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Academic literature on the topic 'CRISPR system'

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Published: 13 April 2024

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Journal articles on the topic "CRISPR system"

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Huescas, C. G. Y., R. I. Pereira, J. Prichula, P. A. Azevedo, J. Frazzon, and A. P. G. Frazzon. "Frequency of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in non-clinical Enterococcus faecalis and Enterococcus faecium strains." Brazilian Journal of Biology 79, no. 3 (September 2019): 460–65. http://dx.doi.org/10.1590/1519-6984.183375.

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Abstract The fidelity of the genomes is defended by mechanism known as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems. Three Type II CRISPR systems (CRISPR1- cas, CRISPR2 and CRISPR3-cas) have been identified in enterococci isolates from clinical and environmental samples. The aim of this study was to observe the distribution of CRISPR1-cas, CRISPR2 and CRISPR3-cas in non-clinical strains of Enterococcus faecalis and Enterococcus faecium isolates from food and fecal samples, including wild marine animals. The presence of CRISPRs was evaluated by PCR in 120 enterococci strains, 67 E. faecalis and 53 E. faecium. It is the first report of the presence of the CRISPRs system in E. faecalis and E. faecium strains isolated from wild marine animal fecal samples. The results showed that in non-clinical strains, the CRISPRs were more frequently detected in E. faecalis than in E. faecium. And the frequencies of CRISPR1-cas and CRISPR2 were higher (60%) in E. faecalis strains isolated from animal feces, compared to food samples. Both strains showed low frequencies of CRISPR3-cas (8.95% and 1.88%). In conclusion, the differences in the habitats of enterococcal species may be related with the results observe in distribution of CRISPRs systems.
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Serbanescu, M. A., M. Cordova, K. Krastel, R. Flick, N. Beloglazova, A. Latos, A. F. Yakunin, D. B. Senadheera, and D. G. Cvitkovitch. "Role of the Streptococcus mutans CRISPR-Cas Systems in Immunity and Cell Physiology." Journal of Bacteriology 197, no. 4 (December 8, 2014): 749–61. http://dx.doi.org/10.1128/jb.02333-14.

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CRISPR-Cas systems provide adaptive microbial immunity against invading viruses and plasmids. The cariogenic bacteriumStreptococcus mutansUA159 has two CRISPR-Cas systems: CRISPR1 (type II-A) and CRISPR2 (type I-C) with several spacers from both CRISPR cassettes matching sequences of phage M102 or genomic sequences of otherS. mutans. The deletion of thecasgenes of CRISPR1 (ΔC1S), CRISPR2 (ΔC2E), or both CRISPR1+2 (ΔC1SC2E) or the removal of spacers 2 and 3 (ΔCR1SP13E) inS. mutansUA159 did not affect phage sensitivity when challenged with virulent phage M102. Using plasmid transformation experiments, we demonstrated that the CRISPR1-Cas system inhibits transformation ofS. mutansby the plasmids matching the spacers 2 and 3. Functional analysis of thecasdeletion mutants revealed that in addition to a role in plasmid targeting, both CRISPR systems also contribute to the regulation of bacterial physiology inS. mutans. Compared to wild-type cells, the ΔC1S strain displayed diminished growth under cell membrane and oxidative stress, enhanced growth under low pH, and had reduced survival under heat shock and DNA-damaging conditions, whereas the ΔC2E strain exhibited increased sensitivity to heat shock. Transcriptional analysis revealed that the two-component signal transduction system VicR/K differentially modulates expression ofcasgenes within CRISPR-Cas systems, suggesting that VicR/K might coordinate the expression of two CRISPR-Cas systems. Collectively, we providein vivoevidence that the type II-A CRISPR-Cas system ofS. mutansmay be targeted to manipulate its stress response and to influence the host to control the uptake and dissemination of antibiotic resistance genes.
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Chapman, Brittany, Jeong Hoon Han, Hong Jo Lee, Isabella Ruud, and Tae Hyun Kim. "Targeted Modulation of Chicken Genes In Vitro Using CRISPRa and CRISPRi Toolkit." Genes 14, no. 4 (April 13, 2023): 906. http://dx.doi.org/10.3390/genes14040906.

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Engineering of clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated protein 9 (Cas9) system has enabled versatile applications of CRISPR beyond targeted DNA cleavage. Combination of nuclease-deactivated Cas9 (dCas9) and transcriptional effector domains allows activation (CRISPRa) or repression (CRISPRi) of target loci. To demonstrate the effectiveness of the CRISPR-mediated transcriptional regulation in chickens, three CRISPRa (VP64, VPR, and p300) and three CRISPRi (dCas9, dCas9-KRAB, and dCas9-KRAB-MeCP2) systems were tested in chicken DF-1 cells. By introducing guide RNAs (gRNAs) targeting near the transcription start site (TSS) of each gene in CRISPRa and CRISPRi effector domain-expressing chicken DF-1 cell lines, significant gene upregulation was induced in dCas9-VPR and dCas9-VP64 cells, while significant downregulation was observed with dCas9 and dCas9-KRAB. We further investigated the effect of gRNA positions across TSS and discovered that the location of gRNA is an important factor for targeted gene regulation. RNA sequencing analysis of IRF7 CRISPRa and CRISPRi- DF-1 cells revealed the specificity of CRISPRa and CRISPRi-based targeted transcriptional regulation with minimal off-target effects. These findings suggest that the CRISPRa and CRISPRi toolkits are an effective and adaptable platform for studying the chicken genome by targeted transcriptional modulation.
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La Russa, Marie F., and Lei S. Qi. "The New State of the Art: Cas9 for Gene Activation and Repression." Molecular and Cellular Biology 35, no. 22 (September 14, 2015): 3800–3809. http://dx.doi.org/10.1128/mcb.00512-15.

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CRISPR-Cas9 technology has rapidly changed the landscape for how biologists and bioengineers study and manipulate the genome. Derived from the bacterial adaptive immune system, CRISPR-Cas9 has been coopted and repurposed for a variety of new functions, including the activation or repression of gene expression (termed CRISPRa or CRISPRi, respectively). This represents an exciting alternative to previously used repression or activation technologies such as RNA interference (RNAi) or the use of gene overexpression vectors. We have only just begun exploring the possibilities that CRISPR technology offers for gene regulation and the control of cell identity and behavior. In this review, we describe the recent advances of CRISPR-Cas9 technology for gene regulation and outline advantages and disadvantages of CRISPRa and CRISPRi (CRISPRa/i) relative to alternative technologies.
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Karlson, Chou Khai Soong, Siti Nurfadhlina Mohd-Noor, Nadja Nolte, and Boon Chin Tan. "CRISPR/dCas9-Based Systems: Mechanisms and Applications in Plant Sciences." Plants 10, no. 10 (September 29, 2021): 2055. http://dx.doi.org/10.3390/plants10102055.

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RNA-guided genomic transcriptional regulation tools, namely clustered regularly interspaced short palindromic repeats interference (CRISPRi) and CRISPR-mediated gene activation (CRISPRa), are a powerful technology for gene functional studies. Deriving from the CRISPR/Cas9 system, both systems consist of a catalytically dead Cas9 (dCas9), a transcriptional effector and a single guide RNA (sgRNA). This type of dCas9 is incapable to cleave DNA but retains its ability to specifically bind to DNA. The binding of the dCas9/sgRNA complex to a target gene results in transcriptional interference. The CRISPR/dCas9 system has been explored as a tool for transcriptional modulation and genome imaging. Despite its potential applications and benefits, the challenges and limitations faced by the CRISPR/dCas9 system include the off-target effects, protospacer adjacent motif (PAM) sequence requirements, efficient delivery methods and the CRISPR/dCas9-interfered crops being labeled as genetically modified organisms in several countries. This review highlights the progression of CRISPR/dCas9 technology as well as its applications and potential challenges in crop improvement.
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Yang, Jiayi. "Applications of the CRISPR-Cas9 system in cancer models." Theoretical and Natural Science 21, no. 1 (December 20, 2023): 28–33. http://dx.doi.org/10.54254/2753-8818/21/20230804.

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Cancer has a high mortality and prevalence rate in the world. CRISPR-Cas9 is one of the novel and most common gene-editing techniques. Compared with the first two generations of gene-editing technologies, CRISPR-Cas9 system has the advantages of easy design, low cost, high efficiency and so on. sgRNA guides Cas9 to the site of the targeted gene, and Cas9 cuts the DNA strand at that site, triggering the NHEJ or HDR mechanism so as to achieve the purpose of deletion or insertion. CRISPR-Cas9 can be combined with other factors for other purposes, such as CRISPRa, CRISPRi, and base editing. The CRISPR system now has been used extensively for research into biological mechanisms and disease treatments. Since cancer is controlled by genes, a number of researchers in recent years have looked at using the CRISPR system to treat cancer. The CRISPR technology has greatly improved our understanding of cancer and the factors that affect it, and has had a major impact on the study and treatment of cancer. CRISPR gene editing can quickly and efficiently generate gene knockouts and regulate gene expression to identify relevant genes that influence cancer growth. This review systematically introduces CRISPR-Cas9 and its application methods, delivery modes, and discusses some studies using cell lines and organoids in vitro and animal models for cancer therapy in vivo.
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Shi, Yuqian. "CRISPR/Cas System in Human Genetic Diseases." Highlights in Science, Engineering and Technology 74 (December 29, 2023): 78–85. http://dx.doi.org/10.54097/ztchmw71.

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Clustered regularly interspaced short palindromic repeats/CRISPR-associated CRISPER/Cas system, as the current most popular gene-editing technology, shows great advantages of simple composition, good specificity and high cutting efficiency compared with other gene editing technology. With the rapid development of CRISPR-Cas systems, such as Cas9, Cas12a and Cas12f, can be used to edit the DNA of eukaryotic cells, and then successively found that Cas13a, Cas13b and Cas13d are targeted to the RNA merons. Through various modifications, scientists also developed a new type of the CRISPR-Cas system. With higher DNA-cutting activity, greater specificity, and smaller size than the natural CRISPR system, these engineered gene-editing systems form a powerful tool set for DNA sequence knockout, replacement, epigenetic editing, and even the activation and suppression of gene expression. Despite the potential problems in the practical application of CRISPR technology to be solved, it is believed that with further improvement, the CRISPR treatment technology will play a more important role in the prevention and treatment of human diseases, more perfectly and precisely. This review introduces the structure, functional mechanism and application of CRISPR/Cas system in human genetic diseases, and the current status and development of CRISPR/Cas system are summarized and prospected.
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Kiro, Ruth, Moran G. Goren, Ido Yosef, and Udi Qimron. "CRISPR adaptation in Escherichia coli subtypeI-E system." Biochemical Society Transactions 41, no. 6 (November 20, 2013): 1412–15. http://dx.doi.org/10.1042/bst20130109.

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The CRISPRs (clustered regularly interspaced short palindromic repeats) and their associated Cas (CRISPR-associated) proteins are a prokaryotic adaptive defence system against foreign nucleic acids. The CRISPR array comprises short repeats flanking short segments, called ‘spacers’, which are derived from foreign nucleic acids. The process of spacer insertion into the CRISPR array is termed ‘adaptation’. Adaptation allows the system to rapidly evolve against emerging threats. In the present article, we review the most recent studies on the adaptation process, and focus primarily on the subtype I-E CRISPR–Cas system of Escherichia coli.
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Heussler, Gary E., Jon L. Miller, Courtney E. Price, Alan J. Collins, and George A. O'Toole. "Requirements for Pseudomonas aeruginosa Type I-F CRISPR-Cas Adaptation Determined Using a Biofilm Enrichment Assay." Journal of Bacteriology 198, no. 22 (August 29, 2016): 3080–90. http://dx.doi.org/10.1128/jb.00458-16.

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ABSTRACTCRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR-associated protein) systems are diverse and found in many archaea and bacteria. These systems have mainly been characterized as adaptive immune systems able to protect against invading mobile genetic elements, including viruses. The first step in this protection is acquisition of spacer sequences from the invader DNA and incorporation of those sequences into the CRISPR array, termed CRISPR adaptation. Progress in understanding the mechanisms and requirements of CRISPR adaptation has largely been accomplished using overexpression ofcasgenes or plasmid loss assays; little work has focused on endogenous CRISPR-acquired immunity from viral predation. Here, we developed a new biofilm-based assay system to enrich forPseudomonas aeruginosastrains with new spacer acquisition. We used this assay to demonstrate thatP. aeruginosarapidly acquires spacers protective against DMS3vir, an engineered lytic variant of the Mu-like bacteriophage DMS3, through primed CRISPR adaptation from spacers present in the native CRISPR2 array. We found that for theP. aeruginosatype I-F system, thecas1gene is required for CRISPR adaptation,recGcontributes to (but is not required for) primed CRISPR adaptation,recDis dispensable for primed CRISPR adaptation, and finally, the ability of a putative priming spacer to prime can vary considerably depending on the specific sequences of the spacer.IMPORTANCEOur understanding of CRISPR adaptation has expanded largely through experiments in type I CRISPR systems using plasmid loss assays, mutants ofEscherichia coli, orcas1-cas2overexpression systems, but there has been little focus on studying the adaptation of endogenous systems protecting against a lytic bacteriophage. Here we describe a biofilm system that allowsP. aeruginosato rapidly gain spacers protective against a lytic bacteriophage. This approach has allowed us to probe the requirements for CRISPR adaptation in the endogenous type I-F system ofP. aeruginosa. Our data suggest that CRISPR-acquired immunity in a biofilm may be one reason that manyP. aeruginosastrains maintain a CRISPR-Cas system.
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Sasaki, Shigenori, Hirohito Ogawa, Hirokazu Katoh, and Tomoyuki Honda. "Suppression of Borna Disease Virus Replication during Its Persistent Infection Using the CRISPR/Cas13b System." International Journal of Molecular Sciences 25, no. 6 (March 20, 2024): 3523. http://dx.doi.org/10.3390/ijms25063523.

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Borna disease virus (BoDV-1) is a bornavirus that infects the central nervous systems of various animal species, including humans, and causes fatal encephalitis. BoDV-1 also establishes persistent infection in neuronal cells and causes neurobehavioral abnormalities. Once neuronal cells or normal neural networks are lost by BoDV-1 infection, it is difficult to regenerate damaged neural networks. Therefore, the development of efficient anti-BoDV-1 treatments is important to improve the outcomes of the infection. Recently, one of the clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) systems, CRISPR/Cas13, has been utilized as antiviral tools. However, it is still unrevealed whether the CRISPR/Cas13 system can suppress RNA viruses in persistently infected cells. In this study, we addressed this question using persistently BoDV-1-infected cells. The CRISPR/Cas13 system targeting viral mRNAs efficiently decreased the levels of target viral mRNAs and genomic RNA (gRNA) in persistently infected cells. Furthermore, the CRISPR/Cas13 system targeting viral mRNAs also suppressed BoDV-1 infection if the system was introduced prior to the infection. Collectively, we demonstrated that the CRISPR/Cas13 system can suppress BoDV-1 in both acute and persistent infections. Our findings will open the avenue to treat prolonged infection with RNA viruses using the CRISPR/Cas13 system.
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Dissertations / Theses on the topic "CRISPR system"

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Stens, Cassandra, Isabella Enoksson, and Sara Berggren. "The CRISPR-Cas system." Thesis, Linköpings universitet, Institutionen för fysik, kemi och biologi, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-171997.

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Derived from and inspired by the adaptive immune system of bacteria, CRISPR has gone from basic biology knowledge to a revolutionizing biotechnological tool, applicable in many research areas such as medicine, industry and agriculture. The full mechanism of CRISPR-Cas9 was first published in 2012 and various CRISPR-Cas systems have already passed the first stages of clinical trials as new gene therapies. The immense research has resulted in continuously growing knowledge of CRISPR systems and the technique seems to have the potential to greatly impact all life on our planet. Therefore, this literature study aims to thoroughly describe the CRISPR-Cas system, and further suggest an undergraduate laboratory exercise involving gene editing with the CRISPR-Cas9 tool. In this paper, we describe the fundamental technical background of the CRISPR-Cas system, especially emphasizing the most studied CRISPR-Cas9 system, its development and applications areas, as well as highlighting its current limitations and ethical concerns. The history of genetic engineering and the discovery of the CRISPR system is also described, along with a comparison with other established gene editing techniques.  This study concludes that a deeper knowledge about CRISPR is important and required since the technique is applicable in many research areas. A laboratory exercise will not only inspire but also provide extended theoretical and practical knowledge for undergraduate students.
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Stachler, Aris-Edda [Verfasser]. "Das CRISPR-Cas-System von Haloferax volcanii: CRISPRi und Autoimmunität / Aris-Edda Stachler." Ulm : Universität Ulm, 2017. http://d-nb.info/1140118145/34.

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Roidos, Paris. "Genome editing with the CRISPR Cas9 system." Thesis, KTH, Skolan för bioteknologi (BIO), 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-163694.

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Ellis, Donald Christian. "Genetic screens in vivo using the CRISPR/Cas9 system." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/109640.

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Thesis: S.M., Massachusetts Institute of Technology, Department of Biology, 2017.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 82-87).
An unmet and paramount need in the field of cancer research is to rapidly translate basic biological findings to clinically relevant therapeutics for cancer patients. Recent technological advances have generated many innovative applications to cancer biology and in a short time have yielded a wealth of information about putative vulnerabilities across a range of cancers. The proposed work involves the development of a technique to quickly probe potential cancer-specific vulnerabilities in vivo adopting methods used in genetic screens. By harnessing the information obtained from large datasets in vitro and the utility of cutting-edge endogenous mouse models, the general aim of this work is to create a method that shortens the gap between findings in the lab to viable treatment options for cancer patients.
by Donald Christian Ellis.
S.M.
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Maikova, Anna. "The CRISPR-Cas system of human pathogen Clostridium difficile : function and regulation." Thesis, Université de Paris (2019-....), 2019. http://www.theses.fr/2019UNIP7091.

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Clostridium difficile (nouveau nom Clostridioides difficile) est une bactérie à Gram-positif, sporulante, anaérobie stricte, présente dans le sol et les environnements aquatiques, ainsi que dans le tractus intestinal des mammifères. C. difficile est l’un des principaux clostridies pathogènes. Cette bactérie est devenue un vrai problème de santé publique associé à l'antibiothérapie dans les pays industrialisés. La diarrhée associée à C. difficile est actuellement la diarrhée nosocomiale la plus fréquente en Europe et dans le monde. Depuis la dernière décennie, la proportion de formes d’infections graves a augmentée en raison de l’émergence des souches hypervirulantes et épidémiques comme la souche R20291 de ribotype 027. L’infection à C. difficile provoque la diarrhée, la colite et même la mort. De nombreux aspects de la pathogenèse de C. difficile restent mal compris. En particulier, les mécanismes moléculaires de son adaptation aux conditions changeantes de l'hôte doivent être examinés.Durant le cycle d'infection, C. difficile survit dans des communautés intestinales riches en bactériophages, en utilisant des systèmes qui contrôlent les échanges génétiques favorisés dans ces environnements complexes. Au cours de la dernière décennie, les systèmes CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (associés aux CRISPR) d'immunité adaptative chez les procaryotes contre des éléments génétiques exogènes sont devenus le centre d'intérêt scientifique parmi les divers systèmes de défense bactérienne.Des études antérieures ont révélé la présence d'ARN CRISPR abondants chez C. difficile. Cette bactérie possède un système CRISPR original, caractérisé par la présence d'un grand nombre de cassettes CRISPR (12 dans la souche 630 et 9 dans la souche hypervirulante R20291), de deux ou trois opérons cas conservés dans la majorité des génomes séquencés de C. difficile et la localisation au sein des prophages de plusieurs cassettes CRISPR. Cependant, le rôle de CRISPR-Cas dans la physiologie et le cycle infectieux de cet important pathogène reste obscur.Les objectifs de ce travail sont les suivants:1) étudier le rôle et la fonctionnalité du système CRISPR-Cas de C. difficile dans les interactions avec des éléments d'ADN étrangers (tels que les plasmides), 2) révéler la manière dont le système CRISPR-Cas de C. difficile est régulé et fonctionne dans des conditions de culture bactérienne différentes, incluant la réponse aux stress.Dans la présente thèse, la fonctionnalité du système CRISPR-Cas de C. difficile a été étudiée (chapitre 2). Grâce à des tests d'efficacité de conjugaison, la fonction défensive (en interférence) du système CRISPR-Cas a été démontrée. La corrélation entre les niveaux d'expression des ARN CRISPR et les niveaux d'interférence observés a également été montrée. De plus, grâce à la série d’expériences d’interférence, la fonctionnalité des motifs PAM (protospacer adjacent motifs) a été confirmée en accord avec des prédictions in silico. Le consensus fonctionnel de PAM a été déterminé expérimentalement avec les bibliothèques des plasmides. La fonction adaptative du système CRISPR-Cas de C. difficile a été également démontrée pour la souche de laboratoire. Le rôle de plusieurs opérons cas dans la fonctionnalité du système CRISPR de C. difficile est démontré aussi dans ce chapitre.Le chapitre 3 montre le lien entre le système CRISPR-Cas et un nouveau système toxine-antitoxine de type I, ainsi que leur possible co-régulation dans des conditions de biofilm et de stress. Ce chapitre définit également le rôle possible du c-di-GMP dans la régulation du système CRISPR-Cas de C. difficile. De plus, le chapitre 4 décrit l'utilisation du système CRISPR-Cas endogène comme nouvel outil pour la rédaction du génome de C. difficile.En conclusion, les données obtenues mettent en évidence les caractéristiques originales du système CRISPR-Cas actif de C. difficile et démontrent son potentiel biotechnologique
Clostridium difficile (the novel name – Clostridioides difficile) is a Gram-positive, strictly anaerobic spore forming bacterium, found in soil and aquatic environments as well as in mammalian intestinal tracts. C. difficile is one of the major pathogenic clostridia. This bacterium has become a key public health issue associated with antibiotic therapy in industrialized countries. C. difficile-associated diarrhoea is currently the most frequently occurring nosocomial diarrhoea in Europe and worldwide. Since the last decade the number of severe infection forms has been rising due to emergence of the hypervirulent and epidemic strains as ribotype 027 R20291 strain. C. difficile infection causes diarrhoea, colitis and even death. Many aspects of C. difficile pathogenesis remain poorly understood. Particularly, the molecular mechanisms of its adaptation to changing conditions inside the host are to be scrutinized. During the infection cycle C. difficile survives in bacteriophage-rich gut communities possibly by relying on some special systems that control the genetic exchanges favored within these complex environments. During the last decade, CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems of adaptive prokaryotic immunity against exogenic genetic elements has become the center of interest among various anti-invader bacterial defense systems.Previous studies revealed the presence of abundant and diverse CRISPR RNAs in C. difficile. C. difficile has an original CRISPR system, which is characterized by the presence of an unusually large set of CRISPR arrays (12 arrays in the laboratory 630 strain and 9 ones in the hypervirulent R20291 strain), of two or three sets of cas genes conserved in the majority of sequenced C. difficile genomes and the prophage location of several CRISPR arrays. However, the role CRISPR-Cas plays in the physiology and infectious cycle of this important pathogen remains obscure.The general aims of this work run as follows: 1) to investigate the role and the functionality of C. difficile CRISPR-Cas system in the interactions with foreign DNA elements (such as plasmids), 2) to reveal the way C. difficile CRISPR-Cas system expression is regulated and functions in different states of bacterial culture, including its response to stresses. In the present PhD thesis the functionality of C. difficile CRISPR-Cas system was investigated (Chapter 2). Through conjugation efficiency assays defensive function (in interference) of C. difficile CRISPR-Cas system was demonstrated. The correlation between the previously known levels of expression of CRISPR RNAs and the observed levels of interference has also been shown. Moreover, through the series of interference experiments the functionality of PAMs (protospacer adjacent motifs) was confirmed, which have already been predicted in silico. Additionally, the general functional PAM consensus was determined using PAM libraries experiments. Furthermore, an adaptive function of C. difficile CRISPR-Cas system was shown for laboratory strain. The role of multiple cas operons in C. difficile CRISPR functionality is also demonstrated in this Chapter.In Chapter 3 the link between C. difficile CRISPR-Cas system and a new type I toxin-antitoxin system is demonstrated, as well as a possible co-regulation under biofilm and stress conditions of CRISPR-Cas system and these toxin-antitoxin modules. This Chapter also defines a possible role of c-di-GMP in regulation of C. difficile CRISPR-Cas system. Additionally, Chapter 4 describes the utilization of endogenous C. difficile CRISPR-Cas system as a novel tool for genome editing in C. difficile. Altogether, the obtained data highlight the original features of active C. difficile CRISPR-Cas system and demonstrate its biotechnological potential
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Arooj, Mahira. "Precision Genome Engineering and Gene Silencing Using CRISPR/dCas9 System." Thesis, Curtin University, 2018. http://hdl.handle.net/20.500.11937/73571.

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This research aimed to repress target genes by modulating their expression through rewriting of aberrant epigenetic landscapes, including DNA methylation and histone post-translational modifications, utilizing epigenetic repressor domains. The epigenetic repressor domains included KRAB, DNMT3A, UHRF1 and CSD, which were delivered via the epigenetic editing tools ZFs, TALEs and the CRISPR/dCas9 system. Our findings suggest that a combination of multiple epigenetic repressor domains targeting epigenetic marks involved in epigenetic cross-talk significantly repressed target genes.
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Dhanjal, Jaspreet Kaur. "Computational insights into CRISPR/Cas9 system for improved genome editing." Thesis, IIT Delhi, 2019. http://eprint.iitd.ac.in:80//handle/2074/8077.

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Cui, Xiucheng. "Targeted Gene Editing Using CRISPR/Cas9 in a Wheat Protoplast System." Thesis, Université d'Ottawa / University of Ottawa, 2017. http://hdl.handle.net/10393/36543.

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The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has become a promising tool for targeted gene editing in a variety of organisms including plants. In this system, a 20 nt sequence on a single guide RNA (sgRNA) is the only gene-specific information required to modify a target gene. Fusarium head blight (FHB) is a devastating disease in wheat caused by the fungus Fusarium graminearum. The trichothecene it produces, deoxynivalenol (DON), is a major mycotoxin contaminant causing food production loss both in quality and yield. In this project, we used the CRISPR/Cas9 system to modify three wheat genes identified in previous experiments, including an ABC transporter (TaABCC6), and the Nuclear Transcription Factor X box-binding-Like 1 (TaNFXL1), both associated with FHB susceptibility, and a non-specific Lipid Transfer Protein (nsLTP) named TansLTP9.4 which correlates with FHB resistance. Two sgRNAs were designed to target each gene and were shown in an in vitro CRISPR/Cas9 assay to guide the sequence-specific cleavage with high efficiency. Another assay for CRISPR/Cas9 was established by the optimization of a wheat protoplast isolation and transformation system. Using a construct expressing a green fluorescent protein (GFP) as a positive control, estimated transformation efficiencies of about 60% were obtained with different batches of protoplasts. High-throughput sequencing of PCR amplicons from protoplasts transformed with editing constructs clearly showed that the three genes have been successfully edited with efficiencies of up to 42.2%. In addition, we also characterized by RT-qPCR the expression pattern of 10 genes in DON-treated protoplasts; seven of the genes were induced by DON in the protoplasts, consistent with their previously identified DON induction in treated wheat heads, while three genes expressed differentially between DON-treated wheat heads and protoplasts. Preliminary bioinformatics analyses showed that these differentially expressed genes are involved in different plant defense mechanisms.
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Amlinger, Lina. "The type I-E CRISPR-Cas system : Biology and applications of an adaptive immune system in bacteria." Doctoral thesis, Uppsala universitet, Mikrobiologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-312234.

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CRISPR-Cas systems are adaptive immune systems in bacteria and archaea, consisting of a clustered regularly interspaced short palindromic repeats (CRISPR) array and CRISPR associated (Cas) proteins. In this work, the type I-E CRISPR-Cas system of Escherichia coli was studied. CRISPR-Cas immunity is divided into three stages. In the first stage, adaptation, Cas1 and Cas2 store memory of invaders in the CRISPR array as short intervening sequences, called spacers. During the expression stage, the array is transcribed, and subsequently processed into small CRISPR RNAs (crRNA), each consisting of one spacer and one repeat. The crRNAs are bound by the Cascade multi-protein complex. During the interference step, Cascade searches for DNA molecules complementary to the crRNA spacer. When a match is found, the target DNA is degraded by the recruited Cas3 nuclease. Host factors required for integration of new spacers into the CRISPR array were first investigated. Deleting recD, involved in DNA repair, abolished memory formation by reducing the concentration of the Cas1-Cas2 expression plasmid, leading to decreased amounts of Cas1 to levels likely insufficient for spacer integration. Deletion of RecD has an indirect effect on adaptation. To facilitate detection of adaptation, a sensitive fluorescent reporter was developed where an out-of-frame yfp reporter gene is moved into frame when a new spacer is integrated, enabling fluorescent detection of adaptation. Integration can be detected in single cells by a variety of fluorescence-based methods. A second aspect of this thesis aimed at investigating spacer elements affecting target interference. Spacers with predicted secondary structures in the crRNA impaired the ability of the CRISPR-Cas system to prevent transformation of targeted plasmids. Lastly, in absence of Cas3, Cascade was successfully used to inhibit transcription of specific genes by preventing RNA polymerase access to the promoter. The CRISPR-Cas field has seen rapid development since the first demonstration of immunity almost ten years ago. However, much research remains to fully understand these interesting adaptive immune systems and the research presented here increases our understanding of the type I-E CRISPR-Cas system.
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Seo, Jooheon. "Modulation of DNA repair pathway after CRISPR/Cas9 mediated Double Stranded Break." Thesis, Virginia Tech, 2017. http://hdl.handle.net/10919/74884.

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The CRISPR/Cas9 system has become the predominant tool for genome editing. Targeted modifications can be introduced while repairing double strand breaks (DSBs), induced by the CRISPR/Cas9 system. The DSB is repaired by either non-homologous end joining (NHEJ) or homologous recombination (HR), and the repair is commonly processed through NHEJ because it is the dominant repair pathway in most cell types. The goal of this study is to modulate DNA repair system of somatic cells to increase the frequency of homology-directed repair (HDR) through HR by chemical treatment and the frequency of NHEJ by serum starvation. CRISPR/Cas9 systems targeting RAG2 gene and donor DNA to replace endogenous RAG2 were transfected into porcine fetal fibroblast (PFF) cells and the cells were treated with various chemicals that were known to inhibit NHEJ or stimulate HR. Among the chemical treated groups, cells treated with thymidine showed an average of 5.85-fold increase in HDR compared to the control group; the difference ranged from 1.37 to 9.59. There was no positive effect on the frequency of HDR after treating transfected cells with other chemicals. Placing PFFs under low amount of serum (serum deprivation) could enrich the cells in G0/G1 phase, but there was little difference in the frequency of NHEJ. Our results indicate that modulating DNA repair pathways during CRISPR/Cas9-mediated gene targeting could change the outcome of the targeted events.
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Books on the topic "CRISPR system"

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Halpin-Healy, Tyler Sheehan. Structure and Function of a Transposon-Encoded CRISPR-Cas System. [New York, N.Y.?]: [publisher not identified], 2021.

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Little, Jamie. Using Genomic Transgenes and the CRISPR/Cas9 Gene Editing System to Understand How Hedgehog Signaling Regulates Costal2 and Cubitus Interruptus in Drosophila melanogaster. [New York, N.Y.?]: [publisher not identified], 2017.

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Barrangou, Rodolphe, and John van der Oost, eds. CRISPR-Cas Systems. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-662-45794-8.

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Barrangou, Rodolphe, and John van der Oost, eds. CRISPR-Cas Systems. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-34657-6.

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Næss, Petter, and Leigh Price, eds. Crisis System. New York : Routledge, 2016. | Series: Ontological explorations: Routledge, 2016. http://dx.doi.org/10.4324/9781315563138.

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Denis, Smith. Key readings in crisis management: Systems and structures for prevention and recovery. New York, NY: Routledge, 2006.

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Dufresne, Todd, and Clara Sacchetti. The economy as cultural system: Theory, capitalism, crisis. New York, NY: Continuum International Pub., 2012.

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Qi, Yiping, ed. Plant Genome Editing with CRISPR Systems. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-8991-1.

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Sohn, Manfred. Hat das System einen Fehler oder ist es der Fehler?: Antworten auf die Finanz- und Wirtschaftskrise von links. Bonn: Pahl-Rugenstein, 2009.

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Konzelmann, Suzanne J., and Marc Fovargue-Davies. Banking systems in the crisis: The faces of liberal capitalism. New York: Routledge, 2012.

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Book chapters on the topic "CRISPR system"

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Munawar, Nayla, and Aftab Ahmad. "CRISPR/Cas System: An Introduction." In CRISPR Crops, 1–35. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-15-7142-8_1.

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Munawar, Nayla, and Aftab Ahmad. "CRISPR/Cas System: An Introduction." In CRISPR Crops, 1–35. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-15-7142-8_1.

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Gopika, Boro Arthi, Arumugam Vijaya Anand, Natchiappan Senthilkumar, Senthil Kalaiselvi, and Santhanu Krishnapriya. "Gene Editing Using CRISPR/Cas9 System." In CRISPR and Plant Functional Genomics, 258–70. Boca Raton: CRC Press, 2024. http://dx.doi.org/10.1201/9781003387060-15.

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Chen, Meng, and Lei Stanley Qi. "Repurposing CRISPR System for Transcriptional Activation." In RNA Activation, 147–57. Singapore: Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-4310-9_10.

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Cong, Le, and Feng Zhang. "Genome Engineering Using CRISPR-Cas9 System." In Chromosomal Mutagenesis, 197–217. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1862-1_10.

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Khan, Zulqurnain, Tahmina Sattar, Maria Siddique, Zulfiqar Ali, Asif Ali Khan, Syed Ovais Aftab, Muhammad Zubair Ghouri, Qaisar Sultan, Nauman Gulzar, and Farooq Ahmad. "Reengineering of the CRISPR/Cas System." In The CRISPR/Cas Tool Kit for Genome Editing, 149–86. Singapore: Springer Singapore, 2022. http://dx.doi.org/10.1007/978-981-16-6305-5_5.

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Balan, Vitaly, and Jianbin Wang. "The CRISPR System and Cancer Immunotherapy Biomarkers." In Biomarkers for Immunotherapy of Cancer, 301–22. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9773-2_14.

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Khan, Sultan Habibullah, Hooran Tariq, Iqra Farooq, Hira Tasleeem, Muhammad Zubair Ghouri, Muhammad Salman Mubarik, and Zulqurnain Khan. "Applications of CRISPR/Cas System in Plants." In The CRISPR/Cas Tool Kit for Genome Editing, 285–309. Singapore: Springer Singapore, 2022. http://dx.doi.org/10.1007/978-981-16-6305-5_9.

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Khan, Zulqurnain, Zulfiqar Ali, Asif Ali Khan, Tahmina Sattar, Ali Zeshan, Tahira Saboor, and Barkha Binyamin. "History and Classification of CRISPR/Cas System." In The CRISPR/Cas Tool Kit for Genome Editing, 29–52. Singapore: Springer Singapore, 2022. http://dx.doi.org/10.1007/978-981-16-6305-5_2.

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Bonamino, Martín Hérnan, and Eduardo Mannarino Correia. "The CRISPR/Cas System in Human Cancer." In Advances in Experimental Medicine and Biology, 59–71. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-33325-5_4.

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Conference papers on the topic "CRISPR system"

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Zhang, Liuyijia. "CRISPR/Cas system in human genetic diseases." In Third International Conference on Biological Engineering and Medical Science (ICBioMed2023), edited by Alan Wang. SPIE, 2024. http://dx.doi.org/10.1117/12.3012830.

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Jiang, Qiancheng. "CRISPR-Cas9 system applications in cancer models." In International Conference on Biological Engineering and Medical Science (ICBIOMed2022), edited by Gary Royle and Steven M. Lipkin. SPIE, 2023. http://dx.doi.org/10.1117/12.2669382.

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Brisson, Jennifer A. "Developing the CRISPR/Cas9 system in the pea aphid." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.105396.

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Zhang, Hanlin. "Therapeutic applications of CRISPR-Cas system in infectious diseases." In Third International Conference on Biological Engineering and Medical Science (ICBioMed2023), edited by Alan Wang. SPIE, 2024. http://dx.doi.org/10.1117/12.3012858.

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Xiao, Zening. "Principle, application and prospect of CRISPR-Cas9 regulatory system." In International Conference on Modern Medicine and Global Health (ICMMGH 2023), edited by Sheiladevi Sukumaran. SPIE, 2023. http://dx.doi.org/10.1117/12.2692261.

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Song, Tianyi, Jingwen Wang, and Yinxuan Wu. "CRISPR-Cas system: revolutionizing plant breeding and gene therapy." In International Conference on Modern Medicine and Global Health (ICMMGH 2023), edited by Sheiladevi Sukumaran. SPIE, 2023. http://dx.doi.org/10.1117/12.2692353.

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Samaniego, Christian Cuba, Hari K. K. Subramanian, and Elisa Franco. "Design of a bistable network using the CRISPR/Cas system." In 2017 IEEE Conference on Control Technology and Applications (CCTA). IEEE, 2017. http://dx.doi.org/10.1109/ccta.2017.8062586.

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Dolzhikova, O. A., O. A. Semikolenova, M. I. Meschaninova, and D. S. Novopashina. "ALLOSTERIC REGULATION OF CRISPR/CAS9 SYSTEM ON THE RNA LEVEL." In X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-71.

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CRISPR/Cas9 systems are commonly used for the introduction of double-strand break at the targeted point of DNA. A possible way to improve its specificity is allosteric regulation. Here, we designed guide RNA containing theophylline-binding or Mango aptamer and investigated their functional activity by the example of the model DNA cleavage either in absence or in presence of theophylline or thiazole orange respectively.
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Hao, Yiqiao. "CRISPR-Cas system: off-target effects and its possible solutions." In Third International Conference on Biological Engineering and Medical Science (ICBioMed2023), edited by Alan Wang. SPIE, 2024. http://dx.doi.org/10.1117/12.3012920.

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You, Donghan. "Development and applications of CRISPR/Cas system in genetic engineering." In Third International Conference on Biological Engineering and Medical Science (ICBioMed2023), edited by Alan Wang. SPIE, 2024. http://dx.doi.org/10.1117/12.3013065.

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Reports on the topic "CRISPR system"

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Morin, S., L. L. Walling, Peter W. Atkinson, J. Li, and B. E. Tabashnik. ets for CRISPR/Cas9-mediated gene drive in Bemisia tabaci. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134170.bard.

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The goal of our BARD proposal was to build both the necessary infrastructure and knowledge for using the CRISPR/Cas9-based gene drive system to control the whitefly Bemisia tabaci. Our research focused on achieving three main goals: (1) establishing a CRISPR/Cas9 gene-editing system for producing genetically-edited B. tabaci; (2) generating and testing CRISPR/Cas9-mediated mutations targeting genes that represent two gene drive strategies: population replacement and population suppression; (3) using computer modeling to optimize strategies for applying CRISPR/Cas9 to control B. tabaci populations in the field. CRISPR gene drive is one of the most promising strategies for diminishing the negative impacts of harmful insects. This technique can introduce mutations into wild populations of pests that reduce their ability to cause damage, reduce their population size, or both. In principle, this can be selfsustaining because mutations carried by relatively few insects can increase in frequency and spread quickly throughout wild populations. Because of this sustainability and the potential benefits to society, agricultural gene-drive systems are most likely to be funded by government agencies, foundations, and grower associations; as with sterile insect releases and most biocontrol programs. Although gene drives have received intensive study in Drosophila and mosquito vectors of human disease, we were one of the first teams pursuing this approach for crop pests. Our project was also one of the first to address CRISPR gene drive in the Hemiptera, an insect order that includes hundreds of pest species. We focused on developing and implementing CRISPR gene drive to reduce the massive damage caused by B. tabaci. This haplodiploid insect is one of the world's most devastating crop pests. Whereas extensive work by others explored CRISPR in diploid species, our project pioneered application of this revolutionary technology to haplodiploids, which have a distinct system of inheritance that presents special challenges and opportunities. Our project has achieved several breakthroughs, including publication of the first paper analyzing CRISPR gene drive in haplodiploids (Li et al. 2020, see next section). Our modeling results from this landmark study demonstrate that CRISPR gene drive can work in haplodiploids, especially if fitness costs associated with the driver allele are low or nil. Our paper was the first to provide a conceptual framework for evaluating and optimizing CRISPR gene drive strategies for managing B. tabaci and other haplodiploid pests. Our breakthroughs in the laboratory have created the infrastructure needed to develop CRISPR for controlling B. tabaci. We established a microinjection system enabling us to introduce CRISPR-derived mutations into B. tabaci embryos. We have used this system to generate and track inherited eye-color mutants of B. tabaci. We have identified and cloned germline promoters, and demonstrated their function in transgenic B. tabaci embryos and other hemipteran insects. We have also developed a tool to easily identify B. tabaci harboring CRISPR-mediated mutations by tagging target genes using a transgenic fluorescent marker. The successful completion of our project provides all the knowledge and infrastructure essential for developing a novel genetic approach for B. tabaci control, which can serve as a non-chemical "green" alternative for managing this global pest. We predict that our discoveries will accelerate the development of the CRISPR gene drive technique for reducing the numbers of this pest and the damage it causes. Still, realization of the benefits of gene-drive technology for pest control will require sustained attention to potential environmental and societal impacts, as well as regulatory and implementation challenges. Given the great promise of this technology and the urgent need for better control methods, we expect that guidance documents and regulations will be in place to allow the scientific community to safely move gene drives for pest control from the laboratory to field trials.
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Vardhaan Ambati, Vardhaan Ambati. Personalized Cancer and Viral Therapy: Clostridium-based Cell Delivery System coupled to CRISPR/Cas9 Nanotherapeutic. Experiment, September 2016. http://dx.doi.org/10.18258/7926.

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Powell, Andrew, and Giovanni Majnoni. On Endogenous Risk, the Amplification Effects of Financial Systems and Macro Prudential Policies. Inter-American Development Bank, November 2011. http://dx.doi.org/10.18235/0011345.

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The recent global financial crisis has put the spotlight on macro-prudential policies to protect firms and households from problems emanating from the financial sector. This paper proposes an analytical framework that combines exogenous and endogenous risks, the latter seen as stemming from frictions in financial markets. Arguing that endogenous risks may be systemic and costly, the paper employs a database of emerging market corporate bond spreads and finds evidence that endogenous risks are present and have amplified the effects of financial crises. Larger financial systems are found to exacerbate the impact of crises, and weaker financial systems are found to exacerbate particularly the impact of banking crises. The results suggest that policymakers should monitor time-varying systemic risks using both price and quantity signals and take actions in good times to mitigate potential amplifying effects at times of stress.
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Sanford, Jack, and John Weldon. The Biology of Native and Adapted CRISPR-Cas Systems. Journal of Young Investigators, November 2018. http://dx.doi.org/10.22186/jyi.35.5.81-91.

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Spivack, Marla. Applying Systems Thinking to Education: The RISE Systems Framework. Research on Improving Systems of Education (RISE), May 2021. http://dx.doi.org/10.35489/bsg-rise-ri_2021/028.

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Many education systems in low- and middle-income countries are experiencing a learning crisis. Many efforts to address this crisis do not account for the system features of education, meaning that they fail to consider the ways that interactions and feedback loops produce outcomes. Thinking through the feedback relationships that produce the education system can be challenging. The RISE Education Systems Framework, which is sufficiently structured to give boundaries to the analysis but sufficiently flexible to be adapted to multiple scenarios, can be helpful. The RISE Framework identifies four key relationships in an education system: politics, compact, management, and voice and choice; and five features that can be used to describe these relationships: delegation, finance, information, support, and motivation. This Framework can be a useful approach for characterising the key actors and interactions in the education system, thinking through how these interactions produce systems outcomes, and identifying ways to intervene that can shift the system towards better outcomes.
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Hausmann, Ricardo, and Michael Gavin. The Roots of Banking Crises: The Macroeconomic Context. Inter-American Development Bank, January 1996. http://dx.doi.org/10.18235/0011541.

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This paper discusses the ways in which macroeconomic developments can put stress on banks, and in extreme cases lead to banking crises. These macroeconomic causes of bank vulnerability and crisis have important implications for regulatory regimes, and for macroeconomic policy itself. Much of the discussion emphasizes the need for monetary policy to be set with an eye on the state of the domestic banking system as an occasionally important consideration. One purpose of this paper is to promote a discussion of how to do a better job of incorporating weak banking systems into macroeconomic policy management.
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Federico, Pablo M. Developing an Index of Liquidity-Risk Exposure: An Application to Latin American and Caribbean Banking Systems. Inter-American Development Bank, November 2012. http://dx.doi.org/10.18235/0009083.

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After the 2007-2009 global financial crisis and previous financial crises in Latin America, the liquidity-risk exposure of banking systems is considered one of the most important vulnerabilities. At the same time, that exposure may also be the most mysterious of those vulnerabilities, as the dimensions of this risk are not yet well understood and good metrics have not been available. This goal of this paper is to provide a thorough review of previous contributions and to develop a set of measures of systemic liquidity-risk exposure of banking systems, with a focus on Latin American and Caribbean economies.
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Soloviev, Vladimir, Andrii Bielinskyi, and Viktoria Solovieva. Entropy Analysis of Crisis Phenomena for DJIA Index. [б. в.], June 2019. http://dx.doi.org/10.31812/123456789/3179.

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The Dow Jones Industrial Average (DJIA) index for the 125-year-old (since 1896) history has experienced many crises of different nature and, reflecting the dynamics of the world stock market, is an ideal model object for the study of quantitative indicators and precursors of crisis phenomena. In this paper, the classification and periodization of crisis events for the DJIA index have been carried out; crashes and critical events have been highlighted. Based on the modern paradigm of the theory of complexity, a spectrum of entropy indicators and precursors of crisis phenomena have been proposed. The entropy of a complex system is not only a measure of uncertainty (like Shannon's entropy) but also a measure of complexity (like the permutation and Tsallis entropy). The complexity of the system in a crisis changes significantly. This fact can be used as an indicator, and in the case of a proactive change as a precursor of a crisis. Complex systems also have the property of scale invariance, which can be taken into account by calculating the Multiscale entropy. The calculations were carried out within the framework of the sliding window algorithm with the subsequent comparison of the entropy measures of complexity with the dynamics of the DJIA index itself. It is shown that Shannon's entropy is an indicator, and the permutation and Tsallis entropy are the precursors of crisis phenomena to the same extent for both crashes and critical events.
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Soloviev, Vladimir, and Andrey Belinskij. Methods of nonlinear dynamics and the construction of cryptocurrency crisis phenomena precursors. [б. в.], 2018. http://dx.doi.org/10.31812/123456789/2851.

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This article demonstrates the possibility of constructing indicators of critical and crisis phenomena in the volatile market of cryptocurrency. For this purpose, the methods of the theory of complex systems such as recurrent analysis of dynamic systems and the calculation of permutation entropy are used. It is shown that it is possible to construct dynamic measures of complexity, both recurrent and entropy, which behave in a proper way during actual pre-crisis periods. This fact is used to build predictors of crisis phenomena on the example of the main five crises recorded in the time series of the key cryptocurrency bitcoin, the effectiveness of the proposed indicators-precursors of crises has been identified.
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Barjum, Daniel. PDIA for Systems Change: Tackling the Learning Crisis in Indonesia. Research on Improving Systems of Education (RISE), September 2022. http://dx.doi.org/10.35489/bsg-rise-ri_2022/046.

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Indonesia is facing a learning crisis. While schooling has increased dramatically in the last 30 years, the quality of education has remained mediocre (Rosser et al., 2022). Teacher capability is an often cited weakness of the system, along with policies and system governance. Approaches focused primarily on adding resources to education have not yielded expected outcomes of increased quality. “It is a tragedy that in the second decade of the twenty-first century, some children in Indonesia are not completing primary school and are turned out into the workforce as functional illiterates.” (Suryadarma and Jones, 2013; Nihayah et al., 2020). In the early 2000s, Indonesia began a process of decentralising service delivery, including education, to the district level. Many responsibilities were transferred from the central government to districts, but some key authorities, such as hiring of civil service teachers, remained with the central government. The Indonesian system is complex and challenging to manage, with more than 300 ethnic groups and networks of authority spread over more than 500 administrative districts (Suryadarma and Jones, 2013). Niken Rarasati and Daniel Suryadarma researchers at SMERU, an Indonesian think tank and NGO, understood this context well. Their prior experience working in the education sector had shown them that improving the quality of education within the classroom required addressing issues at the systems level (Kleden, 2020). Rarasati noted the difference in knowledge between in-classroom teaching and the systems of education: “There are known-technologies, pedagogical theories, practices, etc. for teaching in the classroom. The context [for systems of education] is different for teacher development, recruitment, and student enrollment. Here, there is less known in the public and education sector.” Looking for ways to bring changes to policy implementation and develop capabilities at the district level, SMERU researchers began to apply a new approach they had learned in a free online course offered by the Building State Capability programme at the Center for International Development at Harvard University titled, “The Practice of PDIA: Building Capability by Delivering Results”. The course offered insights on how to implement public policy in complex settings, focused on using Problem Driven Iterative Adaptation (PDIA). The researchers were interested in putting PDIA into practice and seeing if it could be an effective approach for their colleagues in government. This case study reviews Rarasati and Suryadarma’s journey and showcases how they used PDIA to foster relationships between local government and stakeholders, and bring positive changes to the education sector.
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