Academic literature on the topic 'Integrative and mobilizable element'
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Journal articles on the topic "Integrative and mobilizable element"
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Doublet, Benoît, David Boyd, Michael R. Mulvey, and Axel Cloeckaert. "TheSalmonellagenomic island 1 is an integrative mobilizable element." Molecular Microbiology 55, no. 6 (February 4, 2005): 1911–24. http://dx.doi.org/10.1111/j.1365-2958.2005.04520.x.
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Durand, Romain, Florence Deschênes, and Vincent Burrus. "Genomic islands targeting dusA in Vibrio species are distantly related to Salmonella Genomic Island 1 and mobilizable by IncC conjugative plasmids." PLOS Genetics 17, no. 8 (August 20, 2021): e1009669. http://dx.doi.org/10.1371/journal.pgen.1009669.
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Salmonella Genomic Island 1 (SGI1) and its variants are significant contributors to the spread of antibiotic resistance among Gammaproteobacteria. All known SGI1 variants integrate at the 3’ end of trmE, a gene coding for a tRNA modification enzyme. SGI1 variants are mobilized specifically by conjugative plasmids of the incompatibility groups A and C (IncA and IncC). Using a comparative genomics approach based on genes conserved among members of the SGI1 group, we identified diverse integrative elements distantly related to SGI1 in several species of Vibrio, Aeromonas, Salmonella, Pokkaliibacter, and Escherichia. Unlike SGI1, these elements target two alternative chromosomal loci, the 5’ end of dusA and the 3’ end of yicC. Although they share many features with SGI1, they lack antibiotic resistance genes and carry alternative integration/excision modules. Functional characterization of IMEVchUSA3, a dusA-specific integrative element, revealed promoters that respond to AcaCD, the master activator of IncC plasmid transfer genes. Quantitative PCR and mating assays confirmed that IMEVchUSA3 excises from the chromosome and is mobilized by an IncC helper plasmid from Vibrio cholerae to Escherichia coli. IMEVchUSA3 encodes the AcaC homolog SgaC that associates with AcaD to form a hybrid activator complex AcaD/SgaC essential for its excision and mobilization. We identified the dusA-specific recombination directionality factor RdfN required for the integrase-mediated excision of dusA-specific elements from the chromosome. Like xis in SGI1, rdfN is under the control of an AcaCD-responsive promoter. Although the integration of IMEVchUSA3 disrupts dusA, it provides a new promoter sequence and restores the reading frame of dusA for proper expression of the tRNA-dihydrouridine synthase A. Phylogenetic analysis of the conserved proteins encoded by SGI1-like elements targeting dusA, yicC, and trmE gives a fresh perspective on the possible origin of SGI1 and its variants.
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Lorenzo-Diaz, Fabian, Cris Fernández-Lopez, Pierre-Emmanuel Douarre, Adrian Baez-Ortega, Carlos Flores, Philippe Glaser, and Manuel Espinosa. "Streptococcal group B integrative and mobilizable element IMESag- rpsI encodes a functional relaxase involved in its transfer." Open Biology 6, no. 10 (October 2016): 160084. http://dx.doi.org/10.1098/rsob.160084.
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Streptococcus agalactiae or Group B Streptococcus (GBS) are opportunistic bacteria that can cause lethal sepsis in children and immuno-compromised patients. Their genome is a reservoir of mobile genetic elements that can be horizontally transferred. Among them, integrative and conjugative elements (ICEs) and the smaller integrative and mobilizable elements (IMEs) primarily reside in the bacterial chromosome, yet have the ability to be transferred between cells by conjugation. ICEs and IMEs are therefore a source of genetic variability that participates in the spread of antibiotic resistance. Although IMEs seem to be the most prevalent class of elements transferable by conjugation, they are poorly known. Here, we have studied a GBS-IME, termed IMESag- rpsI , which is widely distributed in GBS despite not carrying any apparent virulence trait. Analyses of 240 whole genomes showed that IMESag- rpsI is present in approximately 47% of the genomes, has a roughly constant size (approx. 9 kb) and is always integrated at a single location, the 3′-end of the gene encoding the ribosomal protein S9 ( rpsI ). Based on their genetic variation, several IMESag- rpsI types were defined (A–J) and classified in clonal complexes (CCs). CC1 was the most populated by IMESag- rpsI (more than 95%), mostly of type-A (71%). One CC1 strain ( S. agalactiae HRC) was deep-sequenced to understand the rationale underlying type-A IMESag- rpsI enrichment in GBS. Thirteen open reading frames were identified, one of them encoding a protein (MobSag) belonging to the broadly distributed family of relaxases MOB V1 . Protein MobSag was purified and, by a newly developed method, shown to cleave DNA at a specific dinucleotide. The S. agalactiae HRC-IMESag- rpsI is able to excise from the chromosome, as shown by the presence of circular intermediates, and it harbours a fully functional mobilization module. Further, the mobSag gene encoded by this mobile element is able to promote plasmid transfer among pneumococcal strains, suggesting that MobSag facilitates the spread of IMESag- rpsI and that this spread would explain the presence of the same IMESag- rpsI type in GBS strains belonging to different CCs.
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Lao, Julie, Gérard Guédon, Thomas Lacroix, Florence Charron-Bourgoin, Virginie Libante, Valentin Loux, Hélène Chiapello, Sophie Payot, and Nathalie Leblond-Bourget. "Abundance, Diversity and Role of ICEs and IMEs in the Adaptation of Streptococcus salivarius to the Environment." Genes 11, no. 9 (August 26, 2020): 999. http://dx.doi.org/10.3390/genes11090999.
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Streptococcus salivarius is a significant contributor to the human oral, pharyngeal and gut microbiomes that contribute to the maintenance of health. The high genomic diversity observed in this species is mainly caused by horizontal gene transfer. This work aimed to evaluate the contribution of integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) in S. salivarius genome diversity. For this purpose, we performed an in-depth analysis of 75 genomes of S. salivarius and searched for signature genes of conjugative and mobilizable elements. This analysis led to the retrieval of 69 ICEs, 165 IMEs and many decayed elements showing their high prevalence in S. salivarius genomes. The identification of almost all ICE and IME boundaries allowed the identification of the genes in which these elements are inserted. Furthermore, the exhaustive analysis of the adaptation genes carried by these elements showed that they encode numerous functions such as resistance to stress, to antibiotics or to toxic compounds, and numerous enzymes involved in diverse cellular metabolic pathways. These data support the idea that not only ICEs but also IMEs and decayed elements play an important role in S. salivarius adaptation to the environment.
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Woudstra, Cedric, and Sophie A. Granier. "A Glimpse at the Anti-Phage Defenses Landscape in the Foodborne Pathogen Salmonella enterica subsp. enterica Serovar Typhimurium." Viruses 15, no. 2 (January 24, 2023): 333. http://dx.doi.org/10.3390/v15020333.
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Bacteriophages, which specifically infect and kill bacteria, are currently used as additives to control pathogens such as Salmonella in human food (PhageGuard S®) or animal feed (SalmoFREE®, Bafasal®). Indeed, salmonellosis is among the most important zoonotic foodborne illnesses. The presence of anti-phage defenses protecting bacteria against phage infection could impair phage applications aiming at reducing the burden of foodborne pathogens such as Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) to the food industry. In this study, the landscape of S. Typhimurium anti-phage defenses was bioinformatically investigated in publicly available genomes using the webserver PADLOC. The primary anti-phage systems identified in S. Typhimurium use nucleic acid degradation and abortive infection mechanisms. Reference systems were identified on an integrative and conjugative element, a transposon, a putative integrative and mobilizable element, and prophages. Additionally, the mobile genetic elements (MGEs) containing a subset of anti-phage systems were found in the Salmonella enterica species. Lastly, the MGEs alone were also identified in the Enterobacteriaceae family. The presented diversity assessment of the anti-phage defenses and investigation of their dissemination through MGEs in S. Typhimurium constitute a first step towards the design of preventive measures against the spread of phage resistance that may hinder phage applications.
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Wang, Jun, Nadja B. Shoemaker, Gui-Rong Wang, and Abigail A. Salyers. "Characterization of a Bacteroides Mobilizable Transposon, NBU2, Which Carries a Functional Lincomycin Resistance Gene." Journal of Bacteriology 182, no. 12 (June 15, 2000): 3559–71. http://dx.doi.org/10.1128/jb.182.12.3559-3571.2000.
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ABSTRACT The mobilizable Bacteroides element NBU2 (11 kbp) was found originally in two Bacteroides clinical isolates,Bacteroides fragilis ERL and B. thetaiotaomicron DOT. At first, NBU2 appeared to be very similar to another mobilizable Bacteroides element, NBU1, in a 2.5-kbp internal region, but further examination of the full DNA sequence of NBU2 now reveals that the region of near identity between NBU1 and NBU2 is limited to this small region and that, outside this region, there is little sequence similarity between the two elements. The integrase gene of NBU2, intN2, was located at one end of the element. This gene was necessary and sufficient for the integration of NBU2. The integrase of NBU2 has the conserved amino acids (R-H-R-Y) in the C-terminal end that are found in members of the lambda family of site-specific integrases. This was also the only region in which the NBU1 and NBU2 integrases shared any similarity (28% amino acid sequence identity and 49% sequence similarity). Integration of NBU2 was site specific in Bacteroidesspecies. Integration occurred in two primary sites in B. thetaiotaomicron. Both of these sites were located in the 3′ end of a serine-tRNA gene NBU2 also integrated in Escherichia coli, but integration was much less site specific than inB. thetaiotaomicron. Analysis of the sequence of NBU2 revealed two potential antibiotic resistance genes. The amino acid sequences of the putative proteins encoded by these genes had similarity to resistances found in gram-positive bacteria. Only one of these genes was expressed in B. thetaiotaomicron, the homolog of linA, a lincomycin resistance gene fromStaphylococcus aureus. To determine how widespread elements related to NBU1 and NBU2 are in Bacteroides species, we screened 291 Bacteroides strains. Elements with some sequence similarity to NBU2 and NBU1 were widespread inBacteroides strains, and the presence oflinAN in Bacteroides strains was highly correlated with the presence of NBU2, suggesting that NBU2 has been responsible for the spread of this gene amongBacteroides strains. Our results suggest that the NBU-related elements form a large and heterogeneous family, whose members have similar integration mechanisms but have different target sites and differ in whether they carry resistance genes.
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Libante, Virginie, Nazim Sarica, Abbas Mohamad Ali, Chloé Gapp, Anissa Oussalah, Gérard Guédon, Nathalie Leblond-Bourget, and Sophie Payot. "Mobilization of IMEs Integrated in the oriT of ICEs Involves Their Own Relaxase Belonging to the Rep-Trans Family of Proteins." Genes 11, no. 9 (August 26, 2020): 1004. http://dx.doi.org/10.3390/genes11091004.
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Integrative mobilizable elements (IMEs) are widespread but very poorly studied integrated elements that can excise and hijack the transfer apparatus of co-resident conjugative elements to promote their own spreading. Sixty-four putative IMEs, harboring closely related mobilization and recombination modules, were found in 14 Streptococcus species and in Staphylococcus aureus. Fifty-three are integrated into the origin of transfer (oriT) of a host integrative conjugative element (ICE), encoding a MobT relaxase and belonging to three distant families: ICESt3, Tn916, and ICE6013. The others are integrated into an unrelated IME or in chromosomal sites. After labeling by an antibiotic resistance gene, the conjugative transfer of one of these IMEs (named IME_oriTs) and its host ICE was measured. Although the IME is integrated in an ICE, it does not transfer as a part of the host ICE (no cis-mobilization). The IME excises and transfers separately from the ICE (without impacting its transfer rate) using its own relaxase, distantly related to all known MobT relaxases, and integrates in the oriT of the ICE after transfer. Overall, IME_oriTs use MobT-encoding ICEs both as hosts and as helpers for conjugative transfer. As half of them carry lsa(C), they actively participate in the dissemination of lincosamide–streptogramin A–pleuromutilin resistance among Firmicutes.
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Shoemaker, N. B., G. R. Wang, A. M. Stevens, and A. A. Salyers. "Excision, transfer, and integration of NBU1, a mobilizable site-selective insertion element." Journal of Bacteriology 175, no. 20 (1993): 6578–87. http://dx.doi.org/10.1128/jb.175.20.6578-6587.1993.
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Veschetti, Laura, Angela Sandri, Helle Krogh Johansen, Maria M. Lleò, and Giovanni Malerba. "Hypermutation as an Evolutionary Mechanism for Achromobacter xylosoxidans in Cystic Fibrosis Lung Infection." Pathogens 9, no. 2 (January 21, 2020): 72. http://dx.doi.org/10.3390/pathogens9020072.
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Achromobacter xylosoxidans can cause chronic infections in the lungs of patients with cystic fibrosis (CF) by adapting to the specific environment. The study of longitudinal isolates allows to investigate its within-host evolution to unravel the adaptive mechanisms contributing to successful colonization. In this study, four clinical isolates longitudinally collected from two chronically infected patients underwent whole genome sequencing, de novo assembly and sequence analysis. Phenotypic assays were also performed. The isolates coming from one of the patients (patient A) presented a greater number of genetic variants, diverse integrative and conjugative elements, and different protease secretion. In the first of these isolates (strain A1), we also found a large deletion in the mutS gene, involved in DNA mismatch repair (MMR). In contrast, isolates from patient B showed a lower number of variants, only one integrative and mobilizable element, no phenotypic changes, and no mutations in the MMR system. These results suggest that in the two patients the establishment of a chronic infection was mediated by different adaptive mechanisms. While the strains isolated from patient B showed a longitudinal microevolution, strain A1 can be clearly classified as a hypermutator, confirming the occurrence and importance of this adaptive mechanism in A. xylosoxidans infection.
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Libante, Virginie, Yves Nombre, Charles Coluzzi, Johan Staub, Gérard Guédon, Marcelo Gottschalk, Sarah Teatero, Nahuel Fittipaldi, Nathalie Leblond-Bourget, and Sophie Payot. "Chromosomal Conjugative and Mobilizable Elements in Streptococcus suis: Major Actors in the Spreading of Antimicrobial Resistance and Bacteriocin Synthesis Genes." Pathogens 9, no. 1 (December 25, 2019): 22. http://dx.doi.org/10.3390/pathogens9010022.
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Streptococcus suis is a zoonotic pathogen suspected to be a reservoir of antimicrobial resistance (AMR) genes. The genomes of 214 strains of 27 serotypes were screened for AMR genes and chromosomal Mobile Genetic Elements (MGEs), in particular Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs). The functionality of two ICEs that host IMEs carrying AMR genes was investigated by excision tests and conjugation experiments. In silico search revealed 416 ICE-related and 457 IME-related elements. These MGEs exhibit an impressive diversity and plasticity with tandem accretions, integration of ICEs or IMEs inside ICEs and recombination between the elements. All of the detected 393 AMR genes are carried by MGEs. As previously described, ICEs are major vehicles of AMR genes in S. suis. Tn5252-related ICEs also appear to carry bacteriocin clusters. Furthermore, whereas the association of IME-AMR genes has never been described in S. suis, we found that most AMR genes are actually carried by IMEs. The autonomous transfer of an ICE to another bacterial species (Streptococcus thermophilus)—leading to the cis-mobilization of an IME carrying tet(O)—was obtained. These results show that besides ICEs, IMEs likely play a major role in the dissemination of AMR genes in S. suis.
Dissertations / Theses on the topic "Integrative and mobilizable element"
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Colombini, Lorenzo. "Whole genome sequencing and comparative genomics in lactic acid bacteria." Doctoral thesis, Università di Siena, 2022. http://hdl.handle.net/11365/1182475.
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In the present thesis, the genomes of different microbial species, belonging to the lactic acid bacteria and including Lactobacillus crispatus, Streptococcus pneumoniae and Enterococcus faecalis, were obtained and analyzed using comparative genomics tools. In the first part of the thesis was described the genome of the probiotic L. crispatus strain M247, which contains a novel integrative and mobilizable element named Tn7088. Tn7088 carries a biosynthetic gene cluster coding for a class I bacteriocin which is homologous to the listeriolysin S gene cluster of Listeria monocytogenes and may confer selective advantages towards related bacterial species. Chromosomal rearrangements mediated by insertion sequences and involving two regions of 69.9- kb and 15.4-kb, were detected in the M247 strain. A L. crispatus M247 laboratory strain carried in our laboratory strain collection since 1990 and named M247_Siena, showed an unusual duplication of the 69.9-kb DNA region resulting in the generation of two long inverted repeats (LIRs) and the deletion of the 15.4-kb region. Analysis of ultra-long DNA Nanopore reads showed that the presence of LIRs in strain M247_Siena increased the intrinsic genome instability of strain M247. In the second part, a collection of 41 E. faecalis strains isolated from genital tract samples of infertile couples, was subjected to antimicrobial susceptibility testing and whole genome sequencing. Multi locus sequence typing and antimicrobial susceptibility testing results suggested clonality of infertility-associated E. faecalis isolates resistant to high-level aminoglycosides. Analysis of the genomic location of aminoglycoside modifying enzyme (AME) genes led to the identification of a family of novel composite transposons, whose reference element was denominated Tn7086. Tn7086 and Tn7086-like elements in infertility-associated E. faecalis shared the following traits: i) are flanked by two direct repeats of the IS1216E element, ii) employ the same chromosomal panE gene integration site, iii) excise from the bacterial chromosome leaving an IS1216E copy in the chromosome and form circular intermediates in which the ends are joined by the other IS1216E copy. Finally, the whole genome sequences of the L. crispatus type strain ATCC 33820 and of S. pneumoniae laboratory strains Rx1 and R36A, were obtained and analyzed.
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Coluzzi, Charles. "L'exploration des génomes par l'outil ICEFinder révèle la forte prévalence et l'extrême diversité des ICE et des IME de streptocoques." Thesis, Université de Lorraine, 2017. http://www.theses.fr/2017LORR0352/document.
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Les éléments génétiques mobiles contribuent grandement à la diversité et à l’évolution des génomes bactériens par le biais du transfert horizontal. Parmi eux, les éléments intégratifs conjugatifs (ICE) codent leur propre excision, leur transfert par conjugaison et leur intégration. En revanche, les éléments intégratifs et mobilisables (IME) ne sont autonomes que pour leur excision et intégration et ne codent seulement que certaines des protéines/fonctions (oriT) dont ils ont besoin pour leur transfert conjugatif. Par conséquent, les IME ont besoin d’un élément conjugatif « helper » pour se transférer. Malgré leur impact sur le flux des gènes et l’évolution des génomes, la prévalence des ICE reste peu étudiée et seulement très peu d’IME avaient été identifiés au début de cette étude. De plus, bien que plusieurs méthodes de détection des ilots génomiques existent, aucune d’elles n’est dédiée aux ICE ou aux IME. Ce qui ne facilite pas l’analyse exhaustive de ces éléments. Le genre Streptococcus appartient au phylum des firmicutes. La quasi-totalité des streptocoques sont des bactéries commensales ou pathogènes de l’homme et d’autres animaux. Aussi, 2 espèces de streptocoques sont utilisées en tant que ferments lactiques lors la production de laits fermentés et divers fromages. Globalement, le genre streptocoques représente un groupe d’intérêt pour l’homme, l’étude du flux de gènes au sein de ces organismes et l’impact qu’il peut avoir sur leur mode vie est primordiale. Au cours de cette thèse, nous avons recherché les ICE et les IME dans 124 souches de streptocoques appartenant à 27 espèces en utilisant une base de données de référence comportant des protéines dites « signatures » d’IME et d’ICE (de leurs modules de conjugaison/mobilisation et d’integration/excision). Cette analyse exhaustive a permis l’identification et la délimitation de 131 ICE ou ICE légèrement dégénérés et 144 IME. Tous ces éléments ont été délimités, ce qui nous a permis de déterminer leur spécificité d’intégration dans les génomes. Au total, 17 spécificités d’intégration ont été identifiées pour les ICE dont 8 encore jamais décrites (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG and ybaB/EbfC) et 18 spécificités pour les IME dont seulement 5 étaient connues chez les firmicutes. Les modules d’intégration des ICE codent soit une intégrase à tyrosine pouvant avoir une faible spécificité (1 famille d’intégrase) ou une forte spécificité (13 spécificités différentes), soit des intégrases à sérine seule ou en triplet (4 spécificités différentes), soit une transposase à DDE. Les IME codent soit des intégrases à tyrosine (10 spécificités différentes) soit des intégrases à serine seule (8 spécificités différentes). Les ICE ont été groupés en 7 familles distinctes selon les protéines codées par leur module de conjugaison. Les IME présentaient une très forte diversité au sein de leur module de mobilisation, empêchant ainsi leur regroupement en famille selon les gènes portés par ce module. Les analyses phylogénétiques des protéines signature codées par tous les ICE et les IME ont montré des échanges de modules d’intégration entre les ICE et les IME et de nombreux échanges entre les modules de mobilisation des IME. L’ensemble de ces résultats révèle la forte prévalence et l’extrême diversité des ICE et des IME au sein des génomes de streptocoques. Une meilleure connaissance et compréhension de ces éléments nous a incité à construire un outil informatique semi-automatisé de détection des ICE et des IME de Streptocoques ainsi que leurs sites d’insertionMobile genetic elements largely contribute to the evolution and diversity of bacterial genomes through horizontal gene transfer. Among them, the integrative and conjugative elements (ICEs) encode their own excision, conjugative transfer and integration. On the other hand, integrative mobilizable elements (IMEs) are autonomous for excision and integration but encode only some of the proteins needed for their conjugative transfer. IMEs therefore need a “helper” conjugative element to transfer. Despite their impact on gene flow and genome dynamics, the prevalence of ICEs remains largely underscored and very few IMEs were identified at the beginning of this study. Furthermore, although several in silico methods exist to detect genomic islands, none are dedicated to ICEs or IMEs, thus complicating exhaustive examination of these mobile elements. The Streptococcus genus belongs to the firmicutes’ phylum. Almost all streptococci are commensal bacteria or pathogenes to men and animals. Two species of Streptococcus are also used in the dairy industry as lactic ferments in order to produce fermented milk and different types of cheese. Studying the gene flux of the Steptococci genus and the impact it can have on the lifestyle of these organisms is essential, as it has a lot of interest for human health and activities. In this work, we searched for ICEs and IMEs in 124 strains of streptococci belonging to 27 species using a reference database of ICE and IME signature proteins (from their conjugation, mobilization and integration/excision modules). This exhaustive analysis led to the identification and delimitation of 131 ICEs or slightly decayed ICEs and 144 IMEs. All these elements were delimited, which allowed us to identify their integration specificities in the genomes. In total, 17 ICE integration specificities were identified. Among them, 8 had never been described before (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG and ybaB/EbfC). 18 specificities were also identified for IMEs, among which only 5 were known for the firmicutes. ICEs encode high or low-specificity tyrosine integrases (13 different specificities), single serine intégrases (1 specificity), triplet of serine integrases (3 different specificities), or DDE transposases while IMEs encode either tyrosine integrases (10 different specificities) or single serine integrases (8 different specificities). ICE were grouped in 7 distinct families according to the proteins encoded by their conjugation module whereas the mobilization modules of IMEs were highly diverse, preventing them from grouping into families according to their mobilization modules. The phylogenetic analysis of the signature proteins encoded by all ICEs and IMEs showed integration module exchanges between ICEs and IMEs and several mobilization module exchanges between IMEs. The overall results reveal a strong prevalence and extreme diversity of these elements among Streptococci genomes. Better understanding and knowledge of ICEs and IMEs prompted us to build a semi-automated command-line tool to identify streptococcal ICEs and IMEs as well as to determine their insertion site
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SANTORO, FRANCESCO. "Functional characterization of the pneumococcal Integrative Conjugative Element Tn5253." Doctoral thesis, Università di Siena, 2017. http://hdl.handle.net/11365/1005925.
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Integrative conjugative elements (ICEs) are responsible for pneumococcal genome evolution and more particularly for virulence and drug resistance acquisition. During
conjugation, ICEs transfer from a donor cell containing the genetic element to a recipient cell lacking it. ICEs insert into the bacterial genome, excise from it and form a
covalently closed circular intermediate which can integrate in a different genomic site and/or can integrate in a new genome upon conjugative transfer. Tn5253 is a composite
ICE of Streptococcus pneumoniae conferring resistance to tetracycline and chloramphenicol. The complete nucleotide sequence showed that it is 64,528 bp in size
and contains 79 ORFs, 41 of which could not be annotated. Two distinct genetic elements were found integrated in Tn5253: Tn5251 (18,033 bp), of the Tn916-Tn1545
family of CTs, and Ωcat(pC194) (7,627 bp), which could not conjugate, but was capable of intracellular mobility by homologous recombination. Ωcat(pC194) was
shown to contain a copy of the staphylococcal plasmid pC194 with a 93-bp deletion in the replication origin, to be flanked by two 1,169-bp direct repeats, and to excise from
Tn5253 producing a circular form of the element. The highest transfer frequency of Tn5253 was registered when Streptococcus pyogenes was the donor (6.7 x 10-3
transconjugants/donor). Upon conjugal transfer, Tn5253 was found to always integrate at a single chromosomal site. The target site (attB) was a 83-bp sequence in the rbg
gene of S. pneumoniae. Strains carrying Tn5253 all contained circular forms of the ICE in which the ends were joined by a 84-bp sequence (attTn). attB and attTn differed only
for an extra nucleotide in attTn. When integrated into the chromosome, Tn5253 was flanked by a copy of attB and a copy of attTn: invariably attB was adjacent to the left
end and attTn to the right, suggesting a polarization in the DNA integration process. In order to study the mechanism of integration into pneumococcal chromosome, we
constructed an attB mutant in which the first 63 nts were deleted and 5 nucleotide changes introduced in the remaining 20 nts. The resulting attB mutant was used as
Tn5253 recipient strain in mating experiments. Conjugation frequency of Tn5253 in the attB mutant recipient was considerably lower when compared to a standard recipient (4.8 x 10-7 vs 1.7 x 10-5 transconjugants per donor cell). Five novel Tn5253 alternative insertion sites were found located in: spr1713, coding for an alpha-galactosidase,
spr0540 (cell wall synthesis enzyme), spr1534 (substrate binding protein of an ABC sugar transporter), spr1983 (MFS protein) and spr0546 (nrd, putative nitroreductase).
Transfer of Tn5253 from alternative attB sites occurred at lower frequencies than wild type donor ranging from 2 x 10-7 to < 3.6 x 10-8. One transconjugant harboring 3 copies
of Tn5253 was able to transfer the ICE at a frequency 100-fold higher than wild type donor. Tn5253 has a strong preference for its primary insertion site, even when it is
mutated, but it can also integrate at different sites. The insertion site of Tn5253 affects its transposition rate, which is decreased or abolished when integrated in one of the
alternative attB.
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Harden, Mark Michael Jr. "Interactions between an integrative and conjugative element and its bacterial host." Thesis, Massachusetts Institute of Technology, 2021. https://hdl.handle.net/1721.1/130662.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, February, 2021Cataloged from the official PDF of thesis.
Includes bibliographical references.
Conjugative elements are mobile genetic elements that can transfer from a donor bacterium to a recipient via an element-encoded type IV secretion system. Integrative and conjugative elements (ICEs) are an abundant class of conjugative element. ICEs are typically integrated into the bacterial host chromosome, but under certain conditions, or stochastically, they can excise from the chromosome and transfer to a recipient. ICEs likely interact with their bacterial host at every stage of their life cycle, but few of these interactions have been characterized. In this work I sought to 1) identify bacterial host factors necessary for efficient transfer of the integrative and conjugative element ICEBs1 to a recipient, and 2) determine whether the ICEBs1-encoded cell wall-modifying enzyme CwlT acts on the cell wall of the donor bacterium, the recipient bacterium, or both.
I used CRISPR interference to induce a knockdown of individual essential Bacillus subtilis genes, and then screened for gene knockdowns that caused an acute defect in transfer of ICEBs1. I found that wall teichoic acids were necessary in both ICEBs1 donors and recipients for efficient conjugative transfer. I found that depletion of wall teichoic acids caused cells involved in ICEBs1 conjugation to sustain lethal envelope damage caused by active conjugation machinery. Conjugative elements must bypass the cell wall of both the donor and recipient cells in a mating pair. Conjugative elements encode cell wall hydrolases that are required for efficient transfer, which are presumed to partly degrade the cell wall of the donor bacterium during conjugation. In order to investigate the role of the ICEBs1-encoded cell wall hydrolase CwlT in conjugation, I generated cell wall-less (L-form) strains of B. subtilis which could donate or receive ICEBs1.
In the absence of either the donor or recipient cell wall, CwlT was dispensable for efficient transfer. This finding indicates that CwlT acts on both the donor and recipient cell wall in a mating pair.
by Mark Michael Harden, Jr.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Biology
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Avello, Monika M. M. (Monika Maria Masumi). "Characterization of an exclusion mechanism in an integrative and conjugative element in Bacillus subtilis." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/119980.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2018.Cataloged from PDF version of thesis.
Includes bibliographical references.
Horizontal gene transfer is the acquisition of new genetic material that can confer novel phenotypes to bacteria and contribute to their evolution. Conjugation is an important mechanism of horizontal gene transfer that involves the direct transfer of DNA between two cells and is mediated by mobile genetic elements encoding type IV secretion systems. Conjugative elements prevent redundant transfer by a mechanism known as exclusion that inhibits their cognate secretion systems. Exclusion is prevalent among conjugative elements, suggesting it is advantageous and potentially essential. Yet very few exclusion mechanisms are characterized, and the advantages they provide are not well understood. My work characterizes the exclusion mechanism of an integrative and conjugative element found in a Gram-positive bacterium. In combination with several other studies, my results point to a potentially conserved mechanism and novel benefits of this phenomenon, furthering our understanding of how mobile genetic elements regulate their transfer, impact their bacterial hosts, and mediate horizontal gene transfer.
by Monika M. M. Avello.
Ph. D.
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Vardakis, Ioannis C. "Multicompartmental poroelasticity for the integrative modelling of fluid transport in the brain." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:46541e50-30e4-453b-ab58-be022e884c58.
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The world population is expected to increase to approximately 11 billion by 2100. The ageing population (aged 60 and over) is projected to exceed the number of children in 2047. This will be a situation without precedent. The number of citizens with disorders of old age like Dementia will rise to 115 million worldwide by 2050. The estimated cost of Dementia will also increase, from $604 billion in 2010, to $1,117 billion by 2030. At the same time, medical expertise, evidence-driven policymaking and commissioning of services are increasingly evolving the definitive architecture of comprehensive long-term care to account for these changes. Technological advances, such as those provided by computational science and biomedical engineering, will allow for an expansion in our ability to model and simulate an almost limitless variety of complex problems that have long defied traditional methods of medical practice. Numerical methods and simulation offer the prospect of improved clinically relevant predictive information, and of course optimisation, enabling more efficient use of resources for designing treatment protocols, risk assessment and urgently needed management of a long term care system for a wide spectrum of brain disorders. Within this paradigm, the importance of the relationship of senescence of cerebrospinal fluid transport to dementia in the elderly make the cerebral environment notably worthy of investigation through numerical and computational modelling. Hydrocephalus can be succinctly described as the abnormal accumulation (imbalance between production and circulation) of cerebrospinal fluid (CSF) within the brain. Using hydrocephalus as a test bed, one is able to account for the necessary mechanisms involved in the interaction between cerebral fluid production, transport and drainage. The current state of knowledge about hydrocephalus, and more broadly integrative cerebral dynamics and its associated constitutive requirements, advocates that poroelastic theory provides a suitable framework to better understand the disease. In this work, Multiple-network poroelastic Theory (MPET) is used to develop a novel spatio-temporal model of fluid regulation and tissue displacement in various scales within the cerebral environment. The model is discretised in a variety of formats, through the established finite difference method, finite difference – finite volume coupling and also the finite element method. Both chronic and acute hydrocephalus was investigated in a variety of settings, and accompanied by emerging surgical techniques where appropriate. In the coupled finite difference – finite volume model, a key novelty was the amalgamation of anatomically accurate choroid plexuses with their feeding arteries and a simple relationship relaxing the constraint of a unique permeability for the CSF compartment. This was done in order to account for Aquaporin-4 sensitisation. This model is used to demonstrate the impact of aqueductal stenosis and fourth ventricle outlet obstruction. The implications of treating such a clinical condition with the aid of endoscopic third (ETV) and endoscopic fourth ventriculostomy (EFV) are considered. It was observed that CSF velocity in the aqueduct, along with ventricular displacement, CSF pressure, wall shear stress and pressure difference between lateral and fourth ventricles increased with applied stenosis. The application of ETV reduced the aqueductal velocity, ventricular displacement, CSF pressure, wall shear stress and pressure difference within nominal levels. The greatest reversal of the effects of atresia come by opting for ETV rather than the more complicated procedure of EFV. For the finite difference model incorporating nonlinear permeability, qualitatively similar results were obtained in comparison to the pertinent literature, however, there was an overall amplification of ventriculomegaly and transparenchymal pressure difference using this model. A quantitative and qualitative assessment is made of hydrocephalus cases involving aqueductal stenosis, along with the effects to CSF reabsorption in the parenchyma and subarachnoid space. The finite element discretisation template produced for the nth- dimensional transient MPET system allowed for novel insight into hydrocephalus. In the 1D formulation, imposing the breakdown of the blood-CSF barrier responsible for clearance resulted in an increase in ventricular displacement, transparenchymal venous pressure gradient and transparenchymal CSF pressure gradient, whilst altering the compliance proved to markedly alter the rate of change of displacement and CSF pressure gradient. The influence of Poisson's ratio was investigated through the use of the dual-grid solver in order to distinguish between possible over or under prediction of the ventricular displacement. In the 2D model based on linear triangles, the importance of the MPET boundary conditions is acknowledged, along with the quality of the underlying mesh. Interesting results include that the fluid content is highest in the periventricular region and the skull, whilst after longer time scales, the peak CSF content becomes limited to the periventricular region. Venous fluid content is heavily influenced by the Biot-Willis constant, whilst both the venous and CSF/ISF compartments show to be strongly influenced by breakdown in the blood-CSF barrier. Increasing the venous compliance effects the arterial, capillary and venous compartments. Decreasing the venous compliance shows an accumulation of fluid, possibly helping to explain why the ventricles can be induced to compress rather than expand under decreased compliance. Finally, a successful application of the 3D-MPET template is shown for simple geometries. It is envisaged that future observations into the biology of cerebral fluid flow (such as perivascular CSF-ISF fluid exchange) and its interaction with the surrounding parenchyma, will demand the evolution of the MPET model to reach a level of complexity that could allow for an experimentally guided exploration of areas that would otherwise prove too intricate and intertwined under conventional settings.
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Eidam, Christopher [Verfasser]. "Molecular analysis of multiresistant Mannheimia haemolytica isolates with particular reference to novel macrolide resistance genes and variants of the integrative and conjugative element ICEPmu1 / Christopher Eidam." Hannover : Bibliothek der Tierärztlichen Hochschule Hannover, 2014. http://d-nb.info/106486256X/34.
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fox, Valeria. "Mobile genetic elements carrying stress response systems, antibiotic resistance determinants, and catabolic pathways." Doctoral thesis, Università di Siena, 2021. http://hdl.handle.net/11365/1159250.
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In the present thesis, I studied the activation of an SOS-like response in Streptococcus pneumoniae encoded by the Streptococcus pyogenes prophage φ1207.3. This system leads to the temporary activation of an hypermutable phenotype, which resulted in increased survival and increased mutation rate upon exposure to mitomycin C or UV-C light. Then, a different type of stress response, the Envelope Stress Response (ESR), was exploited as a strategy for sensitization of Escherichia coli to several antibiotics, by disbalancing five pathways, namely σE, Cpx, Rcs, Bae, and Psp. Disbalancing the Psp pathway increased E. coli susceptibility to some beta-lactam antibiotics. Prophage φ1207.3, carrying a two-genes macrolide efflux system, was originally described as an Integrative and Conjugative Element (ICE). In this thesis, φ1207.3 was transferred to the standard pneumococcal laboratory strain Rx1, for which the whole genome sequence was obtained. It was demonstrated that φ1207.3 is a functional phage of the Siphoviridae family, able to form mature phage particles. It was shown that φ1207.3 does not enter the lytic cycle, even upon induction with mitomycin C. Since φ1207.3 transfers through a mechanism requiring cell-to-cell contact resembling conjugation, the cellular localization of φ1207.3 was investigated. It was demonstrated that the number of φ1207.3 phage particles on the bacterial cells exceeds the number of phages in the culture supernatant by 3 orders of magnitude. φ1207.3 transfer to a variety of streptococcal species was obtained by setting up a mating protocol for the transfer of large mobile genetic elements. Tn5253 is a composite ICE of Streptococcus pneumoniae carrying two elements: i) the ICE Tn5251, carrying the tet(M) tetracycline resistance gene, and ii) the Ωcat(pC194) not-conjugative element, harbouring the cat chloramphenicol resistance gene and able of intracellular transposition. The Tn5253 chromosomal integration site (attB) was investigated in S. pneumoniae with different backgrounds and in other streptococcal and enterococcal species. Finally, during the sequencing of two Mycobacterium chimaera strains, it was reported the presence of an ICE carrying putative genes involved in the catabolic degradation of polycyclic aromatic hydrocarbons, important environmental pollutants.
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Purcaro, Michael J. "Analysis, Visualization, and Machine Learning of Epigenomic Data." eScholarship@UMMS, 2017. https://escholarship.umassmed.edu/gsbs_diss/938.
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The goal of the Encyclopedia of DNA Elements (ENCODE) project has been to characterize all the functional elements of the human genome. These elements include expressed transcripts and genomic regions bound by transcription factors (TFs), occupied by nucleosomes, occupied by nucleosomes with modified histones, or hypersensitive to DNase I cleavage, etc. Chromatin Immunoprecipitation (ChIP-seq) is an experimental technique for detecting TF binding in living cells, and the genomic regions bound by TFs are called ChIP-seq peaks. ENCODE has performed and compiled results from tens of thousands of experiments, including ChIP-seq, DNase, RNA-seq and Hi-C.
These efforts have culminated in two web-based resources from our lab—Factorbook and SCREEN—for the exploration of epigenomic data for both human and mouse. Factorbook is a peak-centric resource presenting data such as motif enrichment and histone modification profiles for transcription factor binding sites computed from ENCODE ChIP-seq data. SCREEN provides an encyclopedia of ~2 million regulatory elements, including promoters and enhancers, identified using ENCODE ChIP-seq and DNase data, with an extensive UI for searching and visualization.
While we have successfully utilized the thousands of available ENCODE ChIP-seq experiments to build the Encyclopedia and visualizers, we have also struggled with the practical and theoretical inability to assay every possible experiment on every possible biosample under every conceivable biological scenario. We have used machine learning techniques to predict TF binding sites and enhancers location, and demonstrate machine learning is critical to help decipher functional regions of the genome.
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Carraro, Nicolas. "Analyse comparative de la dynamique de deux éléments intégratifs conjugatifs de streptococcus thermophilus." Thesis, Nancy 1, 2011. http://www.theses.fr/2011NAN10080/document.
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Les éléments intégratifs conjugatifs (ICE) sont des îlots génomiques qui codent leur excision du chromosome, leur transfert par conjugaison et leur intégration. Ils présentent une organisation modulaire, chaque module incluant tous les gènes nécessaires pour conférer une fonction biologique. Ce travail a porté sur l'étude de la régulation ainsi que les modalités de transfert et de maintien d'ICESt1 et ICESt3, deux ICE de Streptococcus thermophilus présentant une région core étroitement apparentée et une région variable non apparentée. Les résultats obtenus ont montré que, bien qu'ICESt3 s'excise et se transfère à beaucoup plus haute fréquence qu'ICESt1, l'excision des deux éléments est activée par des stimuli identiques et est dépendante de la souche hôte. Chacun de ces ICE code des homologues de deux types de régulateurs différents, cI et ImmR, ce qui implique un mécanisme de régulation complexe et original qui pourrait être conservée chez de nombreux ICE apparentés identifiés lors de ce travail. Selon la définition initiale, les ICE se maintiendraient uniquement sous forme intégrée et ne se répliqueraient pas de façon intracellulaire. Cependant, les dommages à l'ADN induisent non seulement l'excision et le transfert d'ICESt3, mais aussi sa présence en copies multiples extrachromosomiques. Les résultats obtenus impliquent une réplication sous forme extrachromosomique, réplication codée par la région core et qui serait impliquée dans le maintien de l'élément. Une telle réplication pourrait être impliquée dans le maintien de nombreux ICE en plus de leur intégrationIntegrative and Conjugative Elements (ICEs) are genomic islands, which excise from the chromosome, self-transfer by conjugation and integrate. They harbor a modular organization: genes and sequences involved in the same biological process are grouped in the same region. This work concerns the modality of transfer and maintenance of ICESt1 and ICESt3, two ICEs of Streptococcus thermophilus that share closely related core region. ICESt1 excises much less frequently than ICESt3. Nevertheless, excision of the two elements is activated by the same stimuli (DNA damage, stationary phase and/or cell density) and depends of the host strain. Bioinformatical and transcriptional analyses highlight several differences in their organization. However, each of these two ICEs would encode two different regulators, cI and ImmR, suggesting that a complex and original pathway govern to ICESt1' and ICESt3' regulation. This regulation would be shared with numerous ICEs that we identified in the genome of various commensal or pathogenic streptococci. According to the original definition, ICE's maintenance would be exclusively due to their integration in the host chromosome, and ICEs would not be able of extracellular replication. However, in addition to the induction of ICESt3' excision and transfer, DNA damage cause replication of its extrachromosomal form. This unexpected property is encoded by the core region and would be implicated in the maintenance of the element. Comparision with data recently published on other ICEs suggest that intracellular replication could be involved in the maintenance of numerous ICEs, besides their integration
Book chapters on the topic "Integrative and mobilizable element"
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Miyazaki, Ryo, Marco Minoia, Nicolas Pradervand, Vladimir Sentchilo, Sandra Sulser, Friedrich Reinhard, and Jan Roelofvan der Meer. "The clc Element and Related Genomic Islands in Proteobacteria." In Bacterial Integrative Mobile Genetic Elements, 261–72. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9780367813925-16.
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Berkmen, Melanie B., Stephanie J. Laurer, Bridget K. Giarusso, and Rodrigo Romero. "The Integrative and Conjugative Element ICEBs1 of Bacillus subtilis." In Bacterial Integrative Mobile Genetic Elements, 201–16. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9780367813925-12.
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Al-Shura, Anika Niambi. "The fire element." In Ayurvedic Perspectives in Integrative Healthcare, 141–47. Elsevier, 2020. http://dx.doi.org/10.1016/b978-0-12-817602-3.00016-9.
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Craigie, Frederic C. "Spirituality, Religion, and Sleep." In Integrative Sleep Medicine, edited by Valerie Cacho and Esther Lum, 227–40. Oxford University Press, 2021. http://dx.doi.org/10.1093/med/9780190885403.003.0014.
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Spirituality is a vital element of integrative health and well-being. Research is demonstrating that spiritual and religious beliefs and practices are associated with sleep quality, as they are for many aspects of waking life. This chapter examines literature and clinical approaches to explore questions about the definition of spirituality and religion, how spirituality influences health, how spirituality influences sleep, what can be gleaned from current descriptive and interventional research, and what mechanisms might underlie associations of spirituality with sleep. The authors then present material on approaches to working with spirituality in the practice of integrative medicine and care, touching on the personal groundedness and well-being of clinicians, clinical approaches to supporting meaningful living in patients, and organizational approaches to creating affirming, empowering, and satisfying work environments. The authors also include a short section on spirituality and dreams.
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"The role of the meta-role: an integrative element in psychology." In Psychodrama, 77–90. Routledge, 2013. http://dx.doi.org/10.4324/9780203961100-10.
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Borziak, Kirill, Irena Parvanova, and Joseph Finkelstein. "Intelligent Integrative Platform for Sharing Heterogenuous Stem Cell Research Data." In Applying the FAIR Principles to Accelerate Health Research in Europe in the Post COVID-19 Era. IOS Press, 2021. http://dx.doi.org/10.3233/shti210826.
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Recent studies demonstrated that comparative analysis of stem cell research data sets originating from multiple studies can produce new information and help with hypotheses generation. Effective approaches for incorporating multiple diverse heterogeneous data sets collected from stem cell projects into a harmonized project-based framework have been lacking. Here, we provide an intelligent informatics solution for integrating comprehensive characterizations of stem cells with research subject and project outcome information. Our platform is the first to seamlessly integrate information from iPSCs and cancer stem cell research into a single platform, using a multi-modular common data element framework. Heterogeneous data is validated using predefined ontologies and stored in a relational database, to ensure data quality and ease of access. Testing was performed using 103 published, publicly-available iPSC and cancer stem cell projects conducted in clinical, preclinical and in vitro evaluations. We validated the robustness of the platform, by seamlessly harmonizing diverse data elements, and demonstrated its potential for knowledge generation through the aggregation and harmonization of data. Future aims of this project include increasing the database size using crowdsourcing and natural language processing functionalities. The platform is publicly available at https://remedy.mssm.edu/.
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Naidenova, Xenia. "Constructing Galois Lattices as a Commonsense Reasoning Process." In Diagnostic Test Approaches to Machine Learning and Commonsense Reasoning Systems, 34–70. IGI Global, 2013. http://dx.doi.org/10.4018/978-1-4666-1900-5.ch003.
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The concept of good classification test is used in this chapter as a dual element of the interconnected algebraic lattices. The operations of lattice generation take their interpretations in human mental acts. Inferring the chains of dual lattice elements ordered by the inclusion relation lies in the foundation of generating good classification tests. The concept of an inductive transition from one element of a chain to its nearest element in the lattice is determined. The special reasoning rules for realizing inductive transitions are formed. The concepts of admissible and essential values (objects) are introduced. Searching for admissible and essential values (objects) as a part of reasoning is based on the inductive diagnostic rules. Next, the chapter discusses the relations between constructing good tests and the Formal Concept Analysis (FCA). The decomposition of inferring good classification tests is advanced into two kinds of subtasks that are in accordance with human mental acts. This decomposition allows modeling incremental inductive-deductive inferences. The problems of creating an integrative inductive-deductive model of commonsense reasoning are discussed in the last section of this chapter.
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Staudinger, Bettina, Herwig Ostermann, and Roland Staudinger. "Process Standardization and Integration for Human Resource Administration." In Encyclopedia of Human Resources Information Systems, 711–18. IGI Global, 2009. http://dx.doi.org/10.4018/978-1-59904-883-3.ch104.
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Personnel administration is a part of general business administration and an integrative element of the process management of an enterprise. However, personnel administration has not been researched and discussed with priority in context with personnel management or the development of human resource management (HRM) but rather has been assumed to be an operative element of the enterprise. The objectives of personnel administration therefore were set in rationalization and automation of internal administration processes. The necessary digitalization and has been realized by stronger operative oriented sciences (e.g., commercial information technology). The scientific research in personnel management rather concentrated in findings of organization theory (Kupsch & Marr, 1985), the instruments of leadership or even in the basic definition of the concept of personnel management as multidisciplinary and operation oriented business task (Remer, 1978). The personnel work has passed different stages of development within the last decades and depending on the time period the terms as well as the focal points of personnel work have been expanded and redefined. Table 1 shows an overview after Scholz (2000).
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Wallis, Neill. "Powers of Place in the Predestined Middle Woodland Village." In The Archaeology of Villages in Eastern North America, 36–53. University Press of Florida, 2018. http://dx.doi.org/10.5744/florida/9781683400462.003.0003.
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The transition of small mobile groups to larger village aggregations poses distinct economic, social, and political challenges. New integrative institutions and practices are necessary, and their stability can be reinforced through inscriptions on the built environment and landscape, particularly as they define the configuration of community spaces in which people interact frequently. In northern Florida and southern Georgia, an effective approach to village proxemics and social grammar emerged in the Woodland Period around ca. AD 200, after which many villages formed with similar U-shaped layouts studded by mounds in similar, or identical, locations. This chapter posits that the origins of this particular village configuration, and ultimately its widespread popularity, were rooted in experiences of non-anthropogenic features on the landscape. The Garden Patch site on the northern peninsular Gulf coast serves as a case study that shows how natural, cosmically aligned features defined the village layout, revealing an element of inevitability that may have legitimated the organization of space and society.
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Seo, Ribin. "Collaborative Entrepreneurship for Continuous Innovation: A Strategic Alliance Perspective." In Entrepreneurship - Contemporary Issues [Working Title]. IntechOpen, 2020. http://dx.doi.org/10.5772/intechopen.93868.
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Strategic alliances act as a platform to implement collaborative entrepreneurship while exposing a range of challenges. By capitalizing on entrepreneurial opportunities for continuous innovation, alliance partners can promote the productive utilization of resource-pooling systems and facilitate innovation processes for value co-creation. Simultaneously, the heterogeneity of partners in terms of different motivations and interests interferes with the advancement of collaborative entrepreneurship for resource exchange and orchestration. The objective of this paper is thus to explore how to deal with the potential coordination issues that can make an alliance vulnerable and its returns diminished through a preliminary integrative approach to the interface between collaborative entrepreneurship and strategic alliances. From this approach, three elements that can contribute to leverage values of collaborative entrepreneurship for continuous innovation are identified: social capital, entrepreneurial orientation, and interorganizational learning. Based on the discussion about the functions of each element in the context of alliance partners’ dynamic interactions, a model of analysis on collaborative entrepreneurship for continuous innovation is proposed. Hence, this chapter contributes to a better understanding of how firms can enact collaborative entrepreneurship productively to gain greater benefit from the alliance configuration for collaborative advantage.
Conference papers on the topic "Integrative and mobilizable element"
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Scharf, Elias, Mariana Medina-Sánchez, Robert Kuschmierz, Oliver G. Schmidt, and Jürgen W. Czarske. "Minimally Invasive Fiber Endoscope with 3D Printed Diffractive Optical Element (DOE) for Biomedicine." In European Conference on Biomedical Optics. Washington, D.C.: Optica Publishing Group, 2021. http://dx.doi.org/10.1364/ecbo.2021.es1a.3.
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Holographic endoscopes with sub-millimeter diameter require the compensation of inter-core phase distortions, which is accomplished often with an SLM. We present the use of 3D printed DOE as a robust integrative technique for biomedicine.
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Lima, Thayane Araújo, and Cláudio Brandão dos Santos Filho. "Neuropsychiatric sequelae of COVID - 19 and factors related to its neurotropic mechanism: an integrative review." In XIII Congresso Paulista de Neurologia. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1516-3180.676.
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Background: Due to the lack of clarification on the pathophysiological mechanism of COVID - 19 in the neurological system, psychological consequences of SARS - CoV-2 infection are questioned. Objective: To describe the neuropsychiatric sequelae of COVID-19, concomitant with flu syndrome or after, and factors related to its neurotropic mechanism. Design and setting: Integrative review based on the Pubmed database. Methods: A reading of titles and abstracts was done by 2 reviewers of 260 articles, in a blind and independent way, followed by a complete reading, resulting in choice of 16 articles. Using following exclusion criteria: complete articles, publication time 2020-2021 and in English language. Results: From articles read, the following are manifested: acute psychotic episode (68.7%), anxiety (56.2%), disorders related to schizophrenia (43.7%), insomnia (43.7%) and depression (37.5%). The mechanism is multifactorial and may include direct factors of infection, corticosteroid therapy, length of stay in the ICU, female gender and stress due to social isolation. There’re reports of association of psychotic symptoms with previous coronaviruses such as SARSCoV and MERS - CoV contributing to neurotrophic hypothesis. Health professionals have an increased risk of developing psychiatric outcomes and also a high probability of having transient psychosis related to environmental stress, including the socio-environmental element to the risk factors. Conclusion: Despite few analytical studies on the topic, there’s a strong relationship between COVID-19 and neuropsychiatric manifestations, of multifactorial cause, but mainly due to the period of social confinement. Long-term follow-up of patients may provide further evidence of correlation and causality.
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Lall, Amrita, Hamid Khakpour Nejadkhaki, and John Hall. "An Integrative Framework for Design and Control Optimization of a Variable-Ratio Gearbox in a Wind Turbine With Active Blades." In ASME 2016 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/detc2016-60244.
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A variable ratio gearbox (VRG) provides discrete variable rotor speed operation, and thus increases wind capture, for small fixed-speed wind turbines. It is a low-cost, reliable alternative to conventional variable speed operation, which requires special power-conditioning equipment. The authors’ previous work has demonstrated the benefit of using a VRG in a fixed-speed system with passive blades. This work characterizes the performance of the VRG when used with active blades. The main contribution of the study is an integrative design framework that maximizes power production while mitigating stress in the blade root. As part of the procedure, three gear ratios are selected for the VRG. It establishes the control rules by defining the gear ratio and pitch angle used in relation to wind speed and mechanical torque. A 300 kW wind turbine model is used for a case study that demonstrates how the framework is implemented. The model consists of aerodynamic, mechanical, and electrical submodels, which work collaboratively to convert kinetic air to electrical power. Blade element momentum theory is used in the aerodynamic model to compute the blade loads. The resulting torque is passed through a mechanical system and subsequently to the induction machine model to generate power. The BEM method also provides the thrust and bending loads that contribute to blade-root stress. The stress in the root of the blade is also computed in response to these loads, as well as those caused by gravity and centrifugal force. Two case studies are performed using wind data that was obtained from the National Renewable Energy Laboratory (NREL). Each of these represents an installation site with a unique set of wind conditions that are used to customize the wind turbine design. The framework uses dynamic programming to simulate the performance of an exhaustive set of combinations. Each combination is evaluated over each set of recorded wind data. The combinations are evaluated in terms of the total energy and stress that is produced over the simulation period. Weights are applied to a multi-objective cost function that identifies the optimal design configurations with respect to the design objectives. As a final design step, a VRG combination is selected, and a control algorithm is established for each set of wind data. During operation, the cost function can also be used to bias the system towards higher power production or lower stress. The results suggest a VRG can improve wind energy production in Region 2 by roughly 10% in both the low and high wind regions. In both cases, stress is also increased in Region 2, as the power increases. However, the stress in Region 3 may be reduced for some wind speeds through the optimal selection of gear combinations.
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Kadau, Kai, Phillip W. Gravett, and Christian Amann. "Probabilistic Fracture Mechanics for Heavy Duty Gas Turbine Rotor Forgings." In ASME Turbo Expo 2017: Turbomachinery Technical Conference and Exposition. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/gt2017-64811.
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We developed and successfully applied a direct simulation Monte-Carlo scheme to quantify the risk of fracture for heavy duty rotors commonly used in the energy sector. The developed Probabilistic Fracture Mechanics high-performance computing methodology and code ProbFM routinely assesses relevant modes of operation for a component by performing billions of individual fracture mechanics simulations. The methodology can be used for new design and life-optimization of components, as well as for the risk of failure quantification of in service rotors and their re-qualifications in conjunction with non-destructive examination techniques, such as ultrasonic testing. The developed probabilistic scheme integrates material data, ultra-sonic testing information, duty-cycle data, and finite element analysis in order to determine the risk of failure. The methodology provides an integrative and robust measure of the fitness for service and allows for a save and reliable operation management of heavy duty rotating equipment.
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Серова, Ольга Евгеньевна. "INTELLECTUAL HISTORY OF THE SCIENTIFIC SCHOOL OF G.I. CHELPANOV AS AN INFORMATION RESOURCE OF THE INTEGRATIVE BASE OF WORLD PSYCHOLOGY: ON THE 110TH ANNIVERSARY OF THE ESTABLISHMENT OF THE PSYCHOLOGICAL INSTITUTEON." In Наука. Исследования. Практика: сборник избранных статей по материалам Международной научной конференции (Санкт-Петербург, Февраль 2022). Crossref, 2022. http://dx.doi.org/10.37539/srp301.2022.57.43.005.
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В контексте проблемы общемировой интеграции научного знания рассмотрены некоторые аспекты истории создания Г.И. Челпановым Психологического института в Москве как эффективной модели организации научного учреждения, направленного на решение комплексных задач, целостное знание структурных компонентах которой выступает неотъемлемым элементом общемирового информационного пространства. In the context of the problem of global integration of scientific knowledge, some aspects of the history of the creation by G.I. Chelpanov of the Psychological Institute in Moscow as an effective model of the organization of a scientific institution aimed at solving complex problems, the integral knowledge of the structural components of which is an integral element of the global information space, are considered.
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Zhen, K., A. Saigal, and T. S. Chan. "Forging of Compressor Blades: Temperature and Ram Velocity Effects." In ASME 1994 International Gas Turbine and Aeroengine Congress and Exposition. American Society of Mechanical Engineers, 1994. http://dx.doi.org/10.1115/94-gt-428.
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Forging is one of the most widely used manufacturing process for making high strength, structurally integrative, impact and creep resistant Ti-6A1-4V compressor blades for jet engines. In addition, in modern metal forming technology, finite element analysis method and computer modeling are being extensively employed for initial evaluation and optimization of various processes, including forging. In this study, DEFORM, a rigid viscoplastic two-dimensional finite element code, was used to study the effects of initial die temperature and initial ram velocity on the forging process. For a given billet, die temperature and ram velocity influence the strain rate, temperature distribution, and thus the flow stress of the material. The die temperature and the ram velocity were varied over the range 300–700°F and 15–25 in/sec, respectively, to estimate the maximum forging load and the total energy required to forge compressor blades. The ram velocity was assumed to vary linearly as a function of stroke. Based on the analysis, it was found that increasing the die temperature from 300–700°F decreases the forging loads by 19.9% and increases the average temperature of the workpiece by 43°F. Similarly, increasing the initial ram velocity from 15–25 in/sec decreases the forging loads by 25.2% and increases the average temperature of the workpiece by 36°F. The nodal temperature distribution is bimodal in each ease. The forging energy required to forge the blades is approximately 18 kips*in/in.
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Samuel, Robello, Rishi Adari, and Nagaraj Srinivasan. "Greenstick Well Engineering: Sustainability Index for Asset Value Chain Management." In SPE Annual Technical Conference and Exhibition. SPE, 2021. http://dx.doi.org/10.2118/205867-ms.
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Abstract Environmental impacts due to exploration to the abandonment of oil and gas wells are a major focus when the wells are planned and drilled. However, there is no industry standard to quantify the impact due to complex indicators and associated variables. So, it is necessary to have an assessment framework and a methodology with the help of the digital transformation that provides an integrative index. This index allows a baseline to estimate the benchmarking for the well engineering not only during planning but also in real-time as the well is drilled and produced. This paper presents and validates a new model for the sustainability index for well design and engineering in the life cycle of the well. This proposed method avoids some of the vagueness of well’s sustainability and can be used and applied practically. It is based on various metrics and weightage assigned when a well is planned, designed, and engineered. Evaluating the index for well engineering is based on the following elements: environmental impact, well design and engineering, functionality and optimization impact, impact of well and maintenance costs, health and safety impact, societal impact. Each element contains sub-elements. This process involves individual indexing through backpropagation of neural networks combined with bat algorithm to obtain the final overall index.
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Šturanović, Petar. "NARODNA SKUPŠTINA PO VIDOVDANSKOM USTAVU." In 100 GODINA OD VIDOVDANSKOG USTAVA. Faculty of law, University of Kragujevac, 2021. http://dx.doi.org/10.46793/zbvu21.221s.
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The author gives his view of the Constitution of the Kingdom of Serbs, Croats and Slovenes of 1921, pointing out its importance at that time, but also its shortcomings. The choice of a centralist, unitary state system is recognized as one of the basic aspirations of the constitution-maker, that resulted in the king's dominant position as an integrative element, which made it impossible to establish (un)wanted balances between the king and parliament. In institutional terms, orleans parliamentarism is analyzed as an established type of parliamentary system of government, and also its functioning in practice. The author analyzed the constitutional position of the National assembly, emphasizing its weakness in relations with the king, explaining instruments such as the absolute legislative veto, through which the king exercised supremacy in the legislative sphere despite the constitutional proclamation to exercise legislative competence jointly. The unlimited right to dissolve the assembly, despite the undivided opinion of the constitutional theory on the prohibition of successive dissolution, further weakened the position of the National assembly, and established the king as an inviolable arbiter in resolving parliamentary crises, which may ultimately confront the people's will. The king's unrestricted right to dissolve parliament usurped the budgetary right of the National assembly, as one of the foundations of the parliamentary system, which further made it possible for the executive to rule without a budget. Constrained by the constitutional arrangement, insufficient representative functions, burdened by the democratic deficit, the National assembly proved to be weak in articulating various political interests, but was the scene of party and national tensions.
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Lall, Amrita, Hamid Khakpour Nejadkhaki, and John Hall. "Design and Control Framework for Selecting Wind Turbine Gear Ratios Based on Optimal Power Generation and Blade Stress." In ASME 2016 Dynamic Systems and Control Conference. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/dscc2016-9716.
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A variable ratio gearbox (VRG) can enable small wind turbines to operate at discrete variable rotor speeds. This reliable, low-cost, alternative does not require power conversion equipment, as is the case with conventional variable speed. Previous work conducted by the author has demonstrated that a VRG can increase the power production for a fixed-speed system with passive blades. The current study characterizes the performance of a wind turbine equipped with a VRG and active blades. The contribution of this work is an integrative framework that optimizes power production with blade root stress. It works by defining a set of control rules that specify the VRG gear ratio and pitch angle that will be used in relation to wind speed. Three ratios are selected through the proposed procedure. A case study based on the simulation of a 300-kW wind turbine model is performed to demonstrate the proposed technique. The model is constructed with aerodynamic, mechanical, and electrical submodels. These drivetrain components work together to simulate the conversion of moving air to electrical power. The blade element momentum (BEM) technique is used here to compute the blade loading. The resulting torque and rotor speed are reduced and increased, respectively, through the mechanical system gearbox. The output from this is then applied to the electrical generator. The BEM technique is also used here to determine the bending and thrust and loads that are applied to the blade. The stress in the root of the blade is then determined based on these loads, and that caused by centrifugal force and gravity. The proposed method devises a VRG design and control algorithm based on the unique wind conditions at a given installation site. Two case studies are conducted using wind data sets provided by the National Renewable Energy Laboratory (NREL). Low and high-speed data set are selected as inputs to demonstrate the versatility of the proposed method. Dynamic programming is used to reduce the computational expense. This enables the simulation of an exhaustive set of potential VRG combinations over each set of recorded wind data. Each possible combination is evaluated in terms of the total energy production and blade-root stress produced over the simulation period. A set of weights is applied to a multi-objective function that computes the cost associated with each combination. A Pareto analysis is then used to identify the VRG combination and establish the control algorithm for both systems. The results suggest that the VRG can improve energy production in the partial-load region by roughly 10% in both cases. Although stress increases in Region 2, it decreases in Region 3, and overall, through the optimal selection of gear combinations.