Academic literature on the topic 'Integrative conjugative element'
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Journal articles on the topic "Integrative conjugative element"
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Iannelli, Francesco, Francesco Santoro, Marco R. Oggioni, and Gianni Pozzi. "Nucleotide Sequence Analysis of Integrative Conjugative Element Tn5253of Streptococcus pneumoniae." Antimicrobial Agents and Chemotherapy 58, no. 2 (December 2, 2013): 1235–39. http://dx.doi.org/10.1128/aac.01764-13.
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ABSTRACTConjugative transposon Tn5253, an integrative conjugative element (ICE) ofStreptococcus pneumoniaecarrying thecatandtet(M) genes, was shown to be 64,528 bp in size and to contain 79 open reading frames, of which only 38 could be annotated. Two distinct genetic elements were found integrated into Tn5253: Tn5251(18,033 bp), of the Tn916-Tn1545family of ICEs, and Ωcat(pC194) (7,627 bp), which could not conjugate but was capable of intracellular mobility by excision, circularization, and integration by homologous recombination. The highest conjugation frequency of Tn5253was observed whenStreptococcus pyogeneswas the donor (6.7 × 10−3transconjugants/donor).
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Ringwald, Kenneth, and Jeffrey Gardner. "The Bacteroides thetaiotaomicron Protein Bacteroides Host Factor A Participates in Integration of the Integrative Conjugative Element CTnDOT into the Chromosome." Journal of Bacteriology 197, no. 8 (February 2, 2015): 1339–49. http://dx.doi.org/10.1128/jb.02198-14.
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ABSTRACTCTnDOT is a conjugative transposon found inBacteroidesspecies. It encodes multiple antibiotic resistances and is stimulated to transfer by exposure to tetracycline. CTnDOT integration into the host chromosome requires IntDOT and a previously unknown host factor. We have identified a protein, designated BHFa (Bacteroideshost factor A), that participates in integrative recombination. BHFa is the first host factor identified for a site-specific recombination reaction in the CTnDOT family of integrative and conjugative elements. Based on the amino acid sequence of BHFa, the ability to bind specifically to 4 sites in theattDOTDNA, and its activity in the integration reaction, BHFa is a member of the IHF/HU family of nucleoid-associated proteins. Other DNA bending proteins that bind DNA nonspecifically can substitute for BHFa in the integration reaction.IMPORTANCEBacteroidesspecies are normal members of the human colonic microbiota. These species can harbor and spread self-transmissible genetic elements (integrative conjugative elements [ICEs]) that contain antibiotic resistance genes. This work describes the role of a protein, BHFa, and its importance in the integration reaction required for the element CTnDOT to persist inBacteroideshost cells.
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Lee, Catherine A., and Alan D. Grossman. "Identification of the Origin of Transfer (oriT) and DNA Relaxase Required for Conjugation of the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis." Journal of Bacteriology 189, no. 20 (August 10, 2007): 7254–61. http://dx.doi.org/10.1128/jb.00932-07.
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ABSTRACT Integrative and conjugative elements (ICEs), also known as conjugative transposons, are mobile genetic elements that can transfer from one bacterial cell to another by conjugation. ICEBs1 is integrated into the trnS-leu2 gene of Bacillus subtilis and is regulated by the SOS response and the RapI-PhrI cell-cell peptide signaling system. When B. subtilis senses DNA damage or high concentrations of potential mating partners that lack the element, ICEBs1 excises from the chromosome and can transfer to recipients. Bacterial conjugation usually requires a DNA relaxase that nicks an origin of transfer (oriT) on the conjugative element and initiates the 5′-to-3′ transfer of one strand of the element into recipient cells. The ICEBs1 ydcR (nicK) gene product is homologous to the pT181 family of plasmid DNA relaxases. We found that transfer of ICEBs1 requires nicK and identified a cis-acting oriT that is also required for transfer. Expression of nicK leads to nicking of ICEBs1 between a GC-rich inverted repeat in oriT, and NicK was the only ICEBs1 gene product needed for nicking. NicK likely mediates conjugation of ICEBs1 by nicking at oriT and facilitating the translocation of a single strand of ICEBs1 DNA through a transmembrane conjugation pore.
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Burrus, Vincent, Yvonne Roussel, Bernard Decaris, and Gérard Guédon. "Characterization of a Novel Integrative Element, ICESt1, in the Lactic Acid BacteriumStreptococcus thermophilus." Applied and Environmental Microbiology 66, no. 4 (April 1, 2000): 1749–53. http://dx.doi.org/10.1128/aem.66.4.1749-1753.2000.
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ABSTRACT The 35.5-kb ICESt1 element of Streptococcus thermophilus CNRZ368 is bordered by a 27-bp repeat and integrated into the 3′ end of a gene encoding a putative fructose-1,6-biphosphate aldolase. This element encodes site-specific integrase and excisionase enzymes related to those of conjugative transposons Tn5276and Tn5252. The integrase was found to be involved in a site-specific excision of a circular form. ICESt1 also encodes putative conjugative transfer proteins related to those of the conjugative transposon Tn916. Therefore, ICESt1could be or could be derived from an integrative conjugative element.
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Belhocine, Kamila, Karen K. Yam, and Benoit Cousineau. "Conjugative Transfer of the Lactococcus lactis Chromosomal Sex Factor Promotes Dissemination of the Ll.LtrB Group II Intron." Journal of Bacteriology 187, no. 3 (February 1, 2005): 930–39. http://dx.doi.org/10.1128/jb.187.3.930-939.2005.
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ABSTRACT The Ll.LtrB group II intron from the low-G+C gram-positive bacterium Lactococcus lactis was the first bacterial group II intron shown to splice and mobilize in vivo. This retroelement interrupts the relaxase gene (ltrB) of three L. lactis conjugative elements: plasmids pRS01 and pAH90 and the chromosomal sex factor. Conjugative transfer of a plasmid harboring a segment of the pRS01 conjugative plasmid including the Ll.LtrB intron allows dissemination of Ll.LtrB among L. lactis strains and lateral transfer of this retroelement from L. lactis to Enterococcus faecalis. Here we report the dissemination of the Ll.LtrB group II intron among L. lactis strains following conjugative transfer of the native chromosomally embedded L. lactis sex factor. We demonstrated that Ll.LtrB dissemination is highly variable and often more efficient from this integrative and conjugative element than from an engineered conjugative plasmid. Cotransfer among L. lactis strains of both Ll.LtrB-containing elements, the conjugative plasmid and the sex factor, was detected and shown to be synergistic. Moreover, following their concurrent transfer, both mobilizable elements supported the spread of their respective copies of the Ll.LtrB intron. Our findings explain the unusually high efficiency of Ll.LtrB mobility observed following conjugation of intron-containing plasmids.
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Berkmen, Melanie B., Catherine A. Lee, Emma-Kate Loveday, and Alan D. Grossman. "Polar Positioning of a Conjugation Protein from the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis." Journal of Bacteriology 192, no. 1 (September 4, 2009): 38–45. http://dx.doi.org/10.1128/jb.00860-09.
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ABSTRACT ICEBs1 is an integrative and conjugative element found in the chromosome of Bacillus subtilis. ICEBs1 encodes functions needed for its excision and transfer to recipient cells. We found that the ICEBs1 gene conE (formerly yddE) is required for conjugation and that conjugative transfer of ICEBs1 requires a conserved ATPase motif of ConE. ConE belongs to the HerA/FtsK superfamily of ATPases, which includes the well-characterized proteins FtsK, SpoIIIE, VirB4, and VirD4. We found that a ConE-GFP (green fluorescent protein) fusion associated with the membrane predominantly at the cell poles in ICEBs1 donor cells. At least one ICEBs1 product likely interacts with ConE to target it to the membrane and cell poles, as ConE-GFP was dispersed throughout the cytoplasm in a strain lacking ICEBs1. We also visualized the subcellular location of ICEBs1. When integrated in the chromosome, ICEBs1 was located near midcell along the length of the cell, a position characteristic of that chromosomal region. Following excision, ICEBs1 was more frequently found near a cell pole. Excision of ICEBs1 also caused altered positioning of at least one component of the replisome. Taken together, our findings indicate that ConE is a critical component of the ICEBs1 conjugation machinery, that conjugative transfer of ICEBs1 from B. subtilis likely initiates at a donor cell pole, and that ICEBs1 affects the subcellular position of the replisome.
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Smyth, Davida S., and D. Ashley Robinson. "Integrative and Sequence Characteristics of a Novel Genetic Element, ICE6013, in Staphylococcus aureus." Journal of Bacteriology 191, no. 19 (July 31, 2009): 5964–75. http://dx.doi.org/10.1128/jb.00352-09.
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ABSTRACT A survey of chromosomal variation in the ST239 clonal group of methicillin-resistant Staphylococcus aureus (MRSA) revealed a novel genetic element, ICE6013. The element is 13,354 bp in length, excluding a 6,551-bp Tn552 insertion. ICE6013 is flanked by 3-bp direct repeats and is demarcated by 8-bp imperfect inverted repeats. The element was present in 6 of 15 genome-sequenced S. aureus strains, and it was detected using genetic markers in 19 of 44 diverse MRSA and methicillin-susceptible strains and in all 111 ST239 strains tested. Low integration site specificity was discerned. Multiple chromosomal copies and the presence of extrachromosomal circular forms of ICE6013 were detected in various strains. The circular forms included 3-bp coupling sequences, located between the 8-bp ends of the element, that corresponded to the 3-bp direct repeats flanking the chromosomal forms. ICE6013 is predicted to encode 15 open reading frames, including an IS30-like DDE transposase in place of a Tyr/Ser recombinase and homologs of gram-positive bacterial conjugation components. Further sequence analyses indicated that ICE6013 is more closely related to ICEBs1 from Bacillus subtilis than to the only other potential integrative conjugative element known from S. aureus, Tn5801. Evidence of recombination between ICE6013 elements is also presented. In summary, ICE6013 is the first member of a new family of active, integrative genetic elements that are widely dispersed within S. aureus strains.
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Heather, Zoe, Matthew T. G. Holden, Karen F. Steward, Julian Parkhill, Lijiang Song, Gregory L. Challis, Carl Robinson, Nicholas Davis-Poynter, and Andrew S. Waller. "A novel streptococcal integrative conjugative element involved in iron acquisition." Molecular Microbiology 70, no. 5 (December 2008): 1274–92. http://dx.doi.org/10.1111/j.1365-2958.2008.06481.x.
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Taviani, Elisa, Christopher J. Grim, Jongsik Chun, Anwar Huq, and R. R. Colwell. "Genomic analysis of a novel integrative conjugative element inVibrio cholerae." FEBS Letters 583, no. 22 (October 20, 2009): 3630–36. http://dx.doi.org/10.1016/j.febslet.2009.10.041.
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Del Grosso, Maria, Romina Camilli, Ermanno Rizzi, Alessandro Pietrelli, Gianluca De Bellis, and Annalisa Pantosti. "ICESpy009, a Conjugative Genetic Element Carryingmef(E) in Streptococcus pyogenes." Antimicrobial Agents and Chemotherapy 60, no. 7 (April 11, 2016): 3906–12. http://dx.doi.org/10.1128/aac.03082-15.
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ABSTRACTEfflux-mediated macrolide resistance due tomef(E) andmel, carried by the mega element, is common inStreptococcus pneumoniae, for which it was originally characterized, but it is rare inStreptococcus pyogenes. InS. pyogenes, mega was previously found to be enclosed in Tn2009, a composite genetic element of the Tn916family containingtet(M) and conferring erythromycin and tetracycline resistance. In this study,S. pyogenesisolates containingmef(E), apparently not associated with other resistance determinants, were examined to characterize the genetic context of mega. By whole-genome sequencing of one isolate, MB56Spyo009, we identified a novel composite integrative and conjugative element (ICE) carrying mega, designated ICESpy009, belonging to the ICESa2603 family. ICESpy009 was 55 kb long, contained 61 putative open reading frames (ORFs), and was found to be integrated intohylA, a novel integration site for the ICESa2603 family. The modular organization of the ICE was similar to that of members of the ICESa2603 family carried by different streptococcal species. In addition, a novel cluster of accessory resistance genes was found inside a region that encloses mega. PCR mapping targeting ICESpy009 revealed the presence of a similar ICE in five other isolates under study. While in three isolates the integration site was the same as that of ICESpy009, in two isolates the ICE was integrated intorplL, the typical integration site of the ICESa2603 family. ICESpy009 was able to transfer macrolide resistance by conjugation to bothS. pyogenesandS. pneumoniae, showing the first evidence of the transferability of mega fromS. pyogenes.
Dissertations / Theses on the topic "Integrative conjugative element"
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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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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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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
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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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Silva, Miriam Lopes da. "Detecção e caracterização de elementos conjugativos integrativos em bactérias isoladas de amostras ambientais." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/6/6135/tde-14052014-155858/.
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O reconhecimento da resistência antimicrobiana como um fenômeno emergente em saúde pública, tem constituído um problema em nível mundial. O abuso na utilização de antibióticos na medicina humana e veterinária, e na agricultura, tem originado incremento na diversidade de micro-organismos resistentes, refletindo em falha terapêutica. Os mecanismos de resistência a antibióticos em micro-organismos são mediados principalmente por genes adquiridos de DNA exógeno. A dinâmica da transferência horizontal é realizada por meio de elementos genéticos móveis que carregam genes de resistência. A ampla distribuição deste tipo de estruturas, como o elemento SXT, isolado inicialmente em V. cholerae, tem contribuído para a disseminação de complexos específicos clonais em determinadas áreas geográficas. Este estudo pioneiro no Brasil pesquisou a presença de elementos SXT, em espécies bacterianas do grupo das gama proteobactérias em espécies ambientais, determinou suas características estruturais e funcionais, incluindo genes de resistência a antibióticos, bem como a sensibilidade aos antibióticos dentre os isolados bacterianos que os abrigam. O resultado foi a classificação de 43 elementos SXT obtidos no Brasil, através da comparação com aqueles descritos na literatura. Dentre os elementos SXT obtidos, quatro são albergados por Morganella morganii, fato inédito na literatura. O conhecimento da evolução bacteriana constitui importante ferramenta para estabelecer estratégias eficazes de controle e tratamento de infecções, sem aumentar a pressão seletiva sobre os micro-organismos, bem como instrumento preciso e de grande importância para subsidiar estudos epidemiológicos.Recognition of antimicrobial resistance as an emerging phenomenon in public health has been a problem worldwide. The abuse in the use of antibiotics in human and veterinary medicine, and agriculture, has caused an increase in the diversity of resistant microorganisms, reflecting in treatment failure. The mechanisms of antibiotic resistance in microorganisms are primarily mediated by genes acquired from exogenous DNA. The dynamics of the horizontal transfer is performed by mobile genetic elements which carry resistance genes. The wide distribution of these structures, such as the SXT element originally isolated from V. cholerae, has contributed to the spread of specific clonal complexes in certain geographical areas. This pioneering study in Brazil researched the presence of SXT elements in the group of bacterial species in environmental gamma-proteobacteria species, determined their structural and functional characteristics, including genes for resistance to antibiotics and the antibiotic susceptibility among bacterial isolates that harbor them. The result was the classification of 43 SXT elements found in Brazil, by comparison with those found in the literature. Among the SXT elements found, four are sheltered by Morganella morganii, unprecedented in the literature. Knowledge of bacterial evolution is an important to establish effective strategies to control and treat infections without increasing the selective pressure on microorganisms, as well as a precise instrument and very important tool to support epidemiological studies.
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Wright, Laurel D. "Autonomous replication of integrative and conjugative elements." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/106738.
Full textAbstract:
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2016.Cataloged from PDF version of thesis.
Includes bibliographical references.
Mobile genetic elements facilitate movement of genes, including those conferring antibiotic resistance and other traits, between bacteria. Integrative and conjugative elements (ICEs), also known as conjugative transposons, are a large family of mobile genetic elements that can transfer between neighboring cells. ICEs are found integrated in the chromosome of their host bacterium, where they are transmitted to daughter cells by chromosomal replication and cell division. Under certain conditions, ICE DNA will excise and form a circular plasmid-like intermediate. It was previously thought that ICEs were incapable of autonomous replication. However, my research, along with the work of others, shows that ICEs can replicate autonomously, and that many ICEs utilize a rolling circle replication mechanism. Plasmids and phages that use rolling circle replication encode a single strand origin (sso) that enhances priming of DNA synthesis. We identified a functional single strand origin, sso1, in the integrative and conjugative element ICEBs1 of Bacillus subtilis. Genetic analyses indicated that ICEBs1 uses sso1 and at least one other region for second strand DNA synthesis. Sso activity was important for autonomous, rolling circle replication of ICEBs1 in host cells, and for stable acquisition of the element in new host cells. I also showed that the broad-host range ICE Tn916 replicates autonomously by a rolling circle mechanism. Replication of Tn916 was dependent on the relaxase encoded by Tn916 orf20. The origin of transfer of Tn916, oriT(916), also functioned as an origin of replication. I found that the relaxase (Orf20) and the two putative helicase processivity factors (Orf22 and Orf23) encoded by Tn916 likely interact in a complex to facilitate replication. Lastly, I identified a functional single strand origin of replication (sso) in Tn916 that I predict primes second strand synthesis during rolling circle replication. The importance of autonomous replication by rolling circle in the ICE lifecycle and horizontal gene transfer processes is discussed.
by Laurel D. Wright.
Ph. D.
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Haskett, Timothy L. "Discovery and characterisation of tripartite Integrative & Conjugative Elements." Thesis, Haskett, Timothy L. (2018) Discovery and characterisation of tripartite Integrative & Conjugative Elements. PhD thesis, Murdoch University, 2018. https://researchrepository.murdoch.edu.au/id/eprint/41086/.
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Bacterial integrative & conjugative elements (ICEs) are chromosomally-integrated DNA islands that excise to form circular molecules capable of horizontal self-transmission via conjugation (cell-to-cell contact). Symbiosis ICEs, such as ICEMlSymR7A of Mesorhizobium loti, are a group of ICEs that carry genes enabling rhizobial bacteria to engage in N2-fixing symbioses with leguminous plants. Transfer of symbiosis ICEs can convert non-symbiotic rhizobia into legume symbionts in a single evolutionary step.
In this thesis, a novel form of “tripartite” ICE (ICE3) is reported that exists as three entirely separated regions of DNA residing in the chromosomes of genetically diverse N2-fixing Mesorhizobium spp. These ICE3 regions did not excise independently, rather through multiple recombinations with the host chromosome they formed a single contiguous region of DNA prior to excision and conjugative transfer. Upon integration into a recipient chromosome, the ICE3 recombined the recipient chromosome to disassemble into the tripartite form. These recombination reactions were catalysed by three Integrase proteins IntG, IntM, and IntS, acting on three associated integrase attachment sites. The “excisive” recombination reactions (i.e. assembly and excision) were stimulated by three recombination directionality factors RdfG, RdfM, and RdfS. Expression of ICE3 transfer and conjugation genes were found to be induced by quorum-sensing. Quorum-sensing activated expression of rdfS, and in turn RdfS stimulated transcription of both rdfG and rdfM. Therefore, RdfS acts as a “master controller” of ICE3 assembly and excision. A model for ICE3 recombination and transfer is presented in this thesis.
The conservation of gene content between symbiosis ICE and ICE3 indicated that these elements share a common evolutionary history. However, the persistence of ICE3 structure in diverse mesorhizobia is perplexing due to its seemingly unnecessary complexity. Bioinformatic comparisons of ICE and ICE3 indicated that the tripartite configuration itself may provide selective benefits to the element, including enhanced host range, host stability and resistance to destabilization by tandem insertion of competing integrative elements.
In congruency with ICEMlSymR7A, ICE3 acquisition can convey upon recipients the ability to form N2-fixing symbiosis with the host-legume of the ICE3 donor. Interestingly, the effectiveness of N2-fixation may be impaired. The consequences of the emergence of sub-optimal N2-fixing strains following ICE3 transfer in agriculture is discussed. If ICE3 transfer poses a barrier for future inoculation success, the elucidation of the mechanism of ICE3 assembly, excision, and transfer will allow for the development of strategies for management.
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Stagg, Georgina. "Creation and characterisation of genetically-marked Mesorhizobium integrative and conjugative elements." Thesis, Stagg, Georgina (2018) Creation and characterisation of genetically-marked Mesorhizobium integrative and conjugative elements. Honours thesis, Murdoch University, 2018. https://researchrepository.murdoch.edu.au/id/eprint/42888/.
Full textAbstract:
Rhizobia are soil-dwelling bacteria capable of forming symbiotic associations with legumes, where they reduce atmospheric dinitrogen (N2) into ammonia (NH3), providing the host plant with a bioavailable nitrogen source. For rhizobia in the genus Mesorhizobium, genes essential to the establishment (nod) and maintenance of nitrogen fixing-legume symbioses (nif and fix) are chromosomally-encoded on mobile segments of DNA known as symbiosis integrative and conjugative elements (ICEs). Symbiosis ICEs are capable of excising from the host chromosome and transferring to a recipient ICE-free cell via bacterial conjugation. In the recipient cell, the invading ICE integrates into the recipient chromosome at conserved sites known as attachment sites. As well as encoding genes for excision, conjugation and integration, symbiosis ICEs often encode genes for vitamin biosynthesis, such as those for the synthesis of nicotinate, biotin and thiamine.
Symbiosis ICEs can be monopartite or tripartite in nature and it appears that these two conformations of elements may be evolutionarily related, with the more complex tripartite ICE hypothesised to have evolved from two recombination reactions between three independent monopartite ancestral ICEs that co-existed in an ancestral bacterial cell. Testing this hypothesis for tripartite ICE evolution requires conjugation experiments between two strains that harbour different symbiosis ICEs, which has not previously been experimentally attempted. Symbiosis ICE transfer studies have been conducted between an ICE donor strain and an ICE-devoid vitamin auxotrophic recipient strain, with ICE transfer exconjugants selected on the basis of vitamin prototrophy. However, this method of selecting exconjugants is ineffective for conjugation experiments between two ICE-harbouring strains, as both usually harbour the operons for nicotinate, biotin and thiamine biosynthesis. Genetically-marking two structurally similar, yet phenotypically distinct monopartite ICEs with a selectable marker, such as an antibiotic resistance gene would allow for screening exconjugants solely on the presence of the selectable marker. Two such ICEs are ICEMcSym1192 from the genome of the Cicer arietinum (chickpea) nodulating microsymbiont Mesorhizobium ciceri CC1192 and ICEMlSymR7A from the genome of the Lotus-nodulating M. loti R7A. Therefore, the aims of this thesis were to first genetically mark the symbiosis ICEs ICEMcSym1192 and ICEMlSymR7A, with antibiotic resistance genes that could facilitate selection of exconjugants in ICE transfer studies. Second, to investigate the free-living growth and symbiotic phenotype of marked symbiosis ICEs. Finally, to test the in vitro mobility of these genetically marked elements.
Using a site-directed mutagenesis approach, M. ciceri CC1192 ICEMcSym1192 was successfully marked within an intergenic region of the symbiosis ICE, with a gene encoding resistance to neomycin/kanamycin (nptII), yielding ICEMcSym1192::nptII. The free-living phenotype of two M. ciceri ICEMcSym1192::nptII derivatives, MCC91 and MCC92, was assessed alongside wild-type CC1192, in a bacterial growth experiment to compare the mean generation times of all three strains cultured in both rich (TY) and minimal (AMS with either glucose or succinate as the sole carbon source) media. Mean generation times were not significantly different between these strains (p > 0.05) in all media tested. Additionally, the symbiotic phenotype of the ICEMcSym1192::nptII derivatives did not differ significantly (p > 0.05) to wild-type CC1192, as measured by mean nodule number, nodule weight and shoot dry weight of inoculated C. arietinum. Using a similar site-directed approach, M. loti R7A ICEMlSymR7A was also marked within an intragenic region, however, with Ω-aadA encoding resistance to spectinomycin/streptomycin, yielding ICEMlSymR7A::Ω-aadA. Two ICEMlSymR7A::Ω-aadA derivatives, MCC93 and MCC94, were completed towards the end of this Honours project, therefore, the free-living and symbiotic phenotype could not be achieved within the scope of this project.
The transfer of ICEMcSym1192::nptII in MCC91 and MCC92, into the ICE-devoid recipient strain, R7ANS, was tested with conjugation mixtures plated onto three different sets of media to select for R7ANS (ICEMcSym1192::nptII) exconjugants. Integration of ICEMcSym1192::nptII in R7ANS should allow exconjugants to be selected solely on the presence of the antibiotic marker conferring neomycin resistance (encoded on ICEMcSym1192::nptII) and tetracycline resistance (encoded on R7ANS plasmid, pFAJ1700). The three selection conditions included rich or minimal media, with reduced tetracycline concentrations and the addition of the vitamin thiamine. While, putative exconjugants were extracted from two selection conditions, PCR screening confirmed these were not R7ANS exconjugants but instead were most likely spontaneous CC1192 tetracycline resistant isolates. The inability to isolate R7ANS (ICEMcSym1192::nptII) exconjugants could be due to a number of reasons, including the use of HEPES-buffered, rather than phosphate-buffered, minimal media, the combination of neomycin and tetracycline in the selection media attenuating the rate of ICE excision and/or transfer or the insertion of the nptII cassette in ICEMcSym1192::nptII affecting ICE mobility. Nevertheless, the marked strains generated in this thesis and the assessment performed on them to date, provides a solid foundation for subsequent experiments to further characterise the mobility of these derivatives.
The discovery that Mesorhizobium symbiosis ICEs can exist in both monopartite and tripartite configurations raises many questions about ICE stability and persistence. The genetically-marked ICEMcSym1192::nptII and ICEMlSymR7A::Ω-aadA produced in this thesis represent an important set of experimental tools necessary to further investigate the evolution of these symbiotic elements.
Books on the topic "Integrative conjugative element"
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Mullany, Peter, and Adam P. Roberts. Bacterial Integrative Mobile Genetic Elements. Taylor & Francis Group, 2022.
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Bacterial Integrative Mobile Genetic Elements. Taylor & Francis Group, 2013.
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Mullany, Peter, and Adam P. Roberts. Bacterial Integrative Mobile Genetic Elements. Taylor & Francis Group, 2022.
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Mullany, Peter, and Adam P. Roberts. Bacterial Integrative Mobile Genetic Elements. Taylor & Francis Group, 2022.
Find full textBook chapters on the topic "Integrative conjugative element"
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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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Cury, Jean, Sophie S. Abby, Olivia Doppelt-Azeroual, Bertrand Néron, and Eduardo P. C. Rocha. "Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan." In Horizontal Gene Transfer, 265–83. New York, NY: Springer US, 2019. http://dx.doi.org/10.1007/978-1-4939-9877-7_19.
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Cunha, Violette Da, Romain Guérillot, Mathieu Brochet, and Philippe Glaser. "Integrative and Conjugative Elements Encoding DDE Transposases." In Bacterial Integrative Mobile Genetic Elements, 250–60. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9780367813925-15.
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Ciric, Lena, Azmiza Jasni, Lisbeth Elvira de Vries, Yvonne Agersø, Peter Mullany, and Adam P. Roberts. "The Tn916/Tn1545 Family of Conjugative Transposons." In Bacterial Integrative Mobile Genetic Elements, 153–70. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9780367813925-9.
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Garriss, Geneviéve, and Vincent Burrus. "Integrating Conjugative Elements of the SXT/R391 Family." In Bacterial Integrative Mobile Genetic Elements, 217–34. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9780367813925-13.
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Salyers, Abigail A., Jeffrey F. Gardner, and Nadja B. Shoemaker. "Excision and Transfer of Bacteroides Conjugative Integrated Elements." In Bacterial Integrative Mobile Genetic Elements, 235–49. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9780367813925-14.
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Esnault, Emilie, Alain Raynal, and Jean-Luc Pernodet. "pSAM2, a Paradigm for a Family of Actinomycete Integrative and Conjugative Elements." In Bacterial Integrative Mobile Genetic Elements, 135–52. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9780367813925-8.
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Burrus, Vincent. "Significance of the SXT/R391 Family of Integrating Conjugative Elements in Vibrio cholerae." In Epidemiological and Molecular Aspects on Cholera, 161–84. New York, NY: Springer New York, 2010. http://dx.doi.org/10.1007/978-1-60327-265-0_9.
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Armshaw, Patricia, and J. Tony Pembroke. "UV Stress-Responsive Genes Associated with Enterobacterial Integrative Conjugative Elements of the ICE SXT/R391 Group." In Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria, 517–27. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2016. http://dx.doi.org/10.1002/9781119004813.ch48.
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Churchward, G., and V. Burrus. "Conjugative Transposons and Integrative and Conjugative Elements ☆." In Reference Module in Life Sciences. Elsevier, 2017. http://dx.doi.org/10.1016/b978-0-12-809633-8.06270-1.
Full textConference papers on the topic "Integrative conjugative element"
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Grigoriev, M. M., and G. F. Dargush. "A Fast Multi-Level Boundary Element Method for the Steady Heat Diffusion Equation." In ASME 2003 Heat Transfer Summer Conference. ASMEDC, 2003. http://dx.doi.org/10.1115/ht2003-47450.
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A fast, accurate and efficient multi-level boundary element method is developed to solve general boundary value problems. Here we concentrate on problems of two-dimensional steady potential flow and present a fast direct boundary element formulation. This novel method extends the pioneering work of Brandt and Lubrecht on multi-level multi-integration (MLMI) in several important ways to address problems with mixed boundary conditions. We utilize bi-conjugate gradient methods (BCGM) and implement the MLMI approach for fast matrix and matrix transpose multiplication for every iteration loop. Furthermore, by introducing a C-cycle multigrid algorithm, we find that the number of iterations for the bi-conjugate gradient methods is independent of the boundary element mesh discretization for problems of steady-state heat diffusion considered in this paper. As a result, the computational complexity of the proposed method is proportional to only N · log(N), where N is the number of degrees of freedom.
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Noymer, Peter D., Megan U. Hazen, and S. C. Yao. "An Integrated Thermal Science Course for Third-Year Mechanical Engineering Students." In ASME 1998 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 1998. http://dx.doi.org/10.1115/imece1998-0636.
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Abstract A new course in the thermal science discipline was introduced in 1998 in the Mechanical Engineering Department at Carnegie Mellon University. The course was titled “Thermal Fluids Engineering” and some of the specific aims were to integrate and extend the students’ knowledge in the areas of heat transfer, thermodynamics and fluid mechanics and provide better preparation for their post-graduate endeavors. The development of this course was part of a larger curriculum re-design within both the Mechanical Engineering Department and the College of Engineering at Carnegie Mellon. The course was offered to students in the second semester of their third year, after they have taken thermodynamics, fluid mechanics and heat transfer in each of the previous three semesters. In addition to integrating the three basic thermal science disciplines, other novel aspects of this course included: a series of computational assignments in which finite-element models were applied to solve conjugate heat transfer problems; a series of laboratory experiments, one of which was used as the basis for the computational assignments; and a series of in-class “case studies” in which the students applied their integrated knowledge to the design and analysis of a complex system. Feedback from the students indicated that the integration aspect of the course was successful although there was still room for improvement in the structure and presentation of the material.
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Rahman, Muhammad M., and Santosh K. Mukka. "Confined Liquid Jet Impingement on a Plate With Discrete Heating Elements." In ASME 2005 Summer Heat Transfer Conference collocated with the ASME 2005 Pacific Rim Technical Conference and Exhibition on Integration and Packaging of MEMS, NEMS, and Electronic Systems. ASMEDC, 2005. http://dx.doi.org/10.1115/ht2005-72408.
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The primary focus of this paper is the conjugate heat transfer during vertical impingement of a two-dimensional (slot) submerged confined liquid jet using liquid ammonia as the working fluid. Numerical model for the heat transfer process has been developed. The solid region has been modeled along with the fluid region as a conjugate problem. Discrete heat sources have been used to study the overall effect on convective heat transfer. Simulation of discrete heat sources was done by introducing localized heat fluxes at various locations and their magnitudes being varied. Simulations are performed for two different substrate materials namely silicon and stainless steel. The equations solved in the liquid region included the conservation of mass, conservation of momentum, and conservation of energy. In the solid region, only the energy equation, which reduced to the heat conduction equation, had to be solved. The solid-fluid interface temperature showed a strong dependence on several geometric, fluid flow, and heat transfer parameters. The Nusselt number increased with Reynolds number. For a given flow rate, a higher heat transfer coefficient was obtained with smaller slot width and lower impingement height. For a constant Reynolds number, jet impingement height and plate thickness, a wider opening of the slot provided higher average heat transfer coefficient and higher average Nusselt number. A higher average heat transfer coefficient was seen at a smaller thickness, whereas a thicker plate provided a more uniform distribution of heat transfer coefficient. Higher thermal conductivity substrates also provided a more uniform heat distribution.
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Khalilollahi, Amir, and Russell L. Warley. "Thermal Stress Reduction and Optimization for Orthotropic Composite Boards." In ASME 2005 Summer Heat Transfer Conference collocated with the ASME 2005 Pacific Rim Technical Conference and Exhibition on Integration and Packaging of MEMS, NEMS, and Electronic Systems. ASMEDC, 2005. http://dx.doi.org/10.1115/ht2005-72570.
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Composite printed electronic boards are susceptible of structural failure or irreversible damage under thermally raised stresses. A thermal/structural finite element model is integrated in this study to enable the predictions of the temperature and stress distribution of vertically clamped parallel circuit boards that include series of symmetrically mounted heated electronic modules (chips). The board is modeled as a thin plate containing four heated flush rectangular areas that represent the electronic modules. The finite element model should be to able to accept the convection heat transfer on the board surface, heat generation in the modules, and directional conduction inside the board. A detailed 3-D CFD model is incorporated to predict the conjugate heat transfer coefficients that strongly affect the temperature distribution in the board and modules. Structural analyses are performed by a FE model that uses the heat transfer coefficients mentioned above, and structural elements capable of handling orthotropic material properties. The stress fields are obtained and compared for the models possessing different fiber orientations and fiber volume fractions. Appreciable differences in stress and thermal gradient fields were observed. The values of fiber volume fraction and fiber orientation at which to conduct analyses was guided by experimental design (DOE) ideas leading to a metamodel of the stress intensity and temperature gradient in the board which was used to represent the complied results of this study.
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Houck, Lonnie, DeAnna Sewell, Megan Burke, and Gregory Vogel. "A Fully Coupled Aero, Thermal, and Structural Lifetime Model for Root Cause Failure Analysis and Robust Redesign of an Industrial F Class Gas Turbine Blade." In ASME Turbo Expo 2015: Turbine Technical Conference and Exposition. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/gt2015-42505.
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Modern large frame F, G, & J class gas turbine flow path component design requires the complex integration of multiple design disciplines that traditionally reside with distinct specialists. A traditional design system for an actively cooled gas turbine blade includes aerodynamicists, heat transfer engineers, structural engineers and a failure or lifetime prediction engineers passing information through a manual process with a small number of iterations between the disciplines. Design or manufacturing engineers can also be involved ensuring manufacturability and policing best practices in a predominantly deterministic design system. Over the past few decades robust design or probabilistic design philosophies along with cluster computing advancements have accelerated the release of commercial software that allows for the automation of multiple analytical evaluations at off design points. These software codes allow for process automation of several independent codes executed multiple times at various conditions for automated design of experiment (DOE), and reliability analysis using Monte Carlo or other advanced approximate probabilistic methods across the entire design system. In this paper, the authors are presenting a novel approach of using a commercially available process integration tool to fully integrate a series of other commercially available tools for a root cause failure analysis of a F class turbine blade rather than a new make design. The analysis incorporated a computational fluid dynamics model (CFD) to define inlet temperatures and pressure profiles, a fully conjugate thermal analysis interacting with a finite element (FEA) solver linked to a proprietary creep lifetime prediction model. A DOE was executed to define the meaningful parameters and help rule out potential causes of failure such as loss of coating or compromised cooling system as a contributing factor of the failure which greatly reduced the amount of time and money needed for the investigation. A probabilistic failure analysis was then executed and surrogate models created for quick probabilistic assessment for different operating conditions. This allowed for validation against fleet history to explain the single engine failure not previously observed. Setting up the non-deterministic models initially allowed for rapid redesign in less than 1 month time with confidence that the true root cause was identified and mitigated. It further allowed for feedback and calibrations to the traditional design system methodology.
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Al-Dojayli, Maher, Ellen Chan, Sunny Leung, Hani Naguib, Francis Dawson, Vincent Adinkrah, and Laszlo Lakatos-Hayward. "Three-Dimensional Multiphysics Analyses of a CPU Integrated Thermal Heat Sink." In ASME 2010 International Mechanical Engineering Congress and Exposition. ASMEDC, 2010. http://dx.doi.org/10.1115/imece2010-40649.
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Recent advances in electronic packaging have led to small, lightweight and highly efficient heat sink designs. Some of these attempts are aiming to integrate the heat sink with the packaging wall structure. In this paper, a three-dimensional multiphysics numerical model is developed for the integrated heat sink to carry out CFD and thermal analyses, stress analyses due to thermal expansion and modal analyses. Finite volumes were used to model the conjugate heat transfer (CHT) for the coupled fluid-structure fields representing the air and heat sink fin walls and base, respectively. In this analysis, both natural and forced convection analyses were considered. The predicted temperature distribution was then used to calculate the mechanical stresses due to thermal expansion, using finite elements. Lastly, modal analyses were conducted to calculate the natural frequencies of the model. The effect of varying the source heat generation rate, air flow speed, and some geometry features such as number of fins and fin’s height on the performance and structural integrity of the assembly have been studied.
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Barrett, G. R., A. K. Powell, and T. J. Hall. "Dynamic Solutions and Instabilities of the Four-wave Mixing Interaction Utilising the Underlying SU(2) Group Symmetry." In Photorefractive Materials, Effects, and Devices II. Washington, D.C.: Optica Publishing Group, 1991. http://dx.doi.org/10.1364/pmed.1991.tuc21.
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Optical phase conjugation is an important nonlinear process, with many applications in the areas of optical communications and optical processing. This is as a result of the wave-front correction properties that phase conjugation offers and this has generated much interest in the area. A common method of producing phase conjugated wavefronts is the four-wave mixing interaction and many publications on the steady state solution to this problem have appeared over the last decade. More recently, however, interest has been focussed upon the temporal behaviour of four-wave mixing systems, with instabilities and chaos being both demonstrated by Gauthier et al [1] and predicted by Królikowski et al [2]. To date, the analysis for the temporal behaviour of anisotropic four wave mixing, in the transmission grating regime, has involved the direct numerical integration of the equations describing four wave mixing. This analysis however, does not utilise the symmetries of the four wave mixing process, and thus results in a more complex problem. Through exploitation of these symmetries the complexity of the problem has been reduced from one containing four complex variables, to one containing three real variables. This has been accomplished through the use of the Special Unitary Group 2, a group providing a two dimensional matrix, whose elements are functions of three real variables. The multiplication of this matrix, together with one containing the boundary conditions for the problem, thus enables the four complex beam amplitudes to be reexpressed in terms of three real quantities. Using this technique, the temporal nature of anisotropic four wave mixing has been studied, and shown under certain conditions, to exhibit chaotic behaviour when an electric field is present. The effect of any material absorption on the chaotic nature is also demonstrated.
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Smith, Evan Oscar, and Andrew J. Neely. "The Effect of Aircraft Integration Design on Gas Turbine Shaft Thermal Bow and the Newkirk Effect." In ASME Turbo Expo 2014: Turbine Technical Conference and Exposition. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/gt2014-25511.
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During the cooling process after shutdown, gas turbines can suffer from differential thermal expansion due to buoyant convection. This process can result in asymmetric cooling of the shaft, which can in turn lead to differential thermal expansion, causing deformation of the shaft, known as thermal bow. Attempts to start a gas turbine in this bowed condition can lead to rotor-to-stator contact, triggering further heating, and subsequently further bow. This phenomenon, known as the Newkirk Effect, can result in severe damage to the engine, representing a risk to both airworthiness and logistics. This study utilises a technique previously developed by the authors for modelling shaft thermal bow in gas turbines using a combination of 3D conjugate heat transfer (CHT) computational fluid dynamics (CFD) and finite element analysis (FEA). A baseline model comprises a simple hollow shaft supported at each end, enveloped inside a simple case. Body temperatures obtained through 3D CHT CFD at set time intervals are transferred to FEA, where the physical distortion associated with the application of an asymmetric thermal load is measured. The baseline model was allowed to cool down from representative operational temperatures, with the shaft thermal bow measured for 90 minutes of flow time. Simple modifications were then made to the baseline model including the addition of representative helicopter and fast jet inlet and exhaust analogues, and the use of porosity to simulate the presence of blades, to analyse their influence on the onset time, duration, and severity of the shaft deformation. While the geometries used in this initial study are basic, the results indicate that these aspects of gas turbine design do have an appreciable effect on the onset time, severity, and duration, as well as the axial distribution of the shaft thermal bow. This also indicates the importance of further work in this area using more realistic geometries.
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Achar P. L., Sukshitha, Huanyu Liao, and Ganesh Subbarayan. "Comparative Evaluation of Algorithms for Achieving Ultrapacked Thermal Greases: Microstructural Models and Effective Behavior." In ASME 2019 International Technical Conference and Exhibition on Packaging and Integration of Electronic and Photonic Microsystems. American Society of Mechanical Engineers, 2019. http://dx.doi.org/10.1115/ipack2019-6501.
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Abstract As device power density increases, there is a need to dissipate generated heat by increasing particle volume loading in thermal interface materials. In this work, we develop and evaluate algorithms for generating ultrapacked microstructures of particles. Simulated microstructures reported in the literature rarely contain particle volume fractions greater than 60%. However, commercially available thermal greases claim to achieve volume fractions in the range of 60–80%. Therefore, to analyze effectiveness of commercially available particle-filled thermal interface materials, there is a need to develop algorithms capable of generating ultrapacked microstructures. The particle packing problem is initially posed as a nonlinear programming problem (NLP), and formal optimization algorithms are applied to generate microstructures that are maximally packed. Since accuracy of the simulated behavior is dependent on the number of particles in the simulation cell, efficiently simulating large number of particles is imperative. However, the packing simulation is computationally expensive. Therefore, various optimization algorithms are systematically evaluated to assess the computational efficiency as measured by the time to generate the microstructures for a system containing a large number of particles. The evaluated algorithms include the penalty function methods, best-in-class sequential programming method, matrix-less conjugate gradient method as well as the augmented Lagrangian method. In addition, heuristic algorithms are also evaluated to achieve computationally efficient packing. The evaluated heuristic algorithms are mainly based on the Drop-Fall-Shake method, but modified to more effectively simulate the mixing process in commercial planetary mixers. With the developed procedures, Representative Volume Elements (RVE) with volume fraction as high as 74% are demonstrated. The simulated microstructures are analyzed using our previously developed random network model to estimate the effective thermal and mechanical behavior given a particle arrangement.
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Smith, E. O., A. J. Neely, and A. P. Butcher. "Experimental Observations of Thermal Bow due to Natural Convection on a Gas Turbine Compressor Rotor Shaft Analogue." In ASME Turbo Expo 2016: Turbomachinery Technical Conference and Exposition. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/gt2016-56800.
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This study describes the development of an experimental apparatus designed to provide initial validation of numerical simulations of a gas turbine compressor rotor shaft under thermal bow due to natural convection. The experimental analogue represents a simplified model developed by the authors in previous works, designed to represent the basic elements of a compressor rotor shaft, as part of an ongoing parametric study into the influence of compressor design and integration on the onset time, duration, and severity of thermal bow, and the propensity of an engine to suffer from the Newkirk Effect. The semi-enclosed steel shaft, mounted on a support frame, was heated to approximately 600K in a convective oven before being removed and allowed to cool under ambient conditions. Observations of the shaft under natural cooling were made using several experimental techniques, including temperature profiling using thermographic imaging and a thermocouple array, and physical distortion measurement using linear variable displacement transducer (LVDT) probes. The behaviour of the buoyant plume was also observed using background oriented schlieren (BOS). Using these techniques, the natural convection-driven thermal gradient and resultant physical deformation were measured and recorded over a period of 60 minutes. The observed thermal gradients and resultant thermal bow distortions were then compared to a one-way fluid thermal structural interaction (FTSI) 3D conjugate heat transfer (CHT) computational fluid dynamics (CFD) and finite element analysis (FEA) model developed by the authors, in order to validate the numerical model. The behaviour of the thermal plume from the BOS imagery was also used as a qualitative validation method. The temperature measurements and overall cooling rate measured on the experimental model showed good agreement with the numerical predictions (within 1%); however, uncertainties in the initial phase of the experiment led to error in the numerical prediction of the thermal gradient and resultant thermal bow measurements (error of up to 63%). Noting the uncertainties in the experiment, the agreement between numerical and experimental results with respect to the overall cooling rate indicates that the numerical approach being employed as part of the larger parametric study into gas turbine compressor rotor shaft thermal bow is appropriate and valid.