,
title = {
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs)
using multiple technical methods for tissue-specific mRNA delivery
},
author = {
Wang, Xu and Liu, Shuai and Sun, Yehui and Yu, Xueliang and Lee, Sang M. and Cheng, Qiang and Wei, Tuo and Gong, Junyu and Robinson, Joshua and Zhang, Di and Lian, Xizhen and Basak, Pratima and Siegwart, Daniel J.
},
year = 2023,
journal = {Nature Protocols},
volume = 18,
pages = {265--291},
doi = {10.1038/s41596-022-00755-x},
url = {https://doi.org/10.1038/s41596-022-00755-x}
}`,`
@article{Wei2023,
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,
journal = {Nature Communications},
volume = 14,
pages = 7322,
doi = {10.1038/s41467-023-42948-2},
url = {https://doi.org/10.1038/s41467-023-42948-2}
}`,`
@article{ZIMMERMANN2022137,
title = {Spray drying siRNA-lipid nanoparticles for dry powder pulmonary delivery},
author = {
Zimmermann, Christoph M. and Baldassi, Domizia and Chan, Karen and Adams, Nathan B.P. and Neumann, Alina and Porras-Gonzalez, Diana Leidy and Wei, Xin and Kneidinger, Nikolaus and Stoleriu, Mircea Gabriel and Burgstaller, Gerald and Witzigmann, Dominik and Luciani, Paola and Merkel, Olivia M.
},
year = 2022,
journal = {Journal of Controlled Release},
volume = 351,
pages = {137--150},
doi = {https://doi.org/10.1016/j.jconrel.2022.09.021},
issn = {0168-3659},
url = {https://www.sciencedirect.com/science/article/pii/S0168365922006137},
keywords = {
Lipid nanoparticles, LNP, Onpattro®, RNA therapeutics, siRNA delivery, Spray
drying, Pulmonary delivery, Respiratory diseases, Human precision-cut lung
slices, Formulation screening
}
}`,`
@article{IWAWAKI2006709,
title = {
Analysis of the XBP1 splicing mechanism using endoplasmic reticulum
stress-indicators
},
author = {Iwawaki, Takao and Akai, Ryoko},
year = 2006,
journal = {Biochemical and Biophysical Research Communications},
volume = 350,
number = 3,
pages = {709--715},
doi = {https://doi.org/10.1016/j.bbrc.2006.09.100},
issn = {0006-291X},
url = {https://www.sciencedirect.com/science/article/pii/S0006291X06021553},
keywords = {ER stress, IRE1, Splicing, Unfolded protein response, XBP1}
}
`
]
src/sources/education-souces.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function EduSources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} special="edu" />
</div>
);
}
const bibtexSources = [
`@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
src/sources/eng-delivery-sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function EngDelsources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} start={30}/>
</div>
);
}
const bibtexSources = [
`
@article{TAHA2022345,
title = {Delivery of CRISPR-Cas tools for in vivo genome editing therapy: Trends and challenges},
author = {Eman A. Taha and Joseph Lee and Akitsu Hotta},
year = 2022,
journal = {Journal of Controlled Release},
volume = 342,
pages = {345--361},
doi = {https://doi.org/10.1016/j.jconrel.2022.01.013},
issn = {0168-3659},
url = {https://www.sciencedirect.com/science/article/pii/S016836592200027X},
keywords = {CRISPR-Cas, Delivery, AAV, Virus-like particle, Lipid nanoparticle, Gene therapy},
abstract = {The discovery of clustered regularly interspaced short palindromic repeats (CRISPR) genome editing technology opened the door to provide a versatile approach for treating multiple diseases. Promising results have been shown in numerous pre-clinical studies and clinical trials. However, a safe and effective method to deliver genome-editing components is still a key challenge for in vivo genome editing therapy. Adeno-associated virus (AAV) is one of the most commonly used vector systems to date, but immunogenicity against capsid, liver toxicity at high dose, and potential genotoxicity caused by off-target mutagenesis and genomic integration remain unsolved. Recently developed transient delivery systems, such as virus-like particle (VLP) and lipid nanoparticle (LNP), may solve some of the issues. This review summarizes existing in vivo delivery systems and possible solutions to overcome their limitations. Also, we highlight the ongoing clinical trials for in vivo genome editing therapy and recently developed genome editing tools for their potential applications.}
}
`,`
@article{verma_landscape_2023,
title = {The landscape for lipid-nanoparticle-based genomic medicines},
author = {Verma, Malvika and Ozer, Imran and Xie, Wen and Gallagher, Ryan and Teixeira, Alexandra and Choy, Michael},
year = 2023,
month = may,
journal = {Nature Reviews Drug Discovery},
volume = 22,
number = 5,
pages = {349--350},
doi = {10.1038/d41573-023-00002-2},
issn = {1474-1776, 1474-1784},
url = {https://www.nature.com/articles/d41573-023-00002-2},
urldate = {2024-09-16},
copyright = {https://www.springernature.com/gp/researchers/text-and-data-mining},
language = {en},
file = {Verma et al. - 2023 - The landscape for lipid-nanoparticle-based genomic.pdf:C\:\\Users\\Isabell\\Zotero\\storage\\ZESPW7JJ\\Verma et al. - 2023 - The landscape for lipid-nanoparticle-based genomic.pdf:application/pdf}
}
`,`
@article{taha_delivery_2022,
title = {Delivery of {CRISPR}-{Cas} tools for in vivo genome editing therapy: {Trends} and challenges},
shorttitle = {Delivery of {CRISPR}-{Cas} tools for in vivo genome editing therapy},
author = {Taha, Eman A. and Lee, Joseph and Hotta, Akitsu},
year = 2022,
month = feb,
journal = {Journal of Controlled Release},
volume = 342,
pages = {345--361},
doi = {10.1016/j.jconrel.2022.01.013},
issn = {01683659},
url = {https://linkinghub.elsevier.com/retrieve/pii/S016836592200027X},
urldate = {2024-09-16},
abstract = {The discovery of clustered regularly interspaced short palindromic repeats (CRISPR) genome editing technology opened the door to provide a versatile approach for treating multiple diseases. Promising results have been shown in numerous pre-clinical studies and clinical trials. However, a safe and effective method to deliver genome-editing components is still a key challenge for in vivo genome editing therapy. Adeno-associated virus (AAV) is one of the most commonly used vector systems to date, but immunogenicity against capsid, liver toxicity at high dose, and potential genotoxicity caused by off-target mutagenesis and genomic integration remain unsolved. Recently developed transient delivery systems, such as virus-like particle (VLP) and lipid nanoparticle (LNP), may solve some of the issues. This review summarizes existing in vivo delivery systems and possible solutions to overcome their limitations. Also, we highlight the ongoing clinical trials for in vivo genome editing therapy and recently developed genome editing tools for their potential applications.},
language = {en}
}
`,`
@manual{cayman_chemical_lipidlaunch_protocol,
title = {LipidLaunch™ LNP-102 Exploration Kit Protocol},
author = {{Cayman Chemical}},
year = 2024,
url = {https://cdn.caymanchem.com/cdn/insert/35425.pdf},
note = {Accessed: 2024-09-16}
}
`,`
@misc{corden_pharma_lnp_2024,
title = {LNP Formulation and Manufacturing},
author = {{Corden Pharma}},
year = 2024,
url = {https://cordenpharma.com/what-you-need/drug-products/support-services/lnp-formulation-manufacturing/},
note = {Accessed: 2024-09-18}
}
`,`
@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}
}
`,`
@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.}
}
`,`
@article{ZIMMERMANN2022137,
title = {Spray drying siRNA-lipid nanoparticles for dry powder pulmonary delivery},
author = {Christoph M. Zimmermann and Domizia Baldassi and Karen Chan and Nathan B.P. Adams and Alina Neumann and Diana Leidy Porras-Gonzalez and Xin Wei and Nikolaus Kneidinger and Mircea Gabriel Stoleriu and Gerald Burgstaller and Dominik Witzigmann and Paola Luciani and Olivia M. Merkel},
year = 2022,
journal = {Journal of Controlled Release},
volume = 351,
pages = {137--150},
doi = {https://doi.org/10.1016/j.jconrel.2022.09.021},
issn = {0168-3659},
url = {https://www.sciencedirect.com/science/article/pii/S0168365922006137},
keywords = {Lipid nanoparticles, LNP, Onpattro®, RNA therapeutics, siRNA delivery, Spray drying, Pulmonary delivery, Respiratory diseases, Human precision-cut lung slices, Formulation screening},
abstract = {While all the siRNA drugs on the market target the liver, the lungs offer a variety of currently undruggable targets which could potentially be treated with RNA therapeutics. Hence, local, pulmonary delivery of RNA nanoparticles could finally enable delivery beyond the liver. The administration of RNA drugs via dry powder inhalers offers many advantages related to physical, chemical and microbial stability of RNA and nanosuspensions. The present study was therefore designed to test the feasibility of engineering spray dried lipid nanoparticle (LNP) powders. Spray drying was performed using 5% lactose solution (m/V), and the targets were set to obtain nanoparticle sizes after redispersion of spray-dried powders around 150 nm, a residual moisture level below 5%, and RNA loss below 15% at maintained RNA bioactivity. The LNPs consisted of an ionizable cationic lipid which is a sulfur-containing analog of DLin-MC3-DMA, a helper lipid, cholesterol, and PEG-DMG encapsulating siRNA. Prior to the spray drying, the latter process was simulated with a novel dual emission fluorescence spectroscopy method to preselect the highest possible drying temperature and excipient solution maintaining LNP integrity and stability. Through characterization of physicochemical and aerodynamic properties of the spray dried powders, administration criteria for delivery to the lower respiratory tract were fulfilled. Spray dried LNPs penetrated the lung mucus layer and maintained bioactivity for >90% protein downregulation with a confirmed safety profile in a lung adenocarcinoma cell line. Additionally, the spray dried LNPs successfully achieved up to 50% gene silencing of the house keeping gene GAPDH in ex vivo human precision-cut lung slices at without increasing cytokine levels. This study verifies the successful spray drying procedure of LNP-siRNA systems maintaining their integrity and mediating strong gene silencing efficiency on mRNA and protein levels both in vitro and ex vivo. The successful spray drying procedure of LNP-siRNA formulations in 5% lactose solution creates a novel siRNA-based therapy option to target respiratory diseases such as lung cancer, asthma, COPD, Cystic Fibrosis and viral infections.}
}
`,`
@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}
}
`,`
@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}
}
`
]
\ No newline at end of file
src/sources/eng-nickases-sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function EngNicksources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} start={24}/>
</div>
);
}
const bibtexSources = [
`
@article{Saito_Xu_Faure_Maguire_Kannan_Altae-Tran_Vo_Desimone_Macrae_Zhang_2023,
title = {Fanzor is a eukaryotic programmable RNA-guided endonuclease},
author = {Saito, Makoto and Xu, Peiyu and Faure, Guilhem and Maguire, Samantha and Kannan, Soumya and Altae-Tran, Han and Vo, Sam and Desimone, AnAn and Macrae, Rhiannon K. and Zhang, Feng},
year = 2023,
month = aug,
journal = {Nature},
publisher = {Nature Publishing Group},
volume = 620,
number = 7974,
pages = {660–668},
doi = {10.1038/s41586-023-06356-2},
issn = {1476-4687},
rights = {2023 The Author(s)},
abstractnote = {RNA-guided systems, which use complementarity between a guide RNA and target nucleic acid sequences for recognition of genetic elements, have a central role in biological processes in both prokaryotes and eukaryotes. For example, the prokaryotic CRISPR–Cas systems provide adaptive immunity for bacteria and archaea against foreign genetic elements. Cas effectors such as Cas9 and Cas12 perform guide-RNA-dependent DNA cleavage1. Although a few eukaryotic RNA-guided systems have been studied, including RNA interference2 and ribosomal RNA modification3, it remains unclear whether eukaryotes have RNA-guided endonucleases. Recently, a new class of prokaryotic RNA-guided systems (termed OMEGA) was reported4,5. The OMEGA effector TnpB is the putative ancestor of Cas12 and has RNA-guided endonuclease activity4,6. TnpB may also be the ancestor of the eukaryotic transposon-encoded Fanzor (Fz) proteins4,7, raising the possibility that eukaryotes are also equipped with CRISPR–Cas or OMEGA-like programmable RNA-guided endonucleases. Here we report the biochemical characterization of Fz, showing that it is an RNA-guided DNA endonuclease. We also show that Fz can be reprogrammed for human genome engineering applications. Finally, we resolve the structure of Spizellomyces punctatus Fz at 2.7 Å using cryogenic electron microscopy, showing the conservation of core regions among Fz, TnpB and Cas12, despite diverse cognate RNA structures. Our results show that Fz is a eukaryotic OMEGA system, demonstrating that RNA-guided endonucleases are present in all three domains of life.},
language = {en}
}
`,`
@article{ijms25031622,
title = {An Efficient Expression and Purification Protocol for SpCas9 Nuclease and Evaluation of Different Delivery Methods of Ribonucleoprotein},
author = {Evmenov, Konstantin and Pustogarov, Nikolay and Panteleev, Dmitri and Safin, Artur and Alkalaeva, Elena},
year = 2024,
journal = {International Journal of Molecular Sciences},
volume = 25,
number = 3,
doi = {10.3390/ijms25031622},
issn = {1422-0067},
url = {https://www.mdpi.com/1422-0067/25/3/1622},
article-number = 1622,
pubmedid = 38338898,
abstract = {The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 system is a revolutionary tool for precise genome editing across various cell types. Ribonucleoproteins (RNPs), encompassing the Cas9 protein and guide RNA (gRNA), have emerged as a promising technique due to their increased specificity and reduced off-target effects. This method eliminates the need for plasmid DNA introduction, thereby preventing potential integration of foreign DNA into the target cell genome. Given the requirement for large quantities of highly purified protein in various Cas9 studies, we present an efficient and simple method for the preparation of recombinant Streptococcus pyogenes Cas9 (SpCas9) protein. This method leverages the Small Ubiquitin Like Modifier(SUMO) tag system, which includes metal-affinity chromatography followed by anion-exchange chromatography purification. Furthermore, we compare two methods of CRISPR-Cas9 system delivery into cells: transfection with plasmid DNA encoding the CRISPR-Cas9 system and RNP transfection with the Cas9-gRNA complex. We estimate the efficiency of genomic editing and protein lifespan post-transfection. Intriguingly, we found that RNP treatment of cells, even in the absence of a transfection system, is a relatively efficient method for RNP delivery into cell culture. This discovery is particularly promising as it can significantly reduce cytotoxicity, which is crucial for certain cell cultures such as induced pluripotent stem cells (iPSCs).}
}
`,`
@article{Hillary2023Review,
title = {A Review on the Mechanism and Applications of CRISPR/Cas9/Cas12/Cas13/Cas14 Proteins Utilized for Genome Engineering},
author = {Hillary, V. E. and Ceasar, S. A.},
year = 2023,
journal = {Molecular Biotechnology},
volume = 65,
pages = {311--325},
doi = {10.1007/s12033-022-00567-0}
}
`,`
@article{10.3389/fgeed.2024.1471720,
title = {Use of paired Cas9-NG nickase and truncated sgRNAs for single-nucleotide microbial genome editing},
author = {Jeong, Song Hee and Lee, Ho Joung and Lee, Sang Jun},
year = 2024,
journal = {Frontiers in Genome Editing},
volume = 6,
doi = {10.3389/fgeed.2024.1471720},
issn = {2673-3439},
url = {https://www.frontiersin.org/journals/genome-editing/articles/10.3389/fgeed.2024.1471720},
abstract = {<p>The paired nickases approach, which utilizes clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) nickase and dual guide RNA, has the advantage of reducing off-target effects by being able to double the target sequence. In this study, our research utilized the Cas9-NG nickase variant to minimize PAM sequence constraints, enabling the generation of paired nicks at desired genomic loci. We performed a systematic investigation into the formation sites for double nicks and the design of donor DNA within a bacterial model system. Although we successfully identified the conditions necessary for the effective formation of double nicks <italic>in vivo</italic>, achieving single-nucleotide level editing directly at the target sites in the genome proved challenging. Nonetheless, our experiments revealed that efficient editing at the single-nucleotide level was achievable on target DNA sequences that are hybridized with 5′-end-truncated dual single-guide RNAs (sgRNAs). Our findings contribute to a deeper understanding of the paired nickases approach, offering a single-mismatch intolerance design strategy for accurate nucleotide editing. This strategy not only enhances the precision of genome editing but also marks a significant step forward in the development of nickase-derived genome editing technologies.</p>}
}
`,`
@article{Badon2024CRISPR,
title = {Recent application of CRISPR-Cas12 and OMEGA system for genome editing},
author = {Badon, Isabel Wen and Oh, Yeonsun and Kim, Ho-Joong and Lee, Seung Hwan},
year = 2024,
month = {January},
journal = {Molecular Therapy},
volume = 32,
number = 1,
pages = {32--43},
doi = {10.1016/j.ymthe.2023.11.013},
url = {https://www.cell.com/molecular-therapy/fulltext/S1525-0016(23)00113-2}
}
`,`
@article{Kim2024Nicking,
title = {Utilization of nicking properties of CRISPR-Cas12a effector for genome editing},
author = {Kim, Chan Hyoung and Lee, Wi-jae and Oh, Yeonsun and Lee, Youngjeon and Lee, Hyomin K. and Seong, Jung Bae and Lim, Kyung-Seob and Park, Sang Je and Huh, Jae-Won and Kim, Young-Hyun and Kim, Kyoung Mi and Hur, Junho K. and Lee, Seung Hwan},
year = 2024,
month = {February},
journal = {Scientific Reports},
volume = 14,
pages = 3352,
doi = {10.1038/s41598-024-53648-2},
issn = {2045-2322},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10858195},
pmid = 38336977,
pmcid = {PMC10858195}
}
`
]
\ No newline at end of file
src/sources/eng-pe-sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function EngPEsystems(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} start={6}/>
</div>
);
}
const bibtexSources = [ /* 1-> 6 */
`@article{Anzalone_Randolph_Davis_Sousa_Koblan_Levy_Chen_Wilson_Newby_Raguram_2019,
title = {Search-and-replace genome editing without double-strand breaks or donor DNA},
author = {Anzalone, Andrew V. and Randolph, Peyton B. and Davis, Jessie R. and Sousa, Alexander A. and Koblan, Luke W. and Levy, Jonathan M. and Chen, Peter J. and Wilson, Christopher and Newby, Gregory A. and Raguram, Aditya and Liu, David R.},
year = 2019,
month = dec,
journal = {Nature},
publisher = {Nature Publishing Group},
volume = 576,
number = 7785,
pages = {149–157},
doi = {10.1038/s41586-019-1711-4},
issn = {1476-4687},
rights = {2019 The Author(s), under exclusive licence to Springer Nature Limited},
abstractnote = {Most genetic variants that contribute to disease1 are challenging to correct efficiently and without excess byproducts2–5. Here we describe prime editing, a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a catalytically impaired Cas9 endonuclease fused to an engineered reverse transcriptase, programmed with a prime editing guide RNA (pegRNA) that both specifies the target site and encodes the desired edit. We performed more than 175 edits in human cells, including targeted insertions, deletions, and all 12 types of point mutation, without requiring double-strand breaks or donor DNA templates. We used prime editing in human cells to correct, efficiently and with few byproducts, the primary genetic causes of sickle cell disease (requiring a transversion in HBB) and Tay–Sachs disease (requiring a deletion in HEXA); to install a protective transversion in PRNP; and to insert various tags and epitopes precisely into target loci. Four human cell lines and primary post-mitotic mouse cortical neurons support prime editing with varying efficiencies. Prime editing shows higher or similar efficiency and fewer byproducts than homology-directed repair, has complementary strengths and weaknesses compared to base editing, and induces much lower off-target editing than Cas9 nuclease at known Cas9 off-target sites. Prime editing substantially expands the scope and capabilities of genome editing, and in principle could correct up to 89% of known genetic variants associated with human diseases.},
language = {en}
}`,
/* 2 -> 7 Ehemals 7, jetzt 13 */
`@article{Jinek_Chylinski_Fonfara_Hauer_Doudna_Charpentier_2012,
title = {A programmable dual RNA-guided DNA endonuclease in adaptive bacterial immunity},
author = {Jinek, Martin and Chylinski, Krzysztof and Fonfara, Ines and Hauer, Michael and Doudna, Jennifer A. and Charpentier, Emmanuelle},
year = 2012,
month = aug,
journal = {Science},
volume = 337,
number = 6096,
pages = {816–821},
doi = {10.1126/science.1225829},
issn = {0036-8075},
abstractnote = {CRISPR/Cas systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using crRNAs to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA base-paired to trans-activating tracrRNA forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand while the Cas9 RuvC-like domain cleaves the non-complementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing., A two-RNA structure directs an endonuclease to cleave target DNA.}
}`,
/* 3 -> 8 Ehemals 8, jetzt 14 */
`@article{Gao_Ravendran_Mikkelsen_Haldrup_Cai_Ding_Paludan_Thomsen_Mikkelsen_Bak_2022,
title = {A truncated reverse transcriptase enhances prime editing by split AAV vectors},
author = {Gao, Zongliang and Ravendran, Sujan and Mikkelsen, Nanna S. and Haldrup, Jakob and Cai, Huiqiang and Ding, Xiangning and Paludan, Søren R. and Thomsen, Martin K. and Mikkelsen, Jacob Giehm and Bak, Rasmus O.},
year = 2022,
month = sep,
journal = {Molecular Therapy},
publisher = {Elsevier},
volume = 30,
number = 9,
pages = {2942–2951},
doi = {10.1016/j.ymthe.2022.07.001},
issn = {1525-0016, 1525-0024},
language = {English}
}`,
/* 4 -> 9 Hemelas 9, jetzt 15 */
`@article{Chen_Hussmann_Yan_Knipping_Ravisankar_Chen_Chen_Nelson_Newby_Sahin_2021,
title = {Enhanced prime editing systems by manipulating cellular determinants of editing outcomes},
author = {Chen, Peter J. and Hussmann, Jeffrey A. and Yan, Jun and Knipping, Friederike and Ravisankar, Purnima and Chen, Pin-Fang and Chen, Cidi and Nelson, James W. and Newby, Gregory A. and Sahin, Mustafa and Osborn, Mark J. and Weissman, Jonathan S. and Adamson, Britt and Liu, David R.},
year = 2021,
month = oct,
journal = {Cell},
volume = 184,
number = 22,
pages = {5635--5652},
doi = {10.1016/j.cell.2021.09.018},
issn = {0092-8674},
abstractnote = {While prime editing enables precise sequence changes in DNA, cellular determinants of prime editing remain poorly understood. Using pooled CRISPRi screens, we discovered that DNA mismatch repair (MMR) impedes prime editing and promotes undesired indel byproducts. We developed PE4 and PE5 prime editing systems in which transient expression of an engineered MMR-inhibiting protein enhances the efficiency of substitution, small insertion, and small deletion prime edits by an average 7.7-fold and 2.0-fold compared to PE2 and PE3 systems, respectively, while improving edit/indel ratios by 3.4-fold in MMR-proficient cell types. Strategic installation of silent mutations near the intended edit can enhance prime editing outcomes by evading MMR. Prime editor protein optimization resulted in a PEmax architecture that enhances editing efficacy by 2.8-fold on average in HeLa cells. These findings enrich our understanding of prime editing and establish prime editing systems that show substantial improvement across 191 edits in seven mammalian cell types.}
}`,
/* 5 -> 10 Ehemals 10, jetzt 16 */
`@article{Tomer_Buermeyer_Nguyen_Liskay_2002,
title = {Contribution of Human Mlh1 and Pms2 ATPase Activities to DNA Mismatch Repair},
author = {Tomer, Guy and Buermeyer, Andrew B. and Nguyen, Megan M. and Liskay, R. Michael},
year = 2002,
month = jun,
journal = {Journal of Biological Chemistry},
volume = 277,
number = 24,
pages = {21801–21809},
doi = {10.1074/jbc.M111342200},
issn = {0021-9258},
abstractnote = {MutLα, a heterodimer composed of Mlh1 and Pms2, is the major MutL activity in mammalian DNA mismatch repair. Highly conserved motifs in the N termini of both subunits predict that the protein is an ATPase. To study the significance of these motifs to mismatch repair, we have expressed in insect cells wild type human MutLα and forms altered in conserved glutamic acid residues, predicted to catalyze ATP hydrolysis of Mlh1, Pms2, or both. Using an in vitro assay, we showed that MutLα proteins altered in either glutamic acid residue were each partially defective in mismatch repair, whereas the double mutant showed no detectable mismatch repair. Neither strand specificity nor directionality of repair was affected in the single mutant proteins. Limited proteolysis studies of MutLα demonstrated that both Mlh1 and Pms2 N-terminal domains undergo ATP-induced conformational changes, but the extent of the conformational change for Mlh1 was more apparent than for Pms2. Furthermore, Mlh1 was protected at lower ATP concentrations than Pms2, suggesting Mlh1 binds ATP with higher affinity. These findings imply that ATP hydrolysis is required for MutLα activity in mismatch repair and that this activity is associated with differential conformational changes in Mlh1 and Pms2.}
}`,
/* 6 -> 11 Ehemals 11, jetzt 17 */
`@article{Wu_Corbett_Berland_2009,
title = {The Intracellular Mobility of Nuclear Import Receptors and NLS Cargoes},
author = {Wu, Jianrong and Corbett, Anita H. and Berland, Keith M.},
year = 2009,
month = may,
journal = {Biophysical Journal},
volume = 96,
number = 9,
pages = {3840–3849},
doi = {10.1016/j.bpj.2009.01.050},
issn = {0006-3495},
abstractnote = {We have investigated classical nuclear localization sequence (NLS) mediated protein trafficking by measuring biomolecular dynamics within living cells using two-photon fluorescence correlation spectroscopy. By directly observing the behavior of specific molecules in their native cellular environment, it is possible to uncover functional details that are not apparent from traditional biochemical investigations or functional assays. We show that the intracellular mobility of NLS cargoes and their import receptor proteins, karyopherin-α and karyopherin-β, can be robustly measured and that quantitative comparison of intracellular diffusion coefficients provides new insights into nuclear transport mechanisms. Import cargo complexes are assembled throughout the cytoplasm, and their diffusion is slower than predicted by molecular weight due to specific interactions. Analysis of NLS cargo diffusion in the cytoplasm indicates that these interactions are likely disrupted by NLS cargo binding. Our results suggest that delivery of import receptors and NLS cargoes to nuclear pores may complement selective translocation through the pores as a functional mechanism for regulating transport of proteins into the nucleus.}
}`,
/* 7 -> 12 Ehemals 12, jetzt 18 */
`@article{Dang_Lee_1988,
title = {Identification of the human c-myc protein nuclear translocation signal},
author = {Dang, C.V. and Lee, W.M.F.},
year = 1988,
journal = {Molecular and Cellular Biology},
volume = 8,
number = 10,
pages = {4048–4054},
doi = {10.1128/MCB.8.10.4048}
}`
,
/* 8 -> 13 */
`@article{Spencer_Zhang_2017,
title = {Deep mutational scanning of S. pyogenes Cas9 reveals important functional domains},
author = {Spencer, J.M. and Zhang, X.},
year = 2017,
journal = {Scientific Reports},
volume = 7,
number = 1,
doi = {10.1038/s41598-017-17081-y},
abstractnote = {RNA-guided endonucleases (RGENs) have invigorated the field of site-specific nucleases. The success of Streptococcus pyogenes Cas9 (SpCas9) has led to the discovery of several other CRISPR-Associated RGENs. As more RGENs become available, it will be necessary to refine their activity before they can be translated into the clinic. With this in mind, we sought to demonstrate how deep mutational scanning (DMS) could provide details about important functional regions in SpCas9 and speed engineering efforts. Consequently, we developed a nuclease screening platform which could distinguish active Cas9 mutants. We screened a library of 1.9 × 107 with over 8500 possible non-synonymous mutations and inferred the effects of each mutation using DMS. We demonstrate that the RuvC and HNH domains are the least tolerant regions to mutation. In contrast, the Rec2 and PI domains tolerate mutation better than other regions. The mutation information defined in this work provides a foundation for further SpCas9 engineering. Together, our results demonstrate how DMS can be a powerful tool to uncover features important to RGEN function. Application of this approach to emerging RGENs should enhance their engineering and optimization for therapeutic and other applications. © 2017 The Author(s).}
}`,
/* 9 -> 14 */
`@article{Doman_Pandey_Neugebauer_An_Davis_Randolph_McElroy_Gao_Raguram_Richter_2023,
title = {Phage-assisted evolution and protein engineering yield compact, efficient prime editors},
author = {Doman, Jordan L. and Pandey, Smriti and Neugebauer, Monica E. and An, Meirui and Davis, Jessie R. and Randolph, Peyton B. and McElroy, Amber and Gao, Xin D. and Raguram, Aditya and Richter, Michelle F. and Everette, Kelcee A. and Banskota, Samagya and Tian, Kathryn and Tao, Y. Allen and Tolar, Jakub and Osborn, Mark J. and Liu, David R.},
year = 2023,
month = aug,
journal = {Cell},
publisher = {Elsevier},
volume = 186,
number = 18,
pages = {3983--4002},
doi = {10.1016/j.cell.2023.07.039},
issn = {0092-8674, 1097-4172},
language = {English}
}`, /* 10 -> 15 */
`@article{Sousa_Hemez_Lei_Traore_Kulhankova_Newby_Doman_Oye_Pandey_Karp_2024,
title = {Systematic optimization of prime editing for the efficient functional correction of CFTR F508del in human airway epithelial cells},
author = {Sousa, Alexander A. and Hemez, Colin and Lei, Lei and Traore, Soumba and Kulhankova, Katarina and Newby, Gregory A. and Doman, Jordan L. and Oye, Keyede and Pandey, Smriti and Karp, Philip H. and McCray, Paul B. and Liu, David R.},
year = 2024,
month = jul,
journal = {Nature Biomedical Engineering},
publisher = {Nature Publishing Group},
pages = {1–15},
doi = {10.1038/s41551-024-01233-3},
issn = {2157-846X},
rights = {2024 The Author(s)},
abstractnote = {Prime editing (PE) enables precise and versatile genome editing without requiring double-stranded DNA breaks. Here we describe the systematic optimization of PE systems to efficiently correct human Cystic Fibrosis (CF) transmembrane conductance regulator (CFTR) F508del, a three-nucleotide deletion that is the predominant cause of CF. By combining six efficiency optimizations for PE—engineered PE guide RNAs, the PEmax architecture, the transient expression of a dominant-negative mismatch repair protein, strategic silent edits, PE6 variants and proximal ‘dead’ single-guide RNAs—we increased correction efficiencies for CFTR F508del from less than 0.5% in HEK293T cells to 58% in immortalized bronchial epithelial cells (a 140-fold improvement) and to 25% in patient-derived airway epithelial cells. The optimizations also resulted in minimal off-target editing, in edit-to-indel ratios 3.5-fold greater than those achieved by nuclease-mediated homology-directed repair, and in the functional restoration of CFTR ion channels to over 50% of wild-type levels (similar to those achieved via combination treatment with elexacaftor, tezacaftor and ivacaftor) in primary airway cells. Our findings support the feasibility of a durable one-time treatment for CF.},
language = {en}
}`,
/* 11 -> 16*/
`@article{Yan_Oyler-Castrillo_Ravisankar_Ward_Levesque_Jing_Simpson_Zhao_Li_Yan_2024,
title = {Improving prime editing with an endogenous small RNA-binding protein},
author = {Yan, Jun and Oyler-Castrillo, Paul and Ravisankar, Purnima and Ward, Carl C. and Levesque, Sébastien and Jing, Yangwode and Simpson, Danny and Zhao, Anqi and Li, Hui and Yan, Weihao and Goudy, Laine and Schmidt, Ralf and Solley, Sabrina C. and Gilbert, Luke A. and Chan, Michelle M. and Bauer, Daniel E. and Marson, Alexander and Parsons, Lance R. and Adamson, Britt},
year = 2024,
month = apr,
journal = {Nature},
volume = 628,
number = 8008,
pages = {639–647},
doi = {10.1038/s41586-024-07259-6},
issn = {0028-0836, 1476-4687},
abstractnote = {Abstract Prime editing enables the precise modification of genomes through reverse transcription of template sequences appended to the 3′ ends of CRISPR–Cas guide RNAs 1 . To identify cellular determinants of prime editing, we developed scalable prime editing reporters and performed genome-scale CRISPR-interference screens. From these screens, a single factor emerged as the strongest mediator of prime editing: the small RNA-binding exonuclease protection factor La. Further investigation revealed that La promotes prime editing across approaches (PE2, PE3, PE4 and PE5), edit types (substitutions, insertions and deletions), endogenous loci and cell types but has no consistent effect on genome-editing approaches that rely on standard, unextended guide RNAs. Previous work has shown that La binds polyuridine tracts at the 3′ ends of RNA polymerase III transcripts 2 . We found that La functionally interacts with the 3′ ends of polyuridylated prime editing guide RNAs (pegRNAs). Guided by these results, we developed a prime editor protein (PE7) fused to the RNA-binding, N-terminal domain of La. This editor improved prime editing with expressed pegRNAs and engineered pegRNAs (epegRNAs), as well as with synthetic pegRNAs optimized for La binding. Together, our results provide key insights into how prime editing components interact with the cellular environment and suggest general strategies for stabilizing exogenous small RNAs therein.},
language = {en}
}`,
/* 12 -> 17*/
`@article{Simon,
title = {PEAR, a flexible fluorescent reporter for the identification and enrichment of successfully prime edited cells},
author = {Simon, Dorottya Anna and Tálas, András and Kulcsár, Péter István and Biczók, Zsuzsanna and Krausz, Sarah Laura and Várady, György and Welker, Ervin},
year = 2022,
month = feb,
journal = {eLife},
publisher = {eLife Sciences Publications, Ltd},
volume = 11,
doi = {10.7554/eLife.69504},
issn = {2050-084X},
abstractnote = {Prime editing is a recently developed CRISPR/Cas9 based gene engineering tool that allows the introduction of short insertions, deletions, and substitutions into the genome. However, the efficiency of prime editing, which typically achieves editing rates of around 10%–30%, has not matched its versatility. Here, we introduce the prime editor activity reporter (PEAR), a sensitive fluorescent tool for identifying single cells with prime editing activity. PEAR has no background fluorescence and specifically indicates prime editing events. Its design provides apparently unlimited flexibility for sequence variation along the entire length of the spacer sequence, making it uniquely suited for systematic investigation of sequence features that influence prime editing activity. The use of PEAR as an enrichment marker for prime editing can increase the edited population by up to 84%, thus significantly improving the applicability of prime editing for basic research and biotechnological applications.},
editor = {Lapinaite, Audrone and Stainier, Didier YR and Hamilton, Jennifer R}
}`
]
\ No newline at end of file
src/sources/eng-peg-sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function EngPegsources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} start={18} />
</div>
);
}
const bibtexSources = [
`
@article{Chow_Chen_Shen_Chen_2021,
title = {A web tool for the design of prime-editing guide RNAs},
author = {Chow, Ryan D. and Chen, Jennifer S. and Shen, Johanna and Chen, Sidi},
year = 2021,
month = feb,
journal = {Nature Biomedical Engineering},
publisher = {Nature Publishing Group},
volume = 5,
number = 2,
pages = {190–194},
doi = {10.1038/s41551-020-00622-8},
issn = {2157-846X},
rights = {2020 The Author(s), under exclusive licence to Springer Nature Limited},
abstractnote = {Prime editing enables diverse genomic alterations to be written into target sites without requiring double-strand breaks or donor templates. The design of prime-editing guide RNAs (pegRNAs), which must be customized for each edit, can however be complex and time consuming. Compared with single guide RNAs (sgRNAs), pegRNAs have an additional 3′ extension composed of a primer binding site and a reverse-transcription template. Here we report a web tool, which we named pegFinder (http://pegfinder.sidichenlab.org), for the rapid design of pegRNAs from reference and edited DNA sequences. pegFinder can incorporate sgRNA on-target and off-target scoring predictions into its ranking system, and nominates secondary nicking sgRNAs for increasing editing efficiency. CRISPR-associated protein 9 variants with expanded targeting ranges are also supported. To facilitate downstream experimentation, pegFinder produces a comprehensive table of candidate pegRNAs, along with oligonucleotide sequences for cloning.},
language = {en}
}
`,`
@article{Anzalone_Randolph_Davis_Sousa_Koblan_Levy_Chen_Wilson_Newby_Raguram_2019,
title = {Search-and-replace genome editing without double-strand breaks or donor DNA},
author = {Anzalone, Andrew V. and Randolph, Peyton B. and Davis, Jessie R. and Sousa, Alexander A. and Koblan, Luke W. and Levy, Jonathan M. and Chen, Peter J. and Wilson, Christopher and Newby, Gregory A. and Raguram, Aditya and Liu, David R.},
year = 2019,
month = dec,
journal = {Nature},
publisher = {Nature Publishing Group},
volume = 576,
number = 7785,
pages = {149–157},
doi = {10.1038/s41586-019-1711-4},
issn = {1476-4687},
rights = {2019 The Author(s), under exclusive licence to Springer Nature Limited},
abstractnote = {Most genetic variants that contribute to disease1 are challenging to correct efficiently and without excess byproducts2–5. Here we describe prime editing, a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a catalytically impaired Cas9 endonuclease fused to an engineered reverse transcriptase, programmed with a prime editing guide RNA (pegRNA) that both specifies the target site and encodes the desired edit. We performed more than 175 edits in human cells, including targeted insertions, deletions, and all 12 types of point mutation, without requiring double-strand breaks or donor DNA templates. We used prime editing in human cells to correct, efficiently and with few byproducts, the primary genetic causes of sickle cell disease (requiring a transversion in HBB) and Tay–Sachs disease (requiring a deletion in HEXA); to install a protective transversion in PRNP; and to insert various tags and epitopes precisely into target loci. Four human cell lines and primary post-mitotic mouse cortical neurons support prime editing with varying efficiencies. Prime editing shows higher or similar efficiency and fewer byproducts than homology-directed repair, has complementary strengths and weaknesses compared to base editing, and induces much lower off-target editing than Cas9 nuclease at known Cas9 off-target sites. Prime editing substantially expands the scope and capabilities of genome editing, and in principle could correct up to 89% of known genetic variants associated with human diseases.},
language = {en}
}
`,`
@misc{Doman2024,
title = {Prime Editing Webinar},
author = {Jordan Doman},
year = 2024,
url = {https://www.youtube.com/watch?v=0Z_ztvkvKUA},
note = {Accessed: May 2024},
howpublished = {YouTube}
}
`,`
@article{Galietta_Haggie_Verkman_2001,
title = {Green fluorescent protein-based halide indicators with improved chloride and iodide affinities},
author = {Galietta, Luis J.V and Haggie, Peter M and Verkman, A.s},
year = 2001,
journal = {FEBS Letters},
volume = 499,
number = 3,
pages = {220–224},
doi = {10.1016/S0014-5793(01)02561-3},
issn = {1873-3468},
rights = {FEBS Letters 499 (2001) 1873-3468 © 2015 Federation of European Biochemical Societies},
abstractnote = {The green fluorescent protein YFP-H148Q is sensitive to halides by a mechanism involving halide binding and a shift in pK a. However, a limitation of YFP-H148Q is its low halide sensitivity, with K d>100 mM for Cl−. Indicators with improved sensitivities are needed for cell transport studies, particularly in drug discovery by high-throughput screening, and for measurement of Cl− concentration in subcellular organelles. YFP-H148Q libraries were generated in which pairs of residues in the vicinity of the halide binding site were randomly mutated. An automated procedure was developed to screen bacterial colonies for improved halide sensitivity. Analysis of 1536 clones revealed improved anion sensitivities with K d down to 2 mM for I− (I152L), 40 mM for Cl− (V163S), and 10 mM for NO3 − (I152L). The anion-sensitive mechanism of these indicators was established and their utility in cells was demonstrated using transfected cells expressing the Cystic Fibrosis transmembrane conductance regulator chloride channel.},
language = {en}
}
`,`
@article{Bulcaen_Kortleven_Liu_Maule_Dreano_Kelly_Ensinck_Thierie_Smits_Ciciani_2024,
title = {Prime editing functionally corrects Cystic Fibrosis-causing CFTR mutations in human organoids and airway epithelial cells},
author = {Bulcaen, Mattijs and Kortleven, Phéline and Liu, Ronald B. and Maule, Giulia and Dreano, Elise and Kelly, Mairead and Ensinck, Marjolein M. and Thierie, Sam and Smits, Maxime and Ciciani, Matteo and Hatton, Aurelie and Chevalier, Benoit and Ramalho, Anabela S. and Casadevall i Solvas, Xavier and Debyser, Zeger and Vermeulen, François and Gijsbers, Rik and Sermet-Gaudelus, Isabelle and Cereseto, Anna and Carlon, Marianne S.},
year = 2024,
month = may,
journal = {Cell Reports Medicine},
pages = 101544,
doi = {10.1016/j.xcrm.2024.101544},
issn = {2666-3791},
abstractnote = {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”).}
}
`,`
@article{Renz_Valdivia-Francia_Sendoel_2020,
title = {Some like it translated: small ORFs in the 5′UTR},
author = {Renz, Peter F. and Valdivia-Francia, Fabiola and Sendoel, Ataman},
year = 2020,
month = nov,
journal = {Experimental Cell Research},
volume = 396,
number = 1,
pages = 112229,
doi = {10.1016/j.yexcr.2020.112229},
issn = {0014-4827},
abstractnote = {The 5′ untranslated region (5′UTR) is critical in determining post-transcriptional control, which is partly mediated by short upstream open reading frames (uORFs) present in half of mammalian transcripts. uORFs are generally considered to provide functionally important repression of the main-ORF by engaging initiating ribosomes, but under specific environmental conditions such as cellular stress, uORFs can become essential to activate the translation of the main coding sequence. In addition, a growing number of uORF-encoded bioactive microproteins have been described, which have the potential to significantly increase cellular protein diversity. Here we review the diverse cellular contexts in which uORFs play a critical role and discuss the molecular mechanisms underlying their function and regulation. The progress over the last decades in dissecting uORF function suggests that the 5′UTR remains an exciting frontier towards understanding how the cellular proteome is shaped in health and disease.}
}
`,`
@article{Liang_He_Zhao_Zhu_Hu_Liu_Gao_Liu_Zhang_Qiu_2024,
title = {Prime editing using CRISPR-Cas12a and circular RNAs in human cells},
author = {Liang, Ronghong and He, Zixin and Zhao, Kevin Tianmeng and Zhu, Haocheng and Hu, Jiacheng and Liu, Guanwen and Gao, Qiang and Liu, Meiyan and Zhang, Rui and Qiu, Jin-Long and Gao, Caixia},
year = 2024,
month = jan,
journal = {Nature Biotechnology},
doi = {10.1038/s41587-023-02095-x},
issn = {1087-0156, 1546-1696},
url = {https://www.nature.com/articles/s41587-023-02095-x},
language = {en}
}
`
]
\ No newline at end of file
src/sources/eng-reporter-sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function EngRepsources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} />
</div>
);
}
const bibtexSources = [
`
@article{Heim_Prasher_Tsien_1994,
title = {Wavelength mutations and posttranslational autoxidation of green fluorescent protein.},
author = {Heim, R and Prasher, D C and Tsien, R Y},
year = 1994,
month = dec,
journal = {Proceedings of the National Academy of Sciences},
publisher = {Proceedings of the National Academy of Sciences},
volume = 91,
number = 26,
pages = {12501–12504},
doi = {10.1073/pnas.91.26.12501},
abstractnote = {The green fluorescent protein (GFP) of the jellyfish Aequorea victoria is an unusual protein with strong visible absorbance and fluorescence from a p-hydroxybenzylidene-imidazolidinone chromophore, which is generated by cyclization and oxidation of the protein’s own Ser-Tyr-Gly sequence at positions 65-67. Cloning of the cDNA and heterologous expression of fluorescent protein in a wide variety of organisms indicate that this unique posttranslational modification must be either spontaneous or dependent only on ubiquitous enzymes and reactants. We report that formation of the final fluorophore requires molecular oxygen and proceeds with a time constant (approximately 4 hr at 22 degrees C and atmospheric pO2) independent of dilution, implying that the oxidation does not require enzymes or cofactors. GFP was mutagenized and screened for variants with altered spectra. The most striking mutant fluoresced blue and contained histidine in place of Tyr-66. The availability of two visibly distinct colors should significantly extend the usefulness of GFP in molecular and cell biology by enabling in vivo visualization of differential gene expression and protein localization and measurement of protein association by fluorescence resonance energy transfer.}
}
`,`
@article{Simon,
title = {PEAR, a flexible fluorescent reporter for the identification and enrichment of successfully prime edited cells},
author = {Simon, Dorottya Anna and Tálas, András and Kulcsár, Péter István and Biczók, Zsuzsanna and Krausz, Sarah Laura and Várady, György and Welker, Ervin},
year = 2022,
month = feb,
journal = {eLife},
publisher = {eLife Sciences Publications, Ltd},
volume = 11,
pages = {e69504},
doi = {10.7554/eLife.69504},
issn = {2050-084X},
abstractnote = {Prime editing is a recently developed CRISPR/Cas9 based gene engineering tool that allows the introduction of short insertions, deletions, and substitutions into the genome. However, the efficiency of prime editing, which typically achieves editing rates of around 10%–30%, has not matched its versatility. Here, we introduce the prime editor activity reporter (PEAR), a sensitive fluorescent tool for identifying single cells with prime editing activity. PEAR has no background fluorescence and specifically indicates prime editing events. Its design provides apparently unlimited flexibility for sequence variation along the entire length of the spacer sequence, making it uniquely suited for systematic investigation of sequence features that influence prime editing activity. The use of PEAR as an enrichment marker for prime editing can increase the edited population by up to 84%, thus significantly improving the applicability of prime editing for basic research and biotechnological applications.},
editor = {Lapinaite, Audrone and Stainier, Didier YR and Hamilton, Jennifer R}
}
`
]
\ No newline at end of file
src/sources/eng-trf-sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function EngTrfsources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} start={3} />
</div>
);
}
const bibtexSources = [
`@article{Graham_Smiley_Russell_Nairn_1977,
title = {Characteristics of a Human Cell Line Transformed by DNA from Human Adenovirus Type 5},
author = {Graham, F. L. and Smiley, J. and Russell, W. C. and Nairn, R.},
year = 1977,
journal = {Journal of General Virology},
publisher = {Microbiology Society,},
volume = 36,
number = 1,
pages = {59–72},
doi = {10.1099/0022-1317-36-1-59},
issn = {1465-2099},
abstractnote = {SUMMARY Human embryonic kidney cells have been transformed by exposing cells to sheared fragments of adenovirus type 5 DNA. The transformed cells (designated 293 cells) exhibited many of the characteristics of transformation including the elaboration of a virus-specific tumour antigen. Analysis of the polypeptides synthesized in the 293 cells by labelling with 35S-methionine and SDS PAGE showed a variable pattern of synthesis, different in a number of respects from that seen in other human cells. On labelling the surface of cells by lactoperoxidase catalysed radio-iodination, the absence of a labelled polypeptide analogous to the 250 K (LETS) glycoprotein was noted. Hybridization of labelled cellular RNA with restriction fragments of adenovirus type 5 DNA indicated transcription of a portion of the adenovirus genome at the conventional left hand end.}
}`,
`@article{Simon,
title = {PEAR, a flexible fluorescent reporter for the identification and enrichment of successfully prime edited cells},
author = {Simon, Dorottya Anna and Tálas, András and Kulcsár, Péter István and Biczók, Zsuzsanna and Krausz, Sarah Laura and Várady, György and Welker, Ervin},
year = 2022,
month = feb,
journal = {eLife},
publisher = {eLife Sciences Publications, Ltd},
volume = 11,
pages = {e69504},
doi = {10.7554/eLife.69504},
issn = {2050-084X},
abstractnote = {Prime editing is a recently developed CRISPR/Cas9 based gene engineering tool that allows the introduction of short insertions, deletions, and substitutions into the genome. However, the efficiency of prime editing, which typically achieves editing rates of around 10%–30%, has not matched its versatility. Here, we introduce the prime editor activity reporter (PEAR), a sensitive fluorescent tool for identifying single cells with prime editing activity. PEAR has no background fluorescence and specifically indicates prime editing events. Its design provides apparently unlimited flexibility for sequence variation along the entire length of the spacer sequence, making it uniquely suited for systematic investigation of sequence features that influence prime editing activity. The use of PEAR as an enrichment marker for prime editing can increase the edited population by up to 84%, thus significantly improving the applicability of prime editing for basic research and biotechnological applications.},
editor = {Lapinaite, Audrone and Stainier, Didier YR and Hamilton, Jennifer R}
}`,
`@article{Anzalone_Randolph_Davis_Sousa_Koblan_Levy_Chen_Wilson_Newby_Raguram_2019,
title = {Search-and-replace genome editing without double-strand breaks or donor DNA},
author = {Anzalone, Andrew V. and Randolph, Peyton B. and Davis, Jessie R. and Sousa, Alexander A. and Koblan, Luke W. and Levy, Jonathan M. and Chen, Peter J. and Wilson, Christopher and Newby, Gregory A. and Raguram, Aditya and Liu, David R.},
year = 2019,
month = dec,
journal = {Nature},
publisher = {Nature Publishing Group},
volume = 576,
number = 7785,
pages = {149–157},
doi = {10.1038/s41586-019-1711-4},
issn = {1476-4687},
rights = {2019 The Author(s), under exclusive licence to Springer Nature Limited},
abstractnote = {Most genetic variants that contribute to disease1 are challenging to correct efficiently and without excess byproducts2–5. Here we describe prime editing, a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a catalytically impaired Cas9 endonuclease fused to an engineered reverse transcriptase, programmed with a prime editing guide RNA (pegRNA) that both specifies the target site and encodes the desired edit. We performed more than 175 edits in human cells, including targeted insertions, deletions, and all 12 types of point mutation, without requiring double-strand breaks or donor DNA templates. We used prime editing in human cells to correct, efficiently and with few byproducts, the primary genetic causes of sickle cell disease (requiring a transversion in HBB) and Tay–Sachs disease (requiring a deletion in HEXA); to install a protective transversion in PRNP; and to insert various tags and epitopes precisely into target loci. Four human cell lines and primary post-mitotic mouse cortical neurons support prime editing with varying efficiencies. Prime editing shows higher or similar efficiency and fewer byproducts than homology-directed repair, has complementary strengths and weaknesses compared to base editing, and induces much lower off-target editing than Cas9 nuclease at known Cas9 off-target sites. Prime editing substantially expands the scope and capabilities of genome editing, and in principle could correct up to 89% of known genetic variants associated with human diseases.},
language = {en}
}`
]
\ No newline at end of file
src/sources/entre-sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function EntrepreneurSources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} special="ent"/>
</div>
);
}
const bibtexSources = [
`
@article{GMI2021CysticFibrosis,
title = {Cystic Fibrosis Therapeutics Market Size - By Treatment Method (Medications [Drug Class {CFTR Modulators, Mucolytics, Bronchodilators, Pancreatic Enzyme Supplements}, Route of Administration], Devices), Distribution Channel & Forecast, 2021 - 2027},
author = {Faizullabhoy, Mariam and Wani, Gauri},
journal = {GMI Insights},
year = {2021},
month = {Sep},
url = {https://www.gminsights.com/industry-analysis/cystic-fibrosis-therapeutics-market},
note = {Report ID: GMI5118}
}
`,
`
@article{Fajac2021,
title={Therapeutic Approaches for Patients with Cystic Fibrosis Not Eligible for Current CFTR Modulators},
author={Fajac, Isabelle and Sermet, Isabelle},
journal={Cells},
volume={10},
number={10},
year={2021},
month={Oct},
doi={10.3390/cells10102793},
url={https://pubmed.ncbi.nlm.nih.gov/34685773/},
}
`,
`
@misc{ExpertMarketResearch2023,
title = {Cystic Fibrosis Treatment Market Report and Forecast 2024-2032},
author = {Rahul Gotadki},
year = {2023},
month = {Feb},
url = {https://www.expertmarketresearch.com/reports/cystic-fibrosis-treatment-market},
note = {ID: MRFR/Pharma/1293-CR}
}
`,
`
@misc{DeWeerdt2016,
author = {Sarah DeWeerdt},
title = {Developing gene therapy to treat cystic fibrosis: challenges and successes},
journal = {The Pharmaceutical Journal},
year = {2016},
month = {Jun},
url = {https://pharmaceutical-journal.com/article/feature/developing-gene-therapy-to-treat-cystic-fibrosis-challenges-and-successes},
note = {Accessed: 30 Sep 2024}
}
`
]
\ No newline at end of file
src/sources/joshua-inv-sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function JoshuaInterviewSources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} />
</div>
);
}
const bibtexSources = [
`
@article{eins,
title = {Prime editing functionally corrects Cystic Fibrosis-causing CFTR mutations in human organoids and airway epithelial cells},
journal = {Cell Reports Medicine},
volume = {5},
number = {5},
pages = {101544},
year = {2024},
issn = {2666-3791},
doi = {https://doi.org/10.1016/j.xcrm.2024.101544},
url = {https://www.sciencedirect.com/science/article/pii/S2666379124002349},
author = {Mattijs Bulcaen and Phéline Kortleven and Ronald B. Liu and Giulia Maule and Elise Dreano and Mairead Kelly and Marjolein M. Ensinck and Sam Thierie and Maxime Smits and Matteo Ciciani and Aurelie Hatton and Benoit Chevalier and Anabela S. Ramalho and Xavier {Casadevall i Solvas} and Zeger Debyser and François Vermeulen and Rik Gijsbers and Isabelle Sermet-Gaudelus and Anna Cereseto and Marianne S. Carlon},
}`,`
@article{zewi,
author = {Teeratakulpisarn, Jamaree and Kosuwon, Pensri and Srinakarin, Jiraporn and Panthongviriyakul, Charnchai and Sutra, Sumitr},
year = {2006},
month = {11},
pages = {1756-61},
title = {Cystic Fibrosis in three northeast Thai infants is CF really a rare disease in the Thai population?},
volume = {89},
journal = {Journal of the Medical Association of Thailand = Chotmaihet thangphaet}
} `,`
@article{drei,
author = {Ahmed, Shakil and Cheok, Gary and Goh, AnneE and Han, Aye and Hong, SJ and Indawati, Wahyuni and Kabir, AR and Kabra, Sushil and Kamalaporn, Harutai and Kim, HyungYoung and Kunling, Shen and Lochindarat, Sorasak and Moslehi, MohammadAshkan and Nathan, AnnaMarie and Ng, Daniel and Phung, NguyenNg and Singh, V and Takase, Masato and Triasih, Rina and Dai, Zen-Kong},
year = {2020},
month = {01},
pages = {8},
title = {Cystic Fibrosis in asia},
volume = {4},
journal = {Pediatric Respirology and Critical Care Medicine},
doi = {10.4103/prcm.prcm_5_20}
} `,`
@article{vier,
author = {Bobbo, Khadijatabubakar and Ahmad, Umar and Chau, De-Ming and Nordin, Norshariza and Abdullah, Syahril},
year = {2023},
month = {05},
pages = {103685},
title = {A comprehensive review of Cystic Fibrosis in Africa and Asia},
volume = {30},
journal = {Saudi Journal of Biological Sciences},
doi = {10.1016/j.sjbs.2023.103685}
} `
]
\ No newline at end of file
src/sources/liu-inv-sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function LiuInterviewSources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} />
</div>
);
}
const bibtexSources = [
`
@article{eins,
title = {Search-and-replace genome editing without double-strand breaks or donor DNA},
volume = {576},
rights = {2019 The Author(s), under exclusive licence to Springer Nature Limited},
ISSN = {1476-4687},
DOI = {10.1038/s41586-019-1711-4},
abstractNote = {Most genetic variants that contribute to disease are challenging to correct efficiently and without excess byproducts. Here we describe prime editing, a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a catalytically impaired Cas9 endonuclease fused to an engineered reverse transcriptase, programmed with a prime editing guide RNA (pegRNA) that both specifies the target site and encodes the desired edit. We performed more than 175 edits in human cells, including targeted insertions, deletions, and all 12 types of point mutation, without requiring double-strand breaks or donor DNA templates. We used prime editing in human cells to correct, efficiently and with few byproducts, the primary genetic causes of sickle cell disease and Tay–Sachs disease; to install a protective transversion in PRNP; and to insert various tags and epitopes precisely into target loci. Four human cell lines and primary post-mitotic mouse cortical neurons support prime editing with varying efficiencies. Prime editing shows higher or similar efficiency and fewer byproducts than homology-directed repair, has complementary strengths and weaknesses compared to base editing, and induces much lower off-target editing than Cas9 nuclease at known Cas9 off-target sites. Prime editing substantially expands the scope and capabilities of genome editing, and in principle could correct up to 89% of known genetic variants associated with human diseases.},
number = {7785},
journal = {Nature},
publisher = {Nature Publishing Group},
author = {Anzalone, Andrew V. and Randolph, Peyton B. and Davis, Jessie R. and Sousa, Alexander A. and Koblan, Luke W. and Levy, Jonathan M. and Chen, Peter J. and Wilson, Christopher and Newby, Gregory A. and Raguram, Aditya and Liu, David R.},
year = {2019},
month = {dec},
pages = {149–157},
language = {en}
}`,`
@article{zwei,
title = {Phage-assisted evolution and protein engineering yield compact, efficient prime editors},
volume = {186},
ISSN = {0092-8674, 1097-4172},
DOI = {10.1016/j.cell.2023.07.039},
number = {18},
journal = {Cell},
publisher = {Elsevier},
author = {Doman, Jordan L. and Pandey, Smriti and Neugebauer, Monica E. and An, Meirui and Davis, Jessie R. and Randolph, Peyton B. and McElroy, Amber and Gao, Xin D. and Raguram, Aditya and Richter, Michelle F. and Everette, Kelcee A. and Banskota, Samagya and Tian, Kathryn and Tao, Y. Allen and Tolar, Jakub and Osborn, Mark J. and Liu, David R.},
year = {2023},
month = {aug},
pages = {3983-4002.e26},
language = {English}
}`,`
@article{drei,
title = {Phage-assisted continuous and non-continuous evolution},
volume = {15},
rights = {2020 The Author(s), under exclusive licence to Springer Nature Limited},
ISSN = {1750-2799},
DOI = {10.1038/s41596-020-00410-3},
abstractNote = {Directed evolution, which applies the principles of Darwinian evolution to a laboratory setting, is a powerful strategy for generating biomolecules with diverse and tailored properties. This technique can be implemented in a highly efficient manner using continuous evolution, which enables the steps of directed evolution to proceed seamlessly over many successive generations with minimal researcher intervention. Phage-assisted continuous evolution (PACE) enables continuous directed evolution in bacteria by mapping the steps of Darwinian evolution onto the bacteriophage life cycle and allows directed evolution to occur on much faster timescales compared to conventional methods. This protocol provides detailed instructions on evolving proteins using PACE and phage-assisted non-continuous evolution (PANCE) and includes information on the preparation of selection phage and host cells, the assembly of a continuous flow apparatus and the performance and analysis of evolution experiments. This protocol can be performed in as little as 2 weeks to complete more than 100 rounds of evolution (complete cycles of mutation, selection and replication) in a single PACE experiment.},
number = {12},
journal = {Nature Protocols},
publisher = {Nature Publishing Group},
author = {Miller, Shannon M. and Wang, Tina and Liu, David R.},
year = {2020},
month = {dec},
pages = {4101–4127},
language = {en}
}`,`
@article{vier,
title = {Systematic optimization of prime editing for the efficient functional correction of CFTR F508del in human airway epithelial cells},
rights = {2024 The Author(s)},
ISSN = {2157-846X},
DOI = {10.1038/s41551-024-01233-3},
abstractNote = {Prime editing (PE) enables precise and versatile genome editing without requiring double-stranded DNA breaks. Here we describe the systematic optimization of PE systems to efficiently correct human Cystic Fibrosis (CF) transmembrane conductance regulator (CFTR) F508del, a three-nucleotide deletion that is the predominant cause of CF. By combining six efficiency optimizations for PE—engineered PE guide RNAs, the PEmax architecture, the transient expression of a dominant-negative mismatch repair protein, strategic silent edits, PE6 variants and proximal ‘dead’ single-guide RNAs—we increased correction efficiencies for CFTR F508del from less than 0.5% in HEK293T cells to 58% in immortalized bronchial epithelial cells (a 140-fold improvement) and to 25% in patient-derived airway epithelial cells. The optimizations also resulted in minimal off-target editing, in edit-to-indel ratios 3.5-fold greater than those achieved by nuclease-mediated homology-directed repair, and in the functional restoration of CFTR ion channels to over 50% of wild-type levels (similar to those achieved via combination treatment with elexacaftor, tezacaftor and ivacaftor) in primary airway cells. Our findings support the feasibility of a durable one-time treatment for CF.},
journal = {Nature Biomedical Engineering},
publisher = {Nature Publishing Group},
author = {Sousa, Alexander A. and Hemez, Colin and Lei, Lei and Traore, Soumba and Kulhankova, Katarina and Newby, Gregory A. and Doman, Jordan L. and Oye, Keyede and Pandey, Smriti and Karp, Philip H. and McCray, Paul B. and Liu, David R.},
year = {2024},
month = {jul},
pages = {1–15},
language = {en}
}`
]
\ No newline at end of file
src/sources/mattij-inv-sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function MattijsInterviewSources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} />
</div>
);
}
const bibtexSources = [
`
@article{Bulcaen_Kortleven_Liu_Maule_Dreano_Kelly_Ensinck_Thierie_Smits_Ciciani_et,
title = {
Prime editing functionally corrects Cystic Fibrosis-causing CFTR mutations in
human organoids and airway epithelial cells
},
author = {
Bulcaen, Mattijs and Kortleven, Phéline and Liu, Ronald B. and Maule, Giulia
and Dreano, Elise and Kelly, Mairead and Ensinck, Marjolein M. and Thierie,
Sam and Smits, Maxime and Ciciani, Matteo and Hatton, Aurelie and Chevalier,
Benoit and Ramalho, Anabela S. and Casadevall i Solvas, Xavier and Debyser,
Zeger and Vermeulen, François and Gijsbers, Rik and Sermet-Gaudelus, Isabelle
and Cereseto, Anna and Carlon, Marianne S.
},
year = 2024,
month = may,
journal = {Cell Reports Medicine},
pages = 101544,
doi = {10.1016/j.xcrm.2024.101544},
issn = {2666-3791},
abstractnote = {
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”).
}
}
`
]
\ No newline at end of file
src/sources/methods-sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function MethodSources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} />
</div>
);
}
const bibtexSources = [
`
@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}
}`,
`
@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},
language = {en},
editor = {Dallas, Mark and Bell, Damian}
}
`,
`
@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.
}
}
`,
`
@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
}
}
`,
`
@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.
}
}
`,
`
@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}
}
`,
`
@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}
}
`,
`
@misc{ignatova2023,
author = {Zoya Ignatova},
title = {Research Group Ignatova at the Institute of Biochemistry and Molecular Biology},
year = {2023},
howpublished = {Hamburg University},
note = {Accessed: 28 September 2024},
institution = {University of Hamburg},
}
`,
`@article{ehrhardt_towards_2006,
title = {Towards an in vitro model of Cystic Fibrosis small airway epithelium: characterisation of the human bronchial epithelial cell line {CFBE41o}-},
shorttitle = {Towards an in vitro model of Cystic Fibrosis small airway epithelium},
author = {Ehrhardt, Carsten and Collnot, Eva-Maria and Baldes, Christiane and Becker, Ulrich and Laue, Michael and Kim, Kwang-Jin and Lehr, Claus-Michael},
year = 2006,
month = mar,
journal = {Cell and Tissue Research},
volume = 323,
number = 3,
pages = {405--415},
doi = {10.1007/s00441-005-0062-7},
issn = {0302-766X, 1432-0878},
url = {http://link.springer.com/10.1007/s00441-005-0062-7},
urldate = {2024-09-09},
copyright = {http://www.springer.com/tdm},
language = {en},
file = {Ehrhardt et al. - 2006 - Towards an in vitro model of Cystic Fibrosis small.pdf:C\:\\Users\\Isabell\\Zotero\\storage\\RXLMCE3V\\Ehrhardt et al. - 2006 - Towards an in vitro model of Cystic Fibrosis small.pdf:application/pdf}
}
`
,
`
@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}
}
`
]
\ No newline at end of file
src/sources/part-sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function PartSources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} />
</div>
);
}
const bibtexSources = [
`
@article {10.7554/eLife.69504,
article_type = {journal},
title = {PEAR, a flexible fluorescent reporter for the identification and enrichment of successfully prime edited cells},
author = {Simon, Dorottya Anna and Tálas, András and Kulcsár, Péter István and Biczók, Zsuzsanna and Krausz, Sarah Laura and Várady, György and Welker, Ervin},
editor = {Lapinaite, Audrone and Stainier, Didier YR and Hamilton, Jennifer R},
volume = 11,
year = 2022,
month = {feb},
pub_date = {2022-02-23},
pages = {e69504},
citation = {eLife 2022;11:e69504},
doi = {10.7554/eLife.69504},
url = {https://doi.org/10.7554/eLife.69504},
abstract = {Prime editing is a recently developed CRISPR/Cas9 based gene engineering tool that allows the introduction of short insertions, deletions, and substitutions into the genome. However, the efficiency of prime editing, which typically achieves editing rates of around 10\%–30\%, has not matched its versatility. Here, we introduce the prime editor activity reporter (PEAR), a sensitive fluorescent tool for identifying single cells with prime editing activity. PEAR has no background fluorescence and specifically indicates prime editing events. Its design provides apparently unlimited flexibility for sequence variation along the entire length of the spacer sequence, making it uniquely suited for systematic investigation of sequence features that influence prime editing activity. The use of PEAR as an enrichment marker for prime editing can increase the edited population by up to 84\%, thus significantly improving the applicability of prime editing for basic research and biotechnological applications.},
keywords = {CRISPR, Cas9, prime editing, fluorescent, fluorescent reporter, reporter, enrichment, genome engineering},
journal = {eLife},
issn = {2050-084X},
publisher = {eLife Sciences Publications, Ltd},
}
`,
`
@misc{nickaseassay2024internet,
author = {Kim et al.},
title = { Utilization of nicking properties of CRISPR-Cas12a effector for genome editing},
year = {2024},
url = { https://doi.org/10.1038/s41598-024-53648-2},
note = {Zugriff am 16. August 2024}
}
`
]
\ No newline at end of file
src/sources/res-sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export default function ResultSources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} />
</div>
);
}
const bibtexSources = [
`
@article{wang2023sortlnps,
author = {Wang, X. and Liu, S. and Sun, Y. and others},
title = {Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery},
journal = {Nature Protocols},
volume = {18},
pages = {265--291},
year = {2023},
doi = {10.1038/s41596-022-00755-},
url = {https://doi.org/10.1038/s41596-022-00755-}
}
`,
`@article{sousa2024primeediting,
author = {Sousa, A. A. and Hemez, C. and Lei, L. and others},
title = {Systematic optimization of prime editing for the efficient functional correction of CFTR F508del in human airway epithelial cells},
journal = {Nature Biomedical Engineering},
year = {2024},
doi = {10.1038/s41551-024-01233-3},
url = {https://doi.org/10.1038/s41551-024-01233-3}
}
`
]
\ No newline at end of file
code/bibtex.bib → src/sources/rnhale-sources.tsx
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
@article{article1,
export default function RnhaleSources(){
return (
<div>
<BibtexParser bibtexSources={bibtexSources} />
</div>
);
}
const bibtexSources = [
`
@article{article,
author={Roth, F. C., Numberger, M., and Draguhn, A.},
......@@ -19,8 +32,9 @@ doi={10.1007/978-3-662-66053-9_1}
}
`,`
@article{article2,
@article{article,
author={Mete, V.},
......@@ -40,9 +54,9 @@ doi={10.17879/98958441905}
}
`,`
@article{article3,
@article{article,
author={Giaever, I. and Keese, C. },
......@@ -60,4 +74,6 @@ journal={Nature},
doi={10.1038/366591a0}
}
\ No newline at end of file
}
`
]
\ No newline at end of file
src/sources/test-sources.tsx 0 → 100644
View file @ 3fd292fd
import BibtexParser from "../components/makeSources";
export function TestSource(){
const bibtexSources = [
`
@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}
}
`
];
return (
<div>
<h1>BibTeX to HTML in React</h1>
<BibtexParser bibtexSources={bibtexSources} />
</div>
);
}
export default TestSource;
\ No newline at end of file