The recent explosion of interest in epigenetics is often portrayed as the dawning of a scientific revolution that promises to transform biomedical science along with developmental and evolutionary biology. Much of this enthusiasm surrounds what we call the epigenetic switch hypothesis, which regards certain examples of epigenetic inheritance as an adaptive organismal response to environmental change. This interpretation overlooks an alternative explanation in terms of coevolutionary dynamics between parasitic transposons and the host genome. This raises a question about whether epigenetics (...) researchers tend to overlook transposon dynamics more generally. To address this question, we surveyed a large sample of scientific publications on the topics of epigenetics and transposons over the past fifty years. We found that enthusiasm for epigenetics is often inversely related to interest in transposon dynamics across the four disciplines we examined. Most surprising was a declining interest in transposons within biomedical science and cellular and molecular biology over the past two decades. Also notable was a delayed and relatively muted enthusiasm for epigenetics within evolutionary biology. An analysis of scientific abstracts from the past twenty-five years further reveals systematic differences among disciplines in their uses of the term epigenetic, especially with respect to heritability commitments and functional interpretations. Taken together, these results paint a nuanced picture of the rise of epigenetics and the possible neglect of transposon dynamics, especially among biomedical scientists. (shrink)

Transposons are ubiquitous genetic elements discovered so far in all investigated prokaryotes and eukaryotes. In remarkable contrast to all other genes, transposable elements are able to move to new locations within their host genomes. Transposition of transposons into coding sequences and their initiation of chromosome rearrangements have tremendous impact on gene expression and genome evolution. While transposons have long been known in bacteria, plants, and animals, only in recent years has there been a significant increase in the number of transposable (...) elements discovered in filamentous fungi. Like those of other eukaryotes, each fungal transposable element is either of class I or of class II. While class I elements transpose by a RNA intermediate and employ reverse transcriptases, class II elements transpose directly at the DNA level. We present structural and functional features for such transposons that have been identified so far in filamentous fungi. Emphasis is given to specific advantages or unique features when fungal systems are used to study transposable elements, e.g., the evolutionary impact of transposons in coenocytic organisms and possible experimental approaches toward horizontal gene transfer. Finally, we focus on the potential of transposons for tagging and identifying fungal genes. BioEssays 20:652–659, 1998.© 1998 John Wiley & Sons Inc. (shrink)

In the October issue of BioEssays (vol. 3, no. 4), H. P. Döring reviewed the general molecular biology of transposable elements in plants. In this review by P. A. Peterson, the effects of transposable genetic elements are considered, with special attention being paid to investigation of mobile‐element‐induced mutations at loci that control identifiable enzymes, and the specific alterations in enzyme properties that result. Together with DNA sequence analysis, these studies have begun to reveal the complexity of insertion/excision events, and their (...) potential in protein evolution. (shrink)

The Sleeping Beauty transposon system is a nonviral DNA transfer tool capable of efficiently mediating transposition‐based, stable integration of DNA sequences of choice into eukaryotic genomes. Continuous refinements of the system, including the emergence of hyperactive transposase mutants and novel approaches in vectorology, greatly improve upon transposition efficiency rivaling viral‐vector‐based methods for stable gene insertion. Current developments, such as reversible transgenesis and proof‐of‐concept RNA‐guided transposition, further expand on possible applications in the future. In addition, innate advantages such as lack (...) of preferential integration into genes reduce insertional mutagenesis‐related safety concerns while comparably low manufacturing costs enable widespread implementation. Accordingly, the system is recognized as a powerful and versatile tool for genetic engineering and is playing a central role in an ever‐expanding number of gene and cell therapy clinical trials with the potential to become a key technology to meet the growing demand for advanced therapy medicinal products. (shrink)

The recent publication by Wylie et al. is reviewed, demonstrating that the p53 protein regulates the movement of transposons. While this work presents genetic evidence for a piRNA‐mediated p53 interaction with transposons in Drosophila and zebrafish, it is herein placed in the context of a decade or so of additional work that demonstrated a role for p53 in regulating transposons and other repetitive elements. The line of thought in those studies began with the observation that transposons damage DNA and p53 (...) regulates DNA damage. The presence of transposon movement can increase the rate of evolution in the germ line and alter genes involved in signal transduction pathways. Transposition can also play an important role in cancers where the p53 gene function is often mutated. This is particularly interesting as recent work has shown that de‐repression of repetitive elements in cancer has important consequences for the immune system and tumor microenvironment. (shrink)

Transposable elements (TEs) are sequences currently or historically mobile, and are present across all eukaryotic genomes. A growing interest in understanding the regulation and function of TEs has revealed seemingly dichotomous roles for these elements in evolution, development, and disease. On the one hand, many gene regulatory networks owe their organization to the spread of cis‐elements and DNA binding sites through TE mobilization during evolution. On the other hand, the uncontrolled activity of transposons can generate mutations and contribute to disease, (...) including cancer, while their increased expression may also trigger immune pathways that result in inflammation or senescence. Interestingly, TEs have recently been found to have novel essential functions during mammalian development. Here, the function and regulation of TEs are discussed, with a focus on LINE1 in mammals. It is proposed that LINE1 is a beneficial endogenous dual regulator of gene expression and genomic diversity during mammalian development, and that both of these functions may be detrimental if deregulated in disease contexts. (shrink)

Expression and transposition of the Suppressor‐mutator (Spm) transposon of maize are controlled by interacting epigenetic and autoregulatory mechanisms. Methylation of critical element sequences prevents both transcription and transposition, heritably inactivating the element. The promoter, comprising the terminal 0.2 kb of the element, and a 0.35‐kb, highly GC‐rich, downstream sequence are the methylation target sequences. The element encodes two proteins necessary for transposition, TnpA and TnpD. There are multiple TnpA binding sites, both in the 5′ terminal promoter region and at (...) the element's 3′ end. In addition to its role in transposition, TnpA is both a positive and a negative regulator of transcription. TnpA represses the element's promoter when it is not methylated. When the element is inactive and its promoter methylated, TnpA activates the methylated promoter and facilitates both its transient and heritable demethylation. (shrink)

Throughout the animal kingdom, p53 genes function to restrain mobile elements and recent observations indicate that transposons become derepressed in human cancers. Together, these emerging lines of evidence suggest that cancers driven by p53 mutations could represent “transpospoathies,” i.e. disease states linked to eruptions of mobile elements. The transposopathy hypothesis predicts that p53 acts through conserved mechanisms to contain transposon movement, and in this way, prevents tumor formation. How transposon eruptions provoke neoplasias is not well understood but, from (...) a broader perspective, this hypothesis also provides an attractive framework to explore unrestrained mobile elements as inciters of late‐onset idiopathic disease.Also see the video abstract here. (shrink)

Horizontal transfer (HT) is the transmission of genetic material between non‐mating species, a phenomenon thought to occur rarely in multicellular eukaryotes. However, many transposable elements (TEs) are not only capable of HT, but have frequently jumped between widely divergent species. Here we review and integrate reported cases of HT in retrotransposons of the BovB family, and DNA transposons, over a broad range of animals spanning all continents. Our conclusions challenge the paradigm that HT in vertebrates is restricted to infective long (...) terminal repeat (LTR) retrotransposons or retroviruses. This raises the possibility that other non‐LTR retrotransposons, such as L1 or CR1 elements, believed to be only vertically transmitted, can horizontally transfer between species. Growing evidence indicates that the process of HT is much more general across different TEs and species than previously believed, and that it likely shapes eukaryotic genomes and catalyses genome evolution. (shrink)

Recent results confirm that long‐term expression of therapeutic transgenes can be achieved by using a transposon‐based system in primary stem cells and in vivo. Transposable elements are natural DNA transfer vehicles that are capable of efficient genomic insertion. The latest generation, Sleeping Beauty transposon‐based hyperactive vector (SB100X), is able to address the basic problem of non‐viral approaches – that is, low efficiency of stable gene transfer. The combination of transposon‐based non‐viral gene transfer with the latest improvements of (...) non‐viral delivery techniques could provide a long‐term therapeutic effect without compromising biosafety. The new challenges of pre‐clinical research will focus on further refinement of the technology in large animal models and improving the safety profile of SB vectors by target‐selected transgene integration into genomic “safe harbors.” The first clinical application of the SB system will help to validate the safety of this approach. (shrink)

The de‐repression of transposable elements (TEs) in mammalian genomes is thought to contribute to genome instability, inflammation, and ageing, yet is viewed as a cell‐autonomous event. In contrast to mammalian cells, prokaryotes constantly exchange genetic material through TEs, crossing both cell and species barriers, contributing to rapid microbial evolution and diversity in complex communities such as the mammalian gut. Here, it is proposed that TEs released from prokaryotes in the microbiome or from pathogenic infections regularly cross the kingdom barrier to (...) the somatic cells of their eukaryotic hosts. It is proposed this horizontal transfer of TEs from microbe to host is a stochastic, ongoing catalyst of genome destabilization, resulting in structural and epigenetic variations, and activation of well‐evolved host defense mechanisms contributing to inflammation, senescence, and biological ageing. It is proposed that innate immunity pathways defend against the horizontal acquisition of microbial TEs, and that activation of this pathway during horizontal transposon transfer promotes chronic inflammation during ageing. Finally, it is suggested that horizontal acquisition of prokaryotic TEs into mammalian genomes has been masked and subsequently under‐reported due to flaws in current sequencing pipelines, and new strategies to uncover these events are proposed. (shrink)

Transposons are well‐known architects of genetic change but their role in insecticide resistance has, until recently, only been speculated upon.1 Transposon insertion, or transposon‐mediated transposition, could alter either metabolic enzymes capable of degrading pesticides or could change the functionality of insecticide targets. The recent work of Aminetzach and coworkers2 suggests an exciting alternative, that transposon insertion can cause resistance by altering gene product function. This hypothesis is discussed in the light of other examples in which transposons have (...) been implicated in insecticide resistance. BioEssays 28:6–8, 2006. © 2005 Wiley Periodicals, Inc. (shrink)

We have synthesized a 582,970-base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce (...) intermediate assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb ("1/4 genome"), which were all cloned as bacterial artificial chromosomes in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments. 10.1126/science.1151721. (shrink)

Written for non-experts, this volume introduces the mechanisms that underlie reticulate evolution. Chapters are either accompanied with glossaries that explain new terminology or timelines that position pioneering scholars and their major discoveries in their historical contexts. The contributing authors outline the history and original context of discovery of symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infectious heredity. By applying key insights from the areas of molecular (phylo)genetics, microbiology, virology, ecology, systematics, immunology, epidemiology and computational science, (...) they demonstrate how reticulate evolution impacts successful survival, fitness and speciation. Reticulate evolution brings forth a challenge to the standard Neo-Darwinian framework, which defines life as the outcome of bifurcation and ramification patterns brought forth by the vertical mechanism of natural selection. Reticulate evolution puts forward a pattern in the tree of life that is characterized by horizontal mergings and lineage crossings induced by symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infective heredity, making the “tree of life” look more like a “web of life.” On an epistemological level, the various means by which hereditary material can be transferred horizontally challenges our classic notions of units and levels of evolution, fitness, modes of transmission, linearity, communities, and biological individuality. The case studies presented examine topics including the origin of the eukaryotic cell and its organelles through symbiogenesis; the origin of algae through primary and secondary symbiosis and dinoflagellates through tertiary symbiosis; the superorganism and holobiont as units of evolution; how endosymbiosis induces speciation in multicellular life forms; transferrable and non-transferrable plasmids and how they symbiotically interact with their host; the means by which pro- and eukaryotic organisms transfer genes laterally (bacterial transformation, transduction and conjugation as well as transposons and other mobile genetic elements); hybridization and divergence with gene flow in sexually-reproducing individuals; current (human) microbiome and viriome studies that impact our knowledge concerning the evolution of organismal health and acquired immunity; and how symbiosis and symbiogenesis can be modelled in computational evolution. (shrink)

Evolution is frequently concentrated in bursts of rapid morphological change and speciation followed by long‐term stasis. We propose that this pattern of punctuated equilibria results from an evolutionary tug‐of‐war between host genomes and transposable elements (TEs) mediated through the epigenome. According to this hypothesis, epigenetic regulatory mechanisms (RNA interference, DNA methylation and histone modifications) maintain stasis by suppressing TE mobilization. However, physiological stress, induced by climate change or invasion of new habitats, disrupts epigenetic regulation and unleashes TEs. With their capacity (...) to drive non‐adaptive host evolution, mobilized TEs can restructure the genome and displace populations from adaptive peaks, thus providing an escape from stasis and generating genetic innovations required for rapid diversification. This “epi‐transposon hypothesis” can not only explain macroevolutionary tempo and mode, but may also resolve other long‐standing controversies, such as Wright's shifting balance theory, Mayr's peripheral isolates model, and McClintock's view of genome restructuring as an adaptive response to challenge. (shrink)

Résumé Au cours des soixante-quinze dernières années, plusieurs traités internationaux ont été adoptés dans le but de promouvoir les droits universels des êtres humains, dont le principe d’égalité homme-femme. Pourtant, de nombreuses violations des _droits de l’homme_ commises contre les femmes en raison de leur sexe perdurent à l’échelle internationale. L’objet de cet article est de répondre à la question suivante: Y a-t-il une marginalisation des femmes et des problématiques qui leur sont propres en droit international? Notre article examine cette (...) question par l’exploration de la présence ou de l’absence de la « femme » en droit international, partant à la « recherche » de cette dernière. Dans un premier temps, nous étudions le silence concernant les femmes dans l’espace temporel sémiotique juridique qu’est le traité et la transmutation du langage français-anglais dans les dispositions pertinentes de la Charte internationale des droits de l’homme. Dans un deuxième temps, nous analysons la marginalisation de problématiques propres aux femmes dans la Charte internationale des droits de l’homme et la Convention sur l’élimination de toutes les formes de discrimination à l’égard des femmes (CEDAW). Nous procédons à une analyse sémiotique des traités internationaux dans le cadre de la théorie de la « signifique » développée par l’éminente sémioticienne Victoria Welby, notamment sa « Triade de Signification », que nous transposons dans le domaine juridique. En dernier lieu, nous proposons des réformes par la déconstruction du paradigme actuel des « _droits de l’homme de la femme_ » à l’échelle internationale. (shrink)

The past three years have seen a dramatic increase in our understanding of the structural organization and expression strategies of the dispersed, repetitive yeast transposon, Ty. These studies have led to a logical comparison of Ty with retroviral proviruses and other mobile, repetitive elements. Such comparisons have culminated in the hypotheses that transposition occurs via the formation of Ty‐encoded virus‐like particles and that these particles represent a basic unit of all ‘retro‐systems’.

Integrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long‐term survival, MGEs must continuously invade new hosts by horizontal transfer. Theoretically, MGEs that persist for millions of years in single lineages, and are thus subject to vertical inheritance, should not exist. Here we draw attention to an exception – a class of MGE termed REPIN. REPINs are non‐autonomous MGEs whose duplication depends on non‐jumping RAYT transposases. (...) Comparisons of REPINs and typical MGEs show that replication rates of REPINs are orders of magnitude lower, REPIN population size fluctuations correlate with changes in available genome space, REPIN conservation depends on RAYT function, and REPIN diversity accumulates within host lineages. These data lead to the hypothesis that REPINs form enduring, beneficial associations with eubacterial chromosomes. Given replicative nesting, our hypothesis predicts conflicts arising from the diverging effects of selection acting simultaneously on REPINs and host genomes. Evidence in support comes from patterns of REPIN abundance and diversity in two distantly related bacterial species. Together this bolsters the conclusion that REPINs are the genetic counterpart of mutualistic endosymbiotic bacteria. (shrink)

Biochemical and genetical analysis of plant transposons has shown that these elements can induce unstable mutations and also that the transposon structure can be altered in different ways. Upon insertion, a transposon can give rise to a variety of chromosomal changes in the vicinity of the insertion site. The alterations range from the nucleotide level to large‐scale rearrangements.

The pituitary hormone prolactin (PRL) is best known for its role in the regulation of lactation. Recent evidence furthermore indicates PRL is required for normal reproduction in rodents. Here, we report on the insertion of two transposon-like DNA sequences in the human prolactin gene, which together function as an alternative promoter directing extrapituitary PRL expression. Indeed, the transposable elements contain transcription factor binding sites that have been shown to mediate PRL transcription in human uterine decidualised endometrial cells and lymphocytes. (...) We hypothesize that the transposon insertion event has resulted in divergent (pituitary versus extrapituitary) expression of prolactin in primates, and in differential actions of pituitary versus extrapituitary prolactin in lactation versus pregnancy respectively. Importantly, the TE insertion might provide a context for some of the conflicting results obtained in studies of PRL function in mice and man. (shrink)

The PIWI-interacting RNA pathway, one of the major eukaryotic small RNA silencing pathways, is a genome surveillance system that silences selfish genes in animal gonads. piRNAs guide PIWI protein to target genes through Watson–Crick RNA–RNA base-parings. Loss of piRNA function causes genome instability, inducing failure in gametogenesis and infertility. Studies using fruit flies and mice as key experimental models have resulted in tremendous progress in understanding the mechanism underlying the piRNA pathway. Recent work using cultured silkworm germline cells has also (...) expanded our knowledge of piRNA biogenesis in particular, since these silkworm cells are the only cells of germline origin that can be cultured. In this review, we describe elucidation of the piRNA pathway using cultured silkworm cells as an experimental model by focusing on recent work in biochemistry and structural biology. Earlier studies that made important contributions to the field are also described. PIWI-interacting RNAs are germline-enriched small RNAs that silence transposons to maintain genome integrity. Recently, cultured silkworm germline cells such as BmN4 made great contributions to understand the mechanism underlying piRNA biogenesis in particular. In this review, we highlight the recent progress in biochemical and structural biology. (shrink)

Recent investigations with non‐model species and whole‐genome approaches have challenged several paradigms in animal epigenetics. They revealed that epigenetic variation in populations is not the mere consequence of genetic variation, but is a semi‐independent or independent source of phenotypic variation, depending on mode of reproduction. DNA methylation is not positively correlated with genome size and phylogenetic position as earlier believed, but has evolved differently between and within higher taxa. Epigenetic marks are usually not completely erased in the zygote and germ (...) cells as generalized from mouse, but often persist and can be transgenerationally inherited, making them evolutionarily relevant. Gene body methylation and promoter methylation are similar in vertebrates and invertebrates with well methylated genomes but transposon silencing through methylation is variable. The new data also suggest that animals use epigenetic mechanisms to cope with rapid environmental changes and to adapt to new environments. The main benefiters are asexual populations, invaders, sessile taxa and long‐lived species. (shrink)

Natural genome editing from a biocommunicative perspective is the competent agent-driven generation and integration of meaningful nucleotide sequences into pre-existing genomic content arrangements, and the ability to (re-)combine and (re-)regulate them according to context-dependent (i.e. adaptational) purposes of the host organism. Natural genome editing integrates both natural editing of genetic code and epigenetic marking that determines genetic reading patterns. As agents that edit genetic code and epigenetically mark genomic structures, viral and subviral agents have been suggested because they may be (...) evolutionarily older than cellular life. This hypothesis that viruses and viral-like agents edit genetic code is developed according to three well investigated examples that represent key evolutionary inventions in which non-lytic viral swarms act symbiotically in a persistent lifestyle within cellular host genomes: origin of eukaryotic nucleus, adaptive immunity, placental mammals. Additionally an abundance of various RNA elements cooperate in a variety of steps and substeps as regulatory and catalytic units with multiple competencies to act on the genetic code. Most of these RNA agents such as transposons, retroposons and small non-coding RNAs act consortially and are remnants of persistent viral infections that now act as co-opted adaptations in cellular key processes. (shrink)

Dawkins in his The Selfish Gene(1) quite aptly applies the term “selfish” to parasitic repetitive DNA sequences endemic to eukaryotic genomes, especially vertebrates. Doolittle and Sapienza(2) as well as Orgel and Crick(3) enlivened this notion of selfish DNA with the identification of such repetitive sequences as remnants of mobile elements such as transposons. In addition, Orgel and Crick(3) associated parasitic DNA with a potential to outgrow their host genomes by propagating both vertically via conventional genome replication as well as infectiously (...) by horizontal gene transfer (HGT) to other genomes. Still later, Doolittle(4) speculated that unchecked HGT between unrelated genomes so complicates phylogeny that the conventional representation of a tree of life would have to be replaced by a thicket or a web of life.(4) In contrast, considerable data now show that reconstructions based on whole genome sequences are consistent with the conventional “tree of life”.(5–10) Here, we identify natural barriers that protect modern genome populations from the inroads of rampant HGT. BioEssays 27:741–747, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

The genomes of virtually all sexually reproducing species contain transposable elements. Although active elements generally transpose more rapidly than they are inactivated by mutation or excision, their number can be kept in check by purifying selection if its effectiveness becomes disproportionately greater as their copy number increases. In sexually reproducing species, such synergistic selection can result from ectopic crossing-over or from homologous recombination under negative epistasis. In addition, there may be controls on transposon activity that are associated with meiosis. (...) Because a sexual lineage that abandons sex must lack such mechanisms, it may be driven to extinction by the unchecked proliferation of deleterious transposons inherited from its sexual progenitor. An important component of the evolutionary advantage of sex over asex may therefore lie in the ability of sex, despite facilitating the spread of deleterious elements within interbreeding populations, also to restrain their intragenomic proliferation. BioEssays 27:76–85, 2005. © 2004 Wiley Periodicals, Inc. (shrink)

The use of Drosophila chromosomal rearrangements and transposon constructs involving the white gene reveals the existence of repressive chromatin domains that can spread over considerable genomic distances. One such type of domain is found in heterochromatin and is responsible for classical position‐effect variegation. Another type of repressive domain is established, beginning at specific sequences, by complexes of Polycomb Group proteins. Such complexes, which normally regulate the expression of many genes, including the homeotic loci, are responsible for silencing, white gene (...) variegation, pairing‐dependent effects and insertional targeting. (shrink)

Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity to the assortment of organisms among ecosystems, some researchers have called for an ecological approach to the study of transposon dynamics. However, there are several ways to adopt such an approach, and it is sometimes unclear what an ecological perspective will add to the existing co-evolutionary framework for explaining transposon-host (...) interactions. This review aims to clarify the conceptual foundations of transposon ecology in order to evaluate its explanatory prospects. We begin by identifying three unanswered questions regarding the abundance and distribution of TEs that potentially call for an ecological explanation. We then offer an operational distinction between evolutionary and ecological approaches to these questions. By determining the amount of variance in transposon abundance and distribution that is explained by ecological and evolutionary factors, respectively, it is possible empirically to assess the prospects for each of these explanatory frameworks. To illustrate how this methodology applies to a concrete example, we analyzed whole-genome data for one set of distantly related mammals and another more closely related group of arthropods. Our expectation was that ecological factors are most informative for explaining differences among individual TE lineages, rather than TE families, and for explaining their distribution among closely related as opposed to distantly related host genomes. We found that, in these data sets, ecological factors do in fact explain most of the variation in TE abundance and distribution among TE lineages across less distantly related host organisms. Evolutionary factors were not significant at these levels. However, the explanatory roles of evolution and ecology become inverted at the level of TE families or among more distantly related genomes. Not only does this example demonstrate the utility of our distinction between ecological and evolutionary perspectives, it further suggests an appropriate explanatory domain for the burgeoning discipline of transposon ecology. The fact that ecological processes appear to be impacting TE lineages over relatively short time scales further raises the possibility that transposons might serve as useful model systems for testing more general hypotheses in ecology. (shrink)

RésuméLes querelles constituent une activité « routinière » plutôt qu’extra ordinaire du monde lettré et savant. Nous montrons ici qu’elles ont un rôle à jouer dans le domaine de la critique historique. Notre apport est double. En nous intéressant aux enjeux épistémologiques de l’écriture baylienne de la querelle, nous transposons sur le terrain de l’historiographie l’apport des études récentes sur la productivité des querelles scientifiques. Nous présentons une perspective nouvelle de compréhension des querelles comme activité structurante de la république des (...) lettres, tant sur le plan social qu’intellectuel. Ce faisant, nous prenons position dans le débat sur le « pyrrhonisme » historique de Bayle en montrant que les querelles sont centrales dans une démarche historio graphique consciente de ses limites comme de ses pouvoirs d’investigation. (shrink)

Résumé Les querelles constituent une activité « routinière » plutôt qu’extra ordinaire du monde lettré et savant. Nous montrons ici qu’elles ont un rôle à jouer dans le domaine de la critique historique. Notre apport est double. En nous intéressant aux enjeux épistémologiques de l’écriture baylienne de la querelle, nous transposons sur le terrain de l’historiographie l’apport des études récentes sur la productivité des querelles scientifiques. Nous présentons une perspective nouvelle de compréhension des querelles comme activité structurante de la république (...) des lettres, tant sur le plan social qu’intellectuel. Ce faisant, nous prenons position dans le débat sur le « pyrrhonisme » historique de Bayle en montrant que les querelles sont centrales dans une démarche historio graphique consciente de ses limites comme de ses pouvoirs d’investigation. (shrink)

Communication is defined as an interaction between at least two living agents which share a repertoire of signs. These are combined according to syntactic, semantic and context-dependent, pragmatic rules in order to coordinate behavior. This volume deals with the important roles of soil bacteria in parasitic and symbiotic interactions with viruses, plants, animals and fungi. Starting with a general overview of the key levels of communication between bacteria, further reviews examine the various aspects of intracellular as well as intercellular biocommunication (...) between soil microorganisms. This includes the various levels of biocommunication between phages and bacteria, between soil algae and bacteria, and between bacteria, fungi and plants in the rhizosphere, the role of plasmids and transposons, horizontal gene transfer, quorum sensing and quorum quenching, bacterial-host cohabitation, phage-mediated genetic exchange and soil viral ecology. (shrink)

Communication is defined as an interaction between at least two living agents which share a repertoire of signs. These are combined according to syntactic, semantic and context dependent, pragmatic rules in order to coordinate behavior. This volume deals with the important roles of soil bacteria in parasitic and symbiotic interactions with viruses, plants, animals and fungi. Starting with a general overview of the key levels of communication between bacteria, further reviews examine the various aspects of intracellular as well as intercellular (...) biocommunication between soil microorganisms. Th is includes the various levels of biocommunication between phages and bacteria, between soil algae and bacteria, and between bacteria, fungi and plants in the rhizosphere, the role of plasmids and transposons, horizontal gene transfer, quorum sensing and quorum quenching, bacterial-host cohabitation, phage-mediated genetic exchange and soil viral ecology. (shrink)

The growing number of cloned eukaryotic genes lacking a defined or proven biological function poses a major challenge in ‘reverse genetics’. A method is described here that permits efficient screening for new lesions in, or close to, genes corresponding to cloned DNA sequences of interest. The technique involves transposon mutagenesis, followed by screening of DNA isolated from a population of mutagenised individuals (or their progeny) for evidence that the population contains at least one individual in which transposon insertion (...) has occurred at the target locus. Detection of rare individuals within the population is facilitated by the use of the polymerase chain reaction (PCR). Once recognised, specific individuals (or their progeny) are isolated from the population by a process of sib‐selection. In cases where insertion of the transposon has occurred close to, but not within, the target locus, secondary events involving imprecise excision of the transposon will nonetheless allow the isolation of mutant individuals. Though the method was developed specifically for the transposon‐mutagenesis of Drosophila, extensions to other organisms and to other mutagenic strategies are feasible and some of the possibilities are discussed. (shrink)

The RNAi machinery is not only involved with post‐transcriptional degradation of messenger RNAs, but also used for targeting of chromatin changes associated with transcriptional silencing. Two recent papers determine the global patterns of gene expression and chromatin modifications produced by the RNAi machinery in fission yeast.(9, 10) The major sites include the outer centromere repeats, the mating‐type locus and subtelomeric regions. By comparison, studies of Arabidopsis heterochromatin also implicate transposons as a major target for silencing. Analyses of siRNA libraries from (...) Drosophila, nematodes and Arabidopsis indicate that major repeats at centromeres, telomeres and transposable elements are likely targets of RNAi. Also, intergenic regions are implicated as targets in Arabidopsis. BioEssays 27:1209–1212, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

It is somewhat ironic that animals that are the prime choice for detailed genetic analysis, such as the fruit fly and the nematode, have thus far been largely refractory to reverse genetic analysis. Their detailed genetic map, and small genome size have made them subjects of ambitious genome analysis projects, but there is still no strategy to introduce desired changes into their genomes by homologous recombination. Some alternative approaches have recently become available; this review describes possibilities and unsolved problems for (...) reverse genetics in the nematode Caenorhabditis elegans. The transposon Tc1 could prove to be very useful for the isolation of knock out mutants, and possibly also for introduction of more subtle alterations. (shrink)

Whoever compares the genomes of distantly related species might find aberrantly high sequence similarity at certain loci. Such anomaly can only be explained by genetic material being transferred through other means than reproduction, that is, a horizontal transfer. Between multicellular organisms, the transferred material will likely turn out to be a transposable element. Because TEs can move between loci and invade chromosomes by replicating themselves, HT of TEs profoundly impacts genome evolution. Yet, very few studies have quantified HTT at large (...) taxonomic scales. Indeed, this task currently faces difficulties that range from the variable quality of available genome sequences to limitations of analytical procedures, some of which have been overlooked. Here we review the many challenges that an extensive analysis of HTT must overcome, we expose biases and limits of current methods, suggest solutions or workarounds, and reflect upon approaches that could be developed to better quantify this phenomenon. With the large amount of genomic resources now available, horizontal transfer of transposable elements can be studied as an evolutionary process, rather than as isolated cases. We discuss some of the difficulties encountered in detecting and counting such transfers and propose guidelines and directions for future research in this area. (shrink)

A combination of cytogenetic and molecular analyses has shown that several different transposable elements are involved in the restructuring of Drosophila chromosomes. Two kinds of elements, P and hobo, are especially prone to induce chromosome rearrangements. The mechanistic details of this process are unclear, but, at least some of the time, it seems to involve ectopic recombination between elements inserted at different chromosomal sites; the available data suggest that these ectopic recombination events are much more likely to occure between elements (...) in the same chromosome than between elements in different chromosomes. Other Drosophila transposons also appear to mediate chromosome restructuring by ectopic recombination; these include the retrotransposons BEL, roo, Docand I and the foldback element FB. In addition, two retrotransposons, HeT‐A and TART, have been found to be associated specifically with the ends of Drosophila chromosomes. Very limited data indicate that transposon‐mediated chromosome restructuring is occurring in natural populations of Drosophila. This suggests that transposable elements may help to shape the structure of the Drosophila genome and implies that they may have a similar role in other organisms. (shrink)

“Antibiotic resistance is usually associated with a fitness cost” is frequently accepted as common knowledge in the field of infectious diseases. However, with the advances in high‐throughput DNA sequencing that allows for a comprehensive analysis of bacterial pathogenesis at the genome scale, including antibiotic resistance genes, it appears that this paradigm might not be as solid as previously thought. Recent studies indicate that antibiotic resistance is able to enhance bacterial fitness in vivo with a concomitant increase in virulence during infections. (...) As a consequence, strategies to minimize antibiotic resistance turn out to be not as simple as initially believed. Indeed, decreased antibiotic use may not be sufficient to let susceptible strains outcompete the resistant ones. Here, we put in perspective these findings and review alternative approaches, such as preventive and therapeutic anti‐bacterial immunotherapies that have the potential to by‐pass the classic antibiotics. (shrink)

Barbara McClintock won the Nobel Prize in 1983 for her discovery of mobile genetic elements. Her Nobel work began in 1944, and by 1950 McClintock began presenting her work on "controlling elements." McClintock performed her studies through the use of controlled breeding experiments with known mutant stocks, and read the action of controlling elements (transposons) in visible patterns of pigment and starch distribution. She taught close colleagues to "read" the patterns in her maize kernels, "seeing" pigment and starch genes turning (...) on and off. McClintock illustrated her talks and papers on controlling elements or transposons with photographs of the spotted and streaked maize kernels which were both her evidence and the key to her explanations. Transposon action could be read in the patterns by the initiated, but those without step by step instruction by McClintock or experience in maize often found her presentations confusing. The photographs she displayed became both McClintock's means of communication, and a barrier to successful presentation of her results. The photographs also had a second and more subtle effect. As images of patterns arrived at through growth and development of the kernel, they highlight what McClintock believed to be the developmental consequences of transposition, which in McClintock's view was her central contribution, over the mechanism of transposition, for which she was eventually recognized by others. Scientific activities are extremely visual, both at the sites of investigation and in communication through drawings, photographs, and movies. Those visual messages deserve greater scrutiny by historians of science. (shrink)

The concept of monophyly is central to much of modern biology. Despite many efforts over many years, important questions remain unanswered that relate both to the concept itself and to its various applications. This essay focuses primarily on four of these: i) Is it possible to define monophyly operationally, specifically with respect to both the structures of genomes and at the levels of the highest phylogenetic categories (kingdoms, phyla, classes)? ii) May the mosaic and chimeric structures of genomes be sufficiently (...) important factors in phylogeny that situations exist in which the concept may not be applicable? iii) In the history of life on earth were there important groups of organisms that probably had polyphyletic, rather than monophyletic, origins? iv) Does the near universal search for monophyletic origins of clades lead, on occasion, to both undesirable narrowing of acceptable options for development of evolutionary scenarios and sometimes actual omission from consideration of less conventional types of both data and modes of thought, possibly at the expense of biological understanding? Three sections in the essay consider possible answers to these questions: i) A reassessment is made of major features of both the concept and some of its applications. Recent research results make it seem improbable that there could have been single basal forms for many of the highest categories of evolutionary differentiation (kingdoms, phyla, classes). The universal tree of life probably had many roots. Facts contributing to this perception include the phylogenetically widespread occurrences of: horizontal transfers of plasmids, viral genomes, and transposons; multiple genomic duplications; the existence and properties of large numbers of gene families and protein families; multiple symbioses; broad-scale hybridizations; and multiple homoplasys. Next, justifications are reassessed for the application of monophyletic frameworks to two major evolutionary developments usually interpreted as having been monophyletic: ii) the origins of life; and iii) the origins of the vertebrate tetrapods. For both cases polyphyletic hypotheses are suggested as more probable than monophyletic hypotheses. Major conclusions are, as answers to the four questions posed above: probably not, yes, yes, and yes. (shrink)