89 results on '"Lgt"'
Search Results
2. The contours of evolution: In defence of Darwin's tree of life paradigm.
- Author
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van der Gulik, Peter T. S., Hoff, Wouter D., and Speijer, Dave
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HORIZONTAL gene transfer , *GENETIC transformation , *TREES - Abstract
Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights of widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL. [ABSTRACT FROM AUTHOR]
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- 2024
- Full Text
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3. Mycoplasmosis in Poultry: An Evaluation of Diagnostic Schemes and Molecular Analysis of Egyptian Mycoplasma gallisepticum Strains.
- Author
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Al-baqir, Ahmed, Hassanin, Ola, Al-Rasheed, Mohammed, Ahmed, Mohamed S., Mohamed, Mahmoud H. A., El Sayed, Mohamed Shawky, Megahed, Mohamed, El-Demerdash, Azza, Hashem, Youserya, and Eid, Amal
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MYCOPLASMA gallisepticum ,POULTRY ,RECEIVER operating characteristic curves ,GENITALIA ,RESPIRATORY organs - Abstract
Infections with Mycoplasma gallisepticum (MG) in poultry are associated with a wide range of disease conditions, including those affecting the respiratory and reproductive systems. The purpose of this study was to endorse the more sensitive diagnostic scheme for MG infection and identify the best molecular marker for MG phylogenetic analysis using six housekeeping genes: mgc2, mraW, atpG, ugpA, DUF31196, and lgT. For these purposes, 55 poultry flocks of different species were screened using either qRT-PCR or PCR techniques analogous to conventional culturing from non-cultured and cultured swabs on PPLO broth. The rate of MG positivity was the highest when using qRT-PCR from cultured broth (89.0%) and the lowest when using conventional culturing (34.5%). Compared to qRT-PCR from broth, statistical analysis using the Roc curve in MedCalc statistical software showed that the PCR schemes (qRT-PCR from swabs and PCR from swabs and broth) performed better than conventional culturing in terms of sensitivity, accuracy, and area under the curve (AUC), suggesting that they may be more reliable schemes. Further support was added by Cohen's kappa test, showing moderate agreement between the molecular approaches. Among the six screened genes, mgc2 and mraW had the highest detection rates (69% and 65.4%, respectively). The comparative phylogenetic analysis revealed that mgc2 or atpG gene sequences distinguished MG isolates into different clades with high discriminatory power. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
4. The contours of evolution: In defence of Darwin's tree of life paradigm
- Author
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Gulik, P.T.S. (Peter) van der, Hoff, W.D. (Wouter), Speijer, D. (Dave), Gulik, P.T.S. (Peter) van der, Hoff, W.D. (Wouter), and Speijer, D. (Dave)
- Abstract
Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights of widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL.
- Published
- 2024
- Full Text
- View/download PDF
5. The extent and characteristics of DNA transfer between plasmids and chromosomes.
- Author
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Kadibalban, A. Samer, Landan, Giddy, and Dagan, Tal
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MOBILE genetic elements , *CHROMOSOMES , *PLASMIDS , *HORIZONTAL gene transfer , *GENETIC variation - Abstract
Plasmids are extrachromosomal genetic elements that reside in prokaryotes. The acquisition of plasmids encoding beneficial traits can facilitate short-term survival in harsh environmental conditions or long-term adaptation of new ecological niches. Due to their ability to transfer between cells, plasmids are considered agents of gene transfer. Nonetheless, the frequency of DNA transfer between plasmids and chromosomes remains understudied. Using a novel approach for detection of homologous loci between genome pairs, we uncover gene sharing with the chromosome in 1,974 (66%) plasmids residing in 1,016 (78%) taxonomically diverse isolates. The majority of homologous loci correspond to mobile elements, which may be duplicated in the host chromosomes in tens of copies. Neighboring shared genes often encode similar functional categories, indicating the transfer of multigene functional units. Rare transfer events of antibiotics resistance genes are observed mainly with mobile elements. The frequent erosion of sequence similarity in homologous regions indicates that the transferred DNA is often devoid of function. DNA transfer between plasmids and chromosomes thus generates genetic variation that is akin to workings of endosymbiotic gene transfer in eukaryotic evolution. Our findings imply that plasmid contribution to gene transfer most often corresponds to transfer of the plasmid entity rather than transfer of protein-coding genes between plasmids and chromosomes. [Display omitted] • A novel approach for detection of homologous loci in replicon pairs • Most shared genes between plasmids and chromosomes are in mobile genetic elements • Transfer of antibiotic resistance genes is rare and mainly with mobile elements • Erosion of sequence similarity indicates non-functionalization of transferred DNA Kadibalban et al. present a novel approach for detection of homologous loci between plasmid-chromosome pairs. Their results show that gene sharing between plasmids and chromosomes corresponds mostly to transferred mobile genetic elements. The transferred DNA is frequently eroded and likely devoid of function. [ABSTRACT FROM AUTHOR]
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- 2024
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6. Characterisation of lipoprotieins of Clostridium difficile and their role in virulence
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Kovacs-Simon, Andrea, Titball, Richard, and Michell, Stephen
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579.364 ,Clostridium difficile ,lipoprotein ,Lgt ,bacterial adherence ,CD0873 - Abstract
Antibiotic-associated diarrhoea (AAD) and colitis, with the causative agent being the Gram-positive anaerobe, Clostridium difficile, are some of the most important hospital-acquired infections and significant burdens to healthcare services worldwide. Treatment of the infection is often ineffective and currently no vaccine is available against C. difficile infection (CDI). Research to identify novel virulence factors potentially leads to the development of new therapeutic and prophylactic drugs. As lipoproteins have been shown to play key roles in the virulence of several pathogens, the aim of this project was to investigate whether lipoproteins are involved in the virulence of C. difficile. Lipoproteins are anchored to the extracellular side of the cytoplasmic membrane in Gram-positive bacteria. Two enzymes are involved in the biosynthesis of lipoproteins: lipoprotein diacylglycerol transferase (Lgt) attaches lipoproteins to the membrane, and lipoprotein signal peptidase (Lsp) cleaves the signal peptide from the amino-terminus of lipoproteins. In order to study lipoprotein processing in C. difficile, lgt and lsp mutants of the C. difficie 630Δerm strain were generated using the ClosTron system. Antibody reactivity of 14 C. difficile lipoproteins was also investigated. It was shown in this study that lgt mutation caused changes in the lipoproteome of C. difficile. Therefore, inactivation of the lgt gene allowed investigation of the global contribution of lipoproteins to bacterial processes. The physiology and virulence of the lgt mutant was studied in vitro and in vivo. Surprisingly, many of the assayed phenotypes were not significantly affected by disruption of the lgt gene. Nevertheless, the ability of the lgt mutant to adhere to Caco-2 cells was markedly reduced. In addition, the phenotype of the lgt mutant observed in mice suggests that the faecal shedding of C. difficile is affected by Lgt inactivation. In further studies, the CD0873 lipoprotein as a potential adhesin of C. difficile was identified by in silico approach. Contribution of the CD0873 lipoprotein to the adherence of C. difficle was investigated by several different assays and the results strongly suggest that the CD0873 lipoprotein is directly involved in adhesion
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- 2013
7. Lipoproteins Contribute to the Anti-inflammatory Capacity of Lactobacillus plantarum WCFS1
- Author
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I-Chiao Lee, Iris I. van Swam, Sjef Boeren, Jacques Vervoort, Marjolein Meijerink, Nico Taverne, Marjo Starrenburg, Peter A. Bron, and Michiel Kleerebezem
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Lactobacillus ,lipoproteins ,human immune system ,proteomics ,prolipoprotein diacylglyceryl transferase ,LGT ,Microbiology ,QR1-502 - Abstract
Bacterial lipoproteins are well-recognized microorganism-associated molecular patterns, which interact with Toll-like receptor (TLR) 2, an important pattern recognition receptor of the host innate immune system. Lipoproteins are conjugated with two- or three-acyl chains (di- or tri-acyl), which is essential for appropriate anchoring in the cell membrane as well as for the interaction with TLR2. Lipoproteins have mostly been studied in pathogens and have established roles in various biological processes, such as nutrient import, cell wall cross-linking and remodeling, and host-cell interaction. By contrast, information on the role of lipoproteins in the physiology and host interaction of probiotic bacteria is scarce. By deletion of lgt, encoding prolipoprotein diacylglyceryl transferase, responsible for lipidation of lipoprotein precursors, we investigated the roles of the collective group of lipoproteins in the physiology of the probiotic model strain Lactobacillus plantarum WCFS1 using proteomic analysis of secreted proteins. To investigate the consequences of the lgt mutation in host-cell interaction, the capacity of mutant and wild-type bacteria to stimulate TLR2 signaling and inflammatory responses was compared using (reporter-) cell-based models. These experiments exemplified the critical contribution of the acyl chains of lipoproteins in immunomodulation. To the best of our knowledge, this is the first study that investigated collective lipoprotein functions in a model strain for probiotic lactobacilli, and we show that the lipoproteins in L. plantarum WCFS1 are critical drivers of anti-inflammatory host responses toward this strain.
- Published
- 2020
- Full Text
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8. Lipoproteins Contribute to the Anti-inflammatory Capacity of Lactobacillus plantarum WCFS1.
- Author
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Lee, I-Chiao, van Swam, Iris I., Boeren, Sjef, Vervoort, Jacques, Meijerink, Marjolein, Taverne, Nico, Starrenburg, Marjo, Bron, Peter A., and Kleerebezem, Michiel
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LIPOPROTEINS ,LACTOBACILLUS ,PATTERN perception receptors ,LACTOBACILLUS plantarum ,INFLAMMATION ,TOLL-like receptors ,CELL membranes - Abstract
Bacterial lipoproteins are well-recognized microorganism-associated molecular patterns, which interact with Toll-like receptor (TLR) 2, an important pattern recognition receptor of the host innate immune system. Lipoproteins are conjugated with two- or three-acyl chains (di- or tri-acyl), which is essential for appropriate anchoring in the cell membrane as well as for the interaction with TLR2. Lipoproteins have mostly been studied in pathogens and have established roles in various biological processes, such as nutrient import, cell wall cross-linking and remodeling, and host-cell interaction. By contrast, information on the role of lipoproteins in the physiology and host interaction of probiotic bacteria is scarce. By deletion of lgt , encoding prolipoprotein diacylglyceryl transferase, responsible for lipidation of lipoprotein precursors, we investigated the roles of the collective group of lipoproteins in the physiology of the probiotic model strain Lactobacillus plantarum WCFS1 using proteomic analysis of secreted proteins. To investigate the consequences of the lgt mutation in host-cell interaction, the capacity of mutant and wild-type bacteria to stimulate TLR2 signaling and inflammatory responses was compared using (reporter-) cell-based models. These experiments exemplified the critical contribution of the acyl chains of lipoproteins in immunomodulation. To the best of our knowledge, this is the first study that investigated collective lipoprotein functions in a model strain for probiotic lactobacilli, and we show that the lipoproteins in L. plantarum WCFS1 are critical drivers of anti-inflammatory host responses toward this strain. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
9. Reflexiones sobre la jurisprudencia aplicable al principio de proporcionalidad en el Derecho sancionador tributario
- Author
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Universidad de Alicante. Departamento de Disciplinas Económicas y Financieras, Martínez Muñoz, Yolanda, Universidad de Alicante. Departamento de Disciplinas Económicas y Financieras, and Martínez Muñoz, Yolanda
- Abstract
El trabajo de la autora realiza una serie de reflexiones sobre el principio de proporcionalidad de las sanciones en la doctrina jurisprudencial tras 20 años de la aprobación de la LGT.
- Published
- 2023
10. Serotype-Independent Protection Against Invasive Pneumococcal Infections Conferred by Live Vaccine With lgt Deletion
- Author
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A-Yeung Jang, Ki Bum Ahn, Yong Zhi, Hyun-Jung Ji, Jing Zhang, Seung Hyun Han, Huichen Guo, Sangyong Lim, Joon Yong Song, Jae Hyang Lim, and Ho Seong Seo
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Streptococcus pneumoniae ,Lgt ,lipoprotein ,live attenuated vaccine ,mucosal immunity ,Immunologic diseases. Allergy ,RC581-607 - Abstract
Streptococcus pneumoniae is the most common respiratory bacterial pathogen among cases of community-acquired infection in young children, older adults, and individuals with underlying medical conditions. Although capsular polysaccharide-based pneumococcal vaccines have contributed to significant decrease in invasive pneumococcal infections, these vaccines have some limitations, including limited serotype coverage, lack of effective mucosal antibody responses, and high costs. In this study, we investigated the safety and immunogenicity of a live, whole-cell pneumococcal vaccine constructed by deleting the gene for prolipoprotein diacylglyceryl transferase (lgt) from the encapsulated pneumococcal strain TIGR4 (TIGR4Δlgt) for protection against heterologous pneumococcal strains. Pneumococcal strain TIGR4 was successfully attenuated by deletion of lgt, resulting in the loss of inflammatory activity and virulence. TIGR4Δlgt colonized the nasopharynx long enough to induce strong mucosal IgA and IgG2b-dominant systemic antibody responses that were cross-reactive to heterologous pneumococcal serotypes. Finally, intranasal immunization with TIGR4Δlgt provided serotype-independent protection against pneumococcal challenge in mice. Taken together, our results suggest that TIGR4Δlgt is an avirulent and attractive broad-spectrum pneumococcal vaccine candidate. More broadly, we assert that modulation of such “master” metabolic genes represents an emerging strategy for developing more effective vaccines against numerous infectious agents.
- Published
- 2019
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11. Lateral Acquisitions Repeatedly Remodel the Oxygen Detoxification Pathway in Diplomonads and Relatives.
- Author
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Jiménez-González, Alejandro, Xu, Feifei, and Andersson, Jan O
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HORIZONTAL gene transfer , *REACTIVE oxygen species , *ANAEROBIC metabolism , *GIARDIA lamblia , *CYSTEINE - Abstract
Oxygen and reactive oxygen species (ROS) are important stress factors for cells because they can oxidize many large molecules. Fornicata, a group of flagellated protists that includes diplomonads, have anaerobic metabolism but are still able to tolerate fluctuating levels of oxygen. We identified 25 protein families putatively involved in detoxification of oxygen and ROS in this group using a bioinformatics approach and propose how these interact in an oxygen detoxification pathway. These protein families were divided into a central oxygen detoxification pathway and accessory pathways for the synthesis of nonprotein thiols. We then used a phylogenetic approach to investigate the evolutionary origin of the components of this putative pathway in Diplomonadida and other Fornicata species. Our analyses suggested that the diplomonad ancestor was adapted to low-oxygen levels, was able to reduce O2 to H2O in a manner similar to extant diplomonads, and was able to synthesize glutathione and l -cysteine. Several genes involved in the pathway have complex evolutionary histories and have apparently been repeatedly acquired through lateral gene transfer and subsequently lost. At least seven genes were acquired independently in different Fornicata lineages, leading to evolutionary convergences. It is likely that acquiring these oxygen detoxification proteins helped anaerobic organisms (like the parasitic Giardia intestinalis) adapt to low-oxygen environments (such as the digestive tract of aerobic hosts). [ABSTRACT FROM AUTHOR]
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- 2019
- Full Text
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12. Serotype-Independent Protection Against Invasive Pneumococcal Infections Conferred by Live Vaccine With lgt Deletion.
- Author
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Jang, A-Yeung, Ahn, Ki Bum, Zhi, Yong, Ji, Hyun-Jung, Zhang, Jing, Han, Seung Hyun, Guo, Huichen, Lim, Sangyong, Song, Joon Yong, Lim, Jae Hyang, and Seo, Ho Seong
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STREPTOCOCCUS pneumoniae ,PNEUMOCOCCAL vaccines ,SEROTYPES ,LIPOPROTEINS ,IMMUNOGLOBULIN A ,IMMUNOGLOBULIN G - Abstract
Streptococcus pneumoniae is the most common respiratory bacterial pathogen among cases of community-acquired infection in young children, older adults, and individuals with underlying medical conditions. Although capsular polysaccharide-based pneumococcal vaccines have contributed to significant decrease in invasive pneumococcal infections, these vaccines have some limitations, including limited serotype coverage, lack of effective mucosal antibody responses, and high costs. In this study, we investigated the safety and immunogenicity of a live, whole-cell pneumococcal vaccine constructed by deleting the gene for prolipoprotein diacylglyceryl transferase (lgt) from the encapsulated pneumococcal strain TIGR4 (TIGR4Δ lgt) for protection against heterologous pneumococcal strains. Pneumococcal strain TIGR4 was successfully attenuated by deletion of lgt , resulting in the loss of inflammatory activity and virulence. TIGR4Δ lgt colonized the nasopharynx long enough to induce strong mucosal IgA and IgG2b-dominant systemic antibody responses that were cross-reactive to heterologous pneumococcal serotypes. Finally, intranasal immunization with TIGR4Δ lgt provided serotype-independent protection against pneumococcal challenge in mice. Taken together, our results suggest that TIGR4Δ lgt is an avirulent and attractive broad-spectrum pneumococcal vaccine candidate. More broadly, we assert that modulation of such "master" metabolic genes represents an emerging strategy for developing more effective vaccines against numerous infectious agents. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
13. Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication.
- Author
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Kapust, Nils, Nelson-Sathi, Shijulal, Schönfeld, Barbara, Hazkani-Covo, Einat, Bryant, David, Lockhart, Peter J, Röttger, Mayo, Xavier, Joana C, and Martin, William F
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HORIZONTAL gene transfer , *SPLIT genes , *BACTERIAL transformation , *GENETIC transformation , *FAMILY size - Abstract
In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation, and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent genome analyses studying gene distributions have uncovered evidence for sporadic, discontinuous events of gene transfer from bacteria to archaea during evolution. Other studies have used traditional models designed to investigate gene family size evolution (Count) to support claims that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here, we show that the methodology used in analyses favoring continuous gene transfers to archaea was misapplied in other studies and does not recover known events of single simultaneous origin for many genes followed by differential loss in real data: plastid genomes. Using the same software and the same settings, we reanalyzed presence/absence pattern data for proteins encoded in plastid genomes and for eukaryotic protein families acquired from plastids. Contrary to expectations under a plastid origin model, we found that the methodology employed inferred that gene acquisitions occurred uniformly across the plant tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, the methodology that recovered gradual and continuous lateral gene transfer among lineages for archaea obtains the same result for plastids, even though it is known that massive gains followed by gradual differential loss is the true evolutionary process that generated plastid gene distribution data. Our findings caution against the use of models designed to study gene family size evolution for investigating gene transfer processes, especially when transfers involving more than one gene per event are possible. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
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14. Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms.
- Author
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Murillo, Tatiana, Ramírez-Vargas, Gabriel, Riedel, Thomas, Overmann, Jörg, Andersen, Joakim M., Guzmán-Verri, Caterina, Chaves-Olarte, Esteban, and Rodríguez, César
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GENETIC recombination , *GENETIC transformation , *SINGLE nucleotide polymorphisms , *GENES , *MICROBIAL virulence - Abstract
Clostridiodes difficile strains fromthe NAPCR1/ST54 andNAP1/ST01 types have caused outbreaks despite of their notable differences in genome diversity. By comparingwhole genome sequences of 32 NAPCR1/ST54 isolates and 17 NAP1/ST01 recovered from patients infected with C. difficile we assessed whether mutation, homologous recombination (r) or nonhomologous recombination (NHR) through lateral gene transfer (LGT) have differentially shaped the microdiversification of these strains. The average number of single nucleotide polymorphisms (SNPs) in coding sequences (NAPCR1/ST54 =24; NAP1/ST01 = 19) and SNP densities (NAPCR1/ST54 =0.54/kb; NAP1/ST01 =0.46/kb) in the NAPCR1/ST54 and NAP1/ST01 isolates was comparable. However, the NAP1/ST01 isolates showed 3× higher average dN/dS rates (8.35) that the NAPCR1/ST54 isolates (2.62). Regarding r, whereas 31 of the NAPCR1/ST54 isolates showed 1 recombination block (3,301-8,226 bp), the NAP1/ST01 isolates showed no bases in recombination. As to NHR, the pangenome of the NAPCR1/ST54 isolates was larger (4,802 gene clusters, 26%noncore genes) andmore heterogeneous (644 ± 33 gene content changes) than that of the NAP1/ST01 isolates (3,829 gene clusters, ca. 6% noncore genes, 129 ± 37 gene content changes). Nearly 55% of the gene content changes seen among the NAPCR1/ST54 isolates (355 ± 31) were traced back to MGEs with putative genes for antimicrobial resistance and virulence factors that were only detected in single isolates or isolate clusters. Congruently, the LGT/SNP rate calculated for the NAPCR1/ST54 isolates (26.8 ± 2.8) was 4× higher than the one obtained for the NAP1/ST1 isolates (6.8 ± 2.0). We conclude that NHR-LGT has had a greater role in the microdiversification of the NAPCR1/ST54 strains, opposite to the NAP1/ST01 strains, where mutation is known to play a more prominent role. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
15. A Defect in Lipoprotein Modification by Lgt Leads to Abnormal Morphology and Cell Death in Escherichia coli That Is Independent of Major Lipoprotein Lpp
- Author
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S. Legood, D. Seng, I. G. Boneca, N. Buddelmeijer, Biologie et Génétique de la Paroi bactérienne - Biology and Genetics of Bacterial Cell Wall, Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), This work was financed by Institut Pasteur and the Pasteur Paris University (PPU)-Oxford International PhD Program with a fellowship to S.L.G. Our research received funding from the Institut Carnot Infectious Diseases Global Care (16 CARN 0023-01 Project iLiNT) and from the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant ANR-10-LABX-62-IBEID)., We thank G. H. Haustant, L. Lemée, and M. Monot from the Biomics Platform, C2RT, Institut Pasteur, Paris, France, who are supported by France Génomique (ANR-10-INBS-09) and IBISA. We thank Sharookh Kapadia for strain MG1655Δlgt and Hajime Tokuda for Lpp antibodies. We are grateful for constructive comments and suggestions from all BGPB lab members., and ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010)
- Subjects
cell envelope ,Cell Death ,Escherichia coli Proteins ,Lipoproteins ,viability ,Lpp ,Arabinose ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,Microbiology ,Anti-Bacterial Agents ,Transferases ,Lgt ,Escherichia coli ,Humans ,Molecular Biology ,Escherichia coli Infections ,cell viability ,Bacterial Outer Membrane Proteins - Abstract
WGS data have been submitted to the NCBI SRA database under accession number PRJNA860548.; International audience; Lgt is an essential enzyme in proteobacteria and therefore a potential target for novel antibiotics. The effect of Lgt depletion on growth, morphology, and viability was studied in Escherichia coli to assess whether absence of Lgt leads to cell death. Two Lgt depletion strains were used in which lgt was under the control of an arabinose-inducible promoter that allowed regulation of Lgt protein levels. Reduced levels of Lgt led to severe growth and morphological defects that could be restored by expressing lgt in trans, demonstrating that only Lgt is responsible for the distorted phenotypes. In the absence of major lipoprotein Lpp, growth defects were partially restored when low levels of Lgt were still present; however, lgt could not be deleted in the absence of Lpp. Our results demonstrate that Lpp is not the main cause of cell death under conditions of Lgt depletion and that other lipoproteins are important in cell envelope biogenesis and cell viability. Specific inhibitors of Lgt are thus promising for the development of novel antibiotics. IMPORTANCE Incomplete maturation and envelope mislocalization of lipoproteins, through inhibition or mutations in lipoprotein modification enzymes or transport to the outer membrane, are lethal in proteobacteria. Resistance to small-molecule inhibition or the appearance of suppressor mutations is often directly correlated with the presence of abundant outer membrane lipoprotein Lpp. Our results show that Lgt, the first enzyme of the lipoprotein modification pathway, is still required for growth and viability in the absence of Lpp and thus is necessary for the function of other essential lipoproteins in the cell envelope. This adds credence to the hypothesis that Lgt is essential in proteobacteria and an attractive target for the development of novel antibiotics.
- Published
- 2022
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16. Stringency of bacterial prolipoprotein signal peptidase (LspA) in recognition of signal peptides – Structure-function correlation.
- Author
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Sangith, Nikhil and Sankaran, Krishnan
- Subjects
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SIGNAL peptidases , *SIGNAL peptides , *POST-translational modification , *PHOSPHATIDYLGLYCEROL , *THREONINE - Abstract
Bacterial lipid modification of proteins is an essential post-translational event committed by Phosphatidylglycerol: prolipoprotein diacylglyceryl transferase (Lgt) by catalysing diacyglyceryl transfer from Phosphatidylglycerol to cysteine present in the characteristic ‘lipobox’ ([LVI] (−3) [ASTVI] (−2) [GAS] (−1) C (+1) ) of prolipoprotein signal peptides. This is then followed by the cleavage of the signal peptide by lipoprotein-specific signal peptidase (LspA). It had been known for long that threonine at the −1 position allows diacylglyceryl modification by Lgt, but not signal peptide cleavage by LspA. We have addressed this unexplained stringency by computational analysis of the recently published 3D structure of LspA with its competitive inhibitor as well as transition state analogue, globomycin using PyMoL viewing tool and VADAR (Volume, Area, Dihedral Angle Reporter) web server. The propensity to form hydrogen bond (2.9 a ) between the hydroxyl group of threonine (not possible with serine) and the NH of the lipid-modified cysteine, possible only in the transition state, will prevent the protonation of NH of the leaving peptide and therefore its cleavage. This knowledge could be useful for designing inhibitors of this essential pathway in bacteria or for engineering LspA. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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17. Investigations on magnetic properties of La3Ga5.5Ta0.5O14 single crystals doped with Er3+ ions.
- Author
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Leniec, G., Kaczmarek, S.M., Berkowski, M., Kazan, S., and Acikgoz, M.
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MAGNETIZATION , *MAGNETIC properties of condensed matter , *ELECTRON paramagnetic resonance , *LARMOR precession , *ERBIUM compounds - Abstract
La 3 Ga 5.5 Ta 0.5 O 14 (LGT) single crystals doped with 3.8 at. % of Er 3+ ions have been investigated by performing Electron Paramagnetic Resonance (EPR) and magnetic susceptibility measurements. The results of EPR measurements show a large anisotropy of spin Hamiltonian parameters belonging to isolated erbium centers. In addition to the isolated erbium centers a small number of pairs of erbium ions was also observed. Based on the obtained spin Hamiltonian parameters we have determined the symmetry of isolated and paired erbium ions as being at least C 4 . From magnetization measurements it does not result strong coupling between Er 3+ ions and the lattice of LGT crystals. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
18. Excited-state absorption in light-scattering, ceramic erbium-doped langatate.
- Author
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Toma, Octavian, Ştefan, Angela, and Georgescu, Şerban
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LIGHT scattering , *CERAMIC materials , *ERBIUM compounds , *DOPING agents (Chemistry) , *EXCITED state chemistry , *ABSORPTION - Abstract
A method for the measurement and calibration of the excited-state absorption spectra in light-scattering media is developed. The method is applied for the recording and calibration of the excited-state absorption spectra of an erbium-doped langatate ceramic sample in the visible range. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
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19. Molecular analysis of an integrative conjugative element, ICEH, present in the chromosome of different strains of Mycoplasma hyopneumoniae
- Author
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Paulo Marcos Pinto, Marcos Oliveira de Carvalho, Leonardo Alves-Junior, Marcelo Brocchi, and Irene Silveira Schrank
- Subjects
LGT ,Mycoplasma ,constins ,Genetics ,QH426-470 - Abstract
Diversification of bacterial species and pathotypes is largely caused by lateral gene transfer (LGT) of diverse mobile DNA elements such as plasmids, phages, transposons and genomic islands. Thus, acquisition of new phenotypes by LGT is very important for bacterial evolution and relationship with hosts. This paper reports a 23 kb region containing fourteen CDSs with similarity to the previous described Integrative Conjugal Element of Mycoplasma fermentans (ICEF). This element, named ICEH, is present as one copy at distinct integration sites in the chromosome of 7448 and 232 pathogenic strains and is absent in the type strain J (non-pathogenic). Notable differences in the nucleotide composition of the insertion sites were detected, and could be correlated to a lack of specificity of the ICEH integrase. Although present in strains of the same organism, the ICEH elements are more divergent than the typical similarity between other chromosomal locus of Mycoplasma hyopneunomiae, suggesting an accelerated evolution of these constins or an ongoing process of degeneration, while maintaining conservation of the tra genes. An extrachromosomal form of this element had been detected in the 7448 strain, suggesting a possible involvement in its mobilization and transference of CDSs to new hosts.
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- 2007
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20. Magnetic properties of La3Ga5.5Ta0.5O14 single crystals doped with Sm3+.
- Author
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Kaczmarek, S.M., Leniec, G., Berkowski, M., Kazan, S., and Açıkgöz, M.
- Subjects
- *
SINGLE crystals , *DOPING agents (Chemistry) , *SAMARIUM isotopes , *METAL crystal growth , *MAGNETIC properties of metals , *MAGNETIC susceptibility - Abstract
Electron Paramagnetic Resonance (EPR) and magnetic susceptibility measurements have been performed for La 3 Ga 5.5 Ta 0.5 O 14 single crystal doped intentionally with 3 wt% of Sm 3+ ions. X-band EPR measurements have been carried out with covering the field range 0–1.4 T and the temperature range 3–300 K. It has been found that two magnetically inequivalent sites having at least C 2 symmetry are responsible for the EPR spectra. The static magnetization measurements as a function of temperature and magnetic field have been done using a vibrating sample magnetometer (VSM). The field and temperature dependences of magnetization are measured in zero-field cooled (ZFC) and field cooled (FC) regimes in an applied field of 100 Oe. It is seen from magnetization measurements that the strong coupling regime is due to the presence of a strong coupling of the Sm 3+ ions to the lattice of LGT crystals. [ABSTRACT FROM AUTHOR]
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- 2016
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21. Inhibition of Escherichia coli Lipoprotein Diacylglyceryl Transferase Is Insensitive to Resistance Caused by Deletion of Braun’s Lipoprotein
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Donghong Yan, Cameron L. Noland, Jingyu Diao, Peter Liu, Anand Kumar Katakam, Mike Reichelt, Haruhiko Ogawa, Cary D. Austin, Susan L. Gloor, Yutian Peng, Min Xu, Hayato Yanagida, Patrick C Reid, Jing Kang, Rie Komura, Homer Pantua, Kelly M. Storek, Yiming Xu, Michael Volny, Wendy Sandoval, Jeremy Murray, Nicholas N. Nickerson, Steven T. Rutherford, Junichi Nishikawa, Tatsuya Sano, Hiroko Inaba, Sharookh B. Kapadia, and Christian N. Cunningham
- Subjects
antibiotic resistance ,Lipoproteins ,Lpp ,Peptidoglycan ,Braun's lipoprotein ,medicine.disease_cause ,Microbiology ,03 medical and health sciences ,Mice ,Bacterial Proteins ,Transferases ,medicine ,Escherichia coli ,Inner membrane ,Transferase ,Animals ,Aspartic Acid Endopeptidases ,Uropathogenic Escherichia coli ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,biology ,030306 microbiology ,Gene Expression Regulation, Bacterial ,biology.organism_classification ,Cell biology ,Anti-Bacterial Agents ,Lgt ,Female ,Bacterial outer membrane ,Biogenesis ,Bacteria ,Gene Deletion ,Lipoprotein ,Research Article - Abstract
Lipoprotein diacylglyceryl transferase (Lgt) catalyzes the first step in the biogenesis of Gram-negative bacterial lipoproteins which play crucial roles in bacterial growth and pathogenesis. We demonstrate that Lgt depletion in a clinical uropathogenic Escherichia coli strain leads to permeabilization of the outer membrane and increased sensitivity to serum killing and antibiotics. Importantly, we identify G2824 as the first-described Lgt inhibitor that potently inhibits Lgt biochemical activity in vitro and is bactericidal against wild-type Acinetobacter baumannii and E. coli strains. While deletion of a gene encoding a major outer membrane lipoprotein, lpp, leads to rescue of bacterial growth after genetic depletion or pharmacologic inhibition of the downstream type II signal peptidase, LspA, no such rescue of growth is detected after Lgt depletion or treatment with G2824. Inhibition of Lgt does not lead to significant accumulation of peptidoglycan-linked Lpp in the inner membrane. Our data validate Lgt as a novel antibacterial target and suggest that, unlike downstream steps in lipoprotein biosynthesis and transport, inhibition of Lgt may not be sensitive to one of the most common resistance mechanisms that invalidate inhibitors of bacterial lipoprotein biosynthesis and transport. IMPORTANCE As the emerging threat of multidrug-resistant (MDR) bacteria continues to increase, no new classes of antibiotics have been discovered in the last 50 years. While previous attempts to inhibit the lipoprotein biosynthetic (LspA) or transport (LolCDE) pathways have been made, most efforts have been hindered by the emergence of a common mechanism leading to resistance, namely, the deletion of the gene encoding a major Gram-negative outer membrane lipoprotein lpp. Our unexpected finding that inhibition of Lgt is not susceptible to lpp deletion-mediated resistance uncovers the complexity of bacterial lipoprotein biogenesis and the corresponding enzymes involved in this essential outer membrane biogenesis pathway and potentially points to new antibacterial targets in this pathway.
- Published
- 2021
22. Lipoproteins Contribute to the Anti-inflammatory Capacity of Lactobacillus plantarum WCFS1
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Lee, Chiao, van Swam, Iris I., Boeren, Sjef, Vervoort, Jacques, Meijerink, Marjolein, Taverne, Nico, Starrenburg, Marjo, Bron, Peter A., Kleerebezem, Michiel, Lee, Chiao, van Swam, Iris I., Boeren, Sjef, Vervoort, Jacques, Meijerink, Marjolein, Taverne, Nico, Starrenburg, Marjo, Bron, Peter A., and Kleerebezem, Michiel
- Abstract
Bacterial lipoproteins are well-recognized microorganism-associated molecular patterns, which interact with Toll-like receptor (TLR) 2, an important pattern recognition receptor of the host innate immune system. Lipoproteins are conjugated with two- or three-acyl chains (di- or tri-acyl), which is essential for appropriate anchoring in the cell membrane as well as for the interaction with TLR2. Lipoproteins have mostly been studied in pathogens and have established roles in various biological processes, such as nutrient import, cell wall cross-linking and remodeling, and host-cell interaction. By contrast, information on the role of lipoproteins in the physiology and host interaction of probiotic bacteria is scarce. By deletion of lgt, encoding prolipoprotein diacylglyceryl transferase, responsible for lipidation of lipoprotein precursors, we investigated the roles of the collective group of lipoproteins in the physiology of the probiotic model strain Lactobacillus plantarum WCFS1 using proteomic analysis of secreted proteins. To investigate the consequences of the lgt mutation in host-cell interaction, the capacity of mutant and wild-type bacteria to stimulate TLR2 signaling and inflammatory responses was compared using (reporter-) cell-based models. These experiments exemplified the critical contribution of the acyl chains of lipoproteins in immunomodulation. To the best of our knowledge, this is the first study that investigated collective lipoprotein functions in a model strain for probiotic lactobacilli, and we show that the lipoproteins in L. plantarum WCFS1 are critical drivers of anti-inflammatory host responses toward this strain.
- Published
- 2020
23. Modularized Evolution in Archaeal Methanogens Phylogenetic Forest.
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Jun Li, Chi-Fat Wong, Mabel Ting Wong, He Huang, and Leung, Frederick C.
- Subjects
- *
METHANOGENS , *ARCHAEBACTERIA , *GENES , *BIOLOGICAL evolution , *PROKARYOTES - Abstract
Methanogens are methane-producing archaea that plays a key role in the global carbon cycle. To date, the evolutionary history of methanogens and closely related nonmethanogen species remains unresolved among studies conducted upon different genetic markers, attributing to horizontal gene transfers (HGTs). With an effort to decipher both congruent and conflicting evolutionary events, reconstruction of coevolved gene clusters and hierarchical structure in the archaeal methanogen phylogenetic forest, comprehensive evolution, and network analyses were performed upon 3,694 gene families from 41methanogens and 33 closely related archaea. Our results show that 1) greater than 50% of genes are in topological dissonance with others; 2) the prevalent interorder HGTs, even for core genes, in methanogen genomes led to their scrambled phylogenetic relationships; 3) most methanogenesisrelated genes have experienced at least one HGT; 4) greater than 20% of the genes in methanogen genomes were transferred horizontally from other archaea, with genes involved in cell-wall synthesis and defense system having been transferred most frequently; 5) the coevolution network contains seven statistically robust modules, where in the centralmodule has the highest average node strength and comprises a majority of the core genes; 6) different coevolutionary module genes boomed in different time and evolutionary lineage, constructing diversified pan-genome structures; 7) the modularized evolution is also closely related to the vertical evolution signals andtheHGTrate of the genes. Overall, this study presented amodularized phylogenetic forest that describes a combination of complicated vertical and nonvertical evolutionary processes for methanogenic archaeal species. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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24. Insilico model for prediction of lateral gene transfer in Rhodopseudomonas paulistris.
- Author
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Shanker, Anuja and Pardasani, Kamal
- Subjects
BIOLOGISTS ,GENETIC transformation ,RHODOPSEUDOMONAS ,PHYLOGENY ,BRADYRHIZOBIUM japonicum - Abstract
Study of evolutionary phenomenon is of great interest to biologists in discovering the secrets of life. The presence of reticulation events due to lateral gene transfer (LGT) among species poses new challenges for such evolutionary studies. In this paper an attempt has been made to develop an insilico model to predict LGT in the Rhodopseudomonas paulistris. Neighbour Joining method is employed to generate phylogenetic tree of 26 sequences of Alphaproteobacteria and one sequence of Cyanobacteria used as an out group. Then Least Squares approach is employed to predict the reticulation branches. Three reticulation branches were detected among these 27 sequences. The lateral gene transfer was predicted between Rhodopseudomonas paulistris 99 D and Rhodobacter sphaeroides, Rhodopseudomonas paulistris HMD 88 and Bradyrhizobium japonicum USDA and Bradyrhizobium japonicum USDA and Rhodobacter blasticus. The results obtained are in agreement with the results obtained by earlier research workers. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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25. Phylogenomic Study Indicates Widespread Lateral Gene Transfer in Entamoeba and Suggests a Past Intimate Relationship with Parabasalids.
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Grant, Jessica R. and Katz, Laura A.
- Subjects
- *
ENTAMOEBA , *HORIZONTAL gene transfer , *EUKARYOTIC evolution , *TRICHOMONAS vaginalis , *MICROBIAL genomics , *PARASITES - Abstract
Lateral gene transfer (LGT) has impacted the evolutionary history of eukaryotes, though to a lesser extent than in bacteria and archaea. Detecting LGT and distinguishing it from single gene tree artifacts is difficult, particularly when considering very ancient events (i.e., over hundreds of millions of years). Here, we use two independent lines of evidence—a taxon-rich phylogenetic approach and an assessment of the patterns of gene presence/absence—to evaluate the extent of LGT in the parasitic amoebozoan genus Entamoeba. Previous work has suggested that a number of genes in the genome of Entamoeba spp. were acquired by LGT. Our approach, using an automated phylogenomic pipeline to build taxon-rich gene trees, suggests that LGT is more extensive than previously thought. Our analyses reveal that genes have frequently entered the Entamoeba genome via nonvertical events, including at least 116 genes acquired directly from bacteria or archaea, plus an additional 22 genes in which Entamoeba plus one other eukaryote are nested among bacteria and/or archaea. These genes may make good candidates for novel therapeutics, as drugs targeting these genes are less likely to impact the human host. Although we recognize the challenges of inferring intradomain transfers given systematic errors in gene trees, we find 109 genes supporting LGT from a eukaryote to Entamoeba spp., and 178 genes unique to Entamoeba spp. and one other eukaryotic taxon (i.e., presence/absence data). Inspection of these intradomain LGTs provide evidence of a common sister relationship between genes of Entamoeba (Amoebozoa) and parabasalids (Excavata). We speculate that this indicates a past close relationship (e.g., symbiosis) between ancestors of these extant lineages. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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26. Subsídios para a compreensão do fenómeno da responsabilidade fiscal no âmbito das pessoas coletivas
- Author
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Caldas, Maria José Silva and Falcão, Pedro Alexandre Ferreira Mendes Marinho
- Subjects
Ónus da prova ,LGT ,Reversão Fiscal ,Culpa ,Responsabilidade subsidiária - Abstract
O estudo da responsabilidade subsidiária pelas dívidas tributárias das pessoas coletivas oferece-nos várias vias de pesquisa possíveis para a abordagem do tema, mas devido aos limites estabelecidos, decidimos então desta forma propomo-nos saber qual o sentido e alcance inerente da responsabilidade subsidiária dos gerentes e administradores das sociedades, decorrente do regime jurídico vigente que consta da aplicação do artigo 24º nº 1 da Lei Geral Tributária. Nos dias de hoje, a crescente utilização da figura da responsabilidade subsidiária por parte da administração fiscal com o objetivo de arrecadar as receitas, sempre indispensáveis, não deixa de merecer o nosso estudo no que toca ao seu desenvolvimento e interpretação, pois, o seu tratamento, tem sido substancialmente abordado pela doutrina e jurisprudência. O presente trabalho resultará fundamentalmente de pesquisas e revisão de literatura jurídica relacionada com o tema, assentando-se na legislação que enquadra o tema, essencialmente a lei geral tributária. Neste contexto ainda, e devido o vínculo entre a responsabilidade tributária e a reversão fiscal que é incontornável, pelo que torna obrigatória abordar esta última, pois, trata-se do instituto que efetiva a responsabilidade tributária subsidiária, acreditamos veramente que tal tratamento possibilita uma melhor análise do instituto da responsabilidade
- Published
- 2020
27. Genetic diversity of rhizobia nodulating common bean ( Phaseolus vulgaris L.) in the Central Black Sea Region of Turkey.
- Author
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Gurkanli, Cem, Ozkoc, Ibrahim, and Gunduz, Islam
- Abstract
We have analyzed 30 rhizobial isolates obtained from common bean ( Phaseolus vulgaris L.) root nodules grown in the Middle Blacksea Region of Turkey, using ARDRA and nucleotide sequence data. ARDRA analysis with enzymes CfoI, HinfI, NdeII, MspI and PstI revealed three patterns. Based on sequence data from 16S rDNA, the patterns were identified as, Rhizobium leguminosarum bv. phaseoli ( n = 16), R. etli bv. phaseoli ( n = 8) and R. phaseoli ( n = 6). On the other hand, nucleotide sequence phylogenies of housekeeping genes ( recA, atpD and glnII) selected to confirm the 16S rDNA phylogeny revealed different evolutionary relationships. These results suggested the possibility of lateral transfers of these genes amongst different rhizobial species (including R. leguminosarum, R. etli and R. phaseoli) sharing the same ecological niche (nodulating P. vulgaris) which also indicates that there may be no true genetic barier among these species. Phylogenetic analysis based on DNA sequence data from the nodA and nifH genes showed that all rhizobial species obtained in this study were carrying nodA and nifH haplotypes which were the same or similar to those of CFN42 ( R. etli type strain), suggesting a further support for the lateral transfer of CFN42 Sym plasmid, p42, amongst Turkish common bean nodulating rhizobial isolates. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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28. GenPhyloData: realistic simulation of gene family evolution.
- Author
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Sjöstrand, Joel, Arvestad, Lars, Lagergren, Jens, and Sennblad, Bengt
- Subjects
- *
PHYLOGENY , *CHROMOSOME duplication , *SYNTHETIC biology , *GENETIC transformation , *MOLECULAR clock , *HOST-parasite relationships , *SIMULATION methods & models - Abstract
Background: PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and--perhaps more interestingly--also supports generation of gene family trees guided by a known (synthetic or biological) species tree while accounting for events such as gene duplication, gene loss, and lateral gene transfer (LGT). The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock. Result: Simulated data created with PrIME-GenPhyloData can be used for benchmarking phylogenetic approaches, or for characterizing models or model parameters with respect to biological data. Conclusion: The concept of tree-in-tree evolution can also be used to model, for instance, biogeography or host-parasite co-evolution. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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29. A Defect in Lipoprotein Modification by Lgt Leads to Abnormal Morphology and Cell Death in Escherichia coli That Is Independent of Major Lipoprotein Lpp.
- Author
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Legood S, Seng D, Boneca IG, and Buddelmeijer N
- Subjects
- Anti-Bacterial Agents metabolism, Anti-Bacterial Agents pharmacology, Arabinose metabolism, Bacterial Outer Membrane Proteins genetics, Bacterial Outer Membrane Proteins metabolism, Cell Death, Escherichia coli metabolism, Humans, Lipoproteins metabolism, Transferases, Escherichia coli Infections, Escherichia coli Proteins genetics, Escherichia coli Proteins metabolism
- Abstract
Lgt is an essential enzyme in proteobacteria and therefore a potential target for novel antibiotics. The effect of Lgt depletion on growth, morphology, and viability was studied in Escherichia coli to assess whether absence of Lgt leads to cell death. Two Lgt depletion strains were used in which lgt was under the control of an arabinose-inducible promoter that allowed regulation of Lgt protein levels. Reduced levels of Lgt led to severe growth and morphological defects that could be restored by expressing lgt in trans , demonstrating that only Lgt is responsible for the distorted phenotypes. In the absence of major lipoprotein Lpp, growth defects were partially restored when low levels of Lgt were still present; however, lgt could not be deleted in the absence of Lpp. Our results demonstrate that Lpp is not the main cause of cell death under conditions of Lgt depletion and that other lipoproteins are important in cell envelope biogenesis and cell viability. Specific inhibitors of Lgt are thus promising for the development of novel antibiotics. IMPORTANCE Incomplete maturation and envelope mislocalization of lipoproteins, through inhibition or mutations in lipoprotein modification enzymes or transport to the outer membrane, are lethal in proteobacteria. Resistance to small-molecule inhibition or the appearance of suppressor mutations is often directly correlated with the presence of abundant outer membrane lipoprotein Lpp. Our results show that Lgt, the first enzyme of the lipoprotein modification pathway, is still required for growth and viability in the absence of Lpp and thus is necessary for the function of other essential lipoproteins in the cell envelope. This adds credence to the hypothesis that Lgt is essential in proteobacteria and an attractive target for the development of novel antibiotics.
- Published
- 2022
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30. A comparison of vibrating beam resonators in Quartz, GaPO4, LGS and LGT
- Author
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Douchet, G., Sthal, F., Bigler, E., and Bourquin, R.
- Subjects
- *
COMPARATIVE studies , *VIBRATION (Mechanics) , *ELECTRIC resonators , *QUARTZ , *GALLIUM compounds , *LANTHANUM compounds , *FLEXURE , *TORSION , *MICROFABRICATION - Abstract
Abstract: The present paper reviews and compares the properties of vibrating beam resonators in length-extensional, flexural and cylindrical-torsional modes; resonators are designed and built with new piezoelectric materials: Gallium orthophosphate (GaPO4), Langasite (LGS) and Langatate (LGT). Their characteristics are compared with the results obtained with the same structures built in classical Quartz crystal. For all 3 new crystals, temperature-compensated cuts have been found for length-extensional and flexural modes by a theoretical analysis. Experiments have been made on test beams fabricated by conventional precision lapping/machining and photolithography to deposit electrodes. The existence of temperature-compensated cuts for length-extensional resonators is experimentally confirmed. The possibilities of using temperature-compensated cylindrical resonators in the torsional modes are analysed and their temperature sensitivity is computed. [Copyright &y& Elsevier]
- Published
- 2010
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31. Staphylococcal lipoproteins and their role in bacterial survival in mice.
- Author
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Schmaler, Mathias, Jann, Naja J., Götz, Friedrich, and Landmann, Regine
- Subjects
LIPOPROTEINS ,STAPHYLOCOCCAL diseases ,BACTERIAL genetics ,LABORATORY mice ,LIPIDS ,CELL membranes ,ANGIOTENSIN converting enzyme ,GLYCERIN ,HOST-virus relationships - Abstract
Abstract: Staphylococcus aureus expresses about 50 lipoproteins (Lpp), which are lipid-anchored in the membrane. The processing of the precursor to the mature Lpp is catalyzed by the phosphatidyl glycerol diacylglyceryl transferase (Lgt) and the lipoprotein-specific type II signal peptidase (LspA) leading to diacylated Lpp. Possibly another acyltransferase attaches a third fatty acid leading to triacylated Lpp. Lpp function as binding proteins for transport of nutrients across the microbial membrane and are involved in processing of other proteins, but most Lpp remain of predicted or unknown function. The di- or triacylated lipid structure is sensed by host pattern recognition receptor TLR2 and induces innate immune responses in professional and non-professional phagocytes. In the host, maturation of Lpp confers optimal metal ion – particularly iron – acquisition, it enhances staphylococcal invasion and phagocytosis, intracellular survival and persistence of infections. However, the advantages of Lpp maturation are counterbalanced by the capability to induce inflammation. In this review, we summarize the current knowledge about the role of Lpp in iron acquisition and TLR2 recognition in the host and describe the consequences of Lpp maturation for survival of S. aureus in the host. [Copyright &y& Elsevier]
- Published
- 2010
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32. Role of prolipoprotein diacylglyceryl transferase (Lgt) and lipoprotein-specific signal peptidase II (LspA) in localization and physiological function of lipoprotein MsmE in Streptococcus mutans.
- Author
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Arimoto, T. and Igarashi, T.
- Subjects
- *
LIPOPROTEINS , *PEPTIDASE , *GENETIC mutation , *STREPTOCOCCUS mutans , *WESTERN immunoblotting , *TRANSFERASES - Abstract
Introduction: To clarify the role that prolipoprotein diacylglyceryl transferase (Lgt) and lipoprotein-specific signal peptidase II (LspA) play in the physiological function of MsmE, we constructed lgt-deficient and lspA-deficient mutants of Streptococcus mutans 109c and examined the potential role of Lgt and LspA in membrane anchoring and growth in a melibiose medium of S. mutans. Methods: The lgt-, lspA-, and msmE-deficient mutants of S. mutans 109c were constructed by double-crossover recombination of their respective genes. Localization of MsmE was demonstrated by Western blot analysis with an MsmE antiserum. The growth of S. mutans cells was examined in a Trypton medium containing melibiose or glucose. Results: In the S. mutans lgt mutant, localization of the surface lipoprotein MsmE changed with the culture supernatant. The growth of the S. mutans lgt and lspA mutants was remarkably reduced in the melibiose medium; however, growth was recovered in the strains complemented with the lgt or the lspA gene. Therefore, lipid-modification by Lgt and subsequent signal peptide cleavage by LspA were crucial for membrane anchoring and the physiological function of MsmE in S. mutans. Conclusion: These results demonstrate that MsmE is required for melibiose metabolism in S. mutans and that modification by Lgt and LspA are important processes for the physiological function of MsmE. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
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33. Immunologic and genetic characterization of lipooligosaccharide variants in a Neisseria meningitidis serogroup C strain
- Author
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Zhu, Peixuan, Tsai, Chao-Ming, and Frasch, Carl E.
- Subjects
- *
NEISSERIA meningitidis , *OLIGOSACCHARIDES , *LIPIDS - Abstract
Neisseria meningitidis shows great variation in expression of structurally different lipooligosaccharides (LOS) on its cell surface. To better understand the LOS diversity that may occur within an individual strain, a group C wild-type strain, BB305-Tr4, and two stable isogenic LOS variants, Tr5 and Tr7, were selected for this study. SDS–PAGE analysis showed a size reduction of Tr5 and Tr7 LOS compared to that of Tr4. Immunoblotting showed that parental Tr4 LOS reacted with L1, L2 and L3,7 antibodies, variant Tr5 LOS with L1 and L6 antibodies, while Tr7 LOS was non-typeable. Genetic analysis showed that the gene organization at the lgt-1 locus in the three strains was lgtZ,C,A,B,H4 in Tr4, lgtZ,C,A,H4 in Tr5 and lgtZ,C,A,H9 in Tr7. The genetic differences in the three strains were consistent with their phenotypic changes. Sequence comparison revealed two independent recombination events. The first was the recombination of repeated DNA fragments in the flanking regions to delete lgtB in Tr5. The second was the recombination of a fragment of two genes, lgtB and lgtH4, to create an inactive lgtH9 allele with a mosaic structure in Tr7. These findings suggest that besides phase variation, homologous recombination can contribute to the genetic diversity of the lgt locus and to the generation of LOS variation in N. meningitidis. [Copyright &y& Elsevier]
- Published
- 2002
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34. Two groups of cocirculating, epidemic clostridiodes difficile strains microdiversify through different mechanisms
- Author
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Caterina Guzmán-Verri, Joakim Mark Andersen, Gabriel Ramírez-Vargas, Esteban Chaves-Olarte, Tatiana Murillo, Thomas Riedel, Jörg Overmann, and César Rodríguez
- Subjects
0301 basic medicine ,Microdiversification ,Gene Transfer, Horizontal ,Genotype ,Virulence ,Single-nucleotide polymorphism ,Biology ,572.86 Genomas ,accessory genome ,Genome ,Disease Outbreaks ,03 medical and health sciences ,Genetic variation ,Drug Resistance, Bacterial ,Genetics ,CORE GENOME ,Humans ,Gene ,Ecology, Evolution, Behavior and Systematics ,SNPS ,Clostridioides difficile ,CLOSTRIDIOIDES DIFFICILE ,Accessory genome ,Genetic Variation ,microdiversification ,INMUNOLOGÍA ,030104 developmental biology ,core genome ,MICROFABRICATION ,LGT ,Horizontal gene transfer ,Mutation ,Clostridium Infections ,Homologous recombination ,Genome, Bacterial ,Research Article ,SNPs - Abstract
Clostridiodes difficile strains from the NAPCR1/ST54 and NAP1/ST01 types have caused outbreaks despite of their notable differences in genome diversity. By comparing whole genome sequences of 32 NAPCR1/ST54 isolates and 17 NAP1/ST01 recovered from patients infected with C. difficile we assessed whether mutation, homologous recombination (r) or nonhomologous recombination (NHR) through lateral gene transfer (LGT) have differentially shaped the microdiversification of these strains. The average number of single nucleotide polymorphisms (SNPs) in coding sequences (NAPCR1/ST54 ¼ 24; NAP1/ST01 ¼ 19) and SNP densities (NAPCR1/ST54 ¼ 0.54/kb; NAP1/ST01 ¼ 0.46/kb) in the NAPCR1/ST54 and NAP1/ST01 isolates was comparable. However, the NAP1/ST01 isolates showed 3 higher average dN/dS rates (8.35) that the NAPCR1/ST54 isolates (2.62). Regarding r, whereas 31 of the NAPCR1/ST54 isolates showed 1 recombination block (3,301–8,226 bp), the NAP1/ ST01 isolates showed no bases in recombination. As to NHR, the pangenome of the NAPCR1/ST54 isolates was larger (4,802 gene clusters, 26% noncore genes) and more heterogeneous (644 6 33 gene content changes) than that of the NAP1/ST01 isolates (3,829 gene clusters, ca. 6% noncore genes, 129 6 37 gene content changes). Nearly 55% of the gene content changes seen among the NAPCR1/ST54 isolates (355 6 31) were traced back to MGEs with putative genes for antimicrobial resistance and virulence factors that were only detected in single isolates or isolate clusters. Congruently, the LGT/SNP rate calculated for the NAPCR1/ST54 isolates (26.8 6 2.8) was 4 higher than the one obtained for the NAP1/ST1 isolates (6.8 6 2.0). We conclude that NHR-LGT has had a greater role in the microdiversification of the NAPCR1/ST54 strains, opposite to the NAP1/ST01 strains, where mutation is known to play a more prominent role. Las cepas de Clostridiodes difficiles de los tipos NAPCR1/ST54 y NAP1/ST01 han causado brotes a pesar de sus notables diferencias en la diversidad del genoma. Comparando las secuencias del genoma completo de 32 aislamientos de NAPCR1/ST54 y 17 NAP1/ST01 recuperados de En el caso de los pacientes infectados con C. difficile, evaluamos si la mutación, la recombinación homóloga (r) o la recombinación no homóloga (NHR) mediante transferencia lateral de genes (LGT) han configurado de forma diferente la microdiversificación de estas cepas. El número medio de polimorfismos de un solo nucleótido (SNP) en las secuencias de codificación (NAPCR1/ST54 ¼ 24; NAP1/ST01 ¼ 19) y las densidades de los SNP (NAPCR1/ST54 ¼ 0,54/kb; NAP1/ST01 ¼ 0,46/kb) en los aislamientos de NAPCR1/ST54 y NAP1/ST01 fue comparable. Sin embargo, los aislamientos NAP1/ST01 mostraron 3 tasas promedio de dN/dS más altas (8,35) que los aislamientos NAPCR1/ST54 (2,62). En cuanto a r, mientras que 31 de los aislados NAPCR1/ST54 mostraron 1 bloque de recombinación (3.301-8.226 pb), los aislados NAP1/ ST01 no mostraron bases en la recombinación. En cuanto a NHR, el pangenoma de los aislamientos NAPCR1/ST54 fue mayor (4.802 (26% de genes no centrales) y más heterogéneo (644 6 33 cambios en el contenido de los genes) que el de los aislados del NAP1/ST01 (3.829 grupos de genes, alrededor del 6% de genes no centrales, 129 6 37 cambios en el contenido de los genes). Casi el 55% de los cambios en el contenido genético observados en los aislados del NAPCR1/ST54 (355 6 31) se remontaban a los GEM con genes putativos de resistencia a los antimicrobianos y factores de virulencia que sólo se detectaron en aislados individuales o en grupos de aislados. Congruentemente, la tasa de LGT/SNP calculado para los aislamientos NAPCR1/ST54 (26,8 6 2,8) fue 4 más alto que el obtenido para los aislamientos NAP1/ST1 (6.8 6 2.0). Concluimos que el NHR-LGT ha tenido un mayor papel en la microdiversificación de las cepas NAPCR1/ST54, frente a las cepas NAP1/ST01, donde se sabe que la mutación juega un papel más prominente. Escuela de Medicina Veterinaria
- Published
- 2018
35. Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication
- Author
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David Bryant, Mayo Roettger, Einat Hazkani-Covo, William Martin, Joana C. Xavier, Nils Kapust, Shijulal Nelson-Sathi, Barbara I. K. Schoenfeld, and Peter J. Lockhart
- Subjects
0106 biological sciences ,0301 basic medicine ,Gene Transfer, Horizontal ,Protein family ,archaea ,Genome, Plastid ,Genomics ,Validation Studies as Topic ,Biology ,010603 evolutionary biology ,01 natural sciences ,Genome ,Evolution, Molecular ,Chloroplast Proteins ,evolutionary models ,03 medical and health sciences ,Phylogenetics ,Genetics ,Gene family ,Plastids ,Plastid ,Symbiosis ,Gene ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Models, Genetic ,plastid genomes ,Computational Biology ,Eukaryota ,030104 developmental biology ,LGT ,Evolutionary biology ,Horizontal gene transfer ,Software ,Research Article - Abstract
In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation, and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent genome analyses studying gene distributions have uncovered evidence for sporadic, discontinuous events of gene transfer from bacteria to archaea during evolution. Other studies have used traditional models designed to investigate gene family size evolution (Count) to support claims that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here, we show that the methodology used in analyses favoring continuous gene transfers to archaea was misapplied in other studies and does not recover known events of single simultaneous origin for many genes followed by differential loss in real data: plastid genomes. Using the same software and the same settings, we reanalyzed presence/absence pattern data for proteins encoded in plastid genomes and for eukaryotic protein families acquired from plastids. Contrary to expectations under a plastid origin model, we found that the methodology employed inferred that gene acquisitions occurred uniformly across the plant tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, the methodology that recovered gradual and continuous lateral gene transfer among lineages for archaea obtains the same result for plastids, even though it is known that massive gains followed by gradual differential loss is the true evolutionary process that generated plastid gene distribution data. Our findings caution against the use of models designed to study gene family size evolution for investigating gene transfer processes, especially when transfers involving more than one gene per event are possible.
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- 2018
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36. Modularized Evolution in Archaeal Methanogens Phylogenetic Forest
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Mabel Ting Wong, Jun Li, Chi-Fat Wong, Frederick C. Leung, and He Huang
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animal structures ,Gene Transfer, Horizontal ,Lineage (evolution) ,Euryarchaeota ,Genome ,Genes, Archaeal ,co-evolution network ,Evolution, Molecular ,Genetics ,Gene family ,Gene ,network analysis ,Ecology, Evolution, Behavior and Systematics ,Coevolution ,Phylogeny ,biology ,Phylogenetic tree ,HGT ,modularized evolution ,phylogenetic forest ,biology.organism_classification ,Methanogen ,Evolutionary biology ,LGT ,Methane ,Archaea ,Research Article - Abstract
Methanogens are methane-producing archaea that plays a key role in the global carbon cycle. To date, the evolutionary history of methanogens and closely related nonmethanogen species remains unresolved among studies conducted upon different genetic markers, attributing to horizontal gene transfers (HGTs). With an effort to decipher both congruent and conflicting evolutionary events, reconstruction of coevolved gene clusters and hierarchical structure in the archaeal methanogen phylogenetic forest, comprehensive evolution, and network analyses were performed upon 3,694 gene families from 41 methanogens and 33 closely related archaea. Our results show that 1) greater than 50% of genes are in topological dissonance with others; 2) the prevalent interorder HGTs, even for core genes, in methanogen genomes led to their scrambled phylogenetic relationships; 3) most methanogenesis-related genes have experienced at least one HGT; 4) greater than 20% of the genes in methanogen genomes were transferred horizontally from other archaea, with genes involved in cell-wall synthesis and defense system having been transferred most frequently; 5) the coevolution network contains seven statistically robust modules, wherein the central module has the highest average node strength and comprises a majority of the core genes; 6) different coevolutionary module genes boomed in different time and evolutionary lineage, constructing diversified pan-genome structures; 7) the modularized evolution is also closely related to the vertical evolution signals and the HGT rate of the genes. Overall, this study presented a modularized phylogenetic forest that describes a combination of complicated vertical and nonvertical evolutionary processes for methanogenic archaeal species.
- Published
- 2014
37. Phylogenomic Study Indicates Widespread Lateral Gene Transfer in Entamoeba and Suggests a Past Intimate Relationship with Parabasalids
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Laura A. Katz and Jessica R. Grant
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Gene Transfer, Horizontal ,microbial eukaryotes ,Parabasalidea ,parasites ,Genome ,Amoebozoa ,Entamoeba ,Evolution, Molecular ,Trichomonas vaginalis ,Genetics ,Gene ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Bacteria ,biology ,Phylogenetic tree ,HGT ,biology.organism_classification ,Archaea ,LGT ,Horizontal gene transfer ,horizontal gene transfer ,Excavata ,Eukaryote ,Research Article - Abstract
Lateral gene transfer (LGT) has impacted the evolutionary history of eukaryotes, though to a lesser extent than in bacteria and archaea. Detecting LGT and distinguishing it from single gene tree artifacts is difficult, particularly when considering very ancient events (i.e., over hundreds of millions of years). Here, we use two independent lines of evidence--a taxon-rich phylogenetic approach and an assessment of the patterns of gene presence/absence--to evaluate the extent of LGT in the parasitic amoebozoan genus Entamoeba. Previous work has suggested that a number of genes in the genome of Entamoeba spp. were acquired by LGT. Our approach, using an automated phylogenomic pipeline to build taxon-rich gene trees, suggests that LGT is more extensive than previously thought. Our analyses reveal that genes have frequently entered the Entamoeba genome via nonvertical events, including at least 116 genes acquired directly from bacteria or archaea, plus an additional 22 genes in which Entamoeba plus one other eukaryote are nested among bacteria and/or archaea. These genes may make good candidates for novel therapeutics, as drugs targeting these genes are less likely to impact the human host. Although we recognize the challenges of inferring intradomain transfers given systematic errors in gene trees, we find 109 genes supporting LGT from a eukaryote to Entamoeba spp., and 178 genes unique to Entamoeba spp. and one other eukaryotic taxon (i.e., presence/absence data). Inspection of these intradomain LGTs provide evidence of a common sister relationship between genes of Entamoeba (Amoebozoa) and parabasalids (Excavata). We speculate that this indicates a past close relationship (e.g., symbiosis) between ancestors of these extant lineages.
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- 2014
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38. Inhibition of Escherichia coli Lipoprotein Diacylglyceryl Transferase Is Insensitive to Resistance Caused by Deletion of Braun's Lipoprotein.
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Diao J, Komura R, Sano T, Pantua H, Storek KM, Inaba H, Ogawa H, Noland CL, Peng Y, Gloor SL, Yan D, Kang J, Katakam AK, Volny M, Liu P, Nickerson NN, Sandoval W, Austin CD, Murray J, Rutherford ST, Reichelt M, Xu Y, Xu M, Yanagida H, Nishikawa J, Reid PC, Cunningham CN, and Kapadia SB
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- Animals, Anti-Bacterial Agents pharmacology, Aspartic Acid Endopeptidases, Bacterial Proteins, Escherichia coli genetics, Female, Gene Deletion, Gene Expression Regulation, Bacterial drug effects, Mice, Peptidoglycan metabolism, Transferases chemistry, Transferases genetics, Uropathogenic Escherichia coli genetics, Uropathogenic Escherichia coli metabolism, Escherichia coli metabolism, Lipoproteins metabolism, Transferases metabolism
- Abstract
Lipoprotein diacylglyceryl transferase (Lgt) catalyzes the first step in the biogenesis of Gram-negative bacterial lipoproteins which play crucial roles in bacterial growth and pathogenesis. We demonstrate that Lgt depletion in a clinical uropathogenic Escherichia coli strain leads to permeabilization of the outer membrane and increased sensitivity to serum killing and antibiotics. Importantly, we identify G2824 as the first-described Lgt inhibitor that potently inhibits Lgt biochemical activity in vitro and is bactericidal against wild-type Acinetobacter baumannii and E. coli strains. While deletion of a gene encoding a major outer membrane lipoprotein, lpp , leads to rescue of bacterial growth after genetic depletion or pharmacologic inhibition of the downstream type II signal peptidase, LspA, no such rescue of growth is detected after Lgt depletion or treatment with G2824. Inhibition of Lgt does not lead to significant accumulation of peptidoglycan-linked Lpp in the inner membrane. Our data validate Lgt as a novel antibacterial target and suggest that, unlike downstream steps in lipoprotein biosynthesis and transport, inhibition of Lgt may not be sensitive to one of the most common resistance mechanisms that invalidate inhibitors of bacterial lipoprotein biosynthesis and transport. IMPORTANCE As the emerging threat of multidrug-resistant (MDR) bacteria continues to increase, no new classes of antibiotics have been discovered in the last 50 years. While previous attempts to inhibit the lipoprotein biosynthetic (LspA) or transport (LolCDE) pathways have been made, most efforts have been hindered by the emergence of a common mechanism leading to resistance, namely, the deletion of the gene encoding a major Gram-negative outer membrane lipoprotein lpp . Our unexpected finding that inhibition of Lgt is not susceptible to lpp deletion-mediated resistance uncovers the complexity of bacterial lipoprotein biogenesis and the corresponding enzymes involved in this essential outer membrane biogenesis pathway and potentially points to new antibacterial targets in this pathway.
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- 2021
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39. Genetic diversity of rhizobia nodulating common bean (Phaseolus vulgaris L.) in the Central Black Sea Region of Turkey
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İslam Gündüz, Ibrahim Ozkoc, Cem Tolga Gürkanli, and Ondokuz Mayıs Üniversitesi
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Diversity ,Genetic diversity ,biology ,Phylogenetic tree ,Beans ,food and beverages ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,medicine.disease_cause ,Applied Microbiology and Biotechnology ,Rhizobium leguminosarum ,Housekeeping gene ,Rhizobia ,LGT ,Phylogenetics ,Botany ,medicine ,Rhizobium ,Phaseolus ,Phylogeny - Abstract
Gunduz, Islam/0000-0002-6436-5397 WOS: 000324058900019 We have analyzed 30 rhizobial isolates obtained from common bean (Phaseolus vulgaris L.) root nodules grown in the Middle Blacksea Region of Turkey, using ARDRA and nucleotide sequence data. ARDRA analysis with enzymes CfoI, HinfI, NdeII, MspI and PstI revealed three patterns. Based on sequence data from 16S rDNA, the patterns were identified as, Rhizobium leguminosarum bv. phaseoli (n = 16), R. etli bv. phaseoli (n = 8) and R. phaseoli (n = 6). On the other hand, nucleotide sequence phylogenies of housekeeping genes (recA, atpD and glnII) selected to confirm the 16S rDNA phylogeny revealed different evolutionary relationships. These results suggested the possibility of lateral transfers of these genes amongst different rhizobial species (including R. leguminosarum, R. etli and R. phaseoli) sharing the same ecological niche (nodulating P. vulgaris) which also indicates that there may be no true genetic barier among these species. Phylogenetic analysis based on DNA sequence data from the nodA and nifH genes showed that all rhizobial species obtained in this study were carrying nodA and nifH haplotypes which were the same or similar to those of CFN42 (R. etli type strain), suggesting a further support for the lateral transfer of CFN42 Sym plasmid, p42, amongst Turkish common bean nodulating rhizobial isolates. Ondokuz Mayis University Research FoundationOndokuz Mayis University We are gratefully acknowledge J.P.W. Young from University of York for critical reading of the manuscript. We would also like to thank Dr. Erkut PEKSEN from Ondokuz Mayis University for his valuable advice. This study was supported by a grant from the Ondokuz Mayis University Research Foundation.
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- 2012
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40. La libertad de información y revelación de datos fiscales
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Aberasturi Gorriño, Unai, F. CC. ECONOMICAS Y EMPRESARIALES, EKONOMIA ETA ENPRESA ZIENTZIEN F., Grado en Fiscalidad y Administración Pública, Zerga Sistemako eta Administrazio Publikoko Gradua, Hernando Irisarri, Maider, Aberasturi Gorriño, Unai, F. CC. ECONOMICAS Y EMPRESARIALES, EKONOMIA ETA ENPRESA ZIENTZIEN F., Grado en Fiscalidad y Administración Pública, Zerga Sistemako eta Administrazio Publikoko Gradua, and Hernando Irisarri, Maider
- Abstract
[ES]Con el desarrollo de las nuevas tecnologías, se han facilitado las relaciones, acortado el tiempo de espera y agilizado los trámites con la Administración Pública. Estos adelantos, sin embargo, han propiciado que sea necesario proporcionar información de carácter personal de los ciudadanos, que en la mayoría de los casos es sensible. Es por esto que en los últimos años se han ido modificando e introduciendo nuevas leyes que permiten proteger estos datos de carácter personal. Cuando un contribuyente realiza sus obligaciones tributarias suministra datos de carácter personal a Hacienda, datos que están protegidos por la Ley Orgánica de Protección de Datos. El Sistema Tributario deber ser eficaz y transparente. Sin embargo, cabe preguntarse dónde se sitúa el límite a esa transparencia. Con el fin de que la transparencia sea máxima y de que la ciudadanía se conciencie de la importancia de cumplir con sus obligaciones tributarias el legislador se ha planteado la posibilidad de publicar una lista de deudores y las sentencias firmes condenatorias de grandes defraudadores. Esta publicación de las listas aparentemente vulneraría los derechos de los ciudadanos en lo referente a la protección de datos con opiniones encontradas. Tras informes de diferentes organismos se ha llegado al Proyecto de Ley de Modificación parcial de la Ley 58/2003, General Tributaria (Boletín Oficial de las Cortes Generales del 30 de abril de 2015), que permitiría publicar las listas con ciertos límites: publicación únicamente del nombre de la persona física o jurídica y DNI o NIF. Además, para permitir la publicación de las sentencias firmes de los defraudadores, recientemente se ha aprobado el Proyecto de reforma de la Ley Orgánica del Poder Judicial., [EN] With the development of the new technologies, the relationship with Public Administration has become easier and procedures are faster. However, these advances mean that the citizen has to provide personal information, which in most cases is sensitive information. That is why, in recent years, laws have been amended and new laws introduced to protect this personal data. When a contributor fulfills their tax obligations, they submit personal information to the tax office, information that is protected by the Organic Law of Data Protection (Ley Orgánica de Protección de Datos). The Tax System of the country has to be effective and transparent. However, the question is where to set the limits of transparency. With the objective of achieving maximum transparence and that the citizen is aware of the importance of fulfilling their tax obligations, the Government has raised the possibility of publishing a list with the debtors to the Tax Office and big fraudsters who have been found guilty with a final judgments. There is an opinion that the publication of this list may infringe the right of the citizen in terms of data protection. Following the reports of different bodies, the bill partially amending Law 58/2003, General Taxation (Official Gazette of the Parliament on April 30, 2015) has been passed, to permit the publication of the list with certain limitations: the sole publication of the name of the natural or legal person and official identity card number (DNI) or tax identification number (NIF). Moreover, to allow the publication of the final judgment convictions of big fraudsters, the bill to amend the Organic Law of Judicial Power (Ley Orgánica del Poder Judicial) has been passed., [EU]Teknologia berrien garapenarekin, Administrazio Publikoarekiko harremanak erraztu, itxaroteko denbora laburtu eta prozedurak arindu egin dira. Aurrerapen handia izan arren, beharrezkoa da karakter pertsonala duen informazioa eskaintzea, askotan pertsonen ohorearekin eta pribatasunarekin lotuta. Honen ondorioz, azken urteotan lege berriak azaleratu eta daudenak aldatuz joan dira datu pertsonalak babesteko asmoarekin. Herritarrek, bere zerga eginbeharrak egitean, informazio pertsonala ematen dio administrazioaren Ogasun Sailari, datu hauek Ley Orgánica de Protección de Datos-rekin (Datuak Babesteko Lege Organikoa) babestuta daude. Zerga Sistema eraginkorra eta argia izan behar du. Hala ere, argitasunaren muga non dagoen jakin behar da. Argitasun handiena lortzeko eta herritarrek haien tributazio betebeharraren garrantzia ikusteko asmoarekin, Gobernuak zordunen zerrendak eta iruzurgileen sententzia tinkoak argitaratzea erabaki du. Argitarapen honek hiritarren datu babesaren eskubidea urratu dezake. Hainbat erakunderen txostenen ondoren, Proyecto de Ley de Modificación parcial de la Ley 58/2003, General Tributaria (Zerga 58/2003 Legearan Modifikazio partzialaren proiektua) onartu egin da, zerrendak argitaratzea baimenduko lukeela: pertsona fisiko edo juridikoen izena eta haien NAN ed NIFa. Bestalde, iruzurgileen sententzia tinkoak argitaratzeko, duela gutxi Proyecto de reforma de la Ley Orgánica del Poder Judicial (Botere Judizialaren Lege Organikoa) onartu egin dute.
- Published
- 2016
41. Bacterial Lipoprotein Biosynthetic Pathway as a Potential Target for Structure-based Design of Antibacterial Agents.
- Author
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Xia J, Feng B, Wen G, Xue W, Ma G, Zhang H, and Wu S
- Subjects
- Bacteria, Bacterial Proteins, Biosynthetic Pathways, Drug Design, Lipoproteins, Anti-Bacterial Agents therapeutic use
- Abstract
Background: Antibiotic resistance is currently a serious problem for global public health. To this end, discovery of new antibacterial drugs that interact with novel targets is important. The biosynthesis of lipoproteins is vital to bacterial survival and its inhibitors have shown efficacy against a range of bacteria, thus bacterial lipoprotein biosynthetic pathway is a potential target., Methods: At first, the literature that covered the basic concept of bacterial lipoprotein biosynthetic pathway as well as biochemical characterization of three key enzymes was reviewed. Then, the recently resolved crystal structures of the three enzymes were retrieved from Protein Data Bank (PDB) and the essential residues in the active sites were analyzed. Lastly, all the available specific inhibitors targeting this pathway and their Structure-activity Relationship (SAR) were discussed., Results: We briefly introduce the bacterial lipoprotein biosynthetic pathway and describe the structures and functions of three key enzymes in detail. In addition, we present much knowledge on ligand recognition that may facilitate structure-based drug design. Moreover, we focus on the SAR of LspA inhibitors and discuss their potency and drug-likeness., Conclusion: This review presents a clear background of lipoprotein biosynthetic pathway and provides practical clues for structure-based drug design. In particular, the most up-to-date knowledge on the SAR of lead compounds targeting this pathway would be a good reference for discovery of a novel class of antibacterial agents., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)
- Published
- 2020
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42. Molecular analysis of an integrative conjugative element, ICEH, present in the chromosome of different strains of Mycoplasma hyopneumoniae
- Author
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Leonardo Alves-Junior, Marcos Oliveira de Carvalho, Paulo Marcos Pinto, Irene Silveira Schrank, and Marcelo Brocchi
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Transposable element ,Genetics ,lcsh:QH426-470 ,Mycoplasma hyopneumoniae ,Locus (genetics) ,Mycoplasma ,Biology ,biology.organism_classification ,medicine.disease_cause ,Genética ,constins ,lcsh:Genetics ,Plasmid ,LGT ,Extrachromosomal DNA ,Horizontal gene transfer ,medicine ,Molecular Biology ,Gene ,Genoma - Abstract
Diversification of bacterial species and pathotypes is largely caused by lateral gene transfer (LGT) of diverse mobile DNA elements such as plasmids, phages, transposons and genomic islands. Thus, acquisition of new phenotypes by LGT is very important for bacterial evolution and relationship with hosts. This paper reports a 23 kb region containing fourteen CDSs with similarity to the previous described Integrative Conjugal Element of Mycoplasma fermentans (ICEF). This element, named ICEH, is present as one copy at distinct integration sites in the chromosome of 7448 and 232 pathogenic strains and is absent in the type strain J (non-pathogenic). Notable differences in the nucleotide composition of the insertion sites were detected, and could be correlated to a lack of specificity of the ICEH integrase. Although present in strains of the same organism, the ICEH elements are more divergent than the typical similarity between other chromosomal locus of Mycoplasma hyopneunomiae, suggesting an accelerated evolution of these constins or an ongoing process of degeneration, while maintaining conservation of the tra genes. An extrachromosomal form of this element had been detected in the 7448 strain, suggesting a possible involvement in its mobilization and transference of CDSs to new hosts.
- Published
- 2007
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43. The apeNEXT project
- Author
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Bodin, F., Boucaud, Ph., Cabibbo, N., Di Carlo, F., De Pietri, R., Di Renzo, F., Errico, W., Kaldass, H., Lonardo, A., De Luca, S., Micheli, J., Morenas, Vincent, Pene, O., Pleiter, D., Paschedag, N., Rapuano, F., Rossetti, D., Sartori, L., Schifano, F., Simma, H., Tripiccione, R., Vicini, P., Laboratoire de Physique Corpusculaire - Clermont-Ferrand (LPC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Bodin, F, Boucaud, P, Cabibbo, N, Di Carlo, F, De Pietri, R, Di Renzo, F, Errico, W, Kaldass, H, Lonardo, A, de Luca, S, Micheli, J, Morenas, V, Pene, O, Pleiter, D, Paschedag, N, Rapuano, F, Rossetti, D, Sartori, L, Schifano, F, Simma, H, Tripiccione, R, and Vicini, P
- Subjects
Lattice QCD, Special Purpose Computers ,Nuclear and High Energy Physics ,[PHYS.HLAT]Physics [physics]/High Energy Physics - Lattice [hep-lat] ,010308 nuclear & particles physics ,High Energy Physics::Lattice ,LGT ,dedicated computing ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,NO ,FIS/02 - FISICA TEORICA, MODELLI E METODI MATEMATICI ,0103 physical sciences ,010306 general physics - Abstract
In this talk I report on the status of the apeNEXT project. apeNEXT is the last of a family of parallel computers designed, in a research environment, to provide multi-teraflops computing power to scientists involved in heavy numerical simulations. The architecture and the custom chip are optimized for Lattice QCD (LQCD) calculations but the favourable price performance ratio and the good efficiency for other kind of calculations make it a quite interesting tool for a large class of scientific problems.
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- 2005
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44. GenPhyloData: realistic simulation of gene family evolution
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Bengt Sennblad, Jens Lagergren, Joel Sjöstrand, and Lars Arvestad
- Subjects
Synthetic data ,Gene duplication ,Gene loss ,Computational biology ,Biology ,Models, Biological ,Biochemistry ,Evolution, Molecular ,Species Specificity ,Biological Clocks ,Structural Biology ,Humans ,Gene family ,Computer Simulation ,Host-parasite co-evolution ,Molecular clock ,Molecular Biology ,Phylogeny ,Genetics ,Biological data ,Phylogenetic tree ,Applied Mathematics ,Gene Transfer Techniques ,Phylogenetic network ,Computer Science Applications ,Phylogenetics ,Tree (data structure) ,Biogeography ,LGT ,Multigene Family ,Horizontal gene transfer ,Software - Abstract
Background PrIME-GenPhyloData is a suite of tools for creating realistic simulated phylogenetic trees, in particular for families of homologous genes. It supports generation of trees based on a birth-death process and—perhaps more interestingly—also supports generation of gene family trees guided by a known (synthetic or biological) species tree while accounting for events such as gene duplication, gene loss, and lateral gene transfer (LGT). The suite also supports a wide range of branch rate models enabling relaxation of the molecular clock. Result Simulated data created with PrIME-GenPhyloData can be used for benchmarking phylogenetic approaches, or for characterizing models or model parameters with respect to biological data. Conclusion The concept of tree-in-tree evolution can also be used to model, for instance, biogeography or host-parasite co-evolution.
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- 2013
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45. Difficulties and disagreements in consolidation of Lithuanian American movements from 15 October 1940 to 15 May 1941 : from Council to aid lithuania to Lithuanian American council
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Skirius, Juozas
- Subjects
Jungtinės Amerikos Valstijos (United States of America ,JAV ,USA) ,Lithuanian American Council ,Povilas Žadeikis ,ALT ,i gelbėti taryba ,Amerikos lietuvių taryba ,USA Lithuanian organizations ,Lietuva (Lithuania) ,LGT ,Lithuanian Americans ,Lithuanian emigration ,Tremtis. Tremtiniai / Deportees. Exile ,Lietuviai / Lithuanians ,Emigrantai. Išeivija. Egzodas / Emigrants. Diaspora ,JAV lietuvių organizacijos ,Council to Aid Lithuania ,Antanas Smetona - Abstract
Straipsnyje nagrinėjamas bandymas suaktyvinti LGT veiklą po jos įkūrimo. Atskleidžiama Lietuvos atstovų JAV, ypač pasiuntinio Povilo Žadeikio, didžiulės pastangos, ieškant būdų ir veiklos formų bendrai išeivijos organizacijai išjudinti. Parodomos pagrindinių patriotinių JAV lietuvių organizacijų (katalikų, tautininkų ir sandarininkų bei socialistų) padėtis tuo metu ir požiūris į LGT. Paaiškinama, kodėl reikėjo LGT reformuoti į ALT ir kaip į tai reagavo skirtingos srovės. Article addresses the attempt to stimulate the activities of the Council to Aid Lithuania after its establishment. It reveals the enormous efforts made by Lithuanian representatives in the US, in particular envoy Povilas Žadeikis, in searching for ways and forms of activity for stirring up the common body of Lithuanians in exile. The article shows the situation of the main patriotic Lithuanian American organizations (Catholics, Nationalists-Sandara members and Socialists) at that time and their approach towards the Council to Aid Lithuania. It explains why the reform of the Council to Aid Lithuania into the Lithuanian American Council was required and how different movements reacted towards it.
- Published
- 2013
46. Evaluating the Evolutionary Origins of Unexpected Character Distributions within the Bacterial Planctomycetes-Verrucomicrobia-Chlamydiae Superphylum
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Aidan Budd and Damien P. Devos
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Microbiology (medical) ,phylogenetic estimation errors ,Protein family ,Lineage (evolution) ,lcsh:QR1-502 ,Biology ,planctomycetes ,Chlamydiae ,Microbiology ,lcsh:Microbiology ,Verrucomicrobia ,Tubulin ,Gene family ,Gene ,Original Research ,Genetics ,Planctomycetes ,gene duplication ,HGT ,gene loss ,biology.organism_classification ,lateral gene transfer ,Evolutionary biology ,LGT ,Horizontal gene transfer ,horizontal gene transfer ,PVC superphylum ,Superphylum - Abstract
Recently, several characters that are absent from most bacteria, but which are found in many eukaryotes or archaea, have been identified within the bacterial Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum. Hypotheses of the evolutionary history of such characters are commonly based on the inference of phylogenies of gene or protein families associated with the traits, estimated from multiple sequence alignments (MSAs). So far, studies of this kind have focused on the distribution of (i) two genes involved in the synthesis of sterol, (ii) tubulin genes, and (iii) c1 transfer genes. In most cases, these analyses have concluded that horizontal gene transfer (HGT) is likely to have played a role in shaping the taxonomic distribution of these gene families. In this article, we describe several issues with the inference of HGT from such analyses, in particular concerning the considerable uncertainty associated with our estimation of both gene family phylogenies (especially those containing ancient lineage divergences) and the Tree of Life (ToL), and the need for wider use and further development of explicit probabilistic models to compare hypotheses of vertical and horizontal genetic transmission. We suggest that data which is often taken as evidence for the occurrence of ancient HGT events may not be as convincing as is commonly described, and consideration of alternative theories is recommended. While focusing on analyses including PVCs, this discussion is also relevant for inferences of HGT involving other groups of organisms.
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- 2012
47. Contribution à l'étude des matériaux piézoélectriques de synthèse LGS et LGT pour des applications micro-résonateurs basse fréquence
- Author
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Douchet, Gabrielle, Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Université de Franche-Comté, and Fabrice STHAL(fabrice.sthal@ens2m.fr)
- Subjects
DRIE ,Langasite ,temperature-compensated cuts ,usinage chimique ,coupe X ,coupes compensées en température ,langatate ,LGS ,micro-resonator ,LGT ,chemical etching ,X-cut ,[SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics ,micro-résonateur - Abstract
The work presented in this thesis concerns the study of synthetic piezoelectric materials (langasite family crystals) and the manufacture of low-frequency micro-resonators with these materials. The first part of the study focuses on the finding of temperature-compensated cuts for X-cut plates of langasite (LGS) and langatate (LGT), for the length-extension along the Y axis and flexure around the X axis modes. The theoretical values of the orientation angle of the temperature-compensated cuts are obtained through an analytical model and finite element simulations. Bar-type devices and tuning forks are then made and used to perform electrical measurements to confirm the existence of these compensated cuts. The second part of the study is about the manufacture of langasite micro-resonators. Several processing methods are considered before the choice of chemical etching in an HCl-based solution. The manufacturing process is detailed and vibration measurements are carried out on the devices.; Les travaux présentés dans ce mémoire portent sur l'étude de matériaux piézoélectriques de synthèse de la famille des langasite et sur la réalisation de micro-résonateurs basse fréquence dans ces matériaux. La première partie de l'étude se concentre sur la recherche des orientations des coupes compensées en température pour les coupes X de la langasite (LGS) et de la langatate (LGT), pour les modes d'extension selon Y et de flexion autour de X. Un modèle analytique simple et des simulations par éléments finis permettent de déterminer les valeurs théoriques de ces orientations. Des dispositifs de types barreau et diapason sont ensuite réalisés afin d'effectuer des mesures électriques pou confirmer l'existence de ces coupes compensées. La seconde partie de l'étude concerne la fabrication de micro-résonateurs en langasite. Plusieurs méthodes d'usinage (mécanique, DRIE,...) sont envisagées avant que notre choix ne se porte sur l'usinage chimique (solution HCl). Le procédé de fabrication est détaillé puis des mesures de vibration sont menées pour les dispositifs obtenus.
- Published
- 2010
48. Measurements of ultra-stable langatate crystal oscillators
- Author
-
Philippe Abbe, R. Bourquin, J. Imbaud, S. Galliou, J.P. Romand, Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), and IEEE
- Subjects
[SPI.OTHER]Engineering Sciences [physics]/Other ,Materials science ,business.industry ,Langatate resonator ,Stability result ,01 natural sciences ,Noise (electronics) ,Low noise ,[SPI.TRON]Engineering Sciences [physics]/Electronics ,Crystal ,Ultra stable oscillator ,LGT ,Q factor ,0103 physical sciences ,Electronic engineering ,Optoelectronics ,business ,010301 acoustics ,Realization (systems) ,Crystal oscillator ,Quartz - Abstract
International audience; The use of the langatate (LGT, La3Ga5.5Ta0.5O14) crystal for the realization of ultra-stable oscillators is very recent. This material proved that it is capable of giving stability results as good as those achieved by quartz crystal. To the knowledge of the authors, until now there was no substitution material for the quartz crystal, for low noise applications. Indeed, investigations had proved that LGT is a good alternative. This paper describes quickly all the essential manufacturing steps related to the development of an oscillator using this pure synthetic crystal. It shows that the performances looked for, in terms of noise, are those obtained with the quartz crystal. Its content is as follows. It begins with the description of the resonator manufacturing, the resonator being the heart of the oscillator. Then, the development of the related electronics is discussed and noise measurements are given as a conclusion. Very first ageing measurements of a set of LGT crystal oscillators are also emphasized. Noise results are given in terms of standard Allan deviation as well as in power spectral density of phase fluctuations. These results are analyzed and finally compared to those of quartz crystal oscillators.
- Published
- 2009
49. Evaluation des potentialités des matériaux du type langasite pour la réalisation d'oscillateurs ultra-stables. Etude et réalisation préliminaires d'un oscillateur cryogénique
- Author
-
Imbaud, Joël, Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Université de Franche-Comté, and Serge Galliou
- Subjects
oscillateur cryogénique ,cryogenic oscillator ,ultra-stable oscillator ,langatate ,résonateur ,LGS ,[SPI.MECA]Engineering Sciences [physics]/Mechanics [physics.med-ph] ,quartz ,langasite ,LGT ,resonator ,[SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics ,[SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing ,Oscillateur ultra-stable - Abstract
The present work is focused on improvement of ultra stable sources of frequencies over short averaging times (typically less than one minute). To do this, two-ways of investigations were selected: - The first one deals with material capabilities of the langasite (LGS) family. A quality factor (Q) classification of LGS and langatate (LGT) materials according to their origin was confirmed. The first prototypes of bulk acoustic waves (BAW) resonators have been made in a high-Q LGT crystal. In this connection, a specific manufacturing process was developed. Oscillator electronics and thermal packaging adapted to the characteristics of these resonators have been designed. Finally, these first prototypes of oscillators have been characterized in terms of time-domain stability and in terms of aging.- The second topic deals with the set-up of an experimental system. This system allows cooling of oscillators equipped with bulk acoustic waves (BAW) resonators at temperatures below that of liquid helium (4.2 K). For that, quartz resonators of SC and LD cuts, and LGT crystal of Y cuts have been characterized at low temperatures. Systematic measurements have revealed outstanding Q-factor coefficients for specific modes of vibration. Furthermore, different models of transistors have been tested and one of them has been modeled at cryogenic temperature. Then, two prototypes of oscillators equipped with SC cut resonators have been developed and tested at low temperatures. Results of this work give the first characterization of stability in the time-domain of such cryogenic oscillators.; Les travaux présentés dans ce mémoire portent sur l'amélioration des sources ultra-stables de fréquences dans le domaine des temps courts (typiquement inferieurs à une minute). Deux voies d'investigations ont été explorées : - La première concerne l'évaluation des potentialités des matériaux de la famille de la langasite (LGS). Une classification des coefficients de qualité (Q) des matériaux LGS et langatate (LGT) en fonction de leurs provenances a été mise en évidence. Les premiers prototypes de résonateurs à ondes de volume ont été réalisés dans un cristal de LGT à fort Q. A cette occasion un procédé de fabrication spécifique a été mis au point. Une électronique d'oscillateur et un packaging thermique adaptés aux caractéristiques de ces résonateurs ont été développés. Enfin, ces premiers prototypes d'oscillateurs ont été caractérisés en terme de stabilité temporelle et de vieillissement.- La seconde voie exploratoire concerne la mise en place d'un ensemble expérimental permettant la réfrigération d'oscillateurs à résonateurs à ondes de volume à des températures inférieures à celles de l'hélium liquide (4,2K). Pour cela, des résonateurs en quartz de coupe SC et LD, et en LGT de coupe Y, ont été caractérisés à basses températures. Une campagne de mesures systématiques a révélé des coefficients de qualité exceptionnels pour certains modes de vibration. Par ailleurs, différents modèles de transistors ont été testés et l'une des références testées a été modélisée simplement, à température cryogénique. Deux premiers prototypes d'oscillateurs à résonateur à quartz de coupe SC ont été développés puis testés à basses températures. Il en résulte les toutes premières caractérisations en terme de stabilité temporelle.
- Published
- 2008
50. MEASUREMENT OF FIRST LANGATATE OSCILLATORS IMPROVED BY AN ORIGINAL SIMULATING METHOD
- Author
-
Imbaud, J., Serge Galliou, Abbe, P., Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), and DGA contract number 04.34.033
- Subjects
Pspice optimizer ,LGT ,Resonator ,Ultra-stable ,High Q-factor ,Oscillator ,Langatate ,Low noise ,ComputingMilieux_MISCELLANEOUS ,Allan variance ,[SPI.TRON]Engineering Sciences [physics]/Electronics - Abstract
International audience; Langasite material family, and more particularly the langatate crystal, is a very good candidate to be an alternative of the quartz crystal in term of material properties for time and frequency applications [1, 2, 3 and 4]. Then, it is interesting to improve ultra-stable oscillators equipped with high-Q langatate crystal resonators and to compare their stability results with those obtained with quartz crystal resonators. Today we do not really know the depth of capabilities in term of noise in the short time domain for oscillators made around langatate crystal resonators. Until now only one LGT oscillator prototype was measured and has achieved an Allan variance stability of σy(τ = 1s) = 8.10^-12. This was a preliminary measurement, but now we are ready to go further: the manufacturing process of resonators is more developed and improvements are in progress on electronics as well as on the thermal aspect.
- Published
- 2008
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