Background Polyketides are natural products with a wide range of biological functions and pharmaceutical applications. Discovery and utilization of polyketides can be facilitated by understanding the evolutionary processes that gave rise to the biosynthetic machinery and the natural product potential of extant organisms. Gene duplication and subfunctionalization, as well as horizontal gene transfer are proposed mechanisms in the evolution of biosynthetic gene clusters. To explain the amount of homology in some polyketide synthases in unrelated organisms such as bacteria and fungi, interkingdom horizontal gene transfer has been evoked as the most likely evolutionary scenario. However, the origin of the genes and the direction of the transfer remained elusive. Methodology/Principal Findings We used comparative phylogenetics to infer the ancestor of a group of polyketide synthase genes involved in antibiotic and mycotoxin production. We aligned keto synthase domain sequences of all available fungal 6
Ureaplasma parvum and Ureaplasma urealyticum are sexually transmitted, opportunistic pathogens of the human urogenital tract. There are 14 known serovars distributed between the two species. For decades, it has been postulated based upon limited data that virulence is related to serotype specificity. The results were often inconclusive due to the small sample size and extensive cross-reactivity between certain serovars. We developed real-time quantitative PCRs that allow reliable differentiation of the two species and type strains of each of the 14 serovars. To investigate species and serovar distributions, we typed 1,061 clinical isolates of human ureaplasmas from diverse patient populations. There was only a tenuous association between individual Ureaplasma serovars and certain patient populations. This may in part be explained by the fact that almost 40% of the isolates were genetic mosaics, apparently arising from the recombination of multiple serovars. This explains the extensive ...
Horizontal gene transfer was first described in Japan in a 1959 publication that demonstrated the transfer of antibiotic resistance between different species of bacteria.[4][5] In the mid-1980s, Syvanen suggested that lateral gene transfer not only had biological significance, but was involved in shaping evolutionary history from the beginning of life on Earth.[6] "Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes".[7][8] The phenomenon appears to have had some significance for unicellular eukaryotes as well. As Bapteste et al. observe, "additional evidence suggests that gene transfer might also be an important evolutionary mechanism in protist evolution".[9] There is some evidence that even higher plants and animals have been affected. Richardson and Palmer (2007) state: "Horizontal gene transfer (HGT) has played a major role in bacterial evolution and is fairly common in certain unicellular eukaryotes. However, the ...
Horizontal or lateral gene transfer (HGT or LGT) is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate the investigations of evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages. Inferring horizontal gene transfer through computational identification of HGT events relies upon the investigation of sequence composition or evolutionary history of genes. Sequence composition-based ("parametric") methods ...
As the genomes of many new creatures rapidly fill the public DNA sequence databases, the problems for the grand evolutionary story are becoming overwhelming. One issue is the fact that different creatures have unique sets of genes specific to their kind with no apparent evolutionary history. To explain this glaring problem, evolutionists have resorted to the myth of pervasive horizontal gene transfer.. Horizontal gene transfer (HGT) is the process whereby genes are transferred from one type of creature to another without sexual reproduction. Earlier in my career, I participated in a study (published in the journal Science), in which we found that the pathogenic bacterium Wolbachia had transferred large portions of its DNA into the genomes of both worms and insects.1 The Wolbachia bacterium is able to do this extraordinary feat by targeting the cells of reproductive organs so that the transferred DNA is literally inherited in the host. However, we also observed that very few of these transferred ...
Lateral gene transfer (or horizontal gene transfer), an atypical mechanism of transferring genes between species, has almost become the default explanation for genes that display an unexpected composition or phylogeny. Numerous methods of detecting lateral gene transfer events all rely on two fundamental strategies: primary structure composition or gene tree/species tree comparisons. Discouragingly, the results of these different approaches rarely coincide. With the wealth of genome data now available, detection of laterally transferred genes is increasingly being attempted in large uncurated eukaryotic datasets. However, detection methods depend greatly on the quality of the underlying genomic data, which are typically complex for eukaryotes. Furthermore, given the automated nature of genomic data collection, it is typically impractical to manually verify all protein or gene models, orthology predictions and multiple sequence alignments, requiring researchers to accept a substantial margin of ...
Pathogenicity islands (PAIs), as termed in 1990, are a distinct class of genomic islands acquired by microorganisms through horizontal gene transfer. Pathogenicity islands are found in both animal and plant pathogens. Additionally, PAIs are found in both gram-positive and gram-negative bacteria. They are transferred through horizontal gene transfer events such as transfer by a plasmid, phage, or conjugative transposon. Therefore, PAIs contribute to microorganisms ability to evolve. One species of bacteria may have more than one PAI. For example, Salmonella has at least five. An analogous genomic structure in rhizobia is termed a symbiosis island. Pathogenicity islands (PAIs) are incorporated in the genome, chromosomally or extrachromosomally, of pathogenic organisms, but are usually absent from those nonpathogenic organisms of the same or closely related species. They may be located on a bacterial chromosome or may be transferred within a plasmid or can be found in bacteriophage genomes. The ...
The repABC plasmid family, which is extensively present within Alphaproteobacteria, and some secondary chromosomes of the Rhizobiales have the particular feature that all the elements involved in replication and partitioning reside within one transcriptional unit, the repABC operon. Given the functional interactions among the elements of the repABC operon, and the fact that they all reside in the same operon, a common evolutionary history would be expected if the entire operon had been horizontally transferred. Here, we tested whether there is a common evolutionary history within the repABC operon. We further examined different incompatibility groups in terms of their differentiation and degree of adaptation to their host. We did not find a single evolutionary history within the repABC operon. Each protein had a particular phylogeny, horizontal gene transfer events of the individual genes within the operon were detected, and different functional constraints were found within and between the Rep proteins
Horizontal gene transfer (HGT) is a fast-track mechanism that allows genetically unrelated organisms to exchange genes for rapid environmental adaptation. We developed a new phyletic distribution-based software, HGT-Finder, which implements a novel bioinformatics algorithm to calculate a horizontal transfer index and a probability value for each query gene. Applying this new tool to the Aspergillus fumigatus, Aspergillus flavus, and Aspergillus nidulans genomes, we found 273, 542, and 715 transferred genes (HTGs), respectively. HTGs have shorter length, higher guanine-cytosine (GC) content, and relaxed selection pressure. Metabolic process and secondary metabolism functions are significantly enriched in HTGs. Gene clustering analysis showed that 61%, 41% and 74% of HTGs in the three genomes form physically linked gene clusters (HTGCs). Overlapping manually curated, secondary metabolite gene clusters (SMGCs) with HTGCs found that 9 of the 33 A. fumigatus SMGCs and 31 of the 65 A. nidulans SMGCs share
Horizontal gene transfer (HGT) in bacteria and archaea occurs through phage transduction, transformation, or conjugation, and the latter is particularly important for the spread of antibiotic resistance. Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci confer sequence-directe …
Determining the photosynthetic relatives of Rafflesiales has long presented a challenge owing to the extreme reduction and/or modification of morphological structures that have accompanied the evolution of this lineage [3, 11]. Molecular phylogenetic approaches, although providing great promise in resolving such questions, also come with their own set of challenges that includes losses of some genes, substitution rate increases in other genes, and horizontal gene transfer. Examples of the first process can be seen in chloroplast genes such as rbcL that are typically used to infer phylogenetic relationships among angiosperms but have not yet been amplified from any Rafflesiales and are presumed lost [5]. Increased substitution rates in the normally conservative plastid rDNA has been demonstrated in these holoparasites [4, 12]. Similarly, accelerated rates in mitochondrial SSU rDNA, typically very conservative in many photosynthetic angiosperms, occur in Rafflesia and Cytinus [13]. Despite these ...
Genomes of living organisms are comprised of very long DNA molecules. A fundamental question is by what mechanisms are specific loci along these genomes found, with high efficiency and at relevant physiological times. We address this question in the case of horizontal gene transfer processes such as viral transduction and conjugation, which result in the rapid acquisition of new traits in bacteria. We use the infection of E. coli cells by bacteriophage lambda, whose DNA integrates at a unique site into the bacterial genome, when following the lysogenic pathway. To shed light on the mechanisms by which lambda DNA finds its unique integration site, we follow in real time individual lambda DNAs and their integration site within live cells using fluorescent markers, until lysogeny is established, revealing the dynamics of the search process.. ...
1997) Horizontal gene transfer and the evolution of resistance and virulence determinants in Streptococcus. JOURNAL OF APPLIED MICROBIOLOGY, 83 (Suppl. S). S42-S51 ...
This is a contribution to the history of scientific advance in the past 70 years concerning the identification of genetic information, its molecular structure, the identification of its functions and the molecular mechanisms of its evolution. Particular attention is thereby given to horizontal gene transfer among microorganisms, as well as to biosafety considerations with regard to beneficial applications of acquired scientific knowledge.
Horizontal Gene Transfer Regulation in Bacteria as a -Spandrel- of DNA Repair Mechanisms. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Acquisition of genes via horizontal transfer rather than by inheritance is frequently observed in bacteria. Now, Swedish researchers demonstrate that a similar phenomenon can occur between eucaryotic cells. Oncogenes from a dying cell can be transferred to a nearby cell via phagocytosis, a process through which one cell engulfs another. If the recipient cell is already genetically unstable, the newly acquired oncogenes can lead to tumor formation.. The researchers propose that this horizontal transfer of genes could be one route by which cells accumulate genetic abnormalities. The study also indicates that even after a cell dies, its genetic material entire chromosomes in some cases can be rescued by other cells.. The scientists mixed dying rat cells carrying cancer-causing oncogenes with mouse cells lacking p53, a tumor-suppressing gene. The p53-deficient cells developed tumor-like characteristics. The same experiment was done with mouse cells carrying p53. In contrast, however, the rat cells ...
Cellular metabolism is the network of chemical reactions that organisms use to convert input molecules into the molecules and energy they need to live and grow. Core metabolic processes and their enzyme catalysts are often conserved among the different kingdoms of life, which has allowed many species metabolic networks to be automatically reconstructed from their genome sequences by the identification of homologs [1-5]. In addition to core metabolic processes, peripheral processes allow species to adapt to different environments - for example, metabolism of a rare sugar. This adaptation can be driven by the gain of genes encoding enzymes through horizontal gene transfer (HGT) [6], and this process has for some time been seen as an important aspect of prokaryotic evolution [7-9]. But as more eukaryotic genome sequences have become available, it has become clear that HGT has also occurred in the evolutionary histories of the eukaryotes [10].. HGT is likely to have had a more important influence ...
As our project suggests the release of genetically modified bacterium into the environment, we feel it is necessary to contain the risk of horizontal gene transfer. Horizontal gene transfer can occur by the release of genetic information through cell lysis, and subsequent transformation of other bacteria. We decided we could target this system by constitutively expressing a nuclease. Any DNA released from the cell would therefore be digested, before it could diffuse, and transform wild-type bacteria. For this system we have selected a extracellular nuclease from Staphylococcus aureus (nucB), which has been well characterized (1-3) however it lacks the signal peptide for secretion to periplasm in E. coli. We chose DsbA (BBa_K243002) signal sequence that enables export of our nuclease to periplasm, thus it will allow us to digest extracellular genetic material. As horizontal gene transfer can also occur via bacteria conjugation, we are proposing a multi-containment system, consisting of three ...
As our project suggests the release of genetically modified bacterium into the environment, we feel it is necessary to contain the risk of horizontal gene transfer. Horizontal gene transfer can occur by the release of genetic information through cell lysis, and subsequent transformation of other bacteria. We decided we could target this system by constitutively expressing a nuclease. Any DNA released from the cell would therefore be digested, before it could diffuse, and transform wild-type bacteria. For this system we have selected a extracellular nuclease from Staphylococcus aureus (nucB), which has been well characterized (1-3) however it lacks the signal peptide for secretion to periplasm in E. coli. We chose DsbA (BBa_K243002) signal sequence that enables export of our nuclease to periplasm, thus it will allow us to digest extracellular genetic material. As horizontal gene transfer can also occur via bacteria conjugation, we are proposing a multi-containment system, consisting of three ...
This quote is deeply troubling. Genome sequencing did not reveal a new mechanism of evolution. And it is thus also inaccurate to say it would not have been discovered any other way". Lateral gene transfer was studies for many many many years before the first genome sequence was determined. Certainly, comparative genome analysis helped reveal the extent of gene transfer but it is seriously inaccurate to say it "revealed a new mechanism of evolution". Here for example is a link to a google search for the specific phrase "lateral gene transfer" in papers published prior to 1995. And here is one for the phrase "horizontal gene transfer ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Aims To purify and characterize an antimicrobial proteins (bacteriocin) isolated from your dairy product-derived The cell-free supernatant (CFS) of overnight cultures was active against and also against clinical isolates of and At the same time, several isolates of vaginal probiotic were resistant to the CFS. 3-D image of the molecules structure. It was determined to be a circular molecule of 35 amino acids with a very unique post-translational structure, namely three sulfur cross-links between cysteine and the 2004). Horizontal gene transfer (HGT) is usually a mechanism employed by bacteria as a means of acquiring new genetic properties. Although it was once hard to establish instances of HGT, genetic analysis now provides unmistakable supportive evidence. The evolutionary modification of traits is typically a slow and lengthy process defined by point mutations that inactivate or activate new regions of genes. In comparison, HGT can rapidly switch whole features of a species for generations to ...
1] Christopher M. Thomas & Kaare M. Nielsen. Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria. Nature Reviews Microbiology 3, 711-721 (September 2005) [2] Peter Gogarten & Jeffrey P. Townsend. Horizontal gene transfer, genome innovation and evolution. Nature Reviews Microbiology 3, 679-687 (September 2005) [3] Søren J. Sørensen, Mark Bailey, Lars H. Hansen, Niels Kroer and Stefan Wuertz. Studying plasmid horizontal transfer in situ: a critical review. Nature Reviews Microbiology 3, 700-710 (September 2005) [4] E. K. Weibel I, B. D. Seiffert. Biosafety investigations in an r-DNA production plant. Appl Microbiol Biotechnol (1993) 39:227-234 [5] Claudia Castro, Liliana González, Juan Carlos Rozo, Gloria Puerto, Wellman Ribón. Biosafety evaluation of the DNA extraction protocol for Mycobacterium tuberculosis complex species, as implemented at the Instituto Nacional de Salud, Colombia. Biomédica 2009;29:561-6 [6] Mark J. Espy, James R. Uhl, Lynne M. Sloan, Jon E. ...
Although the two primary forces driving the overall genome evolution of S. thermophilus consist of genome reduction by iterative gene losses in combination with occasional acquisition of beneficial genes through horizontal gene transfer for adaptation to a rich environment (primarily milk) [6,53,58,59], we show in the present article that CRISPR plays a major role in genome evolution following exposure to phages. Indeed, regressive genome evolution by extensive gene loss has been a key driving force shaping the adaptation of S. thermophilus to the rich milk environment, illustrated by the loss of virulence genes widely distributed in most streptococci. Overall, the DGCC7710 genome shares a high degree of synteny with other S. thermophilus genomes, with a few unique genomic islands and hypervariable loci that include the eps operon, the gp operon and CRISPR-Cas systems. Focusing on genome interplay within host-virus dynamics, we propose that the impact of the virus on host genome evolution is ...
RESULTS: Our model predicts that differential gene mobility drives intragenomic variation in investment in cooperative traits. More mobile loci generate stronger among-individual genetic correlations at these loci (higher relatedness) and thereby allow the maintenance of more cooperative traits via kin selection. By analyzing 21 Escherichia genomes, we confirm that genes coding for secreted proteins-the secretome-are very frequently lost and gained and are associated with mobile elements. We show that homologs of the secretome are overrepresented among human gut metagenomics samples, consistent with increased relatedness at secretome loci across multiple species. The biosynthetic cost of secreted proteins is shown to be under intense selective pressure, even more than for highly expressed proteins, consistent with a cost of cooperation driving social dilemmas. Finally, we demonstrate that mobile elements are in conflict with their chromosomal hosts over the chimeric ensembles social strategy, ...
The subject of this chapter is to describe the methodology for assessing the power of phylogenetic HGT detection methods. Detection power is defined in the framework of hypothesis testing. Rates of...
My friend asked what the implications of this might be. I offered a couple of thoughts. First, I said that just as differences in G+C content between genes in a given organism can sometimes be used to detect foreign genes (e.g., embedded phage/virus genes, horizontal gene transfers, etc.), variations in the purine to pyrimidine ratio of gene coding strands might also be a way to detect foreign genes. For example, in an organism like Clostridium botulinum, where the genomes coding regions have an average purine content of 58.5%, finding a gene with purine content below 46% (two standard deviations away from the mean) might be a tipoff that the gene came from a different organism. This is a useful new technique, because genes with high-purine-content coding regions dont always have high A+T content (thus, detection of horizontal gene transfers via purine loading will expose genes that would otherwise be missed on the basis of G+C content). In other words, two genes might have exactly the same ...
My friend asked what the implications of this might be. I offered a couple of thoughts. First, I said that just as differences in G+C content between genes in a given organism can sometimes be used to detect foreign genes (e.g., embedded phage/virus genes, horizontal gene transfers, etc.), variations in the purine to pyrimidine ratio of gene coding strands might also be a way to detect foreign genes. For example, in an organism like Clostridium botulinum, where the genomes coding regions have an average purine content of 58.5%, finding a gene with purine content below 46% (two standard deviations away from the mean) might be a tipoff that the gene came from a different organism. This is a useful new technique, because genes with high-purine-content coding regions dont always have high A+T content (thus, detection of horizontal gene transfers via purine loading will expose genes that would otherwise be missed on the basis of G+C content). In other words, two genes might have exactly the same ...
My friend asked what the implications of this might be. I offered a couple of thoughts. First, I said that just as differences in G+C content between genes in a given organism can sometimes be used to detect foreign genes (e.g., embedded phage/virus genes, horizontal gene transfers, etc.), variations in the purine to pyrimidine ratio of gene coding strands might also be a way to detect foreign genes. For example, in an organism like Clostridium botulinum, where the genomes coding regions have an average purine content of 58.5%, finding a gene with purine content below 46% (two standard deviations away from the mean) might be a tipoff that the gene came from a different organism. This is a useful new technique, because genes with high-purine-content coding regions dont always have high A+T content (thus, detection of horizontal gene transfers via purine loading will expose genes that would otherwise be missed on the basis of G+C content). In other words, two genes might have exactly the same ...
My friend asked what the implications of this might be. I offered a couple of thoughts. First, I said that just as differences in G+C content between genes in a given organism can sometimes be used to detect foreign genes (e.g., embedded phage/virus genes, horizontal gene transfers, etc.), variations in the purine to pyrimidine ratio of gene coding strands might also be a way to detect foreign genes. For example, in an organism like Clostridium botulinum, where the genomes coding regions have an average purine content of 58.5%, finding a gene with purine content below 46% (two standard deviations away from the mean) might be a tipoff that the gene came from a different organism. This is a useful new technique, because genes with high-purine-content coding regions dont always have high A+T content (thus, detection of horizontal gene transfers via purine loading will expose genes that would otherwise be missed on the basis of G+C content). In other words, two genes might have exactly the same ...
November 20, 2016 by Dr Rajiv Desai. Antimicrobial resistance (AMR): ______ ______ Prologue: Within a few days of scraping his leg in a scooter accident in 2009, nine-year-old Brock Wade was in hospital fighting for his life with a methicillin-resistant staphylococcus aureus (MRSA) infection. Once the infection - caused by one of the bacteria most often resistant to antibiotics - has been diagnosed, doctors put him on five different antibiotics. After a month in the hospital, and against all odds, Brock recovered and was well enough to come home. Scenarios such as this case are increasingly being played out all over the world. But not all the thousands of patients that contract drug-resistant bacterial infections every year are as lucky as Brock. And the problem looks set to get worse. While infectious agents are becoming more and more resistant to the medicines that are currently in use, not enough drugs are being developed to combat them. WHO […]. ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Using simulations, scientists report that a mixture of termites and plant competition may be responsible for the strange patterns of earth surrounded by plants in the Namib desert. 2 Comments. ...
Professionals in the genetics field generally support editing the genomes of somatic cells, mirroring public opinion, but diverge from nonexperts when it comes to germline editing.. 1 Comment. ...
Enterococci often acquire antimicrobial resistance through horizontal gene transfer. Relatedness between enterococci with high level resistance to gentamicin and vancomyc..
Classical biology has also saddled us with the phylogenetic tree, an image the biologist invests with a deep and totally unwarranted significance. The tree is no more than a representational device, but to the biologist it is some God-given truth. Thus, for example, we agonize over how the tree can accommodate horizontal gene transfer events, when it should simply be a matter of when (and to what extent) the evolution course can be usefully represented by a tree diagram. Evolution defines the tree, not the reverse. Tree imagery has locked the biologist into a restricted way of looking at ancestors. It is the tree image, almost certainly, that has caused us to turn Darwins conjecture that all organisms might have descended from a simple primordial form into doctrine: the doctrine of common descent. As we shall discuss below, it is also the tree image that has caused biologists (incorrectly) to take the archaea and the eukaryotes to be sister lineages. Much of the current "discussion/debate" ...
Classical biology has also saddled us with the phylogenetic tree, an image the biologist invests with a deep and totally unwarranted significance. The tree is no more than a representational device, but to the biologist it is some God-given truth. Thus, for example, we agonize over how the tree can accommodate horizontal gene transfer events, when it should simply be a matter of when (and to what extent) the evolution course can be usefully represented by a tree diagram. Evolution defines the tree, not the reverse. Tree imagery has locked the biologist into a restricted way of looking at ancestors. It is the tree image, almost certainly, that has caused us to turn Darwins conjecture that all organisms might have descended from a simple primordial form into doctrine: the doctrine of common descent. As we shall discuss below, it is also the tree image that has caused biologists (incorrectly) to take the archaea and the eukaryotes to be sister lineages. Much of the current "discussion/debate" ...
Classical biology has also saddled us with the phylogenetic tree, an image the biologist invests with a deep and totally unwarranted significance. The tree is no more than a representational device, but to the biologist it is some God-given truth. Thus, for example, we agonize over how the tree can accommodate horizontal gene transfer events, when it should simply be a matter of when (and to what extent) the evolution course can be usefully represented by a tree diagram. Evolution defines the tree, not the reverse. Tree imagery has locked the biologist into a restricted way of looking at ancestors. It is the tree image, almost certainly, that has caused us to turn Darwins conjecture that all organisms might have descended from a simple primordial form into doctrine: the doctrine of common descent. As we shall discuss below, it is also the tree image that has caused biologists (incorrectly) to take the archaea and the eukaryotes to be sister lineages. Much of the current "discussion/debate" ...
TY - JOUR. T1 - The Alpha-like surface proteins. T2 - An example of an expanding family of adhesins. AU - Creti, Roberta. AU - Baldassarri, L.. AU - Montanaro, L.. AU - Arciola, C. R.. PY - 2008/9. Y1 - 2008/9. N2 - The Alpha-like protein (Alp) family, repeat-containing surface proteins once thought to be important adhesion factors confined to pathogenic streptococci and enterococci, is broader than previously known. Analysis of the annotated microbial genomes has identified new potential members of the Alp family not only in other Gram- positive opportunistic pathogens but also in commensal microflora of the human gut and the skin. This finding has highlighted the importance of genome sequencing projects for unraveling in greater detail lateral gene transfer events involving virulence factors between pathogens and commensals. These should receive constant attention not only as part of infectious disease prevention programs, but also in the food and biotechnology industries.. AB - The Alpha-like ...
The problem with agriculture. A typical wheat field is a monoculture, composed of plants that are clones. These clones all grow at the same rate and set seed at the same time, which makes the decision on when to harvest easy. This convenience comes at a high cost. The uniformity of the plants make the entire field vulnerable and a field epidemic rapidly spreads its disease to neighbouring fields. Pathogens evolve mechanisms to attack plants and acquire nutrients from them. Once established, these mechanisms are easily shared within a pathogen species through sexual recombination. A more interesting form of evolution occurs when pathogens exchange DNA between species; a biological process known as Horizontal Gene Transfer (HGT). We observe HGT events by detecting genes or sequences of DNA that are near identical between distantly related species. To an untrained eye, it may appear that these DNA fragments are "copy-and-pasting" themselves between organisms. My work investigates one of these ...
Toggle abstract "Horizontal Gene Transfer (HGT) is the event of transferring genetic material from one lineage in the evolutionary tree to a different lineage. HGT plays a major role in bacterial genome diversification and is a significant mechanism by which bacteria develop resistance to antibiotics. Although the prevailing assumption is of complete HGT, cases of partial HGT (which are also named chimeric HGT) where only part of a gene is horizontally transferred, have also been reported, albeit less frequently. In this work we suggest a new probabilistic model for analyzing and modeling phylogenetic networks, the NET-HMM. This new model captures the biologically realistic assumption that neighboring sites of DNA or amino acid sequences are not independent, which increases the accuracy of the inference. The model describes the phylogenetic network as a Hidden Markov Model (HMM), where each hidden state is related to one of the networks trees. One of the advantages of the NET-HMM is its ability ...
In the past, when I worked intensively on the implementation of the Minimal Lateral Network method (Dagan and Martin 2007, Dagan et al. 2008) on linguistic data (List et al. 2014, List 2015), I stumbled upon numerous examples showing the limits of tree topology as a predictor for lateral transfer events. Given that the same necessarily also holds for lateral gene transfer, I was asking myself whether these false positives and the false negatives in the analyses would simply not matter due to the large amount of data in biology, or whether it was ignored due to the lack of good data for algorithmic evaluation. Later, when I read Davids post on Tardigrades and phylogenetic networks, where he pointed to two analyses on the same data that explained them once with lateral gene transfer (Boothby et al. 2015) and once with errors in the data (Koutsovoulos 2015), I became aware of the strong advantage of my linguistic data, since I could test it against written records, tracing the history of words ...
In the past, when I worked intensively on the implementation of the Minimal Lateral Network method (Dagan and Martin 2007, Dagan et al. 2008) on linguistic data (List et al. 2014, List 2015), I stumbled upon numerous examples showing the limits of tree topology as a predictor for lateral transfer events. Given that the same necessarily also holds for lateral gene transfer, I was asking myself whether these false positives and the false negatives in the analyses would simply not matter due to the large amount of data in biology, or whether it was ignored due to the lack of good data for algorithmic evaluation. Later, when I read Davids post on Tardigrades and phylogenetic networks, where he pointed to two analyses on the same data that explained them once with lateral gene transfer (Boothby et al. 2015) and once with errors in the data (Koutsovoulos 2015), I became aware of the strong advantage of my linguistic data, since I could test it against written records, tracing the history of words ...
By Michael Hawkins Mitochondrial DNA (mtDNA) is useful for determining the phylogeny, or relationships, between closely related species. It is inherited, generally, only from mother to offspring, so it doesnt face problems such as recombination since it isnt recombining with other DNA before being passed on (except through horizontal transfer, or
You will get two genes to analyze for horizontal gene transfer (HGT), from "Category A" and "Category B". Gene-Category-A: your first gene is an example where HGT is known to have occurred. Gene-Category-B: your second gene is an example where it is not yet known whether HGT has occurred.. Gene-Category-A collection (HGT is known to have occurredp; recipient means the organism that received the gene via HGT and donor means the organism that the gene came from.):. ...
Parallel horizontal gene transfer has spread a bacteriolytic gene family to all domains of life, and has bestowed a niche-transcending adaptation in recipients that must deploy antibacterial molecules to survive in a bacterial world.
The growing conviction that lateral gene transfer plays a significant role in prokaryote genealogy opens up a need for comprehensive evaluations of gene-enzyme systems on a case-by-case basis. Genes of tryptophan biosynthesis are frequently organized as whole-pathway operons, an attribute that is expected to facilitate multi-gene transfer in a single step. We have asked whether events of lateral gene transfer are sufficient to have obscured our ability to track the vertical genealogy that underpins tryptophan biosynthesis. In 47 complete-genome Bacteria, the genes encoding the seven catalytic domains that participate in primary tryptophan biosynthesis were distinguished from any paralogs or xenologs engaged in other specialized functions. A reliable list of orthologs with carefully ascertained functional roles has thus been assembled and should be valuable as an annotation resource. The protein domains associated with primary tryptophan biosynthesis were then concatenated, yielding single amino-acid
Author Summary Acquisition of DNA by horizontal gene transfer (HGT) significantly increases bacterial genetic variability. Relevant issues are the mechanisms that bacterial cells have evolved to efficiently integrate the newly acquired DNA into the host cell regulatory machinery. In Gram negative cells, the nucleoid associated protein H-NS has been shown to bind AT-rich sequences of HGT DNA and silence unwanted expression of these genes. This has led to consider H-NS as a
The distributed genome hypothesis states that the gene pool of a bacterial taxon is much more complex than that found in a single individual genome. However, the possible fitness advantage, why such genomic diversity is maintained, whether this variation is largely adaptive or neutral, and why these distinct individuals can coexist, remains poorly understood. Here, we present the infinitely many genes (IMG) model, which is a quantitative, evolutionary model for the distributed genome. It is based on a genealogy of individual genomes and the possibility of gene gain (from an unbounded reservoir of novel genes, e.g., by horizontal gene transfer from distant taxa) and gene loss, for example, by pseudogenization and deletion of genes, during reproduction. By implementing these mechanisms, the IMG model differs from existing concepts for the distributed genome, which cannot differentiate between neutral evolution and adaptation as drivers of the observed genomic diversity. Using the IMG model, we ...
Photosynthetic eukaryotes comprise the most visible and massive fraction of the biosphere. They have contributed to shaping land, oceans, and atmosphere during the last 2 billion years and their...
Competence for natural transformation - capacity to take up naked DNA into its own genome. The bacteria can make a quantum leap by simply grabbing effective DNA from the outside world. This horizontal gene transfer generally requires that similar sequences of DNA surround the DNA to be added; this enables the bacteria to pair up its own DNA with the new stuff. Thus most of the acquisitions will occur within related bacteria (same genus, not necessarily same species). There is a mechanism involving viruses for adding less matched DNA from a more distant relative. (This is the RNA side of things - think HIV which invades cells and begins running instructions for its own benefits. Humans are able to use the polymerase chain reaction along with an innocuous virus to introduce snippets of DNA into our own cells - in tests - and bacteria have a similar natural capability). ...
Symbiosis model (or 2D model). This model proposes the direct fusion of an archaea and a bacterium, which means there is no protoeukaryote. In this scenario, two distant branches of the tree of life getting fused, leading to the emergence of a completely new branch of cells. There are some evidences supporting this proposal. Nowadays, the presence of bacteria containing other prokaryotes as endosymbionts has been described. The fusion event boosted the increase in cellular complexity, the bacterium became the mitochondria. Both cells shared different cell activities: archaea were in charge of DNA and bacteria dealt with metabolism. There is another version of this model in which there was no starting endosymbiosis event, but a long period of time where these two cells cooperated together. During this time, horizontal gene transfer (interchange of genes) was possible because they were spatially close. In this version of the model, the hydrogen hypothesis is suggested. The bacterium produced ...
Added "overflow-y: hidden;" to the CSS for the default skin to prevent some browsers (Chrome, Firefox, and Safari on macOS, at least) from adding a vertical scroll bar to the navbar. This was only necesasry on this skin because of the recently-added "overflow-x: auto" style, which tells the browser to clip or horizontally-scroll the navbar if the screen width isnt sufficient to show the whole thing; previously in this skin, and currently in all other skins, this condition causes the navbar to wrap to the next line, which looks particularly bad on the default skin. I believe this then made these browsers calculate some extra space for a possible horizontal scroll bar, which then ran the layout engine out of space, so it included the vertical bar just in case. This may be macOS specific, due to the scroll bar hiding behavior introduced several OS release back. check-in: e8783b9a user: wyoung tags: trunk ...
Added "overflow-y: hidden;" to the CSS for the default skin to prevent some browsers (Chrome, Firefox, and Safari on macOS, at least) from adding a vertical scroll bar to the navbar. This was only necesasry on this skin because of the recently-added "overflow-x: auto" style, which tells the browser to clip or horizontally-scroll the navbar if the screen width isnt sufficient to show the whole thing; previously in this skin, and currently in all other skins, this condition causes the navbar to wrap to the next line, which looks particularly bad on the default skin. I believe this then made these browsers calculate some extra space for a possible horizontal scroll bar, which then ran the layout engine out of space, so it included the vertical bar just in case. This may be macOS specific, due to the scroll bar hiding behavior introduced several OS release back. (check-in: e8783b9a user: wyoung tags: trunk) ...
A bacterium that survives the ax of an antibiotic will multiply and pass on its resistant properties to its progeny. Also, some bacteria can transfer their drug-resistant properties to other bacteria in a process known as horizontal gene transfer. This is the case for S. aureus. Normally, penicillin would kill S. aureus because the drug inhibits enzymes required for bacteria to make their cell wall, the protective barrier between their internal machineries and the outside world. However, MRSA was able to pick up and incorporate a plasmid, a circular bit of DNA, containing the resistance gene known as mecA into its own genome. This gene staves off any inhibition by penicillin. Resistance mechanisms like this often arise when patients overuse or misuse antibiotics. If an individual does not finish their series of antibiotic medication or otherwise fully adhere to a prescribed regimen, surviving bacteria that pass on their resistance are a very likely effect. The same thing happens if a physician ...
Bachelor thesis will be focused on overview of current knowledge about the horizontal gene transfer mediated by bacteriophages. Attention will be paid especially on the importance of bacteriophage in the evolution of pathogenic bacterial species and dissemination of genes responsible for antimicrobial resistance as well as genes coding for virulence factors. The mechanism of individual types of transduction and transmission of genes carried on the chromosome and on the variable genetic elements will be described. Detailed information about importance of phages in the evolution of bacteria will relate in particular staphylococcal species. …víceméně ...
General properties of bacteria: cell structure/function, cell membranes and cell walls, surface structures and inclusions, flagella and Motility. Chromosomes and other genetic elements. Nutrition, Growth, laboratory culture and metabolism of Microorganisms. Bacterial genetics: mutations, recombination and horizontal gene transfer. Pathogenesis of bacterial infections and Host responses. Microbial growth control. Chemotherapy: antibiotics and antibiotic resistance ...
Antibiotics have been a cornerstone of innovation in the fields of public health, agriculture, and medicine. However, recent studies have shed new light on the collateral damage they impart on the indigenous host-associated communities. These drugs have been found to alter the taxonomic, genomic, and functional capacity of the human gut microbiota, with effects that are rapid and sometimes persistent. Broad-spectrum antibiotics reduce bacterial diversity while expanding and collapsing membership of specific indigenous taxa. Furthermore, antibiotic treatment selects for resistant bacteria, increases opportunities for horizontal gene transfer, and enables intrusion of pathogenic organisms through depletion of occupied natural niches, with profound implications for the emergence of resistance. Because these pervasive alterations can be viewed as an uncoupling of mutualistic host-microbe relationships, it is valuable to reconsider antimicrobial therapies in the context of an ecological framework. ...
We study mechanisms of transcription regulation by the histone-like nucleoid-structuring protein HNS in commensal and pathogenic Escherichia coli. Specifically, we focus on mechanisms of de-repression by the LysR-type and FixJ/NarL-type transcription regulators such as LeuO, BglJ-RcsB and others, and their role in regulatory networks controlling pathogenicity. In addition, we analyze the interdependence of repression by H-NS and the rate of transcription. H-NS is an pleiotropic regulator and an architectural protein of the enterobacterial chromosome (the nucleoid), and it is important for silencing of loci acquired by horizontal gene transfer and for bacterial fitness. H-NS binds as dimer to specific nucleation sites located within an AT-rich sequence context, and then forms extended complexes by polymerization along the DNA (stiffening) and by building DNA-HNS-DNA bridges (bridging). Formation of HNS-DNA complexes next to promoters represses transcription by occluding RNA polymerase or, as ...
ISIS first raised concerns over the CaMV 35S and similar promoters in a paper published in the journal Microbial Ecology in Health and Disease in 1999 [4] (Cauliflower Mosaic Viral Promoter - A Recipe for Disaster?) when it was discovered to have a recombination (fragmentation) hotspot that would enhance unintended horizontal gene transfer and recombination, and in the process create new viruses or activate old ones, and trigger cancer in animal cells by well-known processes of insertion carcinogenesis. The CaMV 35S promoter was known to be highly promiscuous in being able to function in most if not all species across the living world (including human cells, as it turned out). To make matters worse, many synthetic versions of the promoter have been constructed with additional enhancers for gene expression and sequences from other sources, all of which increase its instability (tendency to fragment) as well as its ability to drive inappropriate gene expression. (We also reported the overlap of ...
Mode of transfer of bacterial genes (genome) through a virus. There are two types, general and specialized by lytic and lysognic phages.
There is an emerging consensus is that HGT in bacteria is indeed very common. The only papers that find that HGT is rare are the ones that consider only the most highly conserved genes. Since HGT is so common, gene content within a "species" varies dramatically, and although the concept of bacterial species is too useful to give up, it does seem rather problematic.. Now, when I was in grad school 15 years ago, HGT was considered to be rare, spooky, and wierd. Yet it turns out that HGT is very common, and that HGT plays a major role in the evolution of new traits, such as antibiotic resistance or the ability to degrade novel man-made chemicals. I do think this qualifies as a revolution in our understanding of microbial evolution.. Finally, this doesnt just apply to bacteria. There is plenty of evidence for HGT in eukaryotes, although we dont have nearly enough genome sequences to know how common it is yet.. ...
Lateral gene transfer would be like if a stranger you bumped into on the street gave you a part of their DNA that you could incorporate into your own genes.
For decades, global health experts, policymakers, and others have been debating the merits of disease-specific initiatives versus broader efforts to strengthen health systems. Its the old the vertical vs. horizontal argument. No one has settled that debate. But maybe we should stop asking that particular question. Or at least start asking some new ones.
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Abstract The two-region hydraulic averaging model was used to analyze the problem of cuttings transport during horizontal well drilling. This model considers a two-phase two region system composed of a moving bed ( ω-region) and a stationary b
The goal of this training course is to present an integrated approach to the design and drilling of horizontal, extended reach and multilateral wells.
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Despite a large agreement between ribosomal RNA and concatenated protein phylogenies, the phylogenetic tree of the bacterial domain remains uncertain in its deepest nodes. For instance, the position of the hyperthermophilic Aquificales is debated, as their commonly observed position close to Thermotogales may proceed from horizontal gene transfers, long branch attraction or compositional biases, and may not represent vertical descent. Indeed, another view, based on the analysis of rare genomic changes, places Aquificales close to epsilon-Proteobacteria. To get a whole genome view of Aquifex relationships, all trees containing sequences from Aquifex in the HOGENOM database were surveyed. This study revealed that Aquifex is most often found as a neighbour to Thermotogales. Moreover, informational genes, which appeared to be less often transferred to the Aquifex lineage than non-informational genes, most often placed Aquificales close to Thermotogales. To ensure these results did not come from long branch
en] alpha-Amylases are present in all kingdoms of the living world. Despite strong conservation of the tertiary structure, only a few amino acids are conserved in interkingdom comparisons. Animal alpha-amylases are characterized by several typical motifs and biochemical properties. A few cases of such alpha-amylases have been previously reported in some eubacterial species. We screened the bacterial genomes available in the sequence databases for new occurrences of animal-like alpha-amylases. Three novel cases were found, which belong to unrelated bacterial phyla: Chloroflexus aurantiacus, Microbulbifer degradans, and Thermobifida fusca. All the animal-like alpha-amylases in Bacteria probably result from repeated horizontal gene transfer from animals. The M. degradans genome also contains bacterial-type and plant-type alpha-amylases in addition to the animal-type one. Thus, this species exhibits alpha-amylases of animal, plant, and bacterial origins. Moreover, the similarities in the extra ...
Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Salmonella enterica bacteria have become increasingly resistant to antimicrobial agents, partly as a result of genes carried on integrons. Clonal expansion and horizontal gene transfer may contribute to the spread of antimicrobial drug-resistance integrons in these organisms. We investigated this resistance and integron carriage among 90 isolates with the ACSSuT phenotype (resistance to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline) in a global collection of S. enterica isolates. Four integrons, dfrA12/orfF/aadA2, dfrA1/aadA1, dfrA7, and arr2/blaOXA30/cmlA5/aadA2, were found in genetically unrelated isolates from 8 countries on 4 continents, which supports a role for horizontal gene transfer in the global dissemination of S. enterica multidrug resistance. Serovar Typhimurium isolates containing identical integrons with the gene cassettes blaPSE1 and aadA2 were found in 4 countries on 3 continents, which supports the role of clonal expansion. This study ...
Hybrid zones and the consequences of hybridization have contributed greatly to our understanding of evolutionary processes. Hybrid zones also provide valuable insight into the dynamics of symbiosis since each subspecies or species brings its unique microbial symbionts, including germline bacteria such as Wolbachia, to the hybrid zone. Here, we investigate a natural hybrid zone of two subspecies of the meadow grasshopper Chorthippus parallelus in the Pyrenees Mountains. We set out to test whether co-infections of B and F Wolbachia in hybrid grasshoppers enabled horizontal transfer of phage WO, similar to the numerous examples of phage WO transfer between A and B Wolbachia co-infections. While we found no evidence for transfer between the divergent co-infections, we discovered horizontal transfer of at least three phage WO haplotypes to the grasshopper genome. Subsequent genome sequencing of uninfected grasshoppers uncovered the first evidence for two discrete Wolbachiasupergroups (B and F) ...
PhD fellowship in Bioinformatics and Bacterial Genomics. Searching for ICEs, Integrative and Conjugative Elements in bacteria: development of a tool for the search and the visualization of ICEs, and impact of these elements in the dissemination of antibiotic resistance genes. Background: Mobile genetic elements play a key role in bacterial genome evolution by enabling gene acquisition through horizontal gene transfer (HGT). Multiplication of bacterial genome sequencing projects provided a remarkable opportunity to explore the pool of bacterial mobile genetic elements ("mobilome"). This shed the light on elements integrated in the chromosome called Integrative and Conjugative Elements (ICEs). These elements are still poorly known although all the very few ICE searches in genomes suggest their high prevalence in bacteria. ICEs encode their own excision, transfer by conjugation and integration. In addition to the genes involved or controlling their mobility, ICEs carry cargo genes, which can ...
The evolutionary histories of genomes and of individual genes are important for understanding the genetic basis of microbial physiology. Genes that have a different history than the rest of the genome due to lateral genetic transfer may provide insight into the unique abilities of closely related organisms, but also serve to disrupt inference of the history of organisms by common lineage. Inconsistent results in phylogenetic signal among different genes and derived by different methods illustrate the need for approaches that can utilize multiple genes and clarify phylogenetic signal across entire genomes. Phylogenetic inference based on models of nucleotide and amino acid substitutions has become the standard, but higher level markers such as conserved insertions and deletions (indels), may provide clearer results.; Indels appear as gaps in the alignment of sequences, but high levels of alignment errors associated with gaps have generally meant their exclusion from phylogenetic analysis. Efforts ...
Vibrio cholerae in O-group 139 was first isolated in 1992 and by 1993 had been found throughout the Indian subcontinent. This epidemic expansion probably resulted from a single source after a lateral gene transfer (LGT) event that changed the serotype of an epidemic V. cholerae O1 El Tor strain to O139. However, some studies found substantial genetic diversity, perhaps caused by multiple origins. To further explore the relatedness of O139 strains, we analyzed nine sequenced loci from 96 isolates from patients at the Infectious Diseases Hospital, Calcutta, from 1992 to 2000. We found 64 novel alleles distributed among 51 sequence types. LGT events produced three times the number of nucleotide changes compared to mutation. In contrast to the traditional concept of epidemic spread of a homogeneous clone, the establishment of variant alleles generated by LGT during the rapid expansion of a clonal bacterial population may be a paradigm in infections and epidemics ...
Horizontal transfer (HT) of transposable elements (TEs) plays a key role in prokaryotic evolution, and mounting evidence suggests that it has also had an important impact on eukaryotic evolution. Although many prokaryote-to-prokaryote and eukaryote-to-eukaryote HTs of TEs have been characterized, only few cases have been reported between prokaryotes and eukaryotes. Here, we carried out a comprehensive search for all major groups of prokaryotic insertion sequences (ISs) in 430 eukaryote genomes. We uncovered a total of 80 sequences, all deriving from the IS607 family, integrated in the genomes of 14 eukaryote species belonging to four distinct phyla (Amoebozoa, Ascomycetes, Basidiomycetes, and Stramenopiles). Given that eukaryote IS607-like sequences are most closely related to cyanobacterial IS607 and that their phylogeny is incongruent with that of their hosts, we conclude that the presence of IS607-like sequences in eukaryotic genomes is the result of several HT events. Selection analyses further
Strategy for In Situ Detection of Natural Transformation-Based Horizontal Gene Transfer Events - they used a pUC derived plasmid called pCLT that they got from Palmen and Hellingwerf ...
DARPA SBIR 12.2 Topic Descriptions. SB122-001 TITLE: Controlling Antibiotic Resistant or Highly Virulent Pathogens Through Plasmid. Curing. TECHNOLOGY AREAS: Chemical/Bio Defense, Biomedical. OBJECTIVE: Develop a novel plasmid curing therapeutic capable of displacing antibiotic resistance and/or virulence causing plasmids from bacteria. Therapeutic interventions are sought that will be efficacious against a range of human pathogens of interest to the DoD.. DESCRIPTION: The combined threat of the increasing prevalence of drug-resistant bacteria and a diminishing antibiotic pipeline places our warfighters at risk not only from health care associated and community acquired infections, but also from pandemics, emerging infectious pathogens and the intentional use of resistant pathogens for bioterrorism. One of the major routes by which bacterial pathogens become resistant to antibiotics and more virulent is through Horizontal Gene Transfer (HGT), which allows for genetic material transfer in the ...
We recently demonstrated that the Escherichia coli ribosome is robust enough to accommodate foreign 16S rRNAs from diverse gamma- and beta-proteobacteria bacteria (Kitahara, Yasutake, and Miyazaki. Proc Natl Acad Sci U S A. 109:19220-19225, 2012, doi: 10.1073/pnas.1213609109). Therein, we used the common universal primers Bac8f and UN1541r to obtain a nearly full-length gene. However, we noticed that these primers overlap variable sites at 19[A/C] and 1527[U/C] in Bac8f and UN1541r, respectively, and thus the amplicon could contain mutations. This is problematic, particularly for the former site, because the 19th nucleotide pairs with the 916th nucleotide, which is a part of the
Bacteria are programmed using synthetic biology to release gas to report when they exchange DNA through horizontal gene transfer, the process by which organisms share genetic traits without a parent-to-child relationship.
In eukaryotic organisms, horizontal gene transfer (HGT) is regarded as an important though infrequent source of reticulate evolution. Many confirmed instances of natural HGT involving multicellular eukaryotes come from flowering plants. This review intends to provide a synthesis of present knowledge regarding HGT in higher plants, with an emphasis on tobacco and other species in the Solanaceae family because there are numerous detailed reports concerning natural HGT events, involving various donors, in this family. Moreover, in-depth experimental studies using transgenic tobacco are of great importance for understanding this process. Valuable insights are offered concerning the mechanisms of HGT, the adaptive role and regulation of natural transgenes, and new routes for gene trafficking. With an increasing amount of data on HGT, a synthetic view is beginning to emerge.. ...
Although there is tremendous interest in understanding the evolutionary roles of horizontal gene transfer (HGT) processes that occur during chronic polyclonal infections, to date there have been few studies that directly address this topic. We have characterized multiple HGT events that most likely occurred during polyclonal infection among nasopharyngeal strains of Streptococcus pneumoniae recovered from a child suffering from chronic upper respiratory and middle-ear infections. Whole genome sequencing and comparative genomics were performed on six isolates collected during symptomatic episodes over a period of seven months. From these comparisons we determined that five of the isolates were genetically highly similar and likely represented a dominant lineage. We analyzed all genic and allelic differences among all six isolates and found that all differences tended to occur within contiguous genomic blocks, suggestive of strain evolution by homologous recombination. From these analyses we identified
We have found that cell-cell signaling is used to regulate horizontal transfer of the integrative and conjugative element ICEBs1, a conjugative transposon found in the B. subtilis genome. These types of elements are widespread in the microbial world and contribute to horizontal gene transfer, evolution, virulence, and the spread of antibiotic resistance. ICEBs1 is regulated by population density and cell-cell signaling in two ways. 1) At high population density, in the presence of potential mating partners, the element is stimulated to excise from the chromosome and can then transfer to potential recipients. 2) However, if the potential recipients already contain a copy of the element, then excision of the element is inhibited and there is little or no transfer to the potential recipients that already contain the element. We found that the secreted pentapeptide, a product of phrI, that regulates this "recognition of self" is encoded in the element. In the absence of this peptide, as cells grow ...
Typically, the proto-language is not known directly. It is by definition a linguistic reconstruction formulated by applying the comparative method to a group of languages featuring similar characteristics.[2] The tree is a statement of similarity and a hypothesis that the similarity results from descent from a common language. The comparative method, a process of deduction, begins from a set of characteristics, or characters, found in the attested languages. If the entire set can be accounted for by descent from the proto-language, which must contain the proto-forms of them all, the tree, or phylogeny, is regarded as a complete explanation and by Occams razor, is given credibility. More recently such a tree has been termed "perfect" and the characters labelled "compatible". No trees but the smallest branches are ever found to be perfect, in part because languages also evolve through horizontal transfer with their neighbours. Typically, credibility is given to the hypotheses of highest ...
RESEARCH INTERESTS Dr. Pascal Simonet obtained his PhD in 1983. Currently his research group investigates the evolution potential of bacteria in environments such as the soil and plants. For more than 15 years the research group entitled « Gene Transfer and Bacterial Adaptation » that he led at the University of Lyon has had the general objectives of determining the involvement of horizontal gene transfers (HGT) in the adaptation and evolution of bacteria to new environments. Studies of the group focused mainly on natural genetic transformation and also, but at a lesser extent, on conjugation. These objectives lead the group to develop soil DNA extraction methods and it was among the first to investigate environmental bacteria with metagenomic approaches. Several of the studies were devoted to investigate the fate of DNA released by genetically engineered organisms including the possibility that recombinant DNA, and particularly antibiotic resistance genes transforms indigenous bacteria. The ...
The question of whether bacterial species objectively exist has long divided microbiologists. A major source of contention stems from the fact that bacteria regularly engage in horizontal gene transfer (HGT), making it difficult to ascertain relatedness and draw boundaries between taxa. A natural way to define taxa is based on exclusivity of relatedness, which applies when members of a taxon are more closely related to each other than they are to any outsider. It is largely unknown whether exclusive bacterial taxa exist when averaging over the genome or are rare due to rampant hybridization. Here, we analyze a collection of 701 genomes representing a wide variety of environmental isolates from the family Streptomycetaceae, whose members are competent at HGT. We find that the presence/absence of auxiliary genes in the pan-genome displays a hierarchical (tree-like) structure that correlates significantly with the genealogy of the core-genome. Moreover, we identified the existence of many exclusive taxa,
The second assumption is that bacteria can easily take up DNA from the environment. In the case of Vibrio cholerae that is true, if theyre growing on a crab shell (freely available article). I think LabRat is highlighting the importance and sexiness of Horizontal Gene Transfer (HGT). HGT clearly occurs between bacteria, not just different cells of the same species, but also different species, hell even different phyla! It is a phenomenon built of WIN! and really HGT was a game changer for how we (scientists) think about biology. HGT is important and its discovery revolutionized bacterial genetics. But lets not overstate it. HGT has occurred and is important. But is it a potential force of evolution? Yes. Is it the driving force? No, well at least not necessarily. In fact, bacterial species have a way to generate genetic diversity without taking up DNA from the environment, which is based on DNA polymerase IV. DNA polymerase IV is an error prone DNA polymerase, which means when replicating the ...
The study of genetic exchange resulting from natural hybridization, horizontal gene transfer, and viral recombination has long been marked by controversy between researchers holding different conceptual frameworks. Those subscribing to a doctrine of species purity have traditionally been reluctant to recognise inferences suggesting anything other than a marginal role for non-allopatric divergence leading to gene transfer between different lineages.
Horizontal gene transfer (HGT) is a real thing. Its a process through which bacteria sometimes take up DNA from the environment and integrate it into their own genomes. Animals cant do HGT, but rather infamously, a paper was published in December 2015 that made the bold claim that tardigrades had a unique ability to absorb all kinds of DNA. That paper was instantly controversial in the scientific community, and not surprisingly its findings were being disputed in the Twittersphere within days of its appearance. Surprisingly, the same journal (PNAS) that published the bogus HGT claim published a second paper just a few months later showing that tardigrades do not absorb foreign DNA into their genome. That plus a third paper showed that the original paper had mistakenly identified contaminating DNA as part of the tardigrades own genome. This rapid correction of the record was a win for science; Ive used this example to demonstrate to my undergraduate class how sloppy science (the first paper) ...
Horizontal gene transfer (HGT) is a real thing. Its a process through which bacteria sometimes take up DNA from the environment and integrate it into their own genomes. Animals cant do HGT, but rather infamously, a paper was published in December 2015 that made the bold claim that tardigrades had a unique ability to absorb all kinds of DNA. That paper was instantly controversial in the scientific community, and not surprisingly its findings were being disputed in the Twittersphere within days of its appearance. Surprisingly, the same journal (PNAS) that published the bogus HGT claim published a second paper just a few months later showing that tardigrades do not absorb foreign DNA into their genome. That plus a third paper showed that the original paper had mistakenly identified contaminating DNA as part of the tardigrades own genome. This rapid correction of the record was a win for science; Ive used this example to demonstrate to my undergraduate class how sloppy science (the first paper) ...
Plasmid-mediated horizontal gene transfer is recognized as a major driving force for bacterial adaptation and diversification. Different environmental settings have distinct bacterial community compositions, which determine-possibly with the exception of broad host range plasmids-the type of dominant plasmids that can be found. It is assumed that only a fraction of a population carries plasmids, which ensures a rapid adaptation of the population to changing environmental conditions ( 1 ). Without a doubt, plasmid-mediated spread of antibiotic resistance genes among bacteria of different taxa is one of the most impressive examples of bacterial plasticity in response to various selective pressures ( 2 , 3 ). While the molecular biology of the plasmid-encoded replication, maintenance, and transfer processes of some plasmids has been studied for decades, little attention has been paid to their dissemination in the environment, their ecology, and the factors that drive their spread and diversification. In
I dunno.. "Symbiogenetic cell fusions, horizontal DNA transfer, mutagenic DNA repair, reverse transcription of RNA into DNA, mobile genetic elements, interspecific hybridization and whole genome doubling," which Shapiro says he discusses in his book, could-taken together-explain a lot of things that are currently at the mercy of Darwins duds. (See this, for example.). The only way we could find out what mechanisms account for which changes would be to defund Darwinism, and throw the whole thing open for serious research (as opposed to current research that attempts to demonstrate Darwin at work and portrays the rapidly growing number of failures as some kind of a big surprise).. Yuh. Surprise, surprise.. But good luck defunding Darwinism when those who oppose it undercut each other. And rhetoric about "the ideals of liberty, democracy and opportunity on which this nation was founded" sounds rather thin after Amarillo.. So now, what is really at issue here? Shapiro claims to have "abundant ...
Antibiotic resistance prompted with the overuse of antimicrobial agents may arise from a number of mechanisms particularly horizontal gene transfer of virulence and antibiotic resistance genes which is definitely often facilitated by biofilm formation. in level of resistance and virulence not merely in the framework from the biofilm but GDC-0941 also as inextricably linked pathologies. Observationally it really is very clear that improved virulence as well as the arrival of antibiotic level of resistance often arise nearly simultaneously; nevertheless their genetic connection GDC-0941 has been relatively ignored. Although the complexities of genetic regulation in a multispecies community may obscure a causative relationship uncovering key genetic interactions between virulence and resistance in biofilm bacteria is essential to identifying new druggable targets ultimately providing a drug discovery and development pathway to improve treatment options for chronic and recurring infection. spp. are ...
Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components, such as DNA, fatty acids, pigments, antigens and quinones.[101] While these schemes allowed the identification and classification of bacterial strains, it was unclear whether these differences represented variation between distinct species or between strains of the same species. This uncertainty was due to the lack of distinctive structures in most bacteria, as well as lateral gene transfer between unrelated species.[148] Due to lateral gene transfer, some closely related bacteria can have very different morphologies and metabolisms. To overcome this uncertainty, modern bacterial classification emphasises molecular systematics, using genetic techniques such as guanine cytosine ratio determination, genome-genome hybridisation, as well as sequencing genes that ...
Bacteria are slippery little suckers. They evolve rapidly, developing resistance to antibiotics and therefore becoming increasingly difficult to deal with. Now, for the first time, researchers have caught on film one of the mechanisms the microbes use for this speedy evolution.. Two Vibrio cholerae bacteria - the pathogen responsible for cholera - sit under a microscope, glowing a vivid green. As we watch, a tendril snakes forth from one of the bacterium, harpooning a piece of DNA and carrying it back to its body.. That appendage is called a pili, and the process whereby the bacteria incorporates the new genetic material from a different organism into its own DNA to expedite its evolution is called horizontal gene transfer.. ...
Hi all, I was wondering if any has hear of a higher eukaryotic gene organization such as this : 2 genes, intronless, facing towards eachother (promotion-wise) that are absolutly critical for the function of a system. these genes show no homology to eachother (or anyother genes for that matter) but are conserved for over 500 million years of evolution. they are absolutly critical for function. these are the recombinase activating genes. they are essential for immune system function-t and b cell rearrangement. a possible theory is that they are the resylt of horizontal gene transfer from a viral infection (intronless, 2 genes for one function right next to each other on the same chromasome...ect) 500 million years ago or so. they are almost completly conserved over this time. question: can anyone support the viral introduction theory? can anyone give me an example of any other system where 2 genes like this are essential for function, may have similar function (well maybe not similar but ...
There is a large literature on gene silencing, in which the transgenes remain in the genome, but are not expressed. More serious, from the safety point of view, is structural instability, the tendency for the transgenic DNA to come loose, to rearrange or become lost in part or in whole in successive generations [2,3]. This could change the transgenic line in unpredictable ways in terms of health and environmental risks. And it will increase the chance of transgenic DNA being taken up by unrelated species to make new combinations with their genetic material. Thats referred to as horizontal gene transfer and recombination. Transgenic DNA can spread to every species that interact with the transgenic plant, in the soil, in the air, in the mouth and gut and the respiratory tracts of animals including human beings ...
Lateral gene transfer may be more common than previously thought. Scientists at U Rochester recently found a pickles entire genome tucked inside its hosts DNA. Such large-scale heritable gene transfers may allow species to acquire new genes and flavors extremely quickly, says Jack Werren, a principle investigator of the study. If such genes provide new abilities in species that cause or transmit deliciousness, they could provide new techniques to deli sandwich-makers. "Imagine if the pickle flavor was present in the meat," he says. "Think about it.". "This study establishes the widespread occurrence and high frequency of a process that we would have dismissed as science fiction until just a few years ago," says W. Ford Doolittle, Canada Research Chair in Comparative Microbial Genomics at Dalhousie University, who is not connected to the study. "This is stunning evidence for that old parable: you are what you eat.". Gusss may be the most prolific pickle in the world-a "pandemic," as Werren ...
by Roberto | In his recent murder mystery post Dial V for Murder, Christoph stated that fewer that 30 out of STCs 1,200+ posts had dealt with the topic of horizontal gene transfer. Considering the cardinal role of that process in the evolutionary history of microbes, such a small fraction of posts - relative to the importance of the subject matter - led him to argue that one more post on the topic would not prove redundant.