Relevant bibliographies by topics / Lateral gene transfers

Academic literature on the topic 'Lateral gene transfers'

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Published: 6 July 2024

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Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Journal articles on the topic "Lateral gene transfers":

1

Andersson, Jan O., and Andrew J. Roger. "Evolutionary Analyses of the Small Subunit of Glutamate Synthase: Gene Order Conservation, Gene Fusions, and Prokaryote-to- Eukaryote Lateral Gene Transfers." Eukaryotic Cell 1, no. 2 (April 2002): 304–10. http://dx.doi.org/10.1128/ec.1.2.304-310.2002.

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ABSTRACT Lateral gene transfer has been identified as an important mode of genome evolution within prokaryotes. Except for the special case of gene transfer from organelle genomes to the eukaryotic nucleus, only a few cases of lateral gene transfer involving eukaryotes have been described. Here we present phylogenetic and gene order analyses on the small subunit of glutamate synthase (encoded by gltD) and its homologues, including the large subunit of sulfide dehydrogenase (encoded by sudA). The scattered distribution of the sudA and sudB gene pair and the phylogenetic analysis strongly suggest that lateral gene transfer was involved in the propagation of the genes in the three domains of life. One of these transfers most likely occurred between a prokaryote and an ancestor of diplomonad protists. Furthermore, phylogenetic analyses indicate that the gene for the small subunit of glutamate synthase was transferred from a low-GC gram-positive bacterium to a common ancestor of animals, fungi, and plants. Interestingly, in both examples, the eukaryotes encode a single gene that corresponds to a conserved operon structure in prokaryotes. Our analyses, together with several recent publications, show that lateral gene transfers from prokaryotes to unicellular eukaryotes occur with appreciable frequency. In the case of the genes for sulfide dehydrogenase, the transfer affected only a limited group of eukaryotes—the diplomonads—while the transfer of the glutamate synthase gene probably happened earlier in evolution and affected a wider range of eukaryotes.
2

THUILLARD, MARC, and VINCENT MOULTON. "IDENTIFYING AND RECONSTRUCTING LATERAL TRANSFERS FROM DISTANCE MATRICES BY COMBINING THE MINIMUM CONTRADICTION METHOD AND NEIGHBOR-NET." Journal of Bioinformatics and Computational Biology 09, no. 04 (August 2011): 453–70. http://dx.doi.org/10.1142/s0219720011005409.

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Identifying lateral gene transfers is an important problem in evolutionary biology. Under a simple model of evolution, the expected values of an evolutionary distance matrix describing a phylogenetic tree fulfill the so-called Kalmanson inequalities. The Minimum Contradiction method for identifying lateral gene transfers exploits the fact that lateral transfers may generate large deviations from the Kalmanson inequalities. Here a new approach is presented to deal with such cases that combines the Neighbor-Net algorithm for computing phylogenetic networks with the Minimum Contradiction method. A subset of taxa, prescribed using Neighbor-Net, is obtained by measuring how closely the Kalmanson inequalities are fulfilled by each taxon. A criterion is then used to identify the taxa, possibly involved in a lateral transfer between nonconsecutive taxa. We illustrate the utility of the new approach by applying it to a distance matrix for Archaea, Bacteria, and Eukaryota.
3

Tofigh, A., M. Hallett, and J. Lagergren. "Simultaneous Identification of Duplications and Lateral Gene Transfers." IEEE/ACM Transactions on Computational Biology and Bioinformatics 8, no. 2 (March 2011): 517–35. http://dx.doi.org/10.1109/tcbb.2010.14.

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Marri, Pradeep Reddy, John P. Bannantine, Michael L. Paustian, and G. Brian Golding. "Lateral gene transfer in Mycobacterium avium subspecies paratuberculosis." Canadian Journal of Microbiology 52, no. 6 (June 1, 2006): 560–69. http://dx.doi.org/10.1139/w06-001.

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Lateral gene transfer is an integral part of genome evolution in most bacteria. Bacteria can readily change the contents of their genomes to increase adaptability to ever-changing surroundings and to generate evolutionary novelty. Here, we report instances of lateral gene transfer in Mycobacterium avium subsp. paratuberculosis, a pathogenic bacteria that causes Johne's disease in cattle. A set of 275 genes are identified that are likely to have been recently acquired by lateral gene transfer. The analysis indicated that 53 of the 275 genes were acquired after the divergence of M. avium subsp. paratuberculosis from M. avium subsp. avium, whereas the remaining 222 genes were possibly acquired by a common ancestor of M. avium subsp. paratuberculosis and M. avium subsp. avium after its divergence from the ancestor of M. tuberculosis complex. Many of the acquired genes were from proteobacteria or soil dwelling actinobacteria. Prominent among the predicted laterally transferred genes is the gene rsbR, a possible regulator of sigma factor, and the genes designated MAP3614 and MAP3757, which are similar to genes in eukaryotes. The results of this study suggest that like most other bacteria, lateral gene transfers seem to be a common feature in M. avium subsp. paratuberculosis and that the proteobacteria contribute most of these genetic exchanges.Key words: mycobacteria, M. avium subsp. paratuberculosis, lateral gene transfer, unique genes, phylogeny.
5

Zhi-Zhong Chen, Fei Deng, and Lusheng Wang. "Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers." IEEE/ACM Transactions on Computational Biology and Bioinformatics 9, no. 5 (September 2012): 1515–28. http://dx.doi.org/10.1109/tcbb.2012.79.

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Yubuki, Naoji, Luis Javier Galindo, Guillaume Reboul, Purificación López-García, Matthew W. Brown, Nicolas Pollet, and David Moreira. "Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina–Blastocystis Stramenopile Lineage." Molecular Biology and Evolution 37, no. 3 (November 6, 2019): 651–59. http://dx.doi.org/10.1093/molbev/msz250.

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Abstract Lateral gene transfer is a very common process in bacterial and archaeal evolution, playing an important role in the adaptation to new environments. In eukaryotes, its role and frequency remain highly debated, although recent research supports that gene transfer from bacteria to diverse eukaryotes may be much more common than previously appreciated. However, most of this research focused on animals and the true phylogenetic and functional impact of bacterial genes in less-studied microbial eukaryotic groups remains largely unknown. Here, we have analyzed transcriptome data from the deep-branching stramenopile Opalinidae, common members of frog gut microbiomes, and distantly related to the well-known genus Blastocystis. Phylogenetic analyses suggest the early acquisition of several bacterial genes in a common ancestor of both lineages. Those lateral gene transfers most likely facilitated the adaptation of the free-living ancestor of the Opalinidae–Blastocystis symbiotic group to new niches in the oxygen-depleted animal gut environment.
7

Friedrich, Michael W. "Phylogenetic Analysis Reveals Multiple Lateral Transfers of Adenosine-5′-Phosphosulfate Reductase Genes among Sulfate-Reducing Microorganisms." Journal of Bacteriology 184, no. 1 (January 1, 2002): 278–89. http://dx.doi.org/10.1128/jb.184.1.278-289.2002.

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ABSTRACT Lateral gene transfer affects the evolutionary path of key genes involved in ancient metabolic traits, such as sulfate respiration, even more than previously expected. In this study, the phylogeny of the adenosine-5′-phosphosulfate (APS) reductase was analyzed. APS reductase is a key enzyme in sulfate respiration present in all sulfate-respiring prokaryotes. A newly developed PCR assay was used to amplify and sequence a fragment (∼900 bp) of the APS reductase gene, apsA, from a taxonomically wide range of sulfate-reducing prokaryotes (n = 60). Comparative phylogenetic analysis of all obtained and available ApsA sequences indicated a high degree of sequence conservation in the region analyzed. However, a comparison of ApsA- and 16S rRNA-based phylogenetic trees revealed topological incongruences affecting seven members of the Syntrophobacteraceae and three members of the Nitrospinaceae, which were clearly monophyletic with gram-positive sulfate-reducing bacteria (SRB). In addition, Thermodesulfovibrio islandicus and Thermodesulfobacterium thermophilum, Thermodesulfobacterium commune, and Thermodesulfobacterium hveragerdense clearly branched off between the radiation of the δ-proteobacterial gram-negative SRB and the gram-positive SRB and not close to the root of the tree as expected from 16S rRNA phylogeny. The most parsimonious explanation for these discrepancies in tree topologies is lateral transfer of apsA genes across bacterial divisions. Similar patterns of insertions and deletions in ApsA sequences of donor and recipient lineages provide additional evidence for lateral gene transfer. From a subset of reference strains (n = 25), a fragment of the dissimilatory sulfite reductase genes (dsrAB), which have recently been proposed to have undergone multiple lateral gene transfers (M. Klein et al., J. Bacteriol. 183:6028–6035, 2001), was also amplified and sequenced. Phylogenetic comparison of DsrAB- and ApsA-based trees suggests a frequent involvement of gram-positive and thermophilic SRB in lateral gene transfer events among SRB.
8

Abby, Sophie S., Eric Tannier, Manolo Gouy, and Vincent Daubin. "Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests." BMC Bioinformatics 11, no. 1 (2010): 324. http://dx.doi.org/10.1186/1471-2105-11-324.

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Alsmark, Cecilia, Peter G. Foster, Thomas Sicheritz-Ponten, Sirintra Nakjang, T. Martin Embley, and Robert P. Hirt. "Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes." Genome Biology 14, no. 2 (2013): R19. http://dx.doi.org/10.1186/gb-2013-14-2-r19.

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Gophna, Uri. "Complexity Apparently Is Not a Barrier to Lateral Gene Transfers." Microbe Magazine 4, no. 12 (December 1, 2009): 549–53. http://dx.doi.org/10.1128/microbe.4.549.1.

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Journal articles Dissertations / Theses

Dissertations / Theses on the topic "Lateral gene transfers":

1

Vieira, Rute Gomes Velosa. "Bayesian phylogenetic modelling of lateral gene transfers." Thesis, University of Newcastle upon Tyne, 2015. http://hdl.handle.net/10443/3018.

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Phylogenetic trees represent the evolutionary relationships between a set of species. Inferring these trees from data is particularly challenging sometimes since the transfer of genetic material can occur not only from parents to their o spring but also between organisms via lateral gene transfers (LGTs). Thus, the presence of LGTs means that genes in a genome can each have di erent evolutionary histories, represented by di erent gene trees. A few statistical approaches have been introduced to explore non-vertical evolution through collections of Markov-dependent gene trees. In 2005 Suchard described a Bayesian hierarchical model for joint inference of gene trees and an underlying species tree, where a layer in the model linked gene trees to the species tree via a sequence of unknown lateral gene transfers. In his model LGT was modeled via a random walk in the tree space derived from the subtree prune and regraft (SPR) operator on unrooted trees. However, the use of SPR moves to represent LGT in an unrooted tree is problematic, since the transference of DNA between two organisms implies the contemporaneity of both organisms and therefore it can allow unrealistic LGTs. This thesis describes a related hierarchical Bayesian phylogenetic model for reconstructing phylogenetic trees which imposes a temporal constraint on LGTs, namely that they can only occur between species which exist concurrently. This is achieved by taking into account possible time orderings of divergence events in trees, without explicitly modelling divergence times. An extended version of the SPR operator is introduced as a more adequate mechanism to represent the LGT e ect in a tree. The extended SPR operation respects the time ordering. It additionaly di ers from regular SPR as it maintains a 1-to-1 correspondence between points on the species tree and points on each gene tree. Each point on a gene tree represents the existence of a population containing that gene at some point in time. Hierarchical phylogenetic models were used in the reconstruction of each gene tree from its corresponding gene alignment, enabling the pooling of information across genes. In addition to Suchard's approach, we assume variation in the rate of evolution between di erent sites. The species tree is assumed to be xed. A Markov Chain Monte Carlo (MCMC) algorithm was developed to t the model in a Bayesian framework. A novel MCMC proposal mechanism for jointly proposing the gene tree topology and branch lengths, LGT distance and LGT history has been developed as well as a novel graphical tool to represent LGT history, the LGT Biplot. Our model was applied to simulated and experimental datasets. More speci cally we analysed LGT/reassortment presence in the evolution of 2009 Swine-Origin In uenza Type A virus. Future improvements of our model and algorithm should include joint inference of the species tree, improving the computational e ciency of the MCMC algorithm and better consideration of other factors that can cause discordance of gene trees and species trees such as gene loss.
2

Tofigh, Ali. "Using Trees to Capture Reticulate Evolution : Lateral Gene Transfers and Cancer Progression." Doctoral thesis, KTH, Beräkningsbiologi, CB, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-10608.

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The historic relationship of species and genes are traditionally depicted using trees. However, not all evolutionary histories are adequately captured by bifurcating processes and an increasing amount of research is devoted towards using networks or network-like structures to capture evolutionary history. Lateral gene transfer (LGT) is a previously controversial mechanism responsible for non tree-like evolutionary histories, and is today accepted as a major force of evolution, particularly in the prokaryotic domain. In this thesis, we present models of gene evolution incorporating both LGTs and duplications, together with efficient computational methods for various inference problems. Specifically, we define a biologically sound combinatorial model for reconciliation of species and gene trees that facilitates simultaneous consideration of duplications and LGTs. We prove that finding most parsimonious reconciliations is NP-hard, but that the problem can be solved efficiently if reconciliations are not required to be acyclic—a condition that is satisfied when analyzing most real-world datasets. We also provide a polynomial-time algorithm for parametric tree reconciliation, a problem analogous to parametric sequence alignment, that enables us to study the entire space of optimal reconciliations under all possible cost schemes. Going beyond combinatorial models, we define the first probabilistic model of gene evolution incorporating a birth-death process generating duplications, LGTs, and losses, together with a relaxed molecular clock model of sequence evolution. Algorithms based on Markov chain Monte Carlo (MCMC) techniques, methods from numerical analysis, and dynamic programming are presented for various probability and parameter inference problems. Finally, we develop methods for analysis of cancer progression, a biological process with many similarities to the process of evolution. Cancer progresses by accumulation of harmful genetic aberrations whose patterns of emergence are graph-like. We develop a model of cancer progression based on trees, and mixtures thereof, that admits an efficient structural EM algorithm for finding Maximum Likelihood (ML) solutions from available cross-sectional data.
QC 20100812
3

Belliardo, Carole. "Étude des transferts horizontaux de gènes chez les nématodes phytoparasites par l'exploitation de métagénomes du sol." Electronic Thesis or Diss., Université Côte d'Azur, 2022. http://theses.univ-cotedazur.fr/2022COAZ6032.

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Les nématodes phytoparasites (NPP) sont parmi les plus importants ravageurs des cultures et menacent l'approvisionnement alimentaire mondial. Outre la nécessité de comprendre leur biologie pour développer de nouvelles stratégies de lutte, ces organismes sont fascinants en termes d'évolution génomique. Le parasitisme des plantes a évolué plusieurs fois indépendamment chez les nématodes selon des processus évolutifs convergents. Il semble que tous les NPP aient acquis des gènes bactériens et fongiques par transferts horizontaux de gènes (THG). Certains des gènes acquis horizontalement sont impliqués dans des fonctions parasitaires essentielles comme la dégradation des parois cellulaires des plantes ou l'assimilation des nutriments provenant des plantes. Cependant, plusieurs questions majeures restent encore en suspens concernant l'origine de ces gènes, leur distribution dans les génomes et la chronologie des événements d'acquisition. La plupart des NPP vivent dans le sol; nous pouvons donc supposer que ces gènes proviennent des micro-organismes du sol. Cependant, la sous-représentation de ces micro-organismes dans les librairies de séquences généralistes a probablement limité les précédentes analyses sur les THG. Pour pallier ce problème, nous avons constitué une bibliothèque de protéines provenant de plus de 6 800 métagénomes du sol disponibles publiquement. Un problème important dans les données métagénomiques concerne la qualité des données provenant des organismes eucaryotes due à l'utilisation d'outils dédiés aux génomes procaryotes. Afin de mieux représenter le pool de gènes présents dans les environnements naturels des NPP, nous avons identifié les contigs eucaryotes et re-prédit les gènes et protéines en utilisant un prédicteur de gènes eucaryotes.. Nous avons, ainsi, obtenu une librairie de protéines fiable et non redondante plus représentative de la biodiversité naturelle du sol.En utilisant cette librairie enrichie en protéines de sol, nous avons effectué une détection de THG sur 18 génomes de NPP du clade Tylenchina constituant un groupe très diversifié de modes de parasitisme. Après curation manuelle, la proportion de gènes acquis par transferts horizontaux avec confirmation phylogénétique est comprise entre 0.5 et 1,9% des gènes codant pour des protéines. Les THG dans les génomes de NPP proviennent principalement de bactéries. Nous avons également observé des THG provenant d'organismes eucaryotes tels que des champignons et pour la première fois des protistes et des plantes. Les taxa les plus représentés parmi les donneurs sont des espèces vivant dans le sol des clades bactériens Burkholderiaceae, Proteobacteria, Actinobacteria, Rhizobiales et fongiques (Dikary)a. L'utilisation de données métagénomiques a permis de préciser l'histoire des THG déjà décrits mais aussi d'identifier des centaines de nouveaux THG. Les prédictions fonctionnelles des THG nouvellement identifiées indiquent une large diversité de fonctions potentielles dont les implications biologiques pourront être plus précisément décrites dans le cadre d'expériences biochimiques. L'intégration de données environnementales dans notre librairie de référence a permis d'étendre la détection des THG et de compléter le catalogue des descendants des potentiels donneurs
Plant-parasitic nematodes (PPN) are among the most important crop pests and threaten the world's food production. Besides the need to understand their biology to develop new control strategies, they are fascinating organisms in terms of genomic evolution. Plant parasitism has evolved several times independently in nematodes with some convergent evolutionary processes. For instance, all studied PPN have acquired bacterial and fungal genes by horizontal gene transfers (HGT). Some of the acquired genes are involved in essential parasitic functions like plant cell wall degradation or processing nutrients from the plant. However, several major questions concerning their origin, evolutionary fate and distribution in the genomes and timing of acquisition events remain unsolved. Most PPN live in soil; thus, we hypothesised that these genes originated from soil-dwelling microorganisms. However, the underrepresentation of soil microorganisms in generalist sequence libraries has previously limited HGT analyses.To circumvent this problem, we built a protein library including more than 6,800 soil metagenomes from the Joint Genome Institute's IMG/M server. The first challenge was to make this massive dataset more accurate and suitable for HGT analysis in PPN genomes. An important issue in metagenomic data is the underrepresentation of eukaryotes and their annotation with prokaryotic tools. To better represent the pool of genes present in the natural environments of PPN, we identified eukaryotic contigs and re-predicted proteins using Augustus, a eukaryotic dedicated gene predictor. Moreover, we reduced the protein sequence redundancy and refined the taxonomic assignment. After all these steps, we obtained an improved and non-redundant database that was more representative of the soil's natural biodiversity. This soil protein library, two times larger than the classic library, contains mainly organisms genetically divergent than lab-cultured.Then, we performed an HGT detection on proteins from 18 plant-parasitic nematode genomes of the Tylenchina clade, constituting a highly diverse group of PPN phenotypes, against our library enriched with soil protein. After manual curation, the proportion of genes acquired by horizontal transfers with phylogenetic confirmation is between 0.5 to 1.9% to protein-coding genes originating from HGT in PPN genomes. Those genes mainly originate from bacteria, but we also observed HGT from eukaryotic kingdoms such as fungi, protists and plants. The most represented taxa in donors are soil-dwelling species of clades Burkholderiaceae, Proteobacteria, Actinobacteria, Rhizobiales and Dikarya. The usage of metagenomic data clarified the history of previously described HGTs but also identified hundreds of new HGTs. Functional analyses of the newly identified HGTs indicate a wide diversity of potential functions whose biological implications can be more precisely described in in-vitro experiments. Integrating environmental data in our reference library has allowed us to extend the detection of HGTs and to complete the catalog of potential donor offspring
4

Lester, Leo. "On Lateral Gene Transfer." Thesis, University of Reading, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.487489.

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Is bacterial evolution phylogenetic or reticulate? Darwin showed that life's history W;J.S mappable with trees. For almost everytfillg that we can see about us, this is largely correct, but beyond the limit of our sight thrives the unseen majority: The tiny, singlecelled prokaryotes do not reserve their genes only for the next generation. Through lateral gene transfer they swap genes with contemporaries, regardless of species. Discovered in the war years, the true place of lateral gene transfer within evolution has not yet been settled. As work on it.has multiplied, so its apparent extent has grown. Here a reappraisal of lateral gene transfer is carried out. The methods of its detection are examined and refined. The ~sults show that lateral transfer is not nearly so prevalent as some say. Less frequent, but still important, lateral gene transfer is shown to be a key mover in the evolution of the entire eukaryote domain. Its effect on individual genes, how it can increase rates of evolution and even trigger 'positive selection regimes, is exposed. The interconnectivity of species is then explored. Species that are the source of many genes receive many. Species that receive lots of genes through lateral transfer hold fewer unique genes. In addition, it is as if all species are connected through a massive network of lateral transfers. But any new information must be placed in its proper context: lateral gene transfer is only one of evolution's tools. Convergent evolution is exposed as a problem, both when trying to detect lateral transfer and perhaps also when constructing phylogenies. For all our problems with bacterial phylogenies, with building and interpreting them, the lesson of lateral gene transfer is that we can have faith in the idea of bacterial species and, after almost a hundred and fifty years, in Darwin too.
5

Cheeseman, Kevin. "Aspects of Penicillium genomics : Molecular combing genome assembly, genetic exchange in food and potential for secondary metabolite production." Thesis, Paris 11, 2013. http://www.theses.fr/2013PA112280/document.

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Les Penicilliums sont des champignons filamenteux appartenant au genre Ascomycota. Ces champignons ont été utilisés par l’homme pour la production de nourriture depuis des siècles. Plus récemment, ils ont aussi été utilisés dans l’industrie biotechnologique pour la production de composés chimiques d’intérêts pharmaceutiques. Certaines espèces de Penicillium sont par ailleurs des moisissures contaminants certains aliments, d’autres sont des pathogènes de plantes, y compris de certains fruits. Leur génomique est globalement peut connue. Dans cette étude, nous avons analysé les génomes de deux espèces nouvellement séquencées, Penicillium roqueforti et Penicillium camemberti. Nous reportons ici le développement d’une nouvelle méthodologie pour l’amélioration et la validation d’assemblage de génomes en utilisant une technologie permettant l’observation de molécules d’ADN unique, le Peignage Moléculaire. En utilisant cette méthode, nous avons amélioré l’assemblage de Penicillium roqueforti. Ce manuscrit décrit aussi de multiples occurrences d’un transfert horizontal d’un ilot génomique de plus de cinq cent kilobases entre plusieurs Penicillium. Ce cas de transfert horizontal indique une fréquence d’échange latéral de matériel génétique plus forte qu’attendue. Enfin nous présentons un inventaire préliminaire du potentiel génomique pour la production de métabolites secondaires dans ces importants Penicillium alimentaires
Penicillium are filamentous fungi belonging to the Ascomycota genus. Penicillium species have been used by Man for centuries in food making processes. More recently they have also been used in the biotechnology industry for the production of compounds of pharmaceutical interest. Some Penicillium species are food spoilage agents, pathogens of plants including fruits. Aspects of their genomics are largely unknown. In this study, we analysed the genomes of two newly sequenced species, Penicillium roqueforti and Penicillium camemberti. Here we report the development of a new methodology for improving and validating genome assembly using an original single DNA molecule technology, Molecular Combing. Using this methodology we were able to produce a high quality genome assembly of Penicillium roqueforti. This work also reports the multiple and recurrent horizontal transfer of a large genomic island of over half a megabase between several Penicillium species. This horizontal transfer indicates a higher frequency of lateral genetic exchange between cheesemaking fungi than previously expected. Finally, we present an early assessment of the genomic potential for secondary metabolite production in these important food associated penicilliums
6

Addario-Berry, Dana. "An analysis of models and algorithms for gene duplication and lateral gene transfer /." Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=80161.

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The construction of phylogenetic trees commonly uses molecular sequence data (DNA, RNA or amino acid sequences) for a single gene family over a set of n extant taxa. However, difficulties arise when the phylogenetic gene tree for one gene family disagrees with the phylogenetic gene tree for a different gene family. Several computational problems arise when trying to explain this disagreement (the two gene trees are not equal). Typically, one assumes a (simplified) model of evolution restricted to a small set of events which are assumed to cause the disagreement. Two such well-studied events are gene duplications and lateral gene transfer (a.k.a. horizontal gene transfer).
This thesis explores several aspects of both of these simplifed models of evolution. A brief exposition of the models is presented, along with previous results and various extensions to these models.
The expected number of gene duplications needed to explain disagreements between a random gene and species tree is investigated.
A method for incorporating edge weights into the species tree is proposed.
7

Khan, Mehmood Alam. "Computational Problems in Modeling Evolution and Inferring Gene Families." Doctoral thesis, KTH, Beräkningsvetenskap och beräkningsteknik (CST), 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-193637.

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Over the last few decades, phylogenetics has emerged as a very promising field, facilitating a comparative framework to explain the genetic relationships among all the living organisms on earth. These genetic relationships are typically represented by a bifurcating phylogenetic tree — the tree of life. Reconstructing a phylogenetic tree is one of the central tasks in evolutionary biology. The different evolutionary processes, such as gene duplications, gene losses, speciation, and lateral gene transfer events, make the phylogeny reconstruction task more difficult. However, with the rapid developments in sequencing technologies and availability of genome-scale sequencing data, give us the opportunity to understand these evolutionary processes in a more informed manner, and ultimately, enable us to reconstruct genes and species phylogenies more accurately. This thesis is an attempt to provide computational methods for phylogenetic inference and give tools to conduct genome-scale comparative evolutionary studies, such as detecting homologous sequences and inferring gene families. In the first project, we present FastPhylo as a software package containing fast tools for reconstructing distance-based phylogenies. It implements the previously published efficient algorithms for estimating a distance matrix from the input sequences and reconstructing an un-rooted Neighbour Joining tree from a given distance matrix. Results on simulated datasets reveal that FastPhylo can handles hundred of thousands of sequences in a minimum time and memory efficient manner. The easy to use, well-defined interfaces, and the modular structure of FastPhylo allows it to be used in very large Bioinformatic pipelines. In the second project, we present a synteny-aware gene homology method, called GenFamClust (GFC) that uses gene content and gene order conservation to detect homology. Results on simulated and biological datasets suggest that local synteny information combined with the sequence similarity improves the detection of homologs. In the third project, we introduce a novel phylogeny-based clustering method, PhyloGenClust, which partitions a very large gene family into smaller subfamilies. ROC (receiver operating characteristics) analysis on synthetic datasets show that PhyloGenClust identify subfamilies more accurately. PhyloGenClust can be used as a middle tier clustering method between raw clustering methods, such as sequence similarity methods, and more sophisticated Bayesian-based phylogeny methods. Finally, we introduce a novel probabilistic Bayesian method based on the DLTRS model, to sample reconciliations of a gene tree inside a species tree. The method uses MCMC framework to integrate LGTs, gene duplications, gene losses and sequence evolution under a relaxed molecular clock for substitution rates. The proposed sampling method estimates the posterior distribution of gene trees and provides the temporal information of LGT events over the lineages of a species tree. Analysis on simulated datasets reveal that our method performs well in identifying the true temporal estimates of LGT events. We applied our method to the genome-wide gene families for mollicutes and cyanobacteria, which gave an interesting insight into the potential LGTs highways.

QC 20161010

8

Wilber, Matthew. "Building a History of Horizontal Gene Transfer in E. Coli." Scholarship @ Claremont, 2016. http://scholarship.claremont.edu/hmc_theses/75.

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Bacteria's ability to pass entire genes between one another, a process called Horizontal Gene Transfer (HGT), has a major impact on bacterial evolution. In an ongoing project at Harvey Mudd, computational methods have been used to catalogue the HGT events that have impacted a group of closely related bacteria. This thesis builds on that project, by improving our ability to identify gene families --- groups of genes in different strains that are related. Previously, similarity was measured only by comparing two genes' DNA sequences, ignoring their positions on the organism's DNA. Here, we leverage genes' relative position to make a better measurement of gene similarity. These improved similarity measurements will improve the existing pipeline's ability to identify HGT events.
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Yan, Yongpan. "Computational analyses of microbial genomes operons, protein families and lateral gene transfer /." College Park, Md. : University of Maryland, 2005. http://hdl.handle.net/1903/2596.

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Thesis (Ph. D.) -- University of Maryland, College Park, 2005.
Thesis research directed by: Cell Biology & Molecular Genetics. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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Andam, Cheryl Marie Palacay. "Role of lateral gene transfer in the evolution of legume nodule symbionts." Diss., Online access via UMI:, 2007.

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Books on the topic "Lateral gene transfers":

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Gophna, Uri, ed. Lateral Gene Transfer in Evolution. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7780-8.

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Gophna, Uri. Lateral Gene Transfer in Evolution. Springer New York, 2015.

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Lateral Gene Transfer in Evolution. Springer-Verlag New York Inc., 2013.

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Gophna, Uri. Lateral Gene Transfer in Evolution. Springer London, Limited, 2013.

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Gontier, Nathalie. Reticulate Evolution: Symbiogenesis, Lateral Gene Transfer, Hybridization and Infectious Heredity. Springer, 2015.

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Gontier, Nathalie. Reticulate Evolution: Symbiogenesis, Lateral Gene Transfer, Hybridization and Infectious Heredity. Springer, 2015.

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Magowan, Fiona. Mission Music as a Mode of Intercultural Transmission, Charisma, and Memory in Northern Australia. Edited by Jonathan Dueck and Suzel Ana Reily. Oxford University Press, 2013. http://dx.doi.org/10.1093/oxfordhb/9780199859993.013.001.

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This article, focuses on the durability of Methodist “mission music” among the Yolngu, an Australian Indigenous people, and addresses questions of musical transfer between missionaries and Yolngu over fifty years that have shaped their Christian music politics. “Mission music” is marked as a genre by its association with the early missionaries among the Yolngu, their processes of teaching and transmission and its articulation with some aspects of Yolngu ritual performance practices. Today, mission music is performed together with an array of contemporary Christian musics reflecting its ongoing importance as a local, transnational and international currency. Magowan shows how hymnody has persisted for Yolngu as a musical mode of remembering and celebrating the past, illustrated first in early dialogic approaches to music teaching and choral training, and later recaptured in choral performances for the 50th anniversary festival of a Yolngu mission. She argues that “mission music,” in spite of its introduced, non-local origins, has become an experiential, rhythmical and textual sign of the “local” as it is adopted and used by the Yolngu. Choral singing is shown to be a means of embodying mission memories and facilitating local charismatic leadership, in turn, transforming Yolngu-missionary relationships over time. Ongoing work with missionary evangelists and frequent travel to foreign mission fields have also created new arenas for intercultural dialogue, leading to increasing complexity in Yolngu relationships embodied in Christian performance.

Book chapters on the topic "Lateral gene transfers":

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Davín, Adrián A., Dominik Schrempf, Tom A. Williams, Philip Hugenholtz, and Gergely J. Szöllősi. "Relative Time Inference Using Lateral Gene Transfers." In Methods in Molecular Biology, 75–94. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2691-7_4.

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López-García, Purificación. "Lateral Gene Transfer." In Encyclopedia of Astrobiology, 914–15. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-11274-4_1727.

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López-García, Purificación. "Lateral Gene Transfer." In Encyclopedia of Astrobiology, 1372–73. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-662-44185-5_1727.

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Gooch, Jan W. "Lateral Gene Transfer." In Encyclopedic Dictionary of Polymers, 903. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-6247-8_14096.

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Fritz, Hans-Joachim. "Lateral Gene Transfer." In Encyclopedia of Geobiology, 533–35. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-1-4020-9212-1_126.

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López-García, Purificación. "Lateral Gene Transfer." In Encyclopedia of Astrobiology, 1–2. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-27833-4_1727-3.

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López-García, Purificación. "Lateral Gene Transfer." In Encyclopedia of Astrobiology, 1660–61. Berlin, Heidelberg: Springer Berlin Heidelberg, 2023. http://dx.doi.org/10.1007/978-3-662-65093-6_1727.

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Skippington, Elizabeth, and Mark A. Ragan. "Lateral Genetic Transfer and Cellular Networks." In Lateral Gene Transfer in Evolution, 123–35. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7780-8_6.

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Dunning Hotopp, Julie C. "Lateral Gene Transfer in Multicellular Organisms." In Lateral Gene Transfer in Evolution, 161–79. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7780-8_9.

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Levin, Itay, Moshe Giladi, and Uri Gophna. "Lateral Gene Transfer and the Synthesis of Thymidine." In Lateral Gene Transfer in Evolution, 3–14. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7780-8_1.

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Conference papers on the topic "Lateral gene transfers":

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Chen, Zhi-Zhong, Fei Deng, and Lusheng Wang. "Identifying duplications and lateral gene transfers simultaneously and rapidly." In 2013 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2013. http://dx.doi.org/10.1109/cibcb.2013.6595398.

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Werren, Jack. "How important are bacteria-eukaryote lateral gene transfers to arthropod evolution?" In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.93233.

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ADDARIO-BERRY, L., M. HALLETT, and J. LAGERGREN. "TOWARDS IDENTIFYING LATERAL GENE TRANSFER EVENTS." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2002. http://dx.doi.org/10.1142/9789812776303_0027.

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RAGAN, MARK A. "AUTOMATING THE SEARCH FOR LATERAL GENE TRANSFER." In 4th Asia-Pacific Bioinformatics Conference. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2005. http://dx.doi.org/10.1142/9781860947292_0002.

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Hallett, M. T., and J. Lagergren. "Efficient algorithms for lateral gene transfer problems." In the fifth annual international conference. New York, New York, USA: ACM Press, 2001. http://dx.doi.org/10.1145/369133.369188.

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Dunning-Hotopp, Julie C. "Lateral gene transfer from bacteria to animals, including humans." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.93235.

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Chen, Kuo-Huey, Taeyoung Han, Bahram Khalighi, and Philip Klaus. "Air Cooling Concepts for Li-Ion Battery Pack in Cell Level." In ASME 2017 Heat Transfer Summer Conference. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/ht2017-4701.

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Computational Fluid Dynamics (CFD) modeling is used to study different cooling architectures for the next generation (Gen-2) EREV Li-Ion battery package. There might be advantages of air cooled batteries with respect to complexity, cost and reliability compared to liquid cooled systems like the EREV (Extended Range Electric Vehicle) GEN1 battery. Therefore, the feasibility of air cooling architectures is investigated first and later liquid cooling strategies. In this study, the thermal performance and pressure drop of the cell level for two of the core product designs are reported. The parameters considered in this study include two different heat generations (heat sources) by the battery pack and three cooling flow rates. The heat generations used are 500 W and 1500 W representing the normal driving and peak load conditions, respectively. The cooling flow rates are 100, 200 and 600 m3/h. The battery cell temperatures, both in terms of absolute value and the variation within the cell, and the pressure drop which is related to the required pumping power, are evaluated and presented.
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Daskalakis, Constantinos, and Sebastien Roch. "Species Trees from Gene Trees Despite a High Rate of Lateral Genetic Transfer: A Tight Bound (Extended Abstract)." In Proceedings of the Twenty-Seventh Annual ACM-SIAM Symposium on Discrete Algorithms. Philadelphia, PA: Society for Industrial and Applied Mathematics, 2015. http://dx.doi.org/10.1137/1.9781611974331.ch110.

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Reports on the topic "Lateral gene transfers":

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Barkay, Tamar, and Patricia Sobecky. Lateral gene transfer in the subsurface. Office of Scientific and Technical Information (OSTI), August 2007. http://dx.doi.org/10.2172/913060.

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Howard Ochman. LATERAL GENE TRANSFER AND THE HISTORY OF BACTERIAL GENOMES. Office of Scientific and Technical Information (OSTI), February 2006. http://dx.doi.org/10.2172/876510.

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Sobecky, Patricia A. The Role of the Horizontal Gene Pool and Lateral Gene Transfer in Enhancing Microbial Activities in Marine Sediments. Fort Belvoir, VA: Defense Technical Information Center, May 2006. http://dx.doi.org/10.21236/ada447026.

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Barkay, Tamar. Lateral Gene Transfer Among Subsurface Bacteria: Horizontal Gene Flow in Microbial Communities: A Special Focus Issue, Web Focus and Supplement. Office of Scientific and Technical Information (OSTI), November 2009. http://dx.doi.org/10.2172/967075.

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Newton, Ronald, Joseph Riov, and John Cairney. Isolation and Functional Analysis of Drought-Induced Genes in Pinus. United States Department of Agriculture, September 1993. http://dx.doi.org/10.32747/1993.7568752.bard.

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Drought is a common factor limiting timber production in the U.S. and Israel. Loblolly (Pinus taeda) and alleppo pine (Pinus halepensis) seedling survival is reduced when out planted, and growth and reproduction are often hindered by periodic droughts during later stages of tree development. Molecular and gene responses to drought stress have not been characterized. The objectives were to characterize drought-induced gene clones from these pines, to determine the effects of a growth regulator on drought tolerance, ABA levels, and drought-induced gene expression in alleppo pine, and to develop procedures for loblolly pine transformation. Nearly 20 cDNA clones influenced by gradual, prolonged drought stress have been isolated. Many of these have been shown to be induced by drought stress, whereas several others are down-regulated. These are the first drought-induced genes isolated from a pine species. Two genomic clones (lp5-1 and lp3-1) have been sequenced and characterized, and each has been found to be associated with a gene family. Clone lp5 appears to code for a cell wall protein, and clone lp3 codes for a nuclear protein. The former may be associated with changing the elastic properties of the cell wall, while the latter may be involved in signal transduction and/or protection from desiccation in the nucleus. Clone lp3 is similar to a drought-induced gene from tomato and is regulated by ABA. Several DNA sequences that are specific to induction during growth-retardation in alleppo pine by uniconazole have been identified. The active DNA species is now being identified. Promoters from genomic clones, lp3 and lp5, have been sequenced. Both are functional when fused with the gus reporter gene and transferred to other plant tissues as well as responding to a simulated drought stress. Through exodeletion analysis, it has been established that the promoter ABRE element of lp3 responds to ABA and that drought-induction of lp3 expression may also involve ABA. Stable tobacco transformants carrying either the lp5 or the lp3 promoter fused to a reporter gus gene have been obtained. The lp5lgus fusion was expressed at several stages of tobacco development and differentiation including the reproductive stage. There was no difference in phenotype between the transformants and the wild type. Embryogenesis procedures were developed for slash pine, but attempts to couple this process with gene transfer and plantlet transformation were not successful. Transformation of pine using Agrobacterium appears tractable, but molecular data supporting stable integration of the Agrobacterium-transferred gene are still inconclusive.
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Gera, Abed, Abed Watad, P. Ueng, Hei-Ti Hsu, Kathryn Kamo, Peter Ueng, and A. Lipsky. Genetic Transformation of Flowering Bulb Crops for Virus Resistance. United States Department of Agriculture, January 2001. http://dx.doi.org/10.32747/2001.7575293.bard.

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Objectives. The major aim of the proposed research was to establish an efficient and reproducible genetic transformation system for Easter lily and gladiolus using either biolistics or Agrobacterium. Transgenic plants containing pathogen-derived genes for virus resistance were to be developed and then tested for virus resistance. The proposal was originally aimed at studying cucumber mosaic virus (CMV) resistance in plants, but studies later included bean yellow mosaic virus (BYMV). Monoclonal antibodies were to be tested to determine their effectiveness in interning with virus infection and vector (aphid) transmission. Those antibodies that effectively interfered with virus infection and transmission were to be cloned as single chain fragments and used for developing transgenic plants with the potential to resist virus infection. Background to the topic. Many flower crops, as lily and gladiolus are propagated vegetatively through bulbs and corms, resulting in virus transmission to the next planting generation. Molecular genetics offers the opportunity of conferring transgene-mediated disease resistance to flower crops that cannot be achieved through classical breeding. CMV infects numerous plant species worldwide including both lilies and gladioli. Major conclusions, solutions and achievements. Results from these for future development of collaborative studies have demonstrated the potential transgenic floral bulb crops for virus resistance. In Israel, an efficient and reproducible genetic transformation system for Easter lily using biolistics was developed. Transient as well as solid expression of GUS reporter gene was demonstrated. Putative transgenic lily plantlets containing the disabled CMV replicase transgene have been developed. The in vitro ability of monoclonal antibodies (mAbs) against CMV to neutralize virus infectivity and block virus transmission by M. persicae were demonstrated. In the US, transgenic Gladiolus plants containing either the BYMV coat protein or antisense coat protein genes have been developed and some lines were found to be virus resistant. Long-term expression of the GUS reporter gene demonstrated that transgene silencing did not occur after three seasons of dormancy in the 28 transgenic Gladiolus plants tested. Selected monoclonal antibody lines have been isolated, cloned as single chain fragments and are being used in developing transgenic plants with CMV resistance. Ornamental crops are multi-million dollar industries in both Israel and the US. The increasing economic value of these floral crops and the increasing ban numerous pesticides makes it more important than ever that alternatives to chemical control of pathogens be studied to determine their possible role in the future. The cooperation resulted in the objectives being promoted at national and international meetings. The cooperation also enabled the technology transfer between the two labs, as well as access to instrumentation and specialization particular to the two labs.

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