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Sample records for autonomous non-ltr retrotransposons

  1. Identification of a non-LTR retrotransposon from the gypsy moth

    Science.gov (United States)

    K.J. Garner; J.M. Slavicek

    1999-01-01

    A family of highly repetitive elements, named LDT1, has been identified in the gypsy moth, Lymantria dispar. The complete element is 5.4 kb in length and lacks long-terminal repeats, The element contains two open reading frames with a significant amino acid sequence similarity to several non-LTR retrotransposons. The first open reading frame contains...

  2. Horizontal Transfer of Non-LTR Retrotransposons from Arthropods to Flowering Plants.

    Science.gov (United States)

    Gao, Dongying; Chu, Ye; Xia, Han; Xu, Chunming; Heyduk, Karolina; Abernathy, Brian; Ozias-Akins, Peggy; Leebens-Mack, James H; Jackson, Scott A

    2018-02-01

    Even though lateral movements of transposons across families and even phyla within multicellular eukaryotic kingdoms have been found, little is known about transposon transfer between the kingdoms Animalia and Plantae. We discovered a novel non-LTR retrotransposon, AdLINE3, in a wild peanut species. Sequence comparisons and phylogenetic analyses indicated that AdLINE3 is a member of the RTE clade, originally identified in a nematode and rarely reported in plants. We identified RTE elements in 82 plants, spanning angiosperms to algae, including recently active elements in some flowering plants. RTE elements in flowering plants were likely derived from a single family we refer to as An-RTE. Interestingly, An-RTEs show significant DNA sequence identity with non-LTR retroelements from 42 animals belonging to four phyla. Moreover, the sequence identity of RTEs between two arthropods and two plants was higher than that of homologous genes. Phylogenetic and evolutionary analyses of RTEs from both animals and plants suggest that the An-RTE family was likely transferred horizontally into angiosperms from an ancient aphid(s) or ancestral arthropod(s). Notably, some An-RTEs were recruited as coding sequences of functional genes participating in metabolic or other biochemical processes in plants. This is the first potential example of horizontal transfer of transposons between animals and flowering plants. Our findings help to understand exchanges of genetic material between the kingdom Animalia and Plantae and suggest arthropods likely impacted on plant genome evolution. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  3. Evolutionary dynamics in a novel L2 clade of non-LTR retrotransposons in Deuterostomia.

    Science.gov (United States)

    Lovsin, N; Gubensek, F; Kordi, D

    2001-12-01

    The evolution of the novel L2 clade of non-long terminal repeat (LTR) retrotransposons and their evolutionary dynamics in Deuterostomia has been examined. The short-term evolution of long interspersed nuclear element 2s (LINE2s) has been studied in 18 reptilian species by analysis of a PCR amplified 0.7-kb fragment encoding the palm/fingers subdomain of reverse transcriptase (RT). Most of the reptilian LINE2s examined are inactive since they contain multiple stop codons, indels, or frameshift mutations that disrupt the RT. Analysis of reptilian LINE2s has shown a high degree of sequence divergence and an unexpectedly large number of deletions. The evolutionary dynamics of LINE2s in reptiles has been found to be complex. LINE2s are shown to form a novel clade of non-LTR retrotransposons that is well separated from the CR1 clade. This novel L2 clade is more widely distributed than previously thought, and new representatives have been discovered in echinoderms, insects, teleost fishes, Xenopus, Squamata, and marsupials. There is an apparent absence of LINE2s from different vertebrate classes, such as cartilaginous fishes, Archosauria (birds and crocodiles), and turtles. Whereas the LINE2s are present in echinoderms and teleost fishes in a conserved form, in most tetrapods only highly degenerated pseudogenes can be found. The predominance of inactive LINE2s in Tetrapoda indicates that, in the host genomes, only inactive copies are still present. The present data indicate that the vertical inactivation of LINE2s might have begun at the time of Tetrapoda origin, 400 MYA. The evolutionary dynamics of the L2 clade in Deuterostomia can be described as a gradual vertical inactivation in Tetrapoda, stochastic loss in Archosauria and turtles, and strict vertical transmission in echinoderms and teleost fishes.

  4. Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia.

    Science.gov (United States)

    Kojima, Kenji K; Jurka, Jerzy

    2015-01-01

    Most non-long terminal repeat (non-LTR) retrotransposons encoding a restriction-like endonuclease show target-specific integration into repetitive sequences such as ribosomal RNA genes and microsatellites. However, only a few target-specific lineages of non-LTR retrotransposons are distributed widely and no lineage is found across the eukaryotic kingdoms. Here we report the most widely distributed lineage of target sequence-specific non-LTR retrotransposons, designated Utopia. Utopia is found in three supergroups of eukaryotes: Amoebozoa, SAR, and Opisthokonta. Utopia is inserted into a specific site of U2 small nuclear RNA genes with different strength of specificity for each family. Utopia families from oomycetes and wasps show strong target specificity while only a small number of Utopia copies from reptiles are flanked with U2 snRNA genes. Oomycete Utopia families contain an "archaeal" RNase H domain upstream of reverse transcriptase (RT), which likely originated from a plant RNase H gene. Analysis of Utopia from oomycetes indicates that multiple lineages of Utopia have been maintained inside of U2 genes with few copy numbers. Phylogenetic analysis of RT suggests the monophyly of Utopia, and it likely dates back to the early evolution of eukaryotes.

  5. Ancient Origin of the U2 Small Nuclear RNA Gene-Targeting Non-LTR Retrotransposons Utopia.

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    Kenji K Kojima

    Full Text Available Most non-long terminal repeat (non-LTR retrotransposons encoding a restriction-like endonuclease show target-specific integration into repetitive sequences such as ribosomal RNA genes and microsatellites. However, only a few target-specific lineages of non-LTR retrotransposons are distributed widely and no lineage is found across the eukaryotic kingdoms. Here we report the most widely distributed lineage of target sequence-specific non-LTR retrotransposons, designated Utopia. Utopia is found in three supergroups of eukaryotes: Amoebozoa, SAR, and Opisthokonta. Utopia is inserted into a specific site of U2 small nuclear RNA genes with different strength of specificity for each family. Utopia families from oomycetes and wasps show strong target specificity while only a small number of Utopia copies from reptiles are flanked with U2 snRNA genes. Oomycete Utopia families contain an "archaeal" RNase H domain upstream of reverse transcriptase (RT, which likely originated from a plant RNase H gene. Analysis of Utopia from oomycetes indicates that multiple lineages of Utopia have been maintained inside of U2 genes with few copy numbers. Phylogenetic analysis of RT suggests the monophyly of Utopia, and it likely dates back to the early evolution of eukaryotes.

  6. Obligatory parthenogenesis and TE load: Bacillus stick insects and the R2 non-LTR retrotransposon.

    Science.gov (United States)

    Bonandin, Livia; Scavariello, Claudia; Mingazzini, Valentina; Luchetti, Andrea; Mantovani, Barbara

    2017-06-01

    Transposable elements (TEs) are selfish genetic elements whose self-replication is contrasted by the host genome. In this context, host reproductive strategies are predicted to impact on both TEs load and activity. The presence and insertion distribution of the non-LTR retrotransposon R2 was here studied in populations of the strictly bisexual Bacillus grandii maretimi and of the obligatory parthenogenetic Bacillus atticus atticus. Furthermore, data were also obtained from the offspring of selected B. a. atticus females. At the population level, the gonochoric B. g. maretimi showed a significantly higher R2 load than the obligatory parthenogenetic B. a. atticus. The comparison with bisexual and unisexual Bacillus rossius populations showed that their values were higher than those recorded for B. a. atticus and similar, or even higher, than those of B. g. maretimi. Consistently, an R2 load reduction is scored in B. a. atticus offspring even if with a great variance. On the whole, data here produced indicate that in the obligatory unisexual B. a. atticus R2 is active and that mechanisms of molecular turnover are effective. Furthermore, progeny analyses show that, at variance of the facultative parthenogenetic B. rossius, the R2 activity is held at a lower rate. Modeling parental-offspring inheritance, suggests that in B. a. atticus recombination plays a major role in eliminating insertions rather than selection, as previously suggested for unisexual B. rossius progeny, even if in both cases a high variance is observed. In addition to this, mechanisms of R2 silencing or chances of clonal selection cannot be ruled out. © 2016 Institute of Zoology, Chinese Academy of Sciences.

  7. The Wide Distribution and Change of Target Specificity of R2 Non-LTR Retrotransposons in Animals.

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    Kenji K Kojima

    Full Text Available Transposons, or transposable elements, are the major components of genomes in most eukaryotes. Some groups of transposons have developed target specificity that limits the integration sites to a specific nonessential sequence or a genomic region to avoid gene disruption caused by insertion into an essential gene. R2 is one of the most intensively investigated groups of sequence-specific non-LTR retrotransposons and is inserted at a specific site inside of 28S ribosomal RNA (rRNA genes. R2 is known to be distributed among at least six animal phyla even though its occurrence is reported to be patchy. Here, in order to obtain a more detailed picture of the distribution of R2, we surveyed R2 using both in silico screening and degenerate PCR, particularly focusing on actinopterygian fish. We found two families of the R2C lineage from vertebrates, although it has previously only been found in platyhelminthes. We also revealed the apparent movement of insertion sites of a lineage of actinopterygian R2, which was likely concurrent with the acquisition of a 28S rRNA-derived sequence in their 3' UTR. Outside of actinopterygian fish, we revealed the maintenance of a single R2 lineage in birds; the co-existence of four lineages of R2 in the leafcutter bee Megachile rotundata; the first examples of R2 in Ctenophora, Mollusca, and Hemichordata; and two families of R2 showing no target specificity. These findings indicate that R2 is relatively stable and universal, while differences in the distribution and maintenance of R2 lineages probably reflect characteristics of some combination of both R2 lineages and host organisms.

  8. A subtelomeric non-LTR retrotransposon Hebe in the bdelloid rotifer Adineta vaga is subject to inactivation by deletions but not 5' truncations

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    Gladyshev Eugene A

    2010-04-01

    Full Text Available Abstract Background Rotifers of the class Bdelloidea are microscopic freshwater invertebrates best known for: their capacity for anhydrobiosis; the lack of males and meiosis; and for the ability to capture genes from other non-metazoan species. Although genetic exchange between these animals might take place by non-canonical means, the overall lack of meiosis and syngamy should greatly impair the ability of transposable elements (TEs to spread in bdelloid populations. Previous studies demonstrated that bdelloid chromosome ends, in contrast to gene-rich regions, harbour various kinds of TEs, including specialized telomere-associated retroelements, as well as DNA TEs and retrovirus-like retrotransposons which are prone to horizontal transmission. Vertically-transmitted retrotransposons have not previously been reported in bdelloids and their identification and studies of the patterns of their distribution and evolution could help in the understanding of the high degree of TE compartmentalization within bdelloid genomes. Results We identified and characterized a non-long terminal repeat (LTR retrotransposon residing primarily in subtelomeric regions of the genome in the bdelloid rotifer Adineta vaga. Contrary to the currently prevailing views on the mode of proliferation of non-LTR retrotransposons, which results in frequent formation of 5'-truncated ('dead-on-arrival' copies due to the premature disengagement of the element-encoded reverse transcriptase from its template, this non-LTR element, Hebe, is represented only by non-5'-truncated copies. Most of these copies, however, were subject to internal deletions associated with microhomologies, a hallmark of non-homologous end-joining events. Conclusions The non-LTR retrotransposon Hebe from the bdelloid rotifer A. vaga was found to undergo frequent microhomology-associated deletions, rather than 5'-terminal truncations characteristic of this class of retrotransposons, and to exhibit preference for

  9. R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements

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    Eickbush Danna G

    2012-05-01

    Full Text Available Abstract Background R2 is a non-long terminal repeat (non-LTR retrotransposable element that inserts site specifically into the 28S genes of the ribosomal (rRNA gene loci. Encoded at the 5' end is a ribozyme that generates the precise 5' end by self-cleavage of a 28S gene cotranscript. Sequences at the 3' end are necessary for the R2 protein to bind RNA and initiate the target primed reverse transcription (TPRT reaction. These minimal RNA requirements suggested that if recombination/DNA repair conjoined the 5' and 3' ends of R2, the result would be a non-autonomous element that could survive as long as autonomous R2 elements supplied the TPRT activity. Results A PCR-based survey of 39 Drosophila species aided by genomic sequences from 12 of these species revealed two types of non-autonomous elements. We call these elements SIDEs (for ‘Short Internally Deleted Elements’. The first consisted of a 5' ribozyme and a 3' end of an R2 element as predicted. Variation at the 5' junctions of the R2 SIDE copies was typical for R2 insertions suggesting their propagation by TPRT. The second class of SIDE contained sequences from R1 elements, another non-LTR retrotransposon that inserts into rRNA gene loci. These insertions had an R2 ribozyme immediately upstream of R1 3' end sequences. These hybrid SIDEs were inserted at the R1 site with 14 bp target site duplications typical of R1 insertions suggesting they used the R1 machinery for retrotransposition. Finally, the survey revealed examples of U12 small nuclear (snRNA and tRNA sequences at the 5' end of R2 elements suggesting the R2 reverse transcriptase can template jump from the R2 transcript to a second RNA during TPRT. Conclusions The R2 SIDE and R2/R1 hybrid SIDEs are rare examples of non-autonomous retrotransposons in the Drosophila genome. Associated non-autonomous elements and in vivo template jumps are two additional characteristics R2 shares with other non-LTR retrotransposons such as

  10. Identification of retrotransposon-like sequences in Iranian river buffalo

    African Journals Online (AJOL)

    ONOS

    2010-03-29

    Mar 29, 2010 ... of Bov-tA2 and CHR-2 like elements contain the whole promoter boxes of RNA polymerase III and tRNA- related region with few differences in their ... increase their copy numbers via copy and paste mechanism. Non-LTR retrotransposons ... in eukaryotic genomes. SINEs are defined by the presence of a ...

  11. Characterization of non-LTR retrotransposable TRAS elements in the aphids Acyrthosiphon pisum and Myzus persicae (Aphididae, Hemiptera).

    Science.gov (United States)

    Monti, Valentina; Serafini, Chiara; Manicardi, Gian Carlo; Mandrioli, Mauro

    2013-01-01

    A non-LTR TRAS retrotransposon (identified as TRASAp1) has been amplified in the pea aphid Acyrthosiphon pisum and its presence has been assessed also in the peach potato aphid Myzus persicae. This TRAS element possesses 2 overlapping ORFs (a gag-ORF1 and a pol-ORF2 containing the reverse transcriptase and the endonuclease domains) that show a similarity ranging from 40% to 48% to proteins coded by other TRAS elements identified in insects (including the beetle Tribolium castaneum and the moth Bombyx mori). The study of the TRAS chromosomal insertion sites, performed by standard fluorescent in situ hybridization (FISH) and fiber FISH, showed that TRAS elements were located in a subtelomeric position, just before the telomeric (TTAGG) n repeats. In both the aphid species, TRAS elements were present at all termini of autosomes, but the 2 X chromosome telomeres show a clear-cut structural difference. Indeed, cromomycin A3 staining, together with FISH using a TRAS probe, revealed that TRAS signals only occur at the telomere opposite to the NOR-bearing one. Lastly, the analysis of the distribution of TRAS retrotransposons in a M. persicae strain possessing spontaneous fragmentations of the X chromosomes assessed that TRAS elements were not involved in the healing of de novo telomeres.

  12. Drosophila: Retrotransposons Making up Telomeres.

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    Casacuberta, Elena

    2017-07-19

    Drosophila and extant species are the best-studied telomerase exception. In this organism, telomere elongation is coupled with targeted retrotransposition of Healing Transposon (HeT-A) and Telomere Associated Retrotransposon (TART) with sporadic additions of Telomere Associated and HeT-A Related (TAHRE), all three specialized non-Long Terminal Repeat (non-LTR) retrotransposons. These three very special retroelements transpose in head to tail arrays, always in the same orientation at the end of the chromosomes but never in interior locations. Apparently, retrotransposon and telomerase telomeres might seem very different, but a detailed view of their mechanisms reveals similarities explaining how the loss of telomerase in a Drosophila ancestor could successfully have been replaced by the telomere retrotransposons. In this review, we will discover that although HeT-A, TART, and TAHRE are still the only examples to date where their targeted transposition is perfectly tamed into the telomere biology of Drosophila, there are other examples of retrotransposons that manage to successfully integrate inside and at the end of telomeres. Because the aim of this special issue is viral integration at telomeres, understanding the base of the telomerase exceptions will help to obtain clues on similar strategies that mobile elements and viruses could have acquired in order to ensure their survival in the host genome.

  13. Linking Maternal and Somatic 5S rRNA types with Different Sequence-Specific Non-LTR Retrotransposons

    NARCIS (Netherlands)

    Locati, M.D.; Pagano, J.F.B.; Ensink, W.A.; van Olst, M.; van Leeuwen, S.; Nehrdich, U.; Zhu, K.; Spaink, H.P.; Girard, G.; Rauwerda, H.; Jonker, M.J.; Dekker, R.J.; Breit, T.M.

    5S rRNA is a ribosomal core component, transcribed from many gene copies organized in genomic repeats. Some eukaryotic species have two 5S rRNA types defined by their predominant expression in oogenesis or adult tissue. Our next-generation sequencing study on zebrafish egg, embryo and adult tissue,

  14. Contrasted patterns of evolution of the LINE-1 retrotransposon in perissodactyls: the history of a LINE-1 extinction.

    Science.gov (United States)

    Sookdeo, Akash; Hepp, Crystal M; Boissinot, Stéphane

    2018-01-01

    LINE-1 (L1) is the dominant autonomously replicating non-LTR retrotransposon in mammals. Although our knowledge of L1 evolution across the tree of life has considerably improved in recent years, what we know of L1 evolution in mammals is biased and comes mostly from studies in primates (mostly human) and rodents (mostly mouse). It is unclear if patterns of evolution that are shared between those two groups apply to other mammalian orders. Here we performed a detailed study on the evolution of L1 in perissodactyls by making use of the complete genome of the domestic horse and of the white rhinoceros. This mammalian order offers an excellent model to study the extinction of L1 since the rhinoceros is one of the few mammalian species to have lost active L1. We found that multiple L1 lineages, carrying different 5'UTRs, have been simultaneously active during the evolution of perissodactyls. We also found that L1 has continuously amplified and diversified in horse. In rhinoceros, L1 was very prolific early on. Two successful families were simultaneously active until ~20my ago but became extinct suddenly at exactly the same time. The general pattern of L1 evolution in perissodactyls is very similar to what was previously described in mouse and human, suggesting some commonalities in the way mammalian genomes interact with L1. We confirmed the extinction of L1 in rhinoceros and we discuss several possible mechanisms.

  15. LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species.

    Science.gov (United States)

    Lee, Sung-Il; Kim, Jong-Hwa; Park, Kyong-Cheul; Kim, Nam-Soo

    2015-06-01

    LTR-retrotransposons are ubiquitous and highly abundant in plant genomes. Moreover, LTR-retrotransposons can often cause genome obesity in plants. Although Lilium species have been known carrying large genomes among flowering plants, reports on the LTR-retrotransposons in Lilium species are rather limited. We isolated a novel Ty3/gypsy-like retrotransposon, LIRE-del, and two Ty1/copia-like retrotransposons, a LIRE-del and an unclassified, from a fosmid clone of Lilium longiflorum. Decayed internal ORF sequences indicated that they were non-autonomous elements. IRAP protocol was developed based on the LTR sequences of the isolated LTR-retrotransposons. Fourteen primer combinations showed clear distinctive PCR amplification bands that were highly informative in the analysis of species relationship among Lilium species. The phylogenetic relationship based on the IRAP profile revealed some discordant with phylogenetic studies based on the ITS sequences of 45S ribosomal gene and matK gene variations in a few species. Thus, the phylogenetic relationship among Lilium species may need to be re-evaluated with other tools such as cross compatibility and selectively neutral genetic markers.

  16. Non-LTR R2 element evolutionary patterns: phylogenetic incongruences, rapid radiation and the maintenance of multiple lineages.

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    Andrea Luchetti

    Full Text Available Retrotransposons of the R2 superclade specifically insert within the 28S ribosomal gene. They have been isolated from a variety of metazoan genomes and were found vertically inherited even if their phylogeny does not always agree with that of the host species. This was explained with the diversification/extinction of paralogous lineages, being proved the absence of horizontal transfer. We here analyze the widest available collection of R2 sequences, either newly isolated from recently sequenced genomes or drawn from public databases, in a phylogenetic framework. Results are congruent with previous analyses, but new important issues emerge. First, the N-terminal end of the R2-B clade protein, so far unknown, presents a new zinc fingers configuration. Second, the phylogenetic pattern is consistent with an ancient, rapid radiation of R2 lineages: being the estimated time of R2 origin (850-600 Million years ago placed just before the metazoan Cambrian explosion, the wide element diversity and the incongruence with the host phylogeny could be attributable to the sudden expansion of available niches represented by host's 28S ribosomal genes. Finally, we detect instances of coexisting multiple R2 lineages showing a non-random phylogenetic pattern, strongly similar to that of the "library" model known for tandem repeats: a collection of R2s were present in the ancestral genome and then differentially activated/repressed in the derived species. Models for activation/repression as well as mechanisms for sequence maintenance are also discussed within this framework.

  17. Occurrence of LINE, gypsy-like, and copia-like retrotransposons in the clonally propagated sweet potato (Ipomoea batatas L.).

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    Okpul, Tom; Harding, Robert M; Dieters, Mark J; Godwin, Ian D

    2011-07-01

    Retrotransposons are a class of transposable elements that represent a major fraction of the repetitive DNA of most eukaryotes. Their abundance stems from their expansive replication strategies. We screened and isolated sequence fragments of long terminal repeat (LTR), gypsy-like reverse transcriptase (rt) and gypsy-like envelope (env) domains, and two partial sequences of non-LTR retrotransposons, long interspersed element (LINE), in the clonally propagated allohexaploid sweet potato (Ipomoea batatas (L.) Lam.) genome. Using dot-blot hybridization, these elements were found to be present in the ~1597 Mb haploid sweet potato genome with copy numbers ranging from ~50 to ~4100 as observed in the partial LTR (IbLtr-1) and LINE (IbLi-1) sequences, respectively. The continuous clonal propagation of sweet potato may have contributed to such a multitude of copies of some of these genomic elements. Interestingly, the isolated gypsy-like env and gypsy-like rt sequence fragments, IbGy-1 (~2100 copies) and IbGy-2 (~540 copies), respectively, were found to be homologous to the Bagy-2 cDNA sequences of barley (Hordeum vulgare L.). Although the isolated partial sequences were found to be homologous to other transcriptionally active elements, future studies are required to determine whether they represent elements that are transcriptionally active under normal and (or) stressful conditions.

  18. LTR retrotransposons in fungi.

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    Anna Muszewska

    Full Text Available Transposable elements with long terminal direct repeats (LTR TEs are one of the best studied groups of mobile elements. They are ubiquitous elements present in almost all eukaryotic genomes. Their number and state of conservation can be a highlight of genome dynamics. We searched all published fungal genomes for LTR-containing retrotransposons, including both complete, functional elements and remnant copies. We identified a total of over 66,000 elements, all of which belong to the Ty1/Copia or Ty3/Gypsy superfamilies. Most of the detected Gypsy elements represent Chromoviridae, i.e. they carry a chromodomain in the pol ORF. We analyzed our data from a genome-ecology perspective, looking at the abundance of various types of LTR TEs in individual genomes and at the highest-copy element from each genome. The TE content is very variable among the analyzed genomes. Some genomes are very scarce in LTR TEs (8000 elements. The data shows that transposon expansions in fungi usually involve an increase both in the copy number of individual elements and in the number of element types. The majority of the highest-copy TEs from all genomes are Ty3/Gypsy transposons. Phylogenetic analysis of these elements suggests that TE expansions have appeared independently of each other, in distant genomes and at different taxonomical levels. We also analyzed the evolutionary relationships between protein domains encoded by the transposon pol ORF and we found that the protease is the fastest evolving domain whereas reverse transcriptase and RNase H evolve much slower and in correlation with each other.

  19. iPBS: a universal method for DNA fingerprinting and retrotransposon isolation.

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    Kalendar, Ruslan; Antonius, Kristiina; Smýkal, Petr; Schulman, Alan H

    2010-11-01

    Molecular markers are essential in plant and animal breeding and biodiversity applications, in human forensics, and for map-based cloning of genes. The long terminal repeat (LTR) retrotransposons are well suited as molecular markers. As dispersed and ubiquitous transposable elements, their "copy and paste" life cycle of replicative transposition leads to new genome insertions without excision of the original element. Both the overall structure of retrotransposons and the domains responsible for the various phases of their replication are highly conserved in all eukaryotes. Nevertheless, up to a year has been required to develop a retrotransposon marker system in a new species, involving cloning and sequencing steps as well as the development of custom primers. Here, we describe a novel PCR-based method useful both as a marker system in its own right and for the rapid isolation of retrotransposon termini and full-length elements, making it ideal for "orphan crops" and other species with underdeveloped marker systems. The method, iPBS amplification, is based on the virtually universal presence of a tRNA complement as a reverse transcriptase primer binding site (PBS) in LTR retrotransposons. The method differs from earlier retrotransposon isolation methods because it is applicable not only to endogenous retroviruses and retroviruses, but also to both Gypsy and Copia LTR retrotransposons, as well as to non-autonomous LARD and TRIM elements, throughout the plant kingdom and to animals. Furthermore, the inter-PBS amplification technique as such has proved to be a powerful DNA fingerprinting technology without the need for prior sequence knowledge.

  20. DIRS and Ngaro Retrotransposons in Fungi.

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    Anna Muszewska

    Full Text Available Retrotransposons with a tyrosine recombinase (YR have been discovered recently and lack thorough annotation in fungi. YR retrotransposons are divided into 3 groups: DIRS, Ngaro and VIPER (known only from kinetoplastida. We used comparative genomics to investigate the evolutionary patterns of retrotransposons in the fungal kingdom. The identification of both functional and remnant elements provides a unique view on both recent and past transposition activity. Our searches covering a wide range of fungal genomes allowed us to identify 2241 YR retrotransposons. Based on CLANS clustering of concatenated sequences of the reverse transcriptase (RT, RNase H (RH, DNA N-6-adenine-methyltransferase (MT and YR protein domains we propose a revised classification of YR elements expanded by two new categories of Ngaro elements. A phylogenetic analysis of 477 representatives supports this observation and additionally demonstrates that DIRS and Ngaro abundance changed independently in Basidiomycota and Blastocladiomycota/Mucoromycotina/Kixellomycotina. Interestingly, a single remnant Ngaro element could be identified in an Ascomycota genome. Our analysis revealed also that 3 Pucciniomycotina taxa, known for their overall mobile element abundance and big genome size, encode an elevated number of Ngaro retrotransposons. Considering the presence of DIRS elements in all analyzed Mucoromycotina, Kickxellomycotina and Blastocladiomycota genomes one might assume a common origin of fungal DIRS retrotransposons with a loss in Dicarya. Ngaro elements described to date from Opisthokonta, seem to have invaded the common ancestor of Agaricomycotina and Pucciniomycotina after Ustilagomycotina divergence. Yet, most of analyzed genomes are devoid of YR elements and most identified retrotransposons are incomplete.

  1. Retrotransposon Domestication and Control in Dictyostelium discoideum

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    Marek Malicki

    2017-10-01

    Full Text Available Transposable elements, identified in all eukaryotes, are mobile genetic units that can change their genomic position. Transposons usually employ an excision and reintegration mechanism, by which they change position, but not copy number. In contrast, retrotransposons amplify via RNA intermediates, increasing their genomic copy number. Hence, they represent a particular threat to the structural and informational integrity of the invaded genome. The social amoeba Dictyostelium discoideum, model organism of the evolutionary Amoebozoa supergroup, features a haploid, gene-dense genome that offers limited space for damage-free transposition. Several of its contemporary retrotransposons display intrinsic integration preferences, for example by inserting next to transfer RNA genes or other retroelements. Likely, any retrotransposons that invaded the genome of the amoeba in a non-directed manner were lost during evolution, as this would result in decreased fitness of the organism. Thus, the positional preference of the Dictyostelium retroelements might represent a domestication of the selfish elements. Likewise, the reduced danger of such domesticated transposable elements led to their accumulation, and they represent about 10% of the current genome of D. discoideum. To prevent the uncontrolled spreading of retrotransposons, the amoeba employs control mechanisms including RNA interference and heterochromatization. Here, we review TRE5-A, DIRS-1 and Skipper-1, as representatives of the three retrotransposon classes in D. discoideum, which make up 5.7% of the Dictyostelium genome. We compile open questions with respect to their mobility and cellular regulation, and suggest strategies, how these questions might be addressed experimentally.

  2. [Ulysses retrotransposon aspartate proteinase (Drosophila virilis)].

    Science.gov (United States)

    Volkov, D A; Savvateeva, L V; Dergousova, N I; Rumsh, L D

    2002-01-01

    Retrotransposones are mobile genetic elements occurring in genomes of bacteria, plants or animals. Retrotransposones were found to contain nucleotide sequences encoding proteins which are homological to retroviral aspartic proteinases. Our research has been focused on Ulysses which is mobile genetic element found in Drosophila virilis. We suggested a primary structure of Ulysses proteinase using comparative analysis of amino acid sequences of retroviral proteinases and proteinases from retrotransposones. The appropriate cDNA fragment has been cloned and expressed in E. coli. The purification of recombinant protein (12 kD) has been carried out by affinity chromatography using pepstatine-agarose. The obtained protein has proteolytic activity at optimum pH 5.5 like the majority of aspartic proteinases.

  3. Retrotransposons and non-protein coding RNAs

    DEFF Research Database (Denmark)

    Mourier, Tobias; Willerslev, Eske

    2009-01-01

    does not merely represent spurious transcription. We review examples of functional RNAs transcribed from retrotransposons, and address the collection of non-protein coding RNAs derived from transposable element sequences, including numerous human microRNAs and the neuronal BC RNAs. Finally, we review...

  4. Retrotransposon-Encoded Reverse Transcriptase in the Genesis, Progression and Cellular Plasticity of Human Cancer

    International Nuclear Information System (INIS)

    Sinibaldi-Vallebona, Paola; Matteucci, Claudia; Spadafora, Corrado

    2011-01-01

    LINE-1 (Long Interspersed Nuclear Elements) and HERVs (Human Endogenous Retroviruses) are two families of autonomously replicating retrotransposons that together account for about 28% of the human genome. Genes harbored within LINE-1 and HERV retrotransposons, particularly those encoding the reverse transcriptase (RT) enzyme, are generally expressed at low levels in differentiated cells, but their expression is upregulated in transformed cells and embryonic tissues. Here we discuss a recently discovered RT-dependent mechanism that operates in tumorigenesis and reversibly modulates phenotypic and functional variations associated with tumor progression. Downregulation of active LINE-1 elements drastically reduces the tumorigenic potential of cancer cells, paralleled by reduced proliferation and increased differentiation. Pharmacological RT inhibitors (e.g., nevirapine and efavirenz) exert similar effects on tumorigenic cell lines, both in culture and in animal models. The HERV-K family play a distinct complementary role in stress-dependent transition of melanoma cells from an adherent, non-aggressive, to a non-adherent, highly malignant, growth phenotype. In synthesis, the retrotransposon-encoded RT is increasingly emerging as a key regulator of tumor progression and a promising target in a novel anti-cancer therapy

  5. Obtaining retrotransposon sequences, analysis of their genomic distribution and use of retrotransposon-derived genetic markers in lentil (Lens culinaris Medik..

    Directory of Open Access Journals (Sweden)

    Rita Rey-Baños

    Full Text Available Retrotransposons with long terminal repeats (LTR-RTs are widespread mobile elements in eukaryotic genomes. We obtained a total of 81 partial LTR-RT sequences from lentil corresponding to internal retrotransposon components and LTRs. Sequences were obtained by PCR from genomic DNA. Approximately 37% of the LTR-RT internal sequences presented premature stop codons, pointing out that these elements must be non-autonomous. LTR sequences were obtained using the iPBS technique which amplifies sequences between LTR-RTs. A total of 193 retrotransposon-derived genetic markers, mainly iPBS, were used to obtain a genetic linkage map from 94 F7 inbred recombinant lines derived from the cross between the cultivar Lupa and the wild ancestor L. culinaris subsp. orientalis. The genetic map included 136 markers located in eight linkage groups. Clusters of tightly linked retrotransposon-derived markers were detected in linkage groups LG1, LG2, and LG6, hence denoting a non-random genomic distribution. Phylogenetic analyses identified the LTR-RT families in which internal and LTR sequences are included. Ty3-gypsy elements were more frequent than Ty1-copia, mainly due to the high Ogre element frequency in lentil, as also occurs in other species of the tribe Vicieae. LTR and internal sequences were used to analyze in silico their distribution among the contigs of the lentil draft genome. Up to 8.8% of the lentil contigs evidenced the presence of at least one LTR-RT similar sequence. A statistical analysis suggested a non-random distribution of these elements within of the lentil genome. In most cases (between 97% and 72%, depending on the LTR-RT type none of the internal sequences flanked by the LTR sequence pair was detected, suggesting that defective and non-autonomous LTR-RTs are very frequent in lentil. Results support that LTR-RTs are abundant and widespread throughout of the lentil genome and that they are a suitable source of genetic markers useful to carry

  6. Full Length Research Paper LTR-retrotransposons-based molecular ...

    African Journals Online (AJOL)

    LTR-retrotransposons possess unique properties that make them appropriate for investigating relationships between closely related species and populations. The aim of the current study was to employ Ty1-copia group retrotransposons as molecular markers in cultivated Egyptian cottons, G. barbadense L. Restriction site ...

  7. Copia and Gypsy retrotransposons activity in sunflower (Helianthus annuus L.)

    Science.gov (United States)

    2009-01-01

    Background Retrotransposons are heterogeneous sequences, widespread in eukaryotic genomes, which refer to the so-called mobile DNA. They resemble retroviruses, both in their structure and for their ability to transpose within the host genome, of which they make up a considerable portion. Copia- and Gypsy-like retrotransposons are the two main classes of retroelements shown to be ubiquitous in plant genomes. Ideally, the retrotransposons life cycle results in the synthesis of a messenger RNA and then self-encoded proteins to process retrotransposon mRNA in double stranded extra-chromosomal cDNA copies which may integrate in new chromosomal locations. Results The RT-PCR and IRAP protocol were applied to detect the presence of Copia and Gypsy retrotransposon transcripts and of new events of integration in unstressed plants of a sunflower (Helianthus annuus L.) selfed line. Results show that in sunflower retrotransposons transcription occurs in all analyzed organs (embryos, leaves, roots, and flowers). In one out of sixty-four individuals analyzed, retrotransposons transcription resulted in the integration of a new element into the genome. Conclusion These results indicate that the retrotransposon life cycle is firmly controlled at a post transcriptional level. A possible silencing mechanism is discussed. PMID:20030800

  8. LTR-retrotransposons-based molecular markers in cultivated ...

    African Journals Online (AJOL)

    GRACE

    2006-07-03

    Jul 3, 2006 ... LTR-retrotransposons represent a standard component of the Gossypium Genome (Zaki and Abdel Ghany,. 2003). The analysis of the molecular existence and distribution of ancient and active LTR-retrotransposons, therefore, provides a comprehensive evaluation of the evolutionary history of Gossypium.

  9. Genome-wide analysis of a recently active retrotransposon, Au SINE, in wheat: content, distribution within subgenomes and chromosomes, and gene associations.

    Science.gov (United States)

    Keidar, Danielle; Doron, Chen; Kashkush, Khalil

    2018-02-01

    Here, we show that Au SINE elements have strong associations with protein-coding genes in wheat. Most importantly Au SINE insertion within introns causes allelic variation and might induce intron retention. The impact of transposable elements (TEs) on genome structure and function is intensively studied in eukaryotes, especially in plants where TEs can reach up to 90% of the genome in some cases, such as in wheat. Here, we have performed a genome-wide in-silico analysis using the updated publicly available genome draft of bread wheat (T. aestivum), in addition to the updated genome drafts of the diploid donor species, T. urartu and Ae. tauschii, to retrieve and analyze a non-LTR retrotransposon family, termed Au SINE, which was found to be widespread in plant species. Then, we have performed site-specific PCR and realtime RT-PCR analyses to assess the possible impact of Au SINE on gene structure and function. To this end, we retrieved 133, 180 and 1886 intact Au SINE insertions from T. urartu, Ae. tauschii and T. aestivum genome drafts, respectively. The 1886 Au SINE insertions were distributed in the seven homoeologous chromosomes of T. aestivum, while ~ 67% of the insertions were associated with genes. Detailed analysis of 40 genes harboring Au SINE revealed allelic variation of those genes in the Triticum-Aegilops genus. In addition, expression analysis revealed that both regular transcripts and alternative Au SINE-containing transcripts were simultaneously amplified in the same tissue, indicating retention of Au SINE-containing introns. Analysis of the wheat transcriptome revealed that hundreds of protein-coding genes harbor Au SINE in at least one of their mature splice variants. Au SINE might play a prominent role in speciation by creating transcriptome variation.

  10. Activation of an endogenous retrotransposon associated with epigenetic changes in Lotus japonicus

    DEFF Research Database (Denmark)

    Fukai, Eigo; Stougaard, Jens; Hayashi, Makoto

    2013-01-01

    Long terminal repeat retrotransposons occupy a large portion of genomes in flowering plants. In spite of their abundance, the majority are silenced and rarely transpose. One of the examples of a highly active retrotransposon is Lotus Retrotransposon 1(LORE1), of the model legume Lotus japonicus (...

  11. Retrotransposons. An RNA polymerase III subunit determines sites of retrotransposon integration.

    Science.gov (United States)

    Bridier-Nahmias, Antoine; Tchalikian-Cosson, Aurélie; Baller, Joshua A; Menouni, Rachid; Fayol, Hélène; Flores, Amando; Saïb, Ali; Werner, Michel; Voytas, Daniel F; Lesage, Pascale

    2015-05-01

    Mobile genetic elements are ubiquitous. Their integration site influences genome stability and gene expression. The Ty1 retrotransposon of the yeast Saccharomyces cerevisiae integrates upstream of RNA polymerase III (Pol III)-transcribed genes, yet the primary determinant of target specificity has remained elusive. Here we describe an interaction between Ty1 integrase and the AC40 subunit of Pol III and demonstrate that AC40 is the predominant determinant targeting Ty1 integration upstream of Pol III-transcribed genes. Lack of an integrase-AC40 interaction dramatically alters target site choice, leading to a redistribution of Ty1 insertions in the genome, mainly to chromosome ends. The mechanism of target specificity allows Ty1 to proliferate and yet minimizes genetic damage to its host. Copyright © 2015, American Association for the Advancement of Science.

  12. BARE retrotransposons are translated and replicated via distinct RNA pools.

    Directory of Open Access Journals (Sweden)

    Wei Chang

    Full Text Available The replication of Long Terminal Repeat (LTR retrotransposons, which can constitute over 80% of higher plant genomes, resembles that of retroviruses. A major question for retrotransposons and retroviruses is how the two conflicting roles of their transcripts, in translation and reverse transcription, are balanced. Here, we show that the BARE retrotransposon, despite its organization into just one open reading frame, produces three distinct classes of transcripts. One is capped, polyadenylated, and translated, but cannot be copied into cDNA. The second is not capped or polyadenylated, but is destined for packaging and ultimate reverse transcription. The third class is capped, polyadenylated, and spliced to favor production of a subgenomic RNA encoding only Gag, the protein forming virus-like particles. Moreover, the BARE2 subfamily, which cannot synthesize Gag and is parasitic on BARE1, does not produce the spliced sub-genomic RNA for translation but does make the replication competent transcripts, which are packaged into BARE1 particles. To our knowledge, this is first demonstration of distinct RNA pools for translation and transcription for any retrotransposon.

  13. Characterization of a genome-specific Gypsy-like retrotransposon ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 92; Issue 1. Characterization of a genome-specific Gypsy-like retrotransposon sequence and development of a molecular marker specific for Dasypyrum villosum (L.) Jie Zhang Hai Long Zhifen Pan Junjun Liang Shuiyang Yu Guangbing Deng Maoqun Yu. Research Note ...

  14. Forward and reverse genetics: The LORE1 retrotransposon insertion mutants

    DEFF Research Database (Denmark)

    Fukai, Eigo; Malolepszy, Anna; Sandal, Niels Nørgaard

    2014-01-01

    The endogenous Lotus retrotransposon 1 (LORE1) transposes in the germ line of Lotus japonicus plants that carry an active element. This feature of LORE1 has been exploited for generation of a large non-transgenic insertion mutant population, where insertions have been annotated using next-generat...

  15. Plant centromeric retrotransposons: a structural and cytogenetic perspective

    Directory of Open Access Journals (Sweden)

    Neumann Pavel

    2011-03-01

    Full Text Available Abstract Background The centromeric and pericentromeric regions of plant chromosomes are colonized by Ty3/gypsy retrotransposons, which, on the basis of their reverse transcriptase sequences, form the chromovirus CRM clade. Despite their potential importance for centromere evolution and function, they have remained poorly characterized. In this work, we aimed to carry out a comprehensive survey of CRM clade elements with an emphasis on their diversity, structure, chromosomal distribution and transcriptional activity. Results We have surveyed a set of 190 CRM elements belonging to 81 different retrotransposon families, derived from 33 host species and falling into 12 plant families. The sequences at the C-terminus of their integrases were unexpectedly heterogeneous, despite the understanding that they are responsible for targeting to the centromere. This variation allowed the division of the CRM clade into the three groups A, B and C, and the members of each differed considerably with respect to their chromosomal distribution. The differences in chromosomal distribution coincided with variation in the integrase C-terminus sequences possessing a putative targeting domain (PTD. A majority of the group A elements possess the CR motif and are concentrated in the centromeric region, while members of group C have the type II chromodomain and are dispersed throughout the genome. Although representatives of the group B lack a PTD of any type, they appeared to be localized preferentially in the centromeres of tested species. All tested elements were found to be transcriptionally active. Conclusions Comprehensive analysis of the CRM clade elements showed that genuinely centromeric retrotransposons represent only a fraction of the CRM clade (group A. These centromeric retrotransposons represent an active component of centromeres of a wide range of angiosperm species, implying that they play an important role in plant centromere evolution. In addition, their

  16. Divergent long-terminal-repeat retrotransposon families in the genome of Paragonimus westermani

    Science.gov (United States)

    Bae, Young-An

    2003-01-01

    To gain information on retrotransposons in the genome of Paragonimus westermani, PCR was carried out with degenerate primers, specific to protease and reverse transcriptase (rt) genes of long-terminal-repeat (LTR) retrotransposons. The PCR products were cloned and sequenced, after which 12 different retrotransposon-related sequences were isolated from the trematode genome. These showed various degrees of identity to the polyprotein of divergent retrotransposon families. A phylogenetic analysis demonstrated that these sequences could be classified into three different families of LTR retrotransposons, namely, Xena, Bel, and Gypsy families. Of these, two mRNA transcripts were detected by reverse transcriptase-PCR, showing that these two elements preserved their mobile activities. The genomic distributions of these two sequences were found to be highly repetitive. These results suggest that there are diverse retrotransposons including the ancient Xena family in the genome of P. westermani, which may have been involved in the evolution of the host genome. PMID:14699263

  17. Retrotransposon molecular markers resolve cocoyam (Xanthosoma sagittifolium) and taro (Colocasia esculenta) by type and variety

    OpenAIRE

    Doungous, Oumar; Kalendar, Ruslan; Adiobo, Amayana; Schulman, Alan

    2015-01-01

    Retrotransposon-based molecular markers were applied for the first time within the genera Xanthosoma and Colocasia to assess intraspecific variability among 27 accessions of cocoyam (Xanthosoma sagittifolium) and taro (Colocasia esulenta). Over 16 distinct retrotransposon fragments were isolated, sequenced, and LTR primers were designed to obtain Inter-Retrotransposon Amplified Polymorphism (IRAP) fingerprints. The set of six polymorphic LTR primers yielded 433 reproducible bands across a set...

  18. Plant centromeric retrotransposons: a structural and cytogenetic perspective

    Czech Academy of Sciences Publication Activity Database

    Neumann, Pavel; Navrátilová, Alice; Koblížková, Andrea; Kejnovský, Eduard; Hřibová, Eva; Hobza, Roman; Widmer, A.; Doležel, Jaroslav; Macas, Jiří

    2011-01-01

    Roč. 2, č. 4 (2011), s. 1-16 ISSN 1759-8753 R&D Projects: GA AV ČR KJB500960802; GA MŠk(CZ) LC06004; GA ČR GA522/09/0083 Institutional research plan: CEZ:AV0Z50510513; CEZ:AV0Z50040507; CEZ:AV0Z50040702; CEZ:AV0Z50380511 Keywords : plant chromosomes * retrotransposons * cytogenetic perspective Subject RIV: EB - Genetics ; Molecular Biology

  19. Detection of tolerant and susceptible fusarium wilt somaclones of banana cultivar rastali (Musa AAB) by RAPD and retrotransposon markers

    International Nuclear Information System (INIS)

    Asif, M.J.; Fatimah, K.; Rofina Yasmin Othman; Tan, S.H.

    2002-01-01

    This study was aimed to use DNA markers i.e. RAPD - random amplified polymorphic DNA and retrotransposon - IRAP - inter retrotransposons amplified polymorphism polymerase reaction - to study somaclonal variation in banana. The usefulness of retrotransposons as genetic markers to study somaclonal variability in bananas was further discussed

  20. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

    NARCIS (Netherlands)

    Jacobs, F.M.J.; Greenberg, D.; Nguyen, N.; Haeussler, M.; Ewing, A.D.; Katzman, S.; Paten, B.; Salama, S.R.; Haussler, D.

    2014-01-01

    Throughout evolution primate genomes have been modified by waves of retrotransposon insertions1, 2, 3. For each wave, the host eventually finds a way to repress retrotransposon transcription and prevent further insertions. In mouse embryonic stem cells, transcriptional silencing of retrotransposons

  1. sRNAs as possible regulators of retrotransposon activity in Cryptococcus gattii VGII.

    Science.gov (United States)

    Ferrareze, Patrícia Aline Gröhs; Streit, Rodrigo Silva Araujo; Dos Santos, Francine Melise; Schrank, Augusto; Kmetzsch, Livia; Vainstein, Marilene Henning; Staats, Charley Christian

    2017-04-12

    The absence of Argonaute genes in the fungal pathogen Cryptococcus gattii R265 and other VGII strains indicates that yeasts of this genotype cannot have a functional RNAi pathway, an evolutionarily conserved gene silencing mechanism performed by small RNAs. The success of the R265 strain as a pathogen that caused the Pacific Northwest and Vancouver Island outbreaks may imply that RNAi machinery loss could be beneficial under certain circumstances during evolution. As a result, a hypermutant phenotype would be created with high rates of genome retrotransposition, for instance. This study therefore aimed to evaluate in silicio the effect of retrotransposons and their control mechanisms by small RNAs on genomic stability and synteny loss of C. gattii R265 through retrotransposons sequence comparison and orthology analysis with other 16 C. gattii genomic sequences available. Retrotransposon mining identified a higher sequence count to VGI genotype compared to VGII, VGIII, and VGIV. However, despite the lower retrotransposon number, VGII exhibited increased synteny loss and genome rearrangement events. RNA-Seq analysis indicated highly expressed retrotransposons as well as sRNA production. Genome rearrangement and synteny loss may suggest a greater retrotransposon mobilization caused by RNAi pathway absence, but the effective presence of sRNAs that matches retrotransposon sequences means that an alternative retrotransposon silencing mechanism could be active in genomic integrity maintenance of C. gattii VGII strains.

  2. Characterization of AFLAV, a Tf1/Sushi retrotransposon from Aspergillus flavus.

    Science.gov (United States)

    Hua, Sui-Sheng T; Tarun, Alice S; Pandey, Sonal N; Chang, Leo; Chang, Perng-Kuang

    2007-02-01

    The plasmid, pAF28, a genomic clone from Aspergillus flavus NRRL 6541, has been used as a hybridization probe to fingerprint A. flavus strains isolated in corn and peanut fields. The insert of pAF28 contains a 4.5 kb region which encodes a truncated retrotransposon (AfRTL-1). In search for a full-length and intact copy of retrotransposon, we exploited a novel PCR cloning strategy by amplifying a 3.4 kb region from the genomic DNA of A. flavus NRRL 6541. The fragment was cloned into pCR 4-TOPO. Sequence analysis confirmed that this region encoded putative domains of partial reverse transcriptase, RNase H, and integrase of the predicted retrotransposon. The two flanking long terminal repeats (LTRs) and the sequence between them comprise a putative full-length LTR retrotransposon of 7799 bp in length. This intact retrotransposon sequence is named AFLAV (A. flavus Retrotransposon). The order of the predicted catalytic domains in the polyprotein (Pol) placed AFLAV in the Tf1/sushi subgroup of the Ty3/gypsy retrotransposon family. Primers derived from AFLAV sequence were used to screen this retrotransposon in other strains of A. flavus. More than fifty strains of A. flavus isolated from different geological origins were surveyed and the results show that many strains have extensive deletions in the regions encoding the capsid (Gag) and Pol.

  3. Autonomic neuropathies

    Science.gov (United States)

    Low, P. A.

    1998-01-01

    A limited autonomic neuropathy may underlie some unusual clinical syndromes, including the postural tachycardia syndrome, pseudo-obstruction syndrome, heat intolerance, and perhaps chronic fatigue syndrome. Antibodies to autonomic structures are common in diabetes, but their specificity is unknown. The presence of autonomic failure worsens prognosis in the diabetic state. Some autonomic neuropathies are treatable. Familial amyloid polyneuropathy may respond to liver transplantation. There are anecdotal reports of acute panautonomic neuropathy responding to intravenous gamma globulin. Orthostatic hypotension may respond to erythropoietin or midodrine.

  4. Retrotransposon Proliferation Coincident with the Evolution of Dioecy in Asparagus.

    Science.gov (United States)

    Harkess, Alex; Mercati, Francesco; Abbate, Loredana; McKain, Michael; Pires, J Chris; Sala, Tea; Sunseri, Francesco; Falavigna, Agostino; Leebens-Mack, Jim

    2016-09-08

    Current phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once, or possibly twice, in the genus Asparagus Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n = 2× = 20 is relatively conserved across the Asparagus genus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here, we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion, or to retrotransposon proliferation in dioecious species. We first estimate genome sizes, or use published values, for four hermaphrodites and four dioecious species distributed across the phylogeny, and show that dioecious species typically have larger genomes than hermaphroditic species. Utilizing a phylogenomic approach, we find no evidence for ancient polyploidization contributing to increased genome sizes of sampled dioecious species. We do find support for an ancient whole genome duplication (WGD) event predating the diversification of the Asparagus genus. Repetitive DNA content of the four hermaphroditic and four dioecious species was characterized based on randomly sampled whole genome shotgun sequencing, and common elements were annotated. Across our broad phylogenetic sampling, Ty-1 Copia retroelements, in particular, have undergone a marked proliferation in dioecious species. In the absence of a detectable WGD event, retrotransposon proliferation is the most likely explanation for the precipitous increase in genome size in dioecious Asparagus species. Copyright © 2016 Harkess et al.

  5. Ty1-copia group retrotransposon sequences in amphibia and reptilia.

    Science.gov (United States)

    Flavell, A J; Jackson, V; Iqbal, M P; Riach, I; Waddell, S

    1995-01-06

    We have isolated sequences belonging to Ty1-copia group retrotransposons from the genomes of an amphibian (Pyxicephalus adspersa) and three reptiles (Conolophus subscristatus, Amblyrynchus cristatus and Pytas mucosus). Two different sequences were found in the amphibian (Tpa1 and Tpa2). Each is present in several copies per genome and absent from the genomes of two other amphibian species. The C. subcristatus sequence Tcs1 is present in multiple copies in both its host genome (Galapagos land iguana) and the genome of the related Galapagos marine iguana (A. cristatus). There is little or no polymorphism in Tcs1 insertions between different individual animals, suggesting that this sequence is not transposing rapidly in either iguana genome. The P. mucosus sequence Tpm1 shows a discontinuous distribution in snake species, suggesting that it has either been lost from many lineages during vertical germline transmission or has been transferred horizontally in some snake species. Phylogenetic comparisons of all these sequences with each other and with other members of this retrotransposon group from other animals and plants show that sequences within a particular vertebrate species are most closely related to each other, consistent with a vertical transmission model for their evolution.

  6. Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting.

    Directory of Open Access Journals (Sweden)

    Shunsuke Suzuki

    2007-04-01

    Full Text Available Among mammals, only eutherians and marsupials are viviparous and have genomic imprinting that leads to parent-of-origin-specific differential gene expression. We used comparative analysis to investigate the origin of genomic imprinting in mammals. PEG10 (paternally expressed 10 is a retrotransposon-derived imprinted gene that has an essential role for the formation of the placenta of the mouse. Here, we show that an orthologue of PEG10 exists in another therian mammal, the marsupial tammar wallaby (Macropus eugenii, but not in a prototherian mammal, the egg-laying platypus (Ornithorhynchus anatinus, suggesting its close relationship to the origin of placentation in therian mammals. We have discovered a hitherto missing link of the imprinting mechanism between eutherians and marsupials because tammar PEG10 is the first example of a differentially methylated region (DMR associated with genomic imprinting in marsupials. Surprisingly, the marsupial DMR was strictly limited to the 5' region of PEG10, unlike the eutherian DMR, which covers the promoter regions of both PEG10 and the adjacent imprinted gene SGCE. These results not only demonstrate a common origin of the DMR-associated imprinting mechanism in therian mammals but provide the first demonstration that DMR-associated genomic imprinting in eutherians can originate from the repression of exogenous DNA sequences and/or retrotransposons by DNA methylation.

  7. Autonomous houses. Autonomous house

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, S. (Tokai University, Tokyo (Japan). Faculty of Engineering)

    1991-09-30

    Self-sufficiency type houses are outlined. On condition that people gain a certain amount of income in relation with the society, they self-suffice under the given environment, allowing themselves to accept a minimum of industrial products with small environmental load. Ordinary supply from outside of fossil energy and materials which depend on it is minimized. Types are classified into three: energy, energy materials and perfect self-sufficiency. A study project for environment symbiotic houses is progressing which is planned by the Ministry of Construction and Institute of Building Energy Conservation and is invested by a private company. Its target is making a house for halving an environmental load by CO{sub 2}, for the purpose of creating the environment symbiotic house which is nice to and in harmony with the global environment and human beings. As a part of the studies on energy-saving and resource conservation on houses, introduced is a plan of an autonomous house at Izu-Atagawa. The passive method and high thermal-insulation are used for air conditioning, and hot spring water for hot water supply. Electric power is generated by hydroelectric power generation using mountain streams and by solar cells. Staple food is purchased, while subsidiary food is sufficed. 17 refs., 4 figs., 1 tab.

  8. Regulating retrotransposon activity through the use of alternative transcription start sites

    DEFF Research Database (Denmark)

    Persson, Jenna; Steglich, Babett; Smialowska, Agata

    2016-01-01

    . This enforces the use of a downstream TSS and the production of a truncated RNA incapable of reverse transcription and retrotransposition. However, in stressed cells, nucleosome occupancy at LTR elements is reduced, and the TSS shifts to allow for productive transcription. We propose that controlled...... a new mechanism of retrotransposon regulation through transcription start site (TSS) selection by altered nucleosome occupancy. We show that Fun30 chromatin remodelers cooperate to maintain a high level of nucleosome occupancy at retrotransposon-flanking long terminal repeat (LTR) elements...... retrotransposon transcription from a nonproductive TSS allows for rapid stress-induced activation, while preventing uncontrolled transposon activity in the genome....

  9. New aspartic proteinase of Ulysses retrotransposon from Drosophila virilis.

    Science.gov (United States)

    Volkov, D A; Dergousova, N I; Rumsh, L D

    2004-06-01

    This work is focused on the investigation of a proteinase of Ulysses mobile genetic element from Drosophila virilis. The primary structure of this proteinase is suggested based on comparative analysis of amino acid sequences of aspartic proteinases from retroviruses and retrotransposons. The corresponding cDNA fragment has been cloned and expressed in E. coli. The protein accumulated in inclusion bodies. The recombinant protein (12 kD) was subjected to refolding and purified by affinity chromatography on pepstatin-agarose. Proteolytic activity of the protein was determined using oligopeptide substrates melittin and insulin B-chain. It was found that the maximum of the proteolytic activity is displayed at pH 5.5 as for the majority of aspartic proteinases. We observed that hydrolysis of B-chain of insulin was totally inhibited by pepstatin A in the micromolar concentration range. The molecular weight of the monomer of the Ulysses proteinase was determined by MALDI-TOF mass-spectrometry.

  10. Autonomous search

    CERN Document Server

    Hamadi, Youssef; Saubion, Frédéric

    2012-01-01

    Autonomous combinatorial search (AS) represents a new field in combinatorial problem solving. Its major standpoint and originality is that it considers that problem solvers must be capable of self-improvement operations. This is the first book dedicated to AS.

  11. Switching of dominant retrotransposon silencing strategies from posttranscriptional to transcriptional mechanisms during male germ-cell development in mice.

    Directory of Open Access Journals (Sweden)

    Kota Inoue

    2017-07-01

    Full Text Available Mammalian genomes harbor millions of retrotransposon copies, some of which are transpositionally active. In mouse prospermatogonia, PIWI-interacting small RNAs (piRNAs combat retrotransposon activity to maintain the genomic integrity. The piRNA system destroys retrotransposon-derived RNAs and guides de novo DNA methylation at some retrotransposon promoters. However, it remains unclear whether DNA methylation contributes to retrotransposon silencing in prospermatogonia. We have performed comprehensive studies of DNA methylation and polyA(+ RNAs (transcriptome in developing male germ cells from Pld6/Mitopld and Dnmt3l knockout mice, which are defective in piRNA biogenesis and de novo DNA methylation, respectively. The Dnmt3l mutation greatly reduced DNA methylation levels at most retrotransposons, but its impact on their RNA abundance was limited in prospermatogonia. In Pld6 mutant germ cells, although only a few retrotransposons exhibited reduced DNA methylation, many showed increased expression at the RNA level. More detailed analysis of RNA sequencing, nascent RNA quantification, profiling of cleaved RNA ends, and the results obtained from double knockout mice suggest that PLD6 works mainly at the posttranscriptional level. The increase in retrotransposon expression was larger in Pld6 mutants than it was in Dnmt3l mutants, suggesting that RNA degradation by the piRNA system plays a more important role than does DNA methylation in prospermatogonia. However, DNA methylation had a long-term effect: hypomethylation caused by the Pld6 or Dnmt3l mutation resulted in increased retrotransposon expression in meiotic spermatocytes. Thus, posttranscriptional silencing plays an important role in the early stage of germ cell development, then transcriptional silencing becomes important in later stages. In addition, intergenic and intronic retrotransposon sequences, in particular those containing the antisense L1 promoters, drove ectopic expression of nearby

  12. Functional and structural divergence of an unusual LTR retrotransposon family in plants.

    Science.gov (United States)

    Gao, Dongying; Jimenez-Lopez, Jose C; Iwata, Aiko; Gill, Navdeep; Jackson, Scott A

    2012-01-01

    Retrotransposons with long terminal repeats (LTRs) more than 3 kb are not frequent in most eukaryotic genomes. Rice LTR retrotransposon, Retrosat2, has LTRs greater than 3.2 kb and two open reading frames (ORF): ORF1 encodes enzymes for retrotransposition whereas no function can be assigned to ORF0 as it is not found in any other organism. A variety of experimental and in silico approaches were used to determine the origin of Retrosat2 and putative function of ORF0. Our data show that not only is Retrosat2 highly abundant in the Oryza genus, it may yet be active in rice. Homologs of Retrosat2 were identified in maize, sorghum, Arabidopsis and other plant genomes suggesting that the Retrosat2 family is of ancient origin. Several putatively cis-acting elements, some multicopy, that regulate retrotransposon replication or responsiveness to environmental factors were found in the LTRs of Retrosat2. Unlike the ORF1, the ORF0 sequences from Retrosat2 and homologs are divergent at the sequence level, 3D-structures and predicted biological functions. In contrast to other retrotransposon families, Retrosat2 and its homologs are dispersed throughout genomes and not concentrated in the specific chromosomal regions, such as centromeres. The genomic distribution of Retrosat2 homologs varies across species which likely reflects the differing evolutionary trajectories of this retrotransposon family across diverse species.

  13. Analysis of Hopi/Osr27 and Houba/Tos5/Osr13 retrotransposons in rice

    Directory of Open Access Journals (Sweden)

    Gozde Yuzbasioglu

    2016-03-01

    Full Text Available We investigated Hopi/Osr27 (gypsy and Houba/Tos5/Osr13 (copy retrotransposon movements in 10-day-old roots and leaves of Oryza sativa cvs. Ipsala, Beser and Osmancik-97. Seeds from these three cultivars were germinated between filter papers in Petri dishes for 10 days. Three biologically independent (nonrelated seeds were germinated for each cultivar. Then, roots and leaves grown from the same rice plant were harvested and used for genomic DNA isolation. Inter-retrotransposon amplified polymorphism–polymerase chain reaction with suitable primers was performed with each DNA template to analyze the movements of Hopi/Osr27 and Houba/Tos5/Osr13 retrotransposons. Polymorphism ratios were evaluated both among cultivars and among roots and leaves from the same cultivar. The polymorphism ratios ranged from 0% to 17% for Hopi/Osr27 and from 10% to 87% for Houba/Tos5/Osr13. The obtained results at retrotransposon and varietal levels indicated that the retrotransposon type and genotype dependence are responsible for the occurrence of different variations. Transposable elements are very important for understanding the relationship between cultivars and evolution. Our findings are expected to contribute to the understanding of spontaneous genomic insertion events and their effects on the genetic and epigenetic changes during rice development.

  14. Large-scale transcriptome data reveals transcriptional activity of fission yeast LTR retrotransposons

    DEFF Research Database (Denmark)

    Mourier, Tobias; Willerslev, Eske

    2010-01-01

    makes it difficult to assess which elements are transcriptionally active, but data strongly indicates that only a subset of the LTR retrotransposons contribute significantly to the detected transcription. A considerable level of reverse strand transcription is also detected. Equal levels......BACKGROUND: Retrotransposons are transposable elements that proliferate within eukaryotic genomes through a process involving reverse transcription. The numbers of retrotransposons within genomes and differences between closely related species may yield insight into the evolutionary history......-requisite for retrotransposition is transcription of the elements. Given their intrinsic sequence redundancy, transcriptome-level analyses of transposable elements are scarce. We have used recently published transcriptome data from the fission yeast Schizosaccharomyces pombe to assess the ability to detect and describe...

  15. Evolutionary genomics revealed interkingdom distribution of Tcn1-like chromodomain-containing Gypsy LTR retrotransposons among fungi and plants

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    Blinov Alexander

    2010-04-01

    Full Text Available Abstract Background Chromodomain-containing Gypsy LTR retrotransposons or chromoviruses are widely distributed among eukaryotes and have been found in plants, fungi and vertebrates. The previous comprehensive survey of chromoviruses from mosses (Bryophyta suggested that genomes of non-seed plants contain the clade which is closely related to the retrotransposons from fungi. The origin, distribution and evolutionary history of this clade remained unclear mainly due to the absence of information concerning the diversity and distribution of LTR retrotransposons in other groups of non-seed plants as well as in fungal genomes. Results In present study we preformed in silico analysis of chromodomain-containing LTR retrotransposons in 25 diverse fungi and a number of plant species including spikemoss Selaginella moellendorffii (Lycopodiophyta coupled with an experimental survey of chromodomain-containing Gypsy LTR retrotransposons from diverse non-seed vascular plants (lycophytes, ferns, and horsetails. Our mining of Gypsy LTR retrotransposons in genomic sequences allowed identification of numerous families which have not been described previously in fungi. Two new well-supported clades, Galahad and Mordred, as well as several other previously unknown lineages of chromodomain-containing Gypsy LTR retrotransposons were described based on the results of PCR-mediated survey of LTR retrotransposon fragments from ferns, horsetails and lycophytes. It appeared that one of the clades, namely Tcn1 clade, was present in basidiomycetes and non-seed plants including mosses (Bryophyta and lycophytes (genus Selaginella. Conclusions The interkingdom distribution is not typical for chromodomain-containing LTR retrotransposons clades which are usually very specific for a particular taxonomic group. Tcn1-like LTR retrotransposons from fungi and non-seed plants demonstrated high similarity to each other which can be explained by strong selective constraints and the

  16. Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.).

    Science.gov (United States)

    Syed, N H; Sureshsundar, S; Wilkinson, M J; Bhau, B S; Cavalcanti, J J V; Flavell, A J

    2005-05-01

    The most popular retrotransposon-based molecular marker system in use at the present time is the sequence-specific amplification polymorphism (SSAP) system . This system exploits the insertional polymorphism of long terminal repeat (LTR) retrotransposons around the genome. Because the LTR sequence is used to design primers for this method, its successful application requires sequence information from the terminal region of the mobile elements . In this study, two LTR sequences were isolated from the cashew genome and used successfully to develop SSAP marker systems. These were shown to have higher levels of polymorphism than amplified fragment length polymorphic markers for this species.

  17. Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes.

    Science.gov (United States)

    Mascagni, Flavia; Barghini, Elena; Giordani, Tommaso; Rieseberg, Loren H; Cavallini, Andrea; Natali, Lucia

    2015-11-24

    The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next-generation sequencing (NGS) technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes--7 wild accessions and 8 cultivars--of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads to two sets of sequences, that is, long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was also ascertained for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats.

    Science.gov (United States)

    Konovalov, Fedor A; Goncharov, Nikolay P; Goryunova, Svetlana; Shaturova, Aleksandra; Proshlyakova, Tatyana; Kudryavtsev, Alexander

    2010-06-01

    Molecular markers based on retrotransposon insertions are widely used for various applications including phylogenetic analysis. Multiple cases were described where retrotransposon-based markers, namely sequence-specific amplification polymorphism (SSAP), were superior to other marker types in resolving the phylogenetic relationships due to their higher variability and informativeness. However, the patterns of evolutionary relationships revealed by SSAP may be dependent on the underlying retrotransposon activity in different periods of time. Hence, the proper choice of retrotransposon family is essential for obtaining significant results. We compared the phylogenetic trees for a diverse set of diploid A-genome wheat species (Triticum boeoticum, T. urartu and T. monococcum) based on two unrelated retrotransposon families, BARE-1 and Jeli. BARE-1 belongs to Copia class and has a uniform distribution between common wheat (T. aestivum) genomes of different origin (A, B and D), indicating similar activity in the respective diploid genome donors. Gypsy-class family Jeli was found by us to be an A-genome retrotransposon with >70% copies residing in A genome of hexaploid common wheat, suggesting a burst of transposition in the history of A-genome progenitors. The results indicate that a higher Jeli transpositional activity was associated with T. urartu versus T. boeoticum speciation, while BARE-1 produced more polymorphic insertions during subsequent intraspecific diversification; as an outcome, each retrotransposon provides more informative markers at the corresponding level of phylogenetic relationships. We conclude that multiple retroelement families should be analyzed for an image of evolutionary relationships to be solid and comprehensive.

  19. Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-GenomeOryzaSpecies.

    Science.gov (United States)

    Zhang, Qun-Jie; Gao, Li-Zhi

    2017-06-07

    The dynamics of long terminal repeat (LTR) retrotransposons and their contribution to genome evolution during plant speciation have remained largely unanswered. Here, we perform a genome-wide comparison of all eight Oryza AA-genome species, and identify 3911 intact LTR retrotransposons classified into 790 families. The top 44 most abundant LTR retrotransposon families show patterns of rapid and distinct diversification since the species split over the last ∼4.8 MY (million years). Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive evolutionary landscape of these changes. Compared with Ty1- copia , independent bursts of Ty3- gypsy retrotransposon expansions have occurred with the three largest showing signatures of lineage-specific evolution. The estimated insertion times of 2213 complete retrotransposons from the top 23 most abundant families reveal divergent life histories marked by speedy accumulation, decline, and extinction that differed radically between species. We hypothesize that this rapid evolution of LTR retrotransposons not only divergently shaped the architecture of rice genomes but also contributed to the process of speciation and diversification of rice. Copyright © 2017 Zhang and Gao.

  20. Envelope-like retrotransposons in the plant kingdom: evidence of their presence in gymnosperms (Pinus pinaster).

    Science.gov (United States)

    Miguel, Célia; Simões, Marta; Oliveira, Maria Margarida; Rocheta, Margarida

    2008-11-01

    Retroviruses differ from retrotransposons due to their infective capacity, which depends critically on the encoded envelope. Some plant retroelements contain domains reminiscent of the env of animal retroviruses but the number of such elements described to date is restricted to angiosperms. We show here the first evidence of the presence of putative env-like gene sequences in a gymnosperm species, Pinus pinaster (maritime pine). Using a degenerate primer approach for conserved domains of RNaseH gene, three clones from putative envelope-like retrotransposons (PpRT2, PpRT3, and PpRT4) were identified. The env-like sequences of P. pinaster clones are predicted to encode proteins with transmembrane domains. These sequences showed identity scores of up to 30% with env-like sequences belonging to different organisms. A phylogenetic analysis based on protein alignment of deduced aminoacid sequences revealed that these clones clustered with env-containing plant retrotransposons, as well as with retrotransposons from invertebrate organisms. The differences found among the sequences of maritime pine clones isolated here suggest the existence of different putative classes of env-like retroelements. The identification for the first time of env-like genes in a gymnosperm species may support the ancestrality of retroviruses among plants shedding light on their role in plant evolution.

  1. Insights into the DNA cleavage mechanism of human LINE-1 retrotransposon endonuclease

    NARCIS (Netherlands)

    Repanas, K.; Fuentes, G.; Cohen, S.; Bonvin, A.M.J.J.; Perrakis, A.

    2008-01-01

    The human LINE-1 endonuclease (L1-EN) contributes in defining the genomic integration sites of the abundant human L1 and Alu retrotransposons. LINEs have been considered as possible vehicles for gene delivery and understanding the mechanism of L1-EN could help engineering them as genetic tools. We

  2. How a retrotransposon exploits the plant's heat stress response for its activation.

    Directory of Open Access Journals (Sweden)

    Vladimir V Cavrak

    2014-01-01

    Full Text Available Retrotransposons are major components of plant and animal genomes. They amplify by reverse transcription and reintegration into the host genome but their activity is usually epigenetically silenced. In plants, genomic copies of retrotransposons are typically associated with repressive chromatin modifications installed and maintained by RNA-directed DNA methylation. To escape this tight control, retrotransposons employ various strategies to avoid epigenetic silencing. Here we describe the mechanism developed by ONSEN, an LTR-copia type retrotransposon in Arabidopsis thaliana. ONSEN has acquired a heat-responsive element recognized by plant-derived heat stress defense factors, resulting in transcription and production of full length extrachromosomal DNA under elevated temperatures. Further, the ONSEN promoter is free of CG and CHG sites, and the reduction of DNA methylation at the CHH sites is not sufficient to activate the element. Since dividing cells have a more pronounced heat response, the extrachromosomal ONSEN DNA, capable of reintegrating into the genome, accumulates preferentially in the meristematic tissue of the shoot. The recruitment of a major plant heat shock transcription factor in periods of heat stress exploits the plant's heat stress response to achieve the transposon's activation, making it impossible for the host to respond appropriately to stress without losing control over the invader.

  3. Analysis of heterogeneity of Copia-like retrotransposons in the genome of cassava (Manihot esculenta Crantz).

    Science.gov (United States)

    Gbadegesin, Micheal A; Beeching, John R

    2011-12-20

    Retrotransposons are ubiquitous in eukaryotic genomes and now proving to be useful genetic tools for genetic diversity and phylogenetic analyses, especially in plants. In order to assess the diversity of Ty1/Copia-like retrotransposons of cassava, we used PCR primers anchored on the conserved domains of reverse transcriptases (RTs) to amplify cassava Ty1/Copia-like RT. The PCR product was cloned and sequenced. Sequences analysis of the clones revealed the presence of 69 families of Ty1/Copia-like retrotransposon in the genome of cassava. Comparative analyses of the predicted amino acid sequences of these clones with those of other plants showed that retroelements of this class are very heterogeneous in cassava. Cassava is widely grown for its edible roots in the tropical and subtropical regions of the world. Cassava roots, though poor in protein, are rich in starch (makes up about 80% of the dry matter), vitamin C, carotenes, calcium and potassium. It has a great commercial importance as a source of starch and starch based products. Realizing the importance of cassava, it stands out as a crop to benefit from biotechnology development. Heterogeneity of Mecops (Manihot esculenta copia-like Retrotransposons) showed that they may be useful for genetic diversity and phylogenetic analyses of cassava germplasm.

  4. A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons

    Czech Academy of Sciences Publication Activity Database

    Steinbauerová, Veronika; Neumann, Pavel; Novák, Petr; Macas, Jiří

    2011-01-01

    Roč. 139, 11-12 (2011), s. 1543-1555 ISSN 0016-6707 Institutional research plan: CEZ:AV0Z50510513 Keywords : Additional ORFs * LTR retrotransposons * Repetitive DNA * Plant genome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.148, year: 2011

  5. LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome

    Czech Academy of Sciences Publication Activity Database

    Barghini, E.; Natali, L.; Giordani, T.; Cossu, R.M.; Scalabrin, S.; Cattonaro, F.; Šimková, Hana; Vrána, Jan; Doležel, Jaroslav; Morgante, M.; Cavallini, A.

    2015-01-01

    Roč. 22, č. 1 (2015), s. 91-100 ISSN 1340-2838 R&D Projects: GA ČR GBP501/12/G090; GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : LTR retrotransposons * next-generation sequencing * olive Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.267, year: 2015

  6. The role of retrotransposons in gene family expansions in the human and mouse genomes

    Czech Academy of Sciences Publication Activity Database

    Janoušek, Václav; Laukaitis, C. M.; Yanchukov, Alexey; Karn, R. C.

    2016-01-01

    Roč. 8, č. 9 (2016), s. 2632-2650 ISSN 1759-6653 R&D Projects: GA MŠk EE2.3.20.0303 Institutional support: RVO:68081766 Keywords : gene families * transposable elements * retrotransposons * LINE * LTR * SINE Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.979, year: 2016

  7. MASiVEdb: the Sirevirus Plant Retrotransposon Database

    Directory of Open Access Journals (Sweden)

    Bousios Alexandros

    2012-04-01

    Full Text Available Abstract Background Sireviruses are an ancient genus of the Copia superfamily of LTR retrotransposons, and the only one that has exclusively proliferated within plant genomes. Based on experimental data and phylogenetic analyses, Sireviruses have successfully infiltrated many branches of the plant kingdom, extensively colonizing the genomes of grass species. Notably, it was recently shown that they have been a major force in the make-up and evolution of the maize genome, where they currently occupy ~21% of the nuclear content and ~90% of the Copia population. It is highly likely, therefore, that their life dynamics have been fundamental in the genome composition and organization of a plethora of plant hosts. To assist studies into their impact on plant genome evolution and also facilitate accurate identification and annotation of transposable elements in sequencing projects, we developed MASiVEdb (Mapping and Analysis of SireVirus Elements Database, a collective and systematic resource of Sireviruses in plants. Description Taking advantage of the increasing availability of plant genomic sequences, and using an updated version of MASiVE, an algorithm specifically designed to identify Sireviruses based on their highly conserved genome structure, we populated MASiVEdb (http://bat.infspire.org/databases/masivedb/ with data on 16,243 intact Sireviruses (total length >158Mb discovered in 11 fully-sequenced plant genomes. MASiVEdb is unlike any other transposable element database, providing a multitude of highly curated and detailed information on a specific genus across its hosts, such as complete set of coordinates, insertion age, and an analytical breakdown of the structure and gene complement of each element. All data are readily available through basic and advanced query interfaces, batch retrieval, and downloadable files. A purpose-built system is also offered for detecting and visualizing similarity between user sequences and Sireviruses, as

  8. DNA methylation of retrotransposons, DNA transposons and genes in sugar beet (Beta vulgaris L.).

    Science.gov (United States)

    Zakrzewski, Falk; Schmidt, Martin; Van Lijsebettens, Mieke; Schmidt, Thomas

    2017-06-01

    The methylation of cytosines shapes the epigenetic landscape of plant genomes, coordinates transgenerational epigenetic inheritance, represses the activity of transposable elements (TEs), affects gene expression and, hence, can influence the phenotype. Sugar beet (Beta vulgaris ssp. vulgaris), an important crop that accounts for 30% of worldwide sugar needs, has a relatively small genome size (758 Mbp) consisting of approximately 485 Mbp repetitive DNA (64%), in particular satellite DNA, retrotransposons and DNA transposons. Genome-wide cytosine methylation in the sugar beet genome was studied in leaves and leaf-derived callus with a focus on repetitive sequences, including retrotransposons and DNA transposons, the major groups of repetitive DNA sequences, and compared with gene methylation. Genes showed a specific methylation pattern for CG, CHG (H = A, C, and T) and CHH sites, whereas the TE pattern differed, depending on the TE class (class 1, retrotransposons and class 2, DNA transposons). Along genes and TEs, CG and CHG methylation was higher than that of adjacent genomic regions. In contrast to the relatively low CHH methylation in retrotransposons and genes, the level of CHH methylation in DNA transposons was strongly increased, pointing to a functional role of asymmetric methylation in DNA transposon silencing. Comparison of genome-wide DNA methylation between sugar beet leaves and callus revealed a differential methylation upon tissue culture. Potential epialleles were hypomethylated (lower methylation) at CG and CHG sites in retrotransposons and genes and hypermethylated (higher methylation) at CHH sites in DNA transposons of callus when compared with leaves. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  9. The RNAPII-CTD Maintains Genome Integrity through Inhibition of Retrotransposon Gene Expression and Transposition.

    Directory of Open Access Journals (Sweden)

    Maria J Aristizabal

    2015-10-01

    Full Text Available RNA polymerase II (RNAPII contains a unique C-terminal domain that is composed of heptapeptide repeats and which plays important regulatory roles during gene expression. RNAPII is responsible for the transcription of most protein-coding genes, a subset of non-coding genes, and retrotransposons. Retrotransposon transcription is the first step in their multiplication cycle, given that the RNA intermediate is required for the synthesis of cDNA, the material that is ultimately incorporated into a new genomic location. Retrotransposition can have grave consequences to genome integrity, as integration events can change the gene expression landscape or lead to alteration or loss of genetic information. Given that RNAPII transcribes retrotransposons, we sought to investigate if the RNAPII-CTD played a role in the regulation of retrotransposon gene expression. Importantly, we found that the RNAPII-CTD functioned to maintaining genome integrity through inhibition of retrotransposon gene expression, as reducing CTD length significantly increased expression and transposition rates of Ty1 elements. Mechanistically, the increased Ty1 mRNA levels in the rpb1-CTD11 mutant were partly due to Cdk8-dependent alterations to the RNAPII-CTD phosphorylation status. In addition, Cdk8 alone contributed to Ty1 gene expression regulation by altering the occupancy of the gene-specific transcription factor Ste12. Loss of STE12 and TEC1 suppressed growth phenotypes of the RNAPII-CTD truncation mutant. Collectively, our results implicate Ste12 and Tec1 as general and important contributors to the Cdk8, RNAPII-CTD regulatory circuitry as it relates to the maintenance of genome integrity.

  10. Effects of As2O3 on DNA methylation, genomic instability, and LTR retrotransposon polymorphism in Zea mays.

    Science.gov (United States)

    Erturk, Filiz Aygun; Aydin, Murat; Sigmaz, Burcu; Taspinar, M Sinan; Arslan, Esra; Agar, Guleray; Yagci, Semra

    2015-12-01

    Arsenic is a well-known toxic substance on the living organisms. However, limited efforts have been made to study its DNA methylation, genomic instability, and long terminal repeat (LTR) retrotransposon polymorphism causing properties in different crops. In the present study, effects of As2O3 (arsenic trioxide) on LTR retrotransposon polymorphism and DNA methylation as well as DNA damage in Zea mays seedlings were investigated. The results showed that all of arsenic doses caused a decreasing genomic template stability (GTS) and an increasing Random Amplified Polymorphic DNAs (RAPDs) profile changes (DNA damage). In addition, increasing DNA methylation and LTR retrotransposon polymorphism characterized a model to explain the epigenetically changes in the gene expression were also found. The results of this experiment have clearly shown that arsenic has epigenetic effect as well as its genotoxic effect. Especially, the increasing of polymorphism of some LTR retrotransposon under arsenic stress may be a part of the defense system against the stress.

  11. Retrotransposon expression and incorporation of cloned human and mouse retroelements in human spermatozoa.

    Science.gov (United States)

    Lazaros, Leandros; Kitsou, Chrysoula; Kostoulas, Charilaos; Bellou, Sofia; Hatzi, Elissavet; Ladias, Paris; Stefos, Theodoros; Markoula, Sofia; Galani, Vasiliki; Vartholomatos, Georgios; Tzavaras, Theodore; Georgiou, Ioannis

    2017-03-01

    To investigate the expression of long interspersed element (LINE) 1, human endogenous retrovirus (HERV) K10, and short interspersed element-VNTR-Alu element (SVA) retrotransposons in ejaculated human spermatozoa by means of reverse-transcription (RT) polymerase chain reaction (PCR) analysis as well as the potential incorporation of cloned human and mouse active retroelements in human sperm cell genome. Laboratory study. University research laboratories and academic hospital. Normozoospermic and oligozoospermic white men. RT-PCR analysis was performed to confirm the retrotransposon expression in human spermatozoa. Exogenous retroelements were tagged with a plasmid containing a green fluorescence (EGFP) retrotransposition cassette, and the de novo retrotransposition events were tested with the use of PCR, fluorescence-activated cell sorting analysis, and confocal microscopy. Retroelement expression in human spermatozoa, incorporation of cloned human and mouse active retroelements in human sperm genome, and de novo retrotransposition events in human spermatozoa. RT-PCR products of expressed human LINE-1, HERV-K10, and SVA retrotransposons were observed in ejaculated human sperm samples. The incubation of human spermatozoa with either retrotransposition-active human LINE-1 and HERV-K10 or mouse reverse transcriptase-deficient VL30 retrotransposons tagged with an EGFP-based retrotransposition cassette led to EGFP-positive spermatozo; 16.67% of the samples were positive for retrotransposition. The respective retrotransposition frequencies for the LINE-1, HERV-K10, and VL30 retrotransposons in the positive samples were 0.34 ± 0.13%, 0.37 ± 0.17%, and 0.30 ± 0.14% per sample of 10,000 spermatozoa. Our results show that: 1) LINE-1, HERV-K10, and SVA retrotransposons are transcriptionally expressed in human spermatozoa; 2) cloned active retroelements of human and mammalian origin can be incorporated in human sperm genome; 3) active reverse transcriptases exist in human

  12. Host Noncoding Retrotransposons Induced by DNA Viruses: a SINE of Infection?

    Science.gov (United States)

    Tucker, Jessica M; Glaunsinger, Britt A

    2017-12-01

    Our genomes are dominated by repetitive elements. The majority of these elements derive from retrotransposons, which expand throughout the genome through a process of reverse transcription and integration. Short interspersed nuclear elements, or SINEs, are an abundant class of retrotransposons that are transcribed by RNA polymerase III, thus generating exclusively noncoding RNA (ncRNA) that must hijack the machinery required for their transposition. SINE loci are generally transcriptionally repressed in somatic cells but can be robustly induced upon infection with multiple DNA viruses. Recent research has focused on the gene expression and signaling events that are modulated by SINE ncRNAs, particularly during gammaherpesvirus infection. Here, we review the biology of these SINE ncRNAs, explore how DNA virus infection may lead to their induction, and describe how novel gene regulatory and immune-related functions of these ncRNAs may impact the viral life cycle. Copyright © 2017 American Society for Microbiology.

  13. Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification.

    Science.gov (United States)

    Smýkal, Petr

    2006-01-01

    Fast and efficient DNA fingerprinting of crop cultivars and individuals is frequently used in both theoretical population genetics and in practical breeding. Numerous DNA marker technologies exist and the ratio of speed, cost and accuracy are of importance. Therefore even in species where highly accurate and polymorphic marker systems are available, such as microsatellite SSR (simple sequence repeats), also alternative methods may be of interest. Thanks to their high abundance and ubiquity, temporary mobile retrotransposable elements come into recent focus. Their properties, such as genome wide distribution and well-defined origin of individual insertions by descent, predetermine them for use as molecular markers. In this study, several Ty3-gypsy type retrotransposons have been developed and adopted for the inter-retrotransposon amplified polymorphism (IRAP) method, which is suitable for fast and efficient pea cultivar fingerprinting. The method can easily distinguish even between genetically closely related pea cultivars and provide high polymorphic information content (PIC) in a single PCR analysis.

  14. Mono-allelic retrotransposon insertion addresses epigenetic transcriptional repression in human genome.

    Science.gov (United States)

    Byun, Hyang-Min; Heo, Kyu; Mitchell, Kasey J; Yang, Allen S

    2012-02-02

    Retrotransposons have been extensively studied in plants and animals and have been shown to have an impact on human genome dynamics and evolution. Their ability to move within genomes gives retrotransposons to affect genome instability. we examined the polymorphic inserted AluYa5, evolutionary young Alu, in the progesterone receptor gene to determine the effects of Alu insertion on molecular environment. We used mono-allelic inserted cell lines which carry both Alu-present and Alu-absent alleles. To determine the epigenetic change and gene expression, we performed restriction enzyme digestion, Pyrosequencing, and Chromatin Immunoprecipitation. We observed that the polymorphic insertion of evolutionally young Alu causes increasing levels of DNA methylation in the surrounding genomic area and generates inactive histone tail modifications. Consequently the Alu insertion deleteriously inactivates the neighboring gene expression. The mono-allelic Alu insertion cell line clearly showed that polymorphic inserted repetitive elements cause the inactivation of neighboring gene expression, bringing aberrant epigenetic changes.

  15. Genome-wide analysis of LTR-retrotransposons in oil palm.

    Science.gov (United States)

    Beulé, Thierry; Agbessi, Mawussé Dt; Dussert, Stephane; Jaligot, Estelle; Guyot, Romain

    2015-10-15

    The oil palm (Elaeis guineensis Jacq.) is a major cultivated crop and the world's largest source of edible vegetable oil. The genus Elaeis comprises two species E. guineensis, the commercial African oil palm and E. oleifera, which is used in oil palm genetic breeding. The recent publication of both the African oil palm genome assembly and the first draft sequence of its Latin American relative now allows us to tackle the challenge of understanding the genome composition, structure and evolution of these palm genomes through the annotation of their repeated sequences. In this study, we identified, annotated and compared Transposable Elements (TE) from the African and Latin American oil palms. In a first step, Transposable Element databases were built through de novo detection in both genome sequences then the TE content of both genomes was estimated. Then putative full-length retrotransposons with Long Terminal Repeats (LTRs) were further identified in the E. guineensis genome for characterization of their structural diversity, copy number and chromosomal distribution. Finally, their relative expression in several tissues was determined through in silico analysis of publicly available transcriptome data. Our results reveal a congruence in the transpositional history of LTR retrotransposons between E. oleifera and E. guineensis, especially the Sto-4 family. Also, we have identified and described 583 full-length LTR-retrotransposons in the Elaeis guineensis genome. Our work shows that these elements are most likely no longer mobile and that no recent insertion event has occurred. Moreover, the analysis of chromosomal distribution suggests a preferential insertion of Copia elements in gene-rich regions, whereas Gypsy elements appear to be evenly distributed throughout the genome. Considering the high proportion of LTR retrotransposon in the oil palm genome, our work will contribute to a greater understanding of their impact on genome organization and evolution

  16. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

    DEFF Research Database (Denmark)

    Fort, Alexandre; Hashimoto, Kosuke; Yamada, Daisuke

    2014-01-01

    on nuclear and retrotransposon-derived transcripts. We have performed deep profiling of the nuclear and cytoplasmic transcriptomes of human and mouse stem cells, identifying a class of previously undetected stem cell-specific transcripts. We show that long terminal repeat (LTR)-derived transcripts contribute...... extensively to the complexity of the stem cell nuclear transcriptome. Some LTR-derived transcripts are associated with enhancer regions and are likely to be involved in the maintenance of pluripotency....

  17. Subtracted Diversity Array Identifies Novel Molecular Markers Including Retrotransposons for Fingerprinting Echinacea Species

    Science.gov (United States)

    Olarte, Alexandra; Mantri, Nitin; Nugent, Gregory; Pang, Edwin C. K.

    2013-01-01

    Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationship within the species of this genus is unclear, making the authentication of the species used for the medicinal industry more difficult. We report the construction of a novel Subtracted Diversity Array (SDA) for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences. In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH) was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. Twenty-seven Echinacea genotypes including four that were not used in the array construction could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic retrotransposon sequences. Five out of the eleven most discriminatory features matched to known retrotransposons. This is the first time retrotransposon sequences have been used to fingerprint Echinacea, highlighting the potential of retrotransposons as based molecular markers useful for fingerprinting and studying diversity patterns in Echinacea. PMID:23940565

  18. Identification and chromosomal localization of the monkey retrotransposon in Mesa sp

    Czech Academy of Sciences Publication Activity Database

    Balint-Kurti, P.; Clendennen, S.; Doleželová, Marie; Valárik, Miroslav; Doležel, Jaroslav; Beetham, G. M.

    2000-01-01

    Roč. 263, č. 6 (2000), s. 908-915 ISSN 0026-8925 R&D Projects: GA ČR GV521/96/K117; GA AV ČR IAA5020803; GA MŠk ME 376 Institutional research plan: CEZ:AV0Z5038910 Keywords : In situ hybridization * chromosomal localization * monkey retrotransposon Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.462, year: 2000

  19. Epigenetic Regulation of a Heat-Activated Retrotransposon in Cruciferous Vegetables

    OpenAIRE

    Nozawa, Kosuke; Kawagishi, Yuki; Kawabe, Akira; Sato, Mio; Masuta, Yukari; Kato, Atsushi; Ito, Hidetaka

    2017-01-01

    Transposable elements (TEs) are highly abundant in plant genomes. Environmental stress is one of the critical stimuli that activate TEs. We analyzed a heat-activated retrotransposon, named ONSEN, in cruciferous vegetables. Multiple copies of ONSEN-like elements (OLEs) were found in all of the cruciferous vegetables that were analyzed. The copy number of OLE was high in Brassica oleracea, which includes cabbage, cauliflower, broccoli, Brussels sprout, and kale. Phylogenic analys...

  20. Host factors that promote retrotransposon integration are similar in distantly related eukaryotes.

    Directory of Open Access Journals (Sweden)

    Sudhir Kumar Rai

    2017-12-01

    Full Text Available Retroviruses and Long Terminal Repeat (LTR-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements.

  1. Retrotransposon-associated long non-coding RNAs in mice and men

    Czech Academy of Sciences Publication Activity Database

    Ganesh, Sravya; Svoboda, Petr

    2016-01-01

    Roč. 468, č. 6 (2016), s. 1049-1060 ISSN 0031-6768 R&D Projects: GA ČR(CZ) GBP305/12/G034; GA MŠk LO1419 EU Projects: European Commission 647403; European Commission 607720 Institutional support: RVO:68378050 Keywords : lncRNA * Retrotransposon * line * sine * ltr * MaLR Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.156, year: 2016

  2. LINE retrotransposon RNA is an essential structural and functional epigenetic component of a core neocentromeric chromatin.

    Directory of Open Access Journals (Sweden)

    Anderly C Chueh

    2009-01-01

    Full Text Available We have previously identified and characterized the phenomenon of ectopic human centromeres, known as neocentromeres. Human neocentromeres form epigenetically at euchromatic chromosomal sites and are structurally and functionally similar to normal human centromeres. Recent studies have indicated that neocentromere formation provides a major mechanism for centromere repositioning, karyotype evolution, and speciation. Using a marker chromosome mardel(10 containing a neocentromere formed at the normal chromosomal 10q25 region, we have previously mapped a 330-kb CENP-A-binding domain and described an increased prevalence of L1 retrotransposons in the underlying DNA sequences of the CENP-A-binding clusters. Here, we investigated the potential role of the L1 retrotransposons in the regulation of neocentromere activity. Determination of the transcriptional activity of a panel of full-length L1s (FL-L1s across a 6-Mb region spanning the 10q25 neocentromere chromatin identified one of the FL-L1 retrotransposons, designated FL-L1b and residing centrally within the CENP-A-binding clusters, to be transcriptionally active. We demonstrated the direct incorporation of the FL-L1b RNA transcripts into the CENP-A-associated chromatin. RNAi-mediated knockdown of the FL-L1b RNA transcripts led to a reduction in CENP-A binding and an impaired mitotic function of the 10q25 neocentromere. These results indicate that LINE retrotransposon RNA is a previously undescribed essential structural and functional component of the neocentromeric chromatin and that retrotransposable elements may serve as a critical epigenetic determinant in the chromatin remodelling events leading to neocentromere formation.

  3. Subtracted diversity array identifies novel molecular markers including retrotransposons for fingerprinting Echinacea species.

    Directory of Open Access Journals (Sweden)

    Alexandra Olarte

    Full Text Available Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationship within the species of this genus is unclear, making the authentication of the species used for the medicinal industry more difficult. We report the construction of a novel Subtracted Diversity Array (SDA for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences. In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA fragments were amplified and arrayed. Twenty-seven Echinacea genotypes including four that were not used in the array construction could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic retrotransposon sequences. Five out of the eleven most discriminatory features matched to known retrotransposons. This is the first time retrotransposon sequences have been used to fingerprint Echinacea, highlighting the potential of retrotransposons as based molecular markers useful for fingerprinting and studying diversity patterns in Echinacea.

  4. Host factors that promote retrotransposon integration are similar in distantly related eukaryotes.

    Science.gov (United States)

    Rai, Sudhir Kumar; Sangesland, Maya; Lee, Michael; Esnault, Caroline; Cui, Yujin; Chatterjee, Atreyi Ghatak; Levin, Henry L

    2017-12-01

    Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements.

  5. Two different clades of copia-like retrotransposons in the red alga, Porphyra yezoensis.

    Science.gov (United States)

    Peddigari, Suresh; Zhang, Wenbo; Takechi, Katsuaki; Takano, Hiroyoshi; Takio, Susumu

    2008-11-15

    A copia-like retrotransposon referred to as PyRE1G1 was isolated from the genome of the red alga Porphyra yezoensis. PyRE1G1 is 4807 bp in length, with 204 bp long terminal repeats (LTRs) at both ends. PyRE1G1 has an open reading frame of 1401 residues encoding gag, protease, integrase, reverse transcriptase (RT), and RNase H. From the order of gene arrangement of proteins, PyRE1G1 appears to be a copia-like retrotransposon. Genomic Southern blot analysis suggests that PyRE1G1 consists of a small gene family. From the phylogenetic tree of RT sequences, PyRE1G1 is grouped in the clade of usual copia elements and distinct from the previously isolated red algal copia-like gene PyRE10G in that the latter is closely related to a new clade of aquatic animal-specific copia-like retrotransposons.

  6. Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data

    Directory of Open Access Journals (Sweden)

    Ramos Kenneth

    2010-10-01

    Full Text Available Abstract Background In humans, copies of the Long Interspersed Nuclear Element 1 (LINE-1 retrotransposon comprise 21% of the reference genome, and have been shown to modulate expression and produce novel splice isoforms of transcripts from genes that span or neighbor the LINE-1 insertion site. Results In this work, newly released pilot data from the 1000 Genomes Project is analyzed to detect previously unreported full length insertions of the retrotransposon LINE-1. By direct analysis of the sequence data, we have identified 22 previously unreported LINE-1 insertion sites within the sequence data reported for a mother/father/daughter trio. Conclusions It is demonstrated here that next generation sequencing data, as well as emerging high quality datasets from individual genome projects allow us to assess the amount of heterogeneity with respect to the LINE-1 retrotransposon amongst humans, and provide us with a wealth of testable hypotheses as to the impact that this diversity may have on the health of individuals and populations.

  7. Development of retrotransposon-based markers IRAP and REMAP for cassava (Manihot esculenta).

    Science.gov (United States)

    Kuhn, B C; Mangolin, C A; Souto, E R; Vicient, C M; Machado, M F P S

    2016-04-07

    Retrotransposons are abundant in the genomes of plants. In the present study, inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) markers were developed for the cassava genome (Manihot esculenta Crantz). Four cassava cultivars (Fécula Branca, IPR-União, Olho Junto, and Tamboara, two samples per cultivar) were used to obtain IRAP and REMAP fingerprints. Twelve designed primers were amplified alone and in combinations. The 42 IRAP/REMAP primer combinations amplified 431 DNA segments (bands; markers) of which 36 (8.36%) were polymorphic. The largest number of informative markers (16) was detected using the primers AYF2 and AYF2xAYF4. The number of bands for each primer varied from 3 to 16, with an average of 10.26 amplified segments per primer. The size of the amplified products ranged between 100 and 7000 bp. The AYF2 primer generated the highest number of amplified segments and showed the highest number of polymorphic bands (68.75%). Two samples of each cassava cultivar were used to illustrate the usefulness and the polymorphism of IRAP/REMAP markers. IRAP and REMAP markers produced a high number of reproducible bands, and might be informative and reliable for investigation of genetic diversity and relationships among cassava cultivars.

  8. Quantitative retrotransposon anchored PCR confirms transduction efficiency of transgenes in adult Schistosoma mansoni.

    Science.gov (United States)

    Rinaldi, Gabriel; Suttiprapa, Sutas; Brindley, Paul J

    2011-05-01

    A quantitative retrotransposon anchored PCR (qRAP) that utilizes endogenous retrotransposons as a chromosomal anchor was developed to investigate integration of transgenes in Schistosoma mansoni. The qRAP technique, which builds on earlier techniques, (i) Alu-PCR which has been used to quantify lentiviral (HIV-1) proviral insertions in human chromosomes and (ii) a non-quantitative retrotransposon anchored PCR known to detect the presence of transgenes in the S. mansoni genome, was tested here in a model comparison of retrovirus-transduced adult schistosomes in which one group included intact worms, the other included fragments of adult worms. At the outset, after transducing intact and viable fragments of schistosomes with reporter RNAs, we observed more reporter activity in fragments of worms than in intact worms. We considered this simply reflects the increased surface area in fragments compared to intact worms exposed to the exogenous reporter genes. Subsequently, intact worms and worm fragments were transduced with pseudotyped virions. Transgene integration events in genomic DNA extracted from the virion-exposed worms and worm fragments were quantified by the qRAP, which revealed that fragmenting adult schistosomes resulted in increased density of proviral integrations. The qRAP findings confirmed the likely value of this qRAP technique for quantification of transgenes integrated in schistosome chromosomes. Last, considering the absence of schistosome cell or tissue lines, primary culture of fragmented worms offers an opportunity to optimize transgenesis, and other functional genomic approaches. Copyright © 2011 Elsevier B.V. All rights reserved.

  9. Different histories of two highly variable LTR retrotransposons in sunflower species.

    Science.gov (United States)

    Mascagni, Flavia; Cavallini, Andrea; Giordani, Tommaso; Natali, Lucia

    2017-11-15

    In the Helianthus genus, very large intra- and interspecific variability related to two specific retrotransposons of Helianthus annuus (Helicopia and SURE) exists. When comparing these two sequences to sunflower sequence databases recently produced by our lab, the Helicopia family was shown to belong to the Maximus/SIRE lineage of the Sirevirus genus of the Copia superfamily, whereas the SURE element (whose superfamily was not even previously identified) was classified as a Gypsy element of the Ogre/Tat lineage of the Metavirus genus. Bioinformatic analysis of the two retrotransposon families revealed their genomic abundance and relative proliferation timing. The genomic abundance of these families differed significantly among 12 Helianthus species. The ratio between the abundance of long terminal repeats and their reverse transcriptases suggested that the SURE family has relatively more solo long terminal repeats than does Helicopia. Pairwise comparisons of Illumina reads encoding the reverse transcriptase domain indicated that SURE amplification may have occurred more recently than that of Helicopia. Finally, the analysis of population structure based on the SURE and Helicopia polymorphisms of 32 Helianthus species evidenced two subpopulations, which roughly corresponded to species of the Helianthus and Divaricati/Ciliares sections. However, a number of species showed an admixed structure, confirming the importance of interspecific hybridisation in the evolution of this genus. In general, these two retrotransposon families differentially contributed to interspecific variability, emphasising the need to refer to specific families when studying genome evolution. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Isolation and characterization of genomic retrotransposon sequences from octoploid strawberry (Fragaria x ananassa Duch.).

    Science.gov (United States)

    Ma, Yue; Sun, Haiyue; Zhao, Guiling; Dai, Hongyan; Gao, Xiuyan; Li, He; Zhang, Zhihong

    2008-03-01

    Strawberry (Fragaria spp.) is a kind of herbaceous perennial plant that propagates vegetatively. The conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of LTR retrotransposons were amplified from the cultivated strawberry (Fragaria x ananassa Duch.). Sequence analysis of clones demonstrated that 5 of 19 Ty1-copia group unique sequences and 2 of 10 Ty3-gypsy unique sequences in F. x ananassa genome possessed either stop codon or frameshift. Ty1-copia group sequences are highly heterogeneous (divergence ranged from 1 to 69.8%), but the Ty3-gypsy group sequences are less (divergence ranged from 1 to 10%). Southern dot blot hybridization result suggested that both of the LTR retrotransposons are present in the genome of cultivated strawberry with high copy number (Ty1-copia group 2,875 Ty3-gypsy group 348). RT-PCR amplification from total RNA, which was extracted from leaves of micropropagated strawberry plants, did not yield either of the RT fragments. This is the first report on the presence of RT sequences of Ty1-copia and Ty3-gypsy group retrotransposons in F. x ananassa genome.

  11. Development and Characterisation of Irap Markers From Expressed Retrotransposon-like sequences in Pinus sylvestris L.

    Directory of Open Access Journals (Sweden)

    Voronova Angelika

    2014-07-01

    Full Text Available Conifer genomes are large and stably diploid, in contrast to angiosperms, which are more variable both in genome size and ploidy. Conifer genomes are characterised by multiple gene families and pseudogenes, contain large inter-gene regions and a considerable proportion of repetitive sequences. All members of plant retrotransposon orders have been identified in gymnosperm genomes, however active elements have not been described. Investigation of transposable elements in Scots pine (Pinus sylvestris L. could offer insights into transposon-mediated reorganisation under stress conditions in complex and ancient plant genomes. Nine Pinus sylvestris specific markers were developed to hypothetical long terminal repeats (LTRs from differentially expressed retrotransposon-like fragments after heat stress and insect damage. Genetic diversity of 150 trees from a naturally regenerated pine stand was investigated using the IRAP method. The developed markers revealed high levels of genetic diversity and were able to distinguish subpopulations growing in long-term differential environmental conditions. Somaclonal variation was also investigated using these markers and polymorphic fragments were identified between ramets of Scots pine clones growing in two different plantations, possibly indicating evidence of recent transposition events. Sequencing of the polymorphic fragments identified two groups of sequences containing LTR sequences of an unknown retrotransposon with homology to the LTRs of the Copia-17-PAb-I element.

  12. Evolutionary characterization of Ty3/gypsy-like LTR retrotransposons in the parasitic cestode Echinococcus granulosus.

    Science.gov (United States)

    Bae, Young-An

    2016-11-01

    Cyclophyllidean cestodes including Echinococcus granulosus have a smaller genome and show characteristics such as loss of the gut, a segmented body plan, and accelerated growth rate in hosts compared with other tissue-invading helminths. In an effort to address the molecular mechanism relevant to genome shrinkage, the evolutionary status of long-terminal-repeat (LTR) retrotransposons, which are known as the most potent genomic modulators, was investigated in the E. granulosus draft genome. A majority of the E. granulosus LTR retrotransposons were classified into a novel characteristic clade, named Saci-2, of the Ty3/gypsy family, while the remaining elements belonged to the CsRn1 clade of identical family. Their nucleotide sequences were heavily corrupted by frequent base substitutions and segmental losses. The ceased mobile activity of the major retrotransposons and the following intrinsic DNA loss in their inactive progenies might have contributed to decrease in genome size. Apart from the degenerate copies, a gag gene originating from a CsRn1-like element exhibited substantial evidences suggesting its domestication including a preserved coding profile and transcriptional activity, the presence of syntenic orthologues in cestodes, and selective pressure acting on the gene. To my knowledge, the endogenized gag gene is reported for the first time in invertebrates, though its biological function remains elusive.

  13. LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice

    Directory of Open Access Journals (Sweden)

    Liu Jin-Song

    2008-08-01

    Full Text Available Abstract Background Long terminal repeat retrotransposons (LTR elements are ubiquitous Eukaryotic TEs that transpose through RNA intermediates. Accounting for significant proportion of many plant genomes, LTR elements have been well established as one of the major forces underlying the evolution of plant genome size, structure and function. The accessibility of more than 40% of genomic sequences of the model legume Medicago truncatula (Mt has made the comprehensive study of its LTR elements possible. Results We use a newly developed tool LTR_FINDER to identify LTR retrotransposons in the Mt genome and detect 526 full-length elements as well as a great number of copies related to them. These elements constitute about 9.6% of currently available genomic sequences. They are classified into 85 families of which 64 are reported for the first time. The majority of the LTR retrotransposons belong to either Copia or Gypsy superfamily and the others are categorized as TRIMs or LARDs by their length. We find that the copy-number of Copia-like families is 3 times more than that of Gypsy-like ones but the latter contribute more to the genome. The analysis of PBS and protein-coding domain structure of the LTR families reveals that they tend to use only 4–5 types of tRNAs and many families have quite conservative ORFs besides known TE domains. For several important families, we describe in detail their abundance, conservation, insertion time and structure. We investigate the amplification-deletion pattern of the elements and find that the detectable full-length elements are relatively young and most of them were inserted within the last 0.52 MY. We also estimate that more than ten million bp of the Mt genomic sequences have been removed by the deletion of LTR elements and the removal of the full-length structures in Mt has been more rapid than in rice. Conclusion This report is the first comprehensive description and analysis of LTR retrotransposons in the

  14. Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data

    Science.gov (United States)

    Tetreault, Hannah M.; Ungerer, Mark C.

    2016-01-01

    The most abundant transposable elements (TEs) in plant genomes are Class I long terminal repeat (LTR) retrotransposons represented by superfamilies gypsy and copia. Amplification of these superfamilies directly impacts genome structure and contributes to differential patterns of genome size evolution among plant lineages. Utilizing short-read Illumina data and sequence information from a panel of Helianthus annuus (sunflower) full-length gypsy and copia elements, we explore the contribution of these sequences to genome size variation among eight diploid Helianthus species and an outgroup taxon, Phoebanthus tenuifolius. We also explore transcriptional dynamics of these elements in both leaf and bud tissue via RT-PCR. We demonstrate that most LTR retrotransposon sublineages (i.e., families) display patterns of similar genomic abundance across species. A small number of LTR retrotransposon sublineages exhibit lineage-specific amplification, particularly in the genomes of species with larger estimated nuclear DNA content. RT-PCR assays reveal that some LTR retrotransposon sublineages are transcriptionally active across all species and tissue types, whereas others display species-specific and tissue-specific expression. The species with the largest estimated genome size, H. agrestis, has experienced amplification of LTR retrotransposon sublineages, some of which have proliferated independently in other lineages in the Helianthus phylogeny. PMID:27233667

  15. Autonomic Nervous System Disorders

    Science.gov (United States)

    Your autonomic nervous system is the part of your nervous system that controls involuntary actions, such as the beating of your heart ... breathing and swallowing Erectile dysfunction in men Autonomic nervous system disorders can occur alone or as the result ...

  16. The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story

    NARCIS (Netherlands)

    Bousios, A.; Kourmpetis, Y.I.A.; Pavlidis, P.; Minga, E.; Tsaftaris, A.; Darzentas, N.

    2012-01-01

    Sireviruses are one of the three genera of Copia long terminal repeat (LTR) retrotransposons, exclusive to and highly abundant in plants, and with a unique, among retrotransposons, genome structure. Yet, perhaps due to the few references to the Sirevirus origin of some families, compounded by the

  17. [Characterization of the copy number of RIRE10 retrotransposon and transcriptional activity of its LTR in rice genome].

    Science.gov (United States)

    Wang, Rong; Hong, Guo-Fan; Han, Bin

    2003-08-01

    A full-length Ty3-like retrotransposon, named RIRE10, was identified on the long arm of chromosome 4 in rice genome. The internal region between two LTRs had another open reading frame in the region upstream of gag-pol sequence. The transcripts from LTR region were detected by Northern blot hybridization and RT-PCR. To assess the activity of RIRE10 in rice genome, the copy number of its internal region and long terminal repeat (LTR) domain were determined by dot blot analyses. Nearly 900 solo-LTR of the RIRE10 retrotransposon exist in rice genome, apart from those LTRs that flank 65 intact RIRE retrotransposons. Based on the experimental results, the retrotransposition of RIRE10 was speculated to be influenced by two factors: transcriptional activity of LTR region and homologous recombination resulting in solo-LTR.

  18. Determinants of Genomic RNA Encapsidation in the Saccharomyces cerevisiae Long Terminal Repeat Retrotransposons Ty1 and Ty3

    Directory of Open Access Journals (Sweden)

    Katarzyna Pachulska-Wieczorek

    2016-07-01

    Full Text Available Long-terminal repeat (LTR retrotransposons are transposable genetic elements that replicate intracellularly, and can be considered progenitors of retroviruses. Ty1 and Ty3 are the most extensively characterized LTR retrotransposons whose RNA genomes provide the template for both protein translation and genomic RNA that is packaged into virus-like particles (VLPs and reverse transcribed. Genomic RNAs are not divided into separate pools of translated and packaged RNAs, therefore their trafficking and packaging into VLPs requires an equilibrium between competing events. In this review, we focus on Ty1 and Ty3 genomic RNA trafficking and packaging as essential steps of retrotransposon propagation. We summarize the existing knowledge on genomic RNA sequences and structures essential to these processes, the role of Gag proteins in repression of genomic RNA translation, delivery to VLP assembly sites, and encapsidation.

  19. Extension of Saccharomyces paradoxus chronological lifespan by retrotransposons in certain media conditions is associated with changes in reactive oxygen species.

    Science.gov (United States)

    VanHoute, David; Maxwell, Patrick H

    2014-10-01

    Retrotransposons are mobile DNA elements present throughout eukaryotic genomes that can cause mutations and genome rearrangements when they replicate through reverse transcription. Increased expression and/or mobility of retrotransposons has been correlated with aging in yeast, Caenorhabditis elegans, Drosophila melanogaster, and mammals. The many copies of retrotransposons in humans and various model organisms complicate further pursuit of this relationship. The Saccharomyces cerevisiae Ty1 retrotransposon was introduced into a strain of S. paradoxus that completely lacks retrotransposons to compare chronological lifespans (CLSs) of yeast strains with zero, low, or high Ty1 copy number. Yeast chronological lifespan reflects the progressive loss of cell viability in a nondividing state. Chronological lifespans for the strains were not different in rich medium, but were extended in high Ty1 copy-number strains in synthetic medium and in rich medium containing a low dose of hydroxyurea (HU), an agent that depletes deoxynucleoside triphosphates. Lifespan extension was not strongly correlated with Ty1 mobility or mutation rates for a representative gene. Buffering deoxynucleoside triphosphate levels with threonine supplementation did not substantially affect this lifespan extension, and no substantial differences in cell cycle arrest in the nondividing cells were observed. Lifespan extension was correlated with reduced reactive oxygen species during early stationary phase in high Ty1 copy strains, and antioxidant treatment allowed the zero Ty1 copy strain to live as long as high Ty1 copy-number strains in rich medium with hydroxyurea. This exceptional yeast system has identified an unexpected longevity-promoting role for retrotransposons that may yield novel insights into mechanisms regulating lifespan. Copyright © 2014 by the Genetics Society of America.

  20. Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes.

    Science.gov (United States)

    Vitte, C; Estep, M C; Leebens-Mack, J; Bennetzen, J L

    2013-09-01

    Although monocotyledonous plants comprise one of the two major groups of angiosperms and include >65 000 species, comprehensive genome analysis has been focused mainly on the Poaceae (grass) family. Due to this bias, most of the conclusions that have been drawn for monocot genome evolution are based on grasses. It is not known whether these conclusions apply to many other monocots. To extend our understanding of genome evolution in the monocots, Asparagales genomic sequence data were acquired and the structural properties of asparagus and onion genomes were analysed. Specifically, several available onion and asparagus bacterial artificial chromosomes (BACs) with contig sizes >35 kb were annotated and analysed, with a particular focus on the characterization of long terminal repeat (LTR) retrotransposons. The results reveal that LTR retrotransposons are the major components of the onion and garden asparagus genomes. These elements are mostly intact (i.e. with two LTRs), have mainly inserted within the past 6 million years and are piled up into nested structures. Analysis of shotgun genomic sequence data and the observation of two copies for some transposable elements (TEs) in annotated BACs indicates that some families have become particularly abundant, as high as 4-5 % (asparagus) or 3-4 % (onion) of the genome for the most abundant families, as also seen in large grass genomes such as wheat and maize. Although previous annotations of contiguous genomic sequences have suggested that LTR retrotransposons were highly fragmented in these two Asparagales genomes, the results presented here show that this was largely due to the methodology used. In contrast, this current work indicates an ensemble of genomic features similar to those observed in the Poaceae.

  1. Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes

    Science.gov (United States)

    Vitte, C.; Estep, M. C.; Leebens-Mack, J.; Bennetzen, J. L.

    2013-01-01

    Background and Aims Although monocotyledonous plants comprise one of the two major groups of angiosperms and include >65 000 species, comprehensive genome analysis has been focused mainly on the Poaceae (grass) family. Due to this bias, most of the conclusions that have been drawn for monocot genome evolution are based on grasses. It is not known whether these conclusions apply to many other monocots. Methods To extend our understanding of genome evolution in the monocots, Asparagales genomic sequence data were acquired and the structural properties of asparagus and onion genomes were analysed. Specifically, several available onion and asparagus bacterial artificial chromosomes (BACs) with contig sizes >35 kb were annotated and analysed, with a particular focus on the characterization of long terminal repeat (LTR) retrotransposons. Key Results The results reveal that LTR retrotransposons are the major components of the onion and garden asparagus genomes. These elements are mostly intact (i.e. with two LTRs), have mainly inserted within the past 6 million years and are piled up into nested structures. Analysis of shotgun genomic sequence data and the observation of two copies for some transposable elements (TEs) in annotated BACs indicates that some families have become particularly abundant, as high as 4–5 % (asparagus) or 3–4 % (onion) of the genome for the most abundant families, as also seen in large grass genomes such as wheat and maize. Conclusions Although previous annotations of contiguous genomic sequences have suggested that LTR retrotransposons were highly fragmented in these two Asparagales genomes, the results presented here show that this was largely due to the methodology used. In contrast, this current work indicates an ensemble of genomic features similar to those observed in the Poaceae. PMID:23887091

  2. Recent expansion of heat-activated retrotransposons in the coral symbiont Symbiodinium microadriaticum

    KAUST Repository

    Chen, Jit Ern

    2017-10-20

    Rising sea surface temperature is the main cause of global coral reef decline. Abnormally high temperatures trigger the breakdown of the symbiotic association between corals and their photosynthetic symbionts in the genus Symbiodinium. Higher genetic variation resulting from shorter generation times has previously been proposed to provide increased adaptability to Symbiodinium compared to the host. Retrotransposition is a significant source of genetic variation in eukaryotes and some transposable elements are specifically expressed under adverse environmental conditions. We present transcriptomic and phylogenetic evidence for the existence of heat stress-activated Ty1-copia-type LTR retrotransposons in the coral symbiont Symbiodinium microadriaticum. Genome-wide analyses of emergence patterns of these elements further indicate recent expansion events in the genome of S. microadriaticum. Our findings suggest that acute temperature increases can activate specific retrotransposons in the Symbiodinium genome with potential impacts on the rate of retrotransposition and the generation of genetic variation under heat stress.The ISME Journal advance online publication, 20 October 2017; doi:10.1038/ismej.2017.179.

  3. Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms.

    Directory of Open Access Journals (Sweden)

    Rita Rebollo

    2011-09-01

    Full Text Available The "arms race" relationship between transposable elements (TEs and their host has promoted a series of epigenetic silencing mechanisms directed against TEs. Retrotransposons, a class of TEs, are often located in repressed regions and are thought to induce heterochromatin formation and spreading. However, direct evidence for TE-induced local heterochromatin in mammals is surprisingly scarce. To examine this phenomenon, we chose two mouse embryonic stem (ES cell lines that possess insertionally polymorphic retrotransposons (IAP, ETn/MusD, and LINE elements at specific loci in one cell line but not the other. Employing ChIP-seq data for these cell lines, we show that IAP elements robustly induce H3K9me3 and H4K20me3 marks in flanking genomic DNA. In contrast, such heterochromatin is not induced by LINE copies and only by a minority of polymorphic ETn/MusD copies. DNA methylation is independent of the presence of IAP copies, since it is present in flanking regions of both full and empty sites. Finally, such spreading into genes appears to be rare, since the transcriptional start sites of very few genes are less than one Kb from an IAP. However, the B3galtl gene is subject to transcriptional silencing via IAP-induced heterochromatin. Hence, although rare, IAP-induced local heterochromatin spreading into nearby genes may influence expression and, in turn, host fitness.

  4. RNA helicase domains of viral origin in proteins of insect retrotransposons: possible source for evolutionary advantages

    Directory of Open Access Journals (Sweden)

    Sergey Y. Morozov

    2017-08-01

    Full Text Available Recently, a novel phenomenon of horizontal gene transfer of helicase-encoding sequence from positive-stranded RNA viruses to LINE transposons in insect genomes was described. TRAS family transposons encoding an ORF2 protein, which comprised all typical functional domains and an additional helicase domain, were found to be preserved in many families during the evolution of the order Lepidoptera. In the present paper, in species of orders Hemiptera and Orthoptera, we found helicase domain-encoding sequences integrated into ORF1 of retrotransposons of the Jockey family. RNA helicases encoded by transposons of TRAS and Jockey families represented separate brunches in a phylogenetic tree of helicase domains and thus could be considered as independently originated in the evolution of insect transposons. Transcriptome database analyses revealed that both TRAS and Jockey transposons encoding the helicase domain represented transcribed genome sequences. Moreover, the transposon-encoded helicases were found to contain the full set of conserved motifs essential for their enzymatic activities. Taking into account the previously reported ability of RNA helicase encoded by TRAS ORF2 to suppress post-transcriptional RNA silencing, we propose possible scenarios of evolutionary fixation of actively expressed functional helicases of viral origin in insect retrotransposons as genetic elements advantageous for both transposons and their insect hosts.

  5. Retrotransposon Microsatellite Amplified Polymorphism Strain Fingerprinting Markers Applicable to Various Mushroom Species

    Science.gov (United States)

    Le, Quy Vang; Won, Hyo-Kyung; Lee, Tae-Soo; Lee, Chang-Yun; Lee, Hyun-Sook

    2008-01-01

    The retrotransposon marY1 is a gypsy family retroelement, which is detected ubiquitously within the fungal taxonomic groups in which mushrooms are included. To utilize marY1 as a molecular marker for the DNA fingerprinting of mushrooms, oligonucleotides marY1-LTR-L and marY1-LTR-R were designed on the basis of highly conserved regions from the multiple sequence alignment of 30 marY1 sequences retrieved from a nucleotide sequence database. In accordance with Retrotransposon Microsatellite Amplified Polymorphism (REMAP) fingerprinting methodology, the two oligonucleotides were utilized together with the short sequence repeat primers UBC807 and UBC818 for polymerase chain reaction using templates from different mushroom genomic DNAs. Among the tested oligonucleotides, the marY1-LTR-L and UBC807 primer set yielded the greatest amount of abundance and variation in terms of DNA band numbers and patterns. This method was successfully applied to 10 mushroom species, and the primer set successfully discriminated between different commercial mushroom cultivars of the same strains of 14 Pleurotus ostreatus and 16 P. eryngii. REMAP reproducibility was superior to other popular DNA fingerprinting methodologies including the random amplified polymorphic DNA method. PMID:23997618

  6. Mono-allelic retrotransposon insertion addresses epigenetic transcriptional repression in human genome

    Directory of Open Access Journals (Sweden)

    Byun Hyang-Min

    2012-02-01

    Full Text Available Abstract Background Retrotransposons have been extensively studied in plants and animals and have been shown to have an impact on human genome dynamics and evolution. Their ability to move within genomes gives retrotransposons to affect genome instability. Methods we examined the polymorphic inserted AluYa5, evolutionary young Alu, in the progesterone receptor gene to determine the effects of Alu insertion on molecular environment. We used mono-allelic inserted cell lines which carry both Alu-present and Alu-absent alleles. To determine the epigenetic change and gene expression, we performed restriction enzyme digestion, Pyrosequencing, and Chromatin Immunoprecipitation. Results We observed that the polymorphic insertion of evolutionally young Alu causes increasing levels of DNA methylation in the surrounding genomic area and generates inactive histone tail modifications. Consequently the Alu insertion deleteriously inactivates the neighboring gene expression. Conclusion The mono-allelic Alu insertion cell line clearly showed that polymorphic inserted repetitive elements cause the inactivation of neighboring gene expression, bringing aberrant epigenetic changes.

  7. Coevolution between a family of parasite virulence effectors and a class of LINE-1 retrotransposons.

    Directory of Open Access Journals (Sweden)

    Soledad Sacristán

    2009-10-01

    Full Text Available Parasites are able to evolve rapidly and overcome host defense mechanisms, but the molecular basis of this adaptation is poorly understood. Powdery mildew fungi (Erysiphales, Ascomycota are obligate biotrophic parasites infecting nearly 10,000 plant genera. They obtain their nutrients from host plants through specialized feeding structures known as haustoria. We previously identified the AVR(k1 powdery mildew-specific gene family encoding effectors that contribute to the successful establishment of haustoria. Here, we report the extensive proliferation of the AVR(k1 gene family throughout the genome of B. graminis, with sequences diverging in formae speciales adapted to infect different hosts. Also, importantly, we have discovered that the effectors have coevolved with a particular family of LINE-1 retrotransposons, named TE1a. The coevolution of these two entities indicates a mutual benefit to the association, which could ultimately contribute to parasite adaptation and success. We propose that the association would benefit 1 the powdery mildew fungus, by providing a mechanism for amplifying and diversifying effectors and 2 the associated retrotransposons, by providing a basis for their maintenance through selection in the fungal genome.

  8. Autonomous Mission Operations

    Data.gov (United States)

    National Aeronautics and Space Administration — The AES Autonomous Mission Operations project will develop understanding of the impacts of increasing communication time delays on mission operations and develop...

  9. Chromosomal distribution and evolution of abundant retrotransposons in plants: gypsy elements in diploid and polyploid Brachiaria forage grasses.

    Science.gov (United States)

    Santos, Fabíola Carvalho; Guyot, Romain; do Valle, Cacilda Borges; Chiari, Lucimara; Techio, Vânia Helena; Heslop-Harrison, Pat; Vanzela, André Luís Laforga

    2015-09-01

    Like other eukaryotes, the nuclear genome of plants consists of DNA with a small proportion of low-copy DNA (genes and regulatory sequences) and very abundant DNA sequence motifs that are repeated thousands up to millions of times in the genomes including transposable elements (TEs) and satellite DNA. Retrotransposons, one class of TEs, are sequences that amplify via an RNA intermediate and reinsert into the genome, are often the major fraction of a genome. Here, we put research on retrotransposons into the larger context of plant repetitive DNA and genome behaviour, showing features of genome evolution in a grass genus, Brachiaria, in relation to other plant species. We show the contrasting amplification of different retroelement fractions across the genome with characteristics for various families and domains. The genus Brachiaria includes both diploid and polyploid species, with similar chromosome types and chromosome basic numbers x = 6, 7, 8 and 9. The polyploids reproduce asexually and are apomictic, but there are also sexual species. Cytogenetic studies and flow cytometry indicate a large variation in DNA content (C-value), chromosome sizes and genome organization. In order to evaluate the role of transposable elements in the genome and karyotype organization of species of Brachiaria, we searched for sequences similar to conserved regions of TEs in RNAseq reads library produced in Brachiaria decumbens. Of the 9649 TE-like contigs, 4454 corresponded to LTR-retrotransposons, and of these, 79.5 % were similar to members of the gypsy superfamily. Sequences of conserved protein domains of gypsy were used to design primers for producing the probes. The probes were used in FISH against chromosomes of accesses of B. decumbens, Brachiaria brizantha, Brachiaria ruziziensis and Brachiaria humidicola. Probes showed hybridization signals predominantly in proximal regions, especially those for retrotransposons of the clades CRM and Athila, while elements of Del and Tat

  10. LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons

    Directory of Open Access Journals (Sweden)

    Steinbiss Sascha

    2012-11-01

    Full Text Available Abstract Background Long terminal repeat (LTR retrotransposons are a class of eukaryotic mobile elements characterized by a distinctive sequence similarity-based structure. Hence they are well suited for computational identification. Current software allows for a comprehensive genome-wide de novo detection of such elements. The obvious next step is the classification of newly detected candidates resulting in (super-families. Such a de novo classification approach based on sequence-based clustering of transposon features has been proposed before, resulting in a preliminary assignment of candidates to families as a basis for subsequent manual refinement. However, such a classification workflow is typically split across a heterogeneous set of glue scripts and generic software (for example, spreadsheets, making it tedious for a human expert to inspect, curate and export the putative families produced by the workflow. Results We have developed LTRsift, an interactive graphical software tool for semi-automatic postprocessing of de novo predicted LTR retrotransposon annotations. Its user-friendly interface offers customizable filtering and classification functionality, displaying the putative candidate groups, their members and their internal structure in a hierarchical fashion. To ease manual work, it also supports graphical user interface-driven reassignment, splitting and further annotation of candidates. Export of grouped candidate sets in standard formats is possible. In two case studies, we demonstrate how LTRsift can be employed in the context of a genome-wide LTR retrotransposon survey effort. Conclusions LTRsift is a useful and convenient tool for semi-automated classification of newly detected LTR retrotransposons based on their internal features. Its efficient implementation allows for convenient and seamless filtering and classification in an integrated environment. Developed for life scientists, it is helpful in postprocessing and refining

  11. Semi-Autonomous Systems Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — VisionThe Semi-Autonomous Systems Lab focuses on developing a comprehensive framework for semi-autonomous coordination of networked robotic systems. Semi-autonomous...

  12. Testing for autonomic neuropathy

    DEFF Research Database (Denmark)

    Hilsted, J

    1984-01-01

    of the disease, and may be nonspecific. A number of recently developed quantifiable and reproducible autonomic nerve function tests are reviewed, with emphasis on the physiological basis of the tests and on practical applicability. Finally, diagnostic criteria, based on autonomic nerve function tests...

  13. Efficient DNA Fingerprinting Based on the Targeted Sequencing of Active Retrotransposon Insertion Sites Using a Bench-Top High-Throughput Sequencing Platform

    OpenAIRE

    Monden, Yuki; Yamamoto, Ayaka; Shindo, Akiko; Tahara, Makoto

    2014-01-01

    In many crop species, DNA fingerprinting is required for the precise identification of cultivars to protect the rights of breeders. Many families of retrotransposons have multiple copies throughout the eukaryotic genome and their integrated copies are inherited genetically. Thus, their insertion polymorphisms among cultivars are useful for DNA fingerprinting. In this study, we conducted a DNA fingerprinting based on the insertion polymorphisms of active retrotransposon families (Rtsp-1 and LI...

  14. Acquisition of full-length viral helicase domains by insect retrotransposon-encoded polypeptides

    Directory of Open Access Journals (Sweden)

    Ekaterina eLazareva

    2015-12-01

    Full Text Available Recent metagenomic studies in insects identified many sequences unexpectedly closely related to plant virus genes. Here we describe a new example of this kind, insect R1 LINEs with an additional C-terminal domain in their open reading frame 2. This domain is similar to NTPase/helicase (SF1H domains, which are found in replicative proteins encoded by plant viruses of the genus Tobamovirus. We hypothesize that the SF1H domain could be acquired by LINEs, directly or indirectly, upon insect feeding on virus-infected plants. Possible functions of this domain in LINE transposition and involvement in LINEs counteraction the silencing-based cell defense against retrotransposons are discussed.

  15. Recognizing the SINEs of Infection: Regulation of Retrotransposon Expression and Modulation of Host Cell Processes

    Directory of Open Access Journals (Sweden)

    William Dunker

    2017-12-01

    Full Text Available Short interspersed elements (SINEs are a family of retrotransposons evolutionarily derived from cellular RNA polymerase III transcripts. Over evolutionary time, SINEs have expanded throughout the human genome and today comprise ~11% of total chromosomal DNA. While generally transcriptionally silent in healthy somatic cells, SINE expression increases during a variety of types of stresses, including DNA virus infection. The relevance of SINE expression to viral infection was largely unexplored, however, recent years have seen great progress towards defining the impact of SINE expression on viral replication and host gene expression. Here we review the origin and diversity of SINE elements and their transcriptional control, with an emphasis on how their expression impacts host cell biology during viral infection.

  16. The promoter of the tobacco Tnt1 retrotransposon is induced by wounding and by abiotic stress.

    Science.gov (United States)

    Mhiri, C; Morel, J B; Vernhettes, S; Casacuberta, J M; Lucas, H; Grandbastien, M A

    1997-01-01

    The transcription of the tobacco Tnt1 retrotransposon was previously shown to be induced, in tobacco and in heterologous species, by microbial elicitors and by pathogen infections. We report here that the expression of the Tnt1 promoter is also activated in heterologous species such as tomato and Arabidopsis by wounding, freezing and by other abiotic factors known to induce the plant defence response, such as salicylic acid, CuCl2, or oxidative stress. A similar regulation is observed in tobacco for most treatments. The induction of the Tnt1 promoter expression by wounding remains localized around injury points. In CuCl2-treated Arabidopsis plants, the transcription of Tnt1 is correlated with accumulation of the phytoalexin camalexin and with the expression of the EL13 defence gene. The interest of the Tnt1 promoter as a sensitive indicator of the plant defence responses is discussed.

  17. An epi [c] genetic battle: LINE-1 retrotransposons and intragenomic conflict in humans.

    Science.gov (United States)

    Muñoz-Lopez, Martin; Macia, Angela; Garcia-Cañadas, Marta; Badge, Richard M; Garcia-Perez, Jose L

    2011-07-01

    The ongoing activity of the human retrotransposon Long Interspersed Element 1 (LINE-1 or L1) continues to impact the human genome in various ways. Throughout evolution, mammalian and primate genomes have been under selection to generate strategies to reduce the activity of selfish DNA like L1. Similarly, selfish DNA has evolved to elude these containment systems. This intragenomic conflict has left many inactive versions of LINEs and other Transposable Elements (TEs) littering the human genome, which together account for roughly half of our DNA. Here, we survey the distinct mechanisms operating in the human genome that seem to reduce the mobility of L1s. In addition, we discuss recent findings that strongly suggest epigenetic mechanisms specifically regulate L1 activity in pluripotent human cells.

  18. Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers.

    Science.gov (United States)

    Friesen, N; Brandes, A; Heslop-Harrison, J S

    2001-07-01

    We examined the diversity, evolution, and genomic organization of retroelements in a wide range of gymnosperms. In total, 165 fragments of the reverse transcriptase (RT) gene domain were sequenced from PCR products using newly designed primers for gypsy-like retrotransposons and well-known primers for copia-like retrotransposons; representatives of long interspersed nuclear element (LINE) retroposons were also found. Gypsy and copia-like retroelements are a major component of the gymnosperm genome, and in situ hybridization showed that individual element families were widespread across the chromosomes, consistent with dispersion and amplification via an RNA intermediate. Most of the retroelement families were widely distributed among the gymnosperms, including species with wide taxonomic separation from the Northern and Southern Hemispheres. When the gymnosperm sequences were analyzed together with retroelements from other species, the monophyletic origin of plant copia, gypsy, and LINE groups was well supported, with an additional clade including badnaviral and other, probably virus-related, plant sequences as well as animal and fungal gypsy elements. Plant retroelements showed high diversity within the phylogenetic trees of both copia and gypsy RT domains, with, for example, retroelement sequences from Arabidopsis thaliana being present in many supported groupings. No primary branches divided major taxonomic clades such as angiosperms, monocotyledons, gymnosperms, or conifers or (based on smaller samples) ferns, Gnetales, or Sphenopsida (Equisetum), suggesting that much of the existing diversity was present early in plant evolution, or perhaps that horizontal transfer of sequences has occurred. Within the phylogenetic trees for both gypsy and copia, two clearly monophyletic gymnosperm/conifer clades were revealed, providing evidence against recent horizontal transfer. The results put the evolution of the large and relatively conserved genome structure of

  19. Identification of rtl1, a retrotransposon-derived imprinted gene, as a novel driver of hepatocarcinogenesis.

    Directory of Open Access Journals (Sweden)

    Jesse D Riordan

    2013-04-01

    Full Text Available We previously utilized a Sleeping Beauty (SB transposon mutagenesis screen to discover novel drivers of HCC. This approach identified recurrent mutations within the Dlk1-Dio3 imprinted domain, indicating that alteration of one or more elements within the domain provides a selective advantage to cells during the process of hepatocarcinogenesis. For the current study, we performed transcriptome and small RNA sequencing to profile gene expression in SB-induced HCCs in an attempt to clarify the genetic element(s contributing to tumorigenesis. We identified strong induction of Retrotransposon-like 1 (Rtl1 expression as the only consistent alteration detected in all SB-induced tumors with Dlk1-Dio3 integrations, suggesting that Rtl1 activation serves as a driver of HCC. While previous studies have identified correlations between disrupted expression of multiple Dlk1-Dio3 domain members and HCC, we show here that direct modulation of a single domain member, Rtl1, can promote hepatocarcinogenesis in vivo. Overexpression of Rtl1 in the livers of adult mice using a hydrodynamic gene delivery technique resulted in highly penetrant (86% tumor formation. Additionally, we detected overexpression of RTL1 in 30% of analyzed human HCC samples, indicating the potential relevance of this locus as a therapeutic target for patients. The Rtl1 locus is evolutionarily derived from the domestication of a retrotransposon. In addition to identifying Rtl1 as a novel driver of HCC, our study represents one of the first direct in vivo demonstrations of a role for such a co-opted genetic element in promoting carcinogenesis.

  20. Autonomous Systems and Operations

    Data.gov (United States)

    National Aeronautics and Space Administration — The AES Autonomous Systems and Operations (ASO) project will develop an understanding of the impacts of increasing communication time delays on mission operations,...

  1. Autonomous Systems: Habitat Automation

    Data.gov (United States)

    National Aeronautics and Space Administration — The Habitat Automation Project Element within the Autonomous Systems Project is developing software to automate the automation of habitats and other spacecraft. This...

  2. Autonomous Propellant Loading Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The AES Autonomous Propellant Loading (APL) project consists of three activities. The first is to develop software that will automatically control loading of...

  3. Highly Autonomous Systems Workshop

    OpenAIRE

    Doyle, Richard; Rasmussen, Robert; Man, Guy; Patel, Keyur

    1998-01-01

    Researchers and technology developers from the National Aeronautics and Space Administration (NASA), other government agencies, academia, and industry recently met in Pasadena, California, to take stock of past and current work and future challenges in the application of AI to highly autonomous systems. The meeting was catalyzed by new opportunities in developing autonomous spacecraft for NASA and was in part a celebration of the fictional birth year of the HAL-9000 computer.

  4. Autonomous Intersection Management

    Science.gov (United States)

    2009-12-01

    and analyzing my algorithms for correctness and rigor. Third, Tarun Nimmagadda, for creating the first mixed simulation using my simulator. In addition...Agent Systems, 10(2):131–164, March 2005. [Beeson et al., 2008] Patrick Beeson, Jack O’Quin, Bartley Gillan, Tarun Nimma- gadda, Mickey Ristroph, David...autonomous vehicles at intersections. IEEE Intelligent Systems, 13(3):82–86, May 1998. [Nimmagadda, 2009] Tarun Nimmagadda. Building an autonomous ground

  5. Autonomous Star Tracker Algorithms

    DEFF Research Database (Denmark)

    Betto, Maurizio; Jørgensen, John Leif; Kilsgaard, Søren

    1998-01-01

    Proposal, in response to an ESA R.f.P., to design algorithms for autonomous star tracker operations.The proposal also included the development of a star tracker breadboard to test the algorithms performances.......Proposal, in response to an ESA R.f.P., to design algorithms for autonomous star tracker operations.The proposal also included the development of a star tracker breadboard to test the algorithms performances....

  6. [Idiopathic autonomic neuropathy (pandysautonomia)].

    Science.gov (United States)

    Jankowicz, E; Drozdowski, W; Pogumirski, J

    2001-01-01

    On the basis of current literature, clinical and neuropathologic features of idiopathic autonomic neuropathy is presented. Idiopathic autonomic neuropathy is a disease characterized by acute or subacute onset, monophasic course over a period of several years, it is often preceded by an infection. The spectrum of autonomic changes ranges from cholinergic or adrenergic dysfunction to pandysautonomia, leading to heterogeneity of its clinical features. Possible sympathetic system abnormalities found in autonomic neuropathy are: poor pupillary response to light in darkness, orthostatic hypotension leading to syncope, hypotension without compensatory tachycardia, ejaculation disturbances and vasomotor instability. Possible parasympathetic dysfunctions are: salivation and lacrimation disturbances, absent pupillary constriction to light and near gaze, gastrointestinal tract immobility and impairment of gastrointestinal function, atonic bladder with large residual volume, erectile impotence. Pandysautonomia is thought to result from an immune mediated mechanism and responds well to plasmaferesis and intravenous immunoglobin therapy leading to gradual, sometimes not full, recovery. Moreover in this article we pay attention to the clinical value of many tests like cardiovascular or pharmacological studies in the diagnosis of pandysautonomia and in differentiation of pre- and postganglionic changes. In order to diagnose idiopathic autonomic neuropathy one has to rule out a large number of diseases with autonomic dysfunction e.g.: diabetes, malignant neoplasms, acute intermittent porphyria, Shy-Drager syndrome, Riley-Day's dysautonomia, Parkinson's disease, amyloidosis and others.

  7. Genome-wide survey and comparative analysis of LTR retrotransposons and their captured genes in rice and sorghum.

    Directory of Open Access Journals (Sweden)

    Shu-Ye Jiang

    Full Text Available Long terminal repeat (LTR retrotransposons are the major class I mobile elements in plants. They play crucial roles in gene expansion, diversification and evolution. However, their captured genes are yet to be genome-widely identified and characterized in most of plants although many genomes have been completely sequenced. In this study, we have identified 7,043 and 23,915 full-length LTR retrotransposons in the rice and sorghum genomes, respectively. High percentages of rice full-length LTR retrotransposons were distributed near centromeric region in each of the chromosomes. In contrast, sorghum full-length LTR retrotransposons were not enriched in centromere regions. This dissimilarity could be due to the discrepant retrotransposition during and after divergence from their common ancestor thus might be contributing to species divergence. A total of 672 and 1,343 genes have been captured by these elements in rice and sorghum, respectively. Gene Ontology (GO and gene set enrichment analysis (GSEA showed that no over-represented GO term was identified in LTR captured rice genes. For LTR captured sorghum genes, GO terms with functions in DNA/RNA metabolism and chromatin organization were over-represented. Only 36% of LTR captured rice genes were expressed and expression divergence was estimated as 11.9%. Higher percentage of LTR captured rice genes have evolved into pseudogenes under neutral selection. On the contrary, higher percentage of LTR captured sorghum genes were under purifying selection and 72.4% of them were expressed. Thus, higher percentage of LTR captured sorghum genes was functional. Small RNA analysis suggested that some of LTR captured genes in rice and sorghum might have been involved in negative regulation. On the other hand, positive selection has been observed in both rice and sorghum LTR captured genes and some of them were still expressed and functional. The data suggest that some of these LTR captured genes might have

  8. Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera

    Science.gov (United States)

    Manetti, Maria E; Rossi, Magdalena; Costa, Ana PP; Clausen, Andrea M; Van Sluys, Marie-Anne

    2007-01-01

    Background Tnt1 was the first active plant retrotransposon identified in tobacco after nitrate reductase gene disruption. The Tnt1 superfamily comprises elements from Nicotiana (Tnt1 and Tto1) and Lycopersicon (Retrolyc1 and Tlc1) species. The study presented here was conducted to characterise Tnt1-related sequences in 20 wild species of Solanum and five cultivars of Solanum tuberosum. Results Tnt1-related sequences were amplified from total genomic DNA using a PCR-based approach. Purified fragments were cloned and sequenced, and clustering analysis revealed three groups that differ in their U3 region. Using a network approach with a total of 453 non-redundant sequences isolated from Solanum (197), Nicotiana (140) and Lycopersicon (116) species, it is demonstrated that the Tnt1 superfamily can be treated as a population to resolve previous phylogenetic multifurcations. The resulting RNAseH network revealed that sequences group according to the Solanaceae genus, supporting a strong association with the host genome, whereas tracing the U3 region sequence association characterises the modular evolutionary pattern within the Tnt1 superfamily. Within each genus, and irrespective of species, nearly 20% of Tnt1 sequences analysed are identical, indicative of being part of an active copy. The network approach enabled the identification of putative "master" sequences and provided evidence that within a genus these master sequences are associated with distinct U3 regions. Conclusion The results presented here support the hypothesis that the Tnt1 superfamily was present early in the evolution of Solanaceae. The evidence also suggests that the RNAseH region of Tnt1 became fixed at the host genus level whereas, within each genus, propagation was ensured by the diversification of the U3 region. Different selection pressures seemed to have acted on the U3 and RNAseH modules of ancestral Tnt1 elements, probably due to the distinct functions of these regions in the retrotransposon

  9. A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

    Directory of Open Access Journals (Sweden)

    Palhares Alessandra C

    2012-06-01

    Full Text Available Abstract Background The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results The mapping population parents (‘IAC66-6’ and ‘TUC71-7’ contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs. Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56 were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. Conclusions Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60

  10. Autonomous surveillance for biosecurity.

    Science.gov (United States)

    Jurdak, Raja; Elfes, Alberto; Kusy, Branislav; Tews, Ashley; Hu, Wen; Hernandez, Emili; Kottege, Navinda; Sikka, Pavan

    2015-04-01

    The global movement of people and goods has increased the risk of biosecurity threats and their potential to incur large economic, social, and environmental costs. Conventional manual biosecurity surveillance methods are limited by their scalability in space and time. This article focuses on autonomous surveillance systems, comprising sensor networks, robots, and intelligent algorithms, and their applicability to biosecurity threats. We discuss the spatial and temporal attributes of autonomous surveillance technologies and map them to three broad categories of biosecurity threat: (i) vector-borne diseases; (ii) plant pests; and (iii) aquatic pests. Our discussion reveals a broad range of opportunities to serve biosecurity needs through autonomous surveillance. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

  11. Identification and chromosomal distribution of copia-like retrotransposon sequences in the coffee (Coffea L. genome

    Directory of Open Access Journals (Sweden)

    Juan-Carlos Herrera

    2013-12-01

    Full Text Available The presence of copia-like transposable elements in seven coffee (Coffea sp. species, including the cultivated Coffea arabica, was investigated. The highly conserved domains of the reverse transcriptase (RT present in the copia retrotransposons were amplified by PCR using degenerated primers. Fragments of roughly 300 bp were obtained and the nucleotide sequence was determined for 36 clones, 19 of which showed good quality. The deduced amino acid sequences were compared by multiple alignment analysis. The data suggested two distinct coffee RT groups, designated as CRTG1 and CRTG2. The sequence identities among the groups ranged from 52 to 60% for CRTG1 and 74 to 85% for CRTG2. The multiple alignment analysis revealed that some of the clones in CRTG1 were closely related to the representative elements present in other plant species such as Brassica napus, Populus ciliata and Picea abis. Furthermore, the chromosomal localization of the RT domains in C. arabica and their putative ancestors was investigated by fluorescence in situ hybridization (FISH analysis. FISH signals were observed throughout the chromosomes following a similar dispersed pattern with some localized regions exhibiting higher concentrations of those elements, providing new evidence of their relative conservation and stability in the coffee genome

  12. A Simple and Efficient Method to Isolate LTR Sequences of Plant Retrotransposon

    Directory of Open Access Journals (Sweden)

    Da-Long Guo

    2014-01-01

    Full Text Available Retrotransposons (RTNs have important roles in the formation of plant genome size, structure, and evolution. Ubiquitous distributions, abundant copy numbers, high heterogeneities, and insertional polymorphisms of RTNs have made them as excellent sources for molecular markers development. However, the wide application of RTNs-based molecular markers is restricted by the scarcity of the LTR (long terminal repeat sequences information. A new, simple, and efficient method to isolate LTR sequences of RTNs was presented based on the degenerate RNase H nested primers and PPT (polypurine tract primer of RTNs in tree peony. This method combined the characteristics and advantages of high-efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR, annealing control primer (ACP system, and suppression PCR method. Nineteen LTR sequences were isolated using this new method in tree peony and the applicability of the LTR sequences based markers was validated by further SSAP analysis. The results showed that the new method is simple, of low-cost, and highly efficient, which is just conducted by three rounds of PCR and does not need any restriction enzymes and adapters, much less the hybridizations. This new method is rapid, economical, and cost- and time-saving, which could be easily used to isolate LTR sequences of RTNs.

  13. Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation

    Science.gov (United States)

    Senerchia, Natacha; Felber, François; Parisod, Christian

    2015-01-01

    Interspecific hybridization leads to new interactions among divergent genomes, revealing the nature of genetic incompatibilities having accumulated during and after the origin of species. Conflicts associated with misregulation of transposable elements (TEs) in hybrids expectedly result in their activation and genome-wide changes that may be key to species boundaries. Repetitive genomes of wild wheats have diverged under differential dynamics of specific long terminal repeat retrotransposons (LTR-RTs), offering unparalleled opportunities to address the underpinnings of plant genome reorganization by selfish sequences. Using reciprocal F1 hybrids between three Aegilops species, restructuring and epigenetic repatterning was assessed at random and LTR-RT sequences with amplified fragment length polymorphism and sequence-specific amplified polymorphisms as well as their methylation-sensitive counterparts, respectively. Asymmetrical reorganization of LTR-RT families predicted to cause conflicting interactions matched differential survival of F1 hybrids. Consistent with the genome shock model, increasing divergence of merged LTR-RTs yielded higher levels of changes in corresponding genome fractions and lead to repeated reorganization of LTR-RT sequences in F1 hybrids. Such non-random reorganization of hybrid genomes is coherent with the necessary repression of incompatible TE loci in support of hybrid viability and indicates that TE-driven genomic conflicts may represent an overlooked factor supporting reproductive isolation. PMID:25716787

  14. A LTR copia retrotransposon and Mutator transposons interrupt Pgip genes in cultivated and wild wheats.

    Science.gov (United States)

    Di Giovanni, Michela; Cenci, Alberto; Janni, Michela; D'Ovidio, Renato

    2008-04-01

    Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) proteins involved in plant defence. Wheat pgip genes have been isolated from the B (Tapgip1) and D (Tapgip2) genomes, and now we report the identification of pgip genes from the A genomes of wild and cultivated wheats. By Southern blots and sequence analysis of BAC clones we demonstrated that wheat contains a single copy pgip gene per genome and the one from the A genome, pgip3, is inactivated by the insertion of a long terminal repeat copia retrotranspon within the fourth LRR. We demonstrated also that this retrotransposon insertion is present in Triticum urartu and all the polyploidy wheats assayed, but is absent in T. monococcum (Tmpgip3), suggesting that this insertion took place after the divergence between T. monococcum and T. urartu, but before the formation of the polyploid wheats. We identified also two independent insertion events of new Class II transposable elements, Vacuna, belonging to the Mutator superfamily, that interrupted the Tdipgip1 gene of T. turgidum ssp. dicoccoides. The occurrence of these transposons within the coding region of Tdipgip1 facilitated the mapping of the Pgip locus in the pericentric region of the short arm of chromosome group 7. We speculate that the inactivation of pgip genes are tolerated because of redundancy of PGIP activities in the wheat genome.

  15. Overview of the Autonomic Nervous System

    Science.gov (United States)

    ... be reversible or progressive. Anatomy of the autonomic nervous system The autonomic nervous system is the part of ... organs they connect with. Function of the autonomic nervous system The autonomic nervous system controls internal body processes ...

  16. Autonomous Forest Fire Detection

    NARCIS (Netherlands)

    Breejen, E. den; Breuers, M.; Cremer, F.; Kemp, R.A.W.; Roos, M.; Schutte, K.; Vries, J.S. de

    1998-01-01

    Forest fire detection is a very important issue in the pre-suppression process. Timely detection allows the suppression units to reach the fire in its initial stages and this will reduce the suppression costs considerably. The autonomous forest fire detection principle is based on temporal contrast

  17. Towards autonomous vehicles.

    Science.gov (United States)

    2013-11-01

    We are moving towards an age of autonomous vehicles. Cycles of innovation initiated in the public and private sectors : have led one into another since the 1990s; and out of these efforts have sprung a variety of Advanced Driver Assistance : Systems ...

  18. Experimental Autonomous Vehicle Systems

    DEFF Research Database (Denmark)

    Ravn, Ole; Andersen, Nils Axel

    1998-01-01

    The paper describes the requirements for and a prototype configuration of a software architecture for control of an experimental autonomous vehicle. The test bed nature of the system is emphasised in the choice of architecture making re-configurability, data logging and extendability simple...

  19. ADAM: ADaptive Autonomous Machine

    NARCIS (Netherlands)

    van Oosten, Daan C.; Nijenhuis, Lucas F.J.; Bakkers, André; Vervoort, Wiek

    1996-01-01

    This paper describes a part of the development of an adaptive autonomous machine that is able to move in an unknown world extract knowledge out of the perceived data, has the possibility to reason, and finally has the capability to exchange experiences and knowledge with other agents. The agent is

  20. Comparative genomic analysis reveals multiple long terminal repeats, lineage-specific amplification, and frequent interelement recombination for Cassandra retrotransposon in pear (Pyrus bretschneideri Rehd.).

    Science.gov (United States)

    Yin, Hao; Du, Jianchang; Li, Leiting; Jin, Cong; Fan, Lian; Li, Meng; Wu, Jun; Zhang, Shaoling

    2014-06-04

    Cassandra transposable elements belong to a specific group of terminal-repeat retrotransposons in miniature (TRIM). Although Cassandra TRIM elements have been found in almost all vascular plants, detailed investigations on the nature, abundance, amplification timeframe, and evolution have not been performed in an individual genome. We therefore conducted a comprehensive analysis of Cassandra retrotransposons using the newly sequenced pear genome along with four other Rosaceae species, including apple, peach, mei, and woodland strawberry. Our data reveal several interesting findings for this particular retrotransposon family: 1) A large number of the intact copies contain three, four, or five long terminal repeats (LTRs) (∼20% in pear); 2) intact copies and solo LTRs with or without target site duplications are both common (∼80% vs. 20%) in each genome; 3) the elements exhibit an overall unbiased distribution among the chromosomes; 4) the elements are most successfully amplified in pear (5,032 copies); and 5) the evolutionary relationships of these elements vary among different lineages, species, and evolutionary time. These results indicate that Cassandra retrotransposons contain more complex structures (elements with multiple LTRs) than what we have known previously, and that frequent interelement unequal recombination followed by transposition may play a critical role in shaping and reshaping host genomes. Thus this study provides insights into the property, propensity, and molecular mechanisms governing the formation and amplification of Cassandra retrotransposons, and enhances our understanding of the structural variation, evolutionary history, and transposition process of LTR retrotransposons in plants. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  1. The Hairless Stem Phenotype of Cotton (Gossypium barbadense) Is Linked to a Copia-Like Retrotransposon Insertion in a Homeodomain-Leucine Zipper Gene (HD1).

    Science.gov (United States)

    Ding, Mingquan; Ye, Wuwei; Lin, Lifeng; He, Shae; Du, Xiongming; Chen, Aiqun; Cao, Yuefen; Qin, Yuan; Yang, Fen; Jiang, Yurong; Zhang, Hua; Wang, Xiyin; Paterson, Andrew H; Rong, Junkang

    2015-09-01

    Cotton (Gossypium) stem trichomes are mostly single cells that arise from stem epidermal cells. In this study, a homeodomain-leucine zipper gene (HD1) was found to cosegregate with the dominant trichome locus previously designated as T1 and mapped to chromosome 6. Characterization of HD1 orthologs revealed that the absence of stem trichomes in modern Gossypium barbadense varieties is linked to a large retrotransposon insertion in the ninth exon, 2565 bp downstream from the initial codon in the At subgenome HD1 gene (At-GbHD1). In both the At and Dt subgenomes, reduced transcription of GbHD1 genes is caused by this insertion. The disruption of At-HD1 further affects the expression of downstream GbMYB25 and GbHOX3 genes. Analyses of primitive cultivated accessions identified another retrotransposon insertion event in the sixth exon of At-GbHD1 that might predate the previously identified retrotransposon in modern varieties. Although both retrotransposon insertions results in similar phenotypic changes, the timing of these two retrotransposon insertion events fits well with our current understanding of the history of cotton speciation and dispersal. Taken together, the results of genetics mapping, gene expression and association analyses suggest that GbHD1 is an important component that controls stem trichome development and is a promising candidate gene for the T1 locus. The interspecific phenotypic difference in stem trichome traits also may be attributable to HD1 inactivation associated with retrotransposon insertion. Copyright © 2015 by the Genetics Society of America.

  2. Diversity of LTR-retrotransposons and Enhancer/Suppressor Mutator-like transposons in cassava (Manihot esculenta Crantz).

    Science.gov (United States)

    Gbadegesin, Michael A; Wills, Matthew A; Beeching, John R

    2008-10-01

    Cassava (Manihot esculenta Crantz), though a major world crop with enormous potential, is very under studied. Little is known about its genome structure and organisation. Transposable elements have a key role in the evolution of genome structure, and can be used as important tools in applied genetics. This paper sets out to survey the diversity of members of three major classes of transposable element within the cassava genome and in relation to similar elements in other plants. Members of two classes of LTR-retrotransposons, Ty1/copia-like and Ty3/gypsy-like, and of Enhancer/Suppressor Mutator (En/Spm)-like transposons were isolated and characterised. Analyses revealed 59 families of Ty1/copia, 26 families of Ty3/gypsy retrotransposons, and 40 families of En/Spm in the cassava genome. In the comparative analyses, the predicted amino acid sequences for these transposon classes were compared with those of related elements from other plant species. These revealed that there were multiple lineages of Ty1/copia-like retrotransposons in the genome of cassava and suggested that vertical and horizontal transmission as the source of cassava Mecops may not be mutually exclusive. For the Ty3/gypsy elements network, two groups of cassava Megyps were evident including the Arabidopsis Athila lineage. However, cassava En/Spm-like elements (Meens) constituted a single group within a network of plant En/Spm-like elements. Hybridisation analysis supported the presence of transposons in the genome of cassava in medium (Ty3/gypsy and En/Spm) to high (Ty1/copia) copy numbers. Thus the cassava genome was shown to contain diverse members of three major classes of transposable element; however, the different classes exhibited contrasting evolutionary histories.

  3. Insertion of a solo LTR retrotransposon associates with spur mutations in 'Red Delicious' apple (Malus × domestica).

    Science.gov (United States)

    Han, Mengxue; Sun, Qibao; Zhou, Junyong; Qiu, Huarong; Guo, Jing; Lu, Lijuan; Mu, Wenlei; Sun, Jun

    2017-09-01

    Insertion of a solo LTR, which possesses strong bidirectional, stem-specific promoter activities, is associated with the evolution of a dwarfing apple spur mutation. Spur mutations in apple scions revolutionized global apple production. Since long terminal repeat (LTR) retrotransposons are tightly related to natural mutations, inter-retrotransposon-amplified polymorphism technique and genome walking were used to find sequences in the apple genome based on these LTRs. In 'Red Delicious' spur mutants, a novel, 2190-bp insertion was identified as a spur-specific, solo LTR (sLTR) located at the 1038th nucleotide of another sLTR, which was 1536 bp in length. This insertion-within-an-insertion was localized within a preexisting Gypsy-50 retrotransposon at position 3,762,767 on chromosome 4. The analysis of transcriptional activity of the two sLTRs (the 2190- and 1536-bp inserts) indicated that the 2190-bp sLTR is a promoter, capable of bidirectional transcription. GUS expression in the 2190-bp-sense and 2190-bp-antisense transgenic lines was prominent in stems. In contrast, no promoter activity from either the sense or the antisense strand of the 1536-bp sLTR was detected. From ~150 kb of DNA on each side of the 2190 bp, sLTR insertion site, corresponding to 300 kb of the 'Golden Delicious' genome, 23 genes were predicted. Ten genes had predicted functions that could affect shoot development. This first report, of a sLTR insertion associated with the evolution of apple spur mutation, will facilitate apple breeding, cloning of spur-related genes, and discovery of mechanisms behind dwarf habit.

  4. Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae).

    Science.gov (United States)

    Kolano, Bozena; Bednara, Edyta; Weiss-Schneeweiss, Hanna

    2013-10-01

    High heterogeneity was observed among conserved domains of reverse transcriptase ( rt ) isolated from quinoa. Only one Ty1- copia rt was highly amplified. Reverse transcriptase sequences were located predominantly in pericentromeric region of quinoa chromosomes. The heterogeneity, genomic abundance, and chromosomal distribution of reverse transcriptase (rt)-coding fragments of Ty1-copia and Ty3-gypsy long terminal repeat retrotransposons were analyzed in the Chenopodium quinoa genome. Conserved domains of the rt gene were amplified and characterized using degenerate oligonucleotide primer pairs. Sequence analyses indicated that half of Ty1-copia rt (51 %) and 39 % of Ty3-gypsy rt fragments contained intact reading frames. High heterogeneity among rt sequences was observed for both Ty1-copia and Ty3-gypsy rt amplicons, with Ty1-copia more heterogeneous than Ty3-gypsy. Most of the isolated rt fragments were present in quinoa genome in low copy numbers, with only one highly amplified Ty1-copia rt sequence family. The gypsy-like RNase H fragments co-amplified with Ty1-copia-degenerate primers were shown to be highly amplified in the quinoa genome indicating either higher abundance of some gypsy families of which rt domains could not be amplified, or independent evolution of this gypsy-region in quinoa. Both Ty1-copia and Ty3-gypsy retrotransposons were preferentially located in pericentromeric heterochromatin of quinoa chromosomes. Phylogenetic analyses of newly amplified rt fragments together with well-characterized retrotransposon families from other organisms allowed identification of major lineages of retroelements in the genome of quinoa and provided preliminary insight into their evolutionary dynamics.

  5. Isolation of two new retrotransposon sequences and development of molecular and cytological markers for Dasypyrum villosum (L.).

    Science.gov (United States)

    Zhang, Jie; Jiang, Yun; Xuan, Pu; Guo, Yuanlin; Deng, Guangbing; Yu, Maoqun; Long, Hai

    2017-10-01

    Dasypyrum villosum is a valuable genetic resource for wheat improvement. With the aim to efficiently monitor the D. villosum chromatin introduced into common wheat, two novel retrotransposon sequences were isolated by RAPD, and were successfully converted to D. villosum-specific SCAR markers. In addition, we constructed a chromosomal karyotype of D. villosum. Our results revealed that different accessions of D. villosum showed slightly different signal patterns, indicating that distribution of repeats did not diverge significantly among D. villosum accessions. The two SCAR markers and FISH karyotype of D. villosum could be used for efficient and precise identification of D. villosum chromatin in wheat breeding.

  6. Partial retrotransposon-like DNA sequence in the genomic clone of Aspergillus flavus, pAF28.

    Science.gov (United States)

    Okubara, Patricia A; Tibbot, Brian K; Tarun, Alice S; McAlpin, Cesaria E; Hua, Sui-Sheng T

    2003-07-01

    A genomic clone of the aflatoxin-producing fungus Aspergillus flavus, designated pAF28, has been used as a probe for Southern blot fingerprinting of fungal strains. A large number of A. flavus strains isolated from corn fields and tree-nut orchards can be distinguished because the DNA fingerprint patterns are highly polymorphic. We have completed the sequencing of a 6355 bp insert in pAF28. The sequence features motifs and open reading frames characteristic of transposable elements of the gypsy class. We have named this new element AfRTL-1, for A. flavus retrotransposon-like DNA.

  7. Control of gag-pol gene expression in the Candida albicans retrotransposon Tca2

    Directory of Open Access Journals (Sweden)

    Gibson Joanne

    2007-10-01

    Full Text Available Abstract Background In the C. albicans retrotransposon Tca2, the gag and pol ORFs are separated by a UGA stop codon, 3' of which is a potential RNA pseudoknot. It is unclear how the Tca2 gag UGA codon is bypassed to allow pol expression. However, in other retroelements, translational readthrough of the gag stop codon can be directed by its flanking sequence, including a 3' pseudoknot. Results The hypothesis was tested that in Tca2, gag stop codon flanking sequences direct translational readthrough and synthesis of a gag-pol fusion protein. Sequence from the Tca2 gag-UGA-pol junction (300 nt was inserted between fused lacZ and luciferase (luc genes in a Saccharomyces cerevisiae dual reporter construct. Although downstream of UGA, luc was expressed, but its expression was unaffected by inserting additional stop codons at the 3' end of lacZ. Luc expression was instead being driven by a previously unknown minor promoter activity within the gag-pol junction region. Evidence together indicated that junction sequence alone cannot direct UGA readthrough. Using reporter genes in C. albicans, the activities of this gag-pol junction promoter and the Tca2 long terminal repeat (LTR promoter were compared. Of the two promoters, only the LTR promoter was induced by heat-shock, which also triggers retrotransposition. Tca2 pol protein, epitope-tagged in C. albicans to allow detection, was also heat-shock induced, indicating that pol proteins were expressed from a gag-UGA-pol RNA. Conclusion This is the first demonstration that the LTR promoter directs Tca2 pol protein expression, and that pol proteins are translated from a gag-pol RNA, which thus requires a mechanism for stop codon bypass. However, in contrast to most other retroelement and viral readthrough signals, immediate gag UGA-flanking sequences were insufficient to direct stop readthrough in S. cerevisiae, indicating non-canonical mechanisms direct gag UGA bypass in Tca2.

  8. Expression of the Retrotransposon Helena Reveals a Complex Pattern of TE Deregulation in Drosophila Hybrids.

    Directory of Open Access Journals (Sweden)

    Valèria Romero-Soriano

    Full Text Available Transposable elements (TEs, repeated mobile sequences, are ubiquitous in the eukaryotic kingdom. Their mobilizing capacity confers on them a high mutagenic potential, which must be strongly regulated to guarantee genome stability. In the Drosophila germline, a small RNA-mediated silencing system, the piRNA (Piwi-interacting RNA pathway, is the main responsible TE regulating mechanism, but some stressful conditions can destabilize it. For instance, during interspecific hybridization, genomic stress caused by the shock of two different genomes can lead, in both animals and plants, to higher transposition rates. A recent study in D. buzatii-D. koepferae hybrids detected mobilization of 28 TEs, yet little is known about the molecular mechanisms explaining this transposition release. We have characterized one of the mobilized TEs, the retrotransposon Helena, and used quantitative expression to assess whether its high transposition rates in hybrids are preceded by increased expression. We have also localized Helena expression in the gonads to see if cellular expression patterns have changed in the hybrids. To give more insight into changes in TE regulation in hybrids, we analysed Helena-specific piRNA populations of hybrids and parental species. Helena expression is not globally altered in somatic tissues, but male and female gonads have different patterns of deregulation. In testes, Helena is repressed in F1, increasing then its expression up to parental values. This is linked with a mislocation of Helena transcripts along with an increase of their specific piRNA levels. Ovaries have additive levels of Helena expression, but the ping-pong cycle efficiency seems to be reduced in F1 hybrids. This could be at the origin of new Helena insertions in hybrids, which would be transmitted to F1 hybrid female progeny.

  9. Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element.

    Science.gov (United States)

    Leung, Wilson; Shaffer, Christopher D; Chen, Elizabeth J; Quisenberry, Thomas J; Ko, Kevin; Braverman, John M; Giarla, Thomas C; Mortimer, Nathan T; Reed, Laura K; Smith, Sheryl T; Robic, Srebrenka; McCartha, Shannon R; Perry, Danielle R; Prescod, Lindsay M; Sheppard, Zenyth A; Saville, Ken J; McClish, Allison; Morlock, Emily A; Sochor, Victoria R; Stanton, Brittney; Veysey-White, Isaac C; Revie, Dennis; Jimenez, Luis A; Palomino, Jennifer J; Patao, Melissa D; Patao, Shane M; Himelblau, Edward T; Campbell, Jaclyn D; Hertz, Alexandra L; McEvilly, Maddison F; Wagner, Allison R; Youngblom, James; Bedi, Baljit; Bettincourt, Jeffery; Duso, Erin; Her, Maiye; Hilton, William; House, Samantha; Karimi, Masud; Kumimoto, Kevin; Lee, Rebekah; Lopez, Darryl; Odisho, George; Prasad, Ricky; Robbins, Holly Lyn; Sandhu, Tanveer; Selfridge, Tracy; Tsukashima, Kara; Yosif, Hani; Kokan, Nighat P; Britt, Latia; Zoellner, Alycia; Spana, Eric P; Chlebina, Ben T; Chong, Insun; Friedman, Harrison; Mammo, Danny A; Ng, Chun L; Nikam, Vinayak S; Schwartz, Nicholas U; Xu, Thomas Q; Burg, Martin G; Batten, Spencer M; Corbeill, Lindsay M; Enoch, Erica; Ensign, Jesse J; Franks, Mary E; Haiker, Breanna; Ingles, Judith A; Kirkland, Lyndsay D; Lorenz-Guertin, Joshua M; Matthews, Jordan; Mittig, Cody M; Monsma, Nicholaus; Olson, Katherine J; Perez-Aragon, Guillermo; Ramic, Alen; Ramirez, Jordan R; Scheiber, Christopher; Schneider, Patrick A; Schultz, Devon E; Simon, Matthew; Spencer, Eric; Wernette, Adam C; Wykle, Maxine E; Zavala-Arellano, Elizabeth; McDonald, Mitchell J; Ostby, Kristine; Wendland, Peter; DiAngelo, Justin R; Ceasrine, Alexis M; Cox, Amanda H; Docherty, James E B; Gingras, Robert M; Grieb, Stephanie M; Pavia, Michael J; Personius, Casey L; Polak, Grzegorz L; Beach, Dale L; Cerritos, Heaven L; Horansky, Edward A; Sharif, Karim A; Moran, Ryan; Parrish, Susan; Bickford, Kirsten; Bland, Jennifer; Broussard, Juliana; Campbell, Kerry; Deibel, Katelynn E; Forka, Richard; Lemke, Monika C; Nelson, Marlee B; O'Keeffe, Catherine; Ramey, S Mariel; Schmidt, Luke; Villegas, Paola; Jones, Christopher J; Christ, Stephanie L; Mamari, Sami; Rinaldi, Adam S; Stity, Ghazal; Hark, Amy T; Scheuerman, Mark; Silver Key, S Catherine; McRae, Briana D; Haberman, Adam S; Asinof, Sam; Carrington, Harriette; Drumm, Kelly; Embry, Terrance; McGuire, Richard; Miller-Foreman, Drew; Rosen, Stella; Safa, Nadia; Schultz, Darrin; Segal, Matt; Shevin, Yakov; Svoronos, Petros; Vuong, Tam; Skuse, Gary; Paetkau, Don W; Bridgman, Rachael K; Brown, Charlotte M; Carroll, Alicia R; Gifford, Francesca M; Gillespie, Julie Beth; Herman, Susan E; Holtcamp, Krystal L; Host, Misha A; Hussey, Gabrielle; Kramer, Danielle M; Lawrence, Joan Q; Martin, Madeline M; Niemiec, Ellen N; O'Reilly, Ashleigh P; Pahl, Olivia A; Quintana, Guadalupe; Rettie, Elizabeth A S; Richardson, Torie L; Rodriguez, Arianne E; Rodriguez, Mona O; Schiraldi, Laura; Smith, Joanna J; Sugrue, Kelsey F; Suriano, Lindsey J; Takach, Kaitlyn E; Vasquez, Arielle M; Velez, Ximena; Villafuerte, Elizabeth J; Vives, Laura T; Zellmer, Victoria R; Hauke, Jeanette; Hauser, Charles R; Barker, Karolyn; Cannon, Laurie; Parsamian, Perouza; Parsons, Samantha; Wichman, Zachariah; Bazinet, Christopher W; Johnson, Diana E; Bangura, Abubakarr; Black, Jordan A; Chevee, Victoria; Einsteen, Sarah A; Hilton, Sarah K; Kollmer, Max; Nadendla, Rahul; Stamm, Joyce; Fafara-Thompson, Antoinette E; Gygi, Amber M; Ogawa, Emmy E; Van Camp, Matt; Kocsisova, Zuzana; Leatherman, Judith L; Modahl, Cassie M; Rubin, Michael R; Apiz-Saab, Susana S; Arias-Mejias, Suzette M; Carrion-Ortiz, Carlos F; Claudio-Vazquez, Patricia N; Espada-Green, Debbie M; Feliciano-Camacho, Marium; Gonzalez-Bonilla, Karina M; Taboas-Arroyo, Mariela; Vargas-Franco, Dorianmarie; Montañez-Gonzalez, Raquel; Perez-Otero, Joseph; Rivera-Burgos, Myrielis; Rivera-Rosario, Francisco J; Eisler, Heather L; Alexander, Jackie; Begley, Samatha K; Gabbard, Deana; Allen, Robert J; Aung, Wint Yan; Barshop, William D; Boozalis, Amanda; Chu, Vanessa P; Davis, Jeremy S; Duggal, Ryan N; Franklin, Robert; Gavinski, Katherine; Gebreyesus, Heran; Gong, Henry Z; Greenstein, Rachel A; Guo, Averill D; Hanson, Casey; Homa, Kaitlin E; Hsu, Simon C; Huang, Yi; Huo, Lucy; Jacobs, Sarah; Jia, Sasha; Jung, Kyle L; Wai-Chee Kong, Sarah; Kroll, Matthew R; Lee, Brandon M; Lee, Paul F; Levine, Kevin M; Li, Amy S; Liu, Chengyu; Liu, Max Mian; Lousararian, Adam P; Lowery, Peter B; Mallya, Allyson P; Marcus, Joseph E; Ng, Patrick C; Nguyen, Hien P; Patel, Ruchik; Precht, Hashini; Rastogi, Suchita; Sarezky, Jonathan M; Schefkind, Adam; Schultz, Michael B; Shen, Delia; Skorupa, Tara; Spies, Nicholas C; Stancu, Gabriel; Vivian Tsang, Hiu Man; Turski, Alice L; Venkat, Rohit; Waldman, Leah E; Wang, Kaidi; Wang, Tracy; Wei, Jeffrey W; Wu, Dennis Y; Xiong, David D; Yu, Jack; Zhou, Karen; McNeil, Gerard P; Fernandez, Robert W; Menzies, Patrick Gomez; Gu, Tingting; Buhler, Jeremy; Mardis, Elaine R; Elgin, Sarah C R

    2017-08-07

    The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome in Drosophila melanogaster , but it is substantially larger (>18.7 Mb) in D. ananassae To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes ( e.g. , larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in D. ananassae Compared to D. melanogaster , the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 5' ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains. Copyright © 2017 Leung et al.

  10. Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element

    Directory of Open Access Journals (Sweden)

    Wilson Leung

    2017-08-01

    Full Text Available The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb in D. ananassae. To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons are major contributors to this expansion (78.6%, while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%. Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes (e.g., larger coding spans, larger introns, more coding exons, and lower codon bias, but these differences are exaggerated in D. ananassae. Compared to D. melanogaster, the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 5′ ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2, while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains.

  11. Diagnostic use of computational retrotransposon detection: Successful definition of pathogenetic mechanism in a ciliopathy phenotype.

    Science.gov (United States)

    Takenouchi, Toshiki; Kuchikata, Tomu; Yoshihashi, Hiroshi; Fujiwara, Mineko; Uehara, Tomoko; Miyama, Sahoko; Yamada, Shiro; Kosaki, Kenjiro

    2017-05-01

    Among more than 5,000 human monogenic disorders with known causative genes, transposable element insertion of a Long Interspersed Nuclear Element 1 (LINE1, L1) is known as the mechanistic basis in only 13 genetic conditions. Meckel-Gruber syndrome is a rare ciliopathy characterized by occipital encephalocele and cystic kidney disease. Here, we document a boy with occipital encephalocele, post-axial polydactyly, and multicystic renal disease. A medical exome analysis detected a heterozygous frameshift mutation, c.4582_4583delCG p.(Arg1528Serfs*17) in CC2D2A in the maternally derived allele. The further use of a dedicated bioinformatics algorithm for detecting retrotransposon insertions led to the detection of an L1 insertion affecting exon 7 in the paternally derived allele. The complete sequencing and sequence homology analysis of the inserted L1 element showed that the L1 element was classified as L1HS (L1 human specific) and that the element had intact open reading frames in the two L1-encoded proteins. This observation ranks Meckel-Gruber syndrome as only the 14th disorder to be caused by an L1 insertion among more than 5,000 known human genetic disorders. Although a transposable element detection algorithm is not included in the current best-practice next-generation sequencing analysis, the present observation illustrates the utility of such an algorithm, which would require modest computational time and resources. Whether the seemingly infrequent recognition of L1 insertion in the pathogenesis of human genetic diseases might simply reflect a lack of appropriate detection methods remains to be seen. © 2017 Wiley Periodicals, Inc.

  12. The reverse transcriptase encoded by LINE-1 retrotransposons in the genesis, progression and therapy of cancer

    Science.gov (United States)

    Sciamanna, Ilaria; De Luca, Chiara; Spadafora, Corrado

    2016-02-01

    In higher eukaryotic genomes, Long Interspersed Nuclear Element 1 (LINE-1) retrotransposons represent a large family of repeated genomic elements. They transpose using a reverse transcriptase (RT), which they encode as part of the ORF2p product. RT inhibition in cancer cells, either via RNA interference-dependent silencing of active LINE-1 elements, or using RT inhibitory drugs, reduces cancer cell proliferation, promotes their differentiation and antagonizes tumor progression in animal models. Indeed, the nonnucleoside RT inhibitor efavirenz has recently been tested in a phase II clinical trial with metastatic prostate cancer patients. An in-depth analysis of ORF2p in a mouse model of breast cancer showed ORF2p to be precociously expressed in precancerous lesions and highly abundant in advanced cancer stages, while being barely detectable in normal breast tissue, providing a rationale for the finding that RT-expressing tumours are therapeutically sensitive to RT inhibitors. We summarise mechanistic and gene profiling studies indicating that highly abundant LINE-1-derived RT can “sequester” RNA substrates for reverse transcription in tumor cells, entailing the formation of RNA:DNA hybrid molecules and impairing the overall production of regulatory miRNAs, with a global impact on the cell transcriptome. Based on these data, LINE-1-ORF2 encoded RT has a tumor-promoting potential that is exerted at an epigenetic level. We propose a model whereby LINE1-RT drives a previously unrecognized global regulatory process, the deregulation of which drives cell transformation and tumorigenesis and possibly implicated in cancer cell heterogeneity.

  13. Evolution of the R2 retrotransposon ribozyme and its self-cleavage site.

    Directory of Open Access Journals (Sweden)

    Danna G Eickbush

    Full Text Available R2 is a non-long terminal repeat retrotransposon that inserts site-specifically in the tandem 28S rRNA genes of many animals. Previously, R2 RNA from various species of Drosophila was shown to self-cleave from the 28S rRNA/R2 co-transcript by a hepatitis D virus (HDV-like ribozyme encoded at its 5' end. RNA cleavage was at the precise 5' junction of the element with the 28S gene. Here we report that RNAs encompassing the 5' ends of R2 elements from throughout its species range fold into HDV-like ribozymes. In vitro assays of RNA self-cleavage conducted in many R2 lineages confirmed activity. For many R2s, RNA self-cleavage was not at the 5' end of the element but at 28S rRNA sequences up to 36 nucleotides upstream of the junction. The location of cleavage correlated well with the types of endogenous R2 5' junctions from different species. R2 5' junctions were uniform for most R2s in which RNA cleavage was upstream in the rRNA sequences. The 28S sequences remaining on the first DNA strand synthesized during retrotransposition are postulated to anneal to the target site and uniformly prime second strand DNA synthesis. In species where RNA cleavage occurred at the R2 5' end, the 5' junctions were variable. This junction variation is postulated to result from the priming of second strand DNA synthesis by chance microhomologies between the target site and the first DNA strand. Finally, features of R2 ribozyme evolution, especially changes in cleavage site and convergence on the same active site sequences, are discussed.

  14. Autonomous Robot Retrieval System

    OpenAIRE

    Ahern, S.

    2015-01-01

    Mobile robots are increasingly being deployed in environments hazardous to humans. However, many of these robots require remote control operation or are tethered, requiring the human operator to remain within a potentially hazardous radius of the area of operation. To resolve this issue an Autonomous Robot Retrieval System (ARRS) utilising Open RatSLAM based on the Lego NXT 2.0 robotics platform is proposed but could not be implemented due to memory limitations of the hardware. An occupancy g...

  15. Nature's Autonomous Oscillators

    Science.gov (United States)

    Mayr, H. G.; Yee, J.-H.; Mayr, M.; Schnetzler, R.

    2012-01-01

    Nonlinearity is required to produce autonomous oscillations without external time dependent source, and an example is the pendulum clock. The escapement mechanism of the clock imparts an impulse for each swing direction, which keeps the pendulum oscillating at the resonance frequency. Among nature's observed autonomous oscillators, examples are the quasi-biennial oscillation and bimonthly oscillation of the Earth atmosphere, and the 22-year solar oscillation. The oscillations have been simulated in numerical models without external time dependent source, and in Section 2 we summarize the results. Specifically, we shall discuss the nonlinearities that are involved in generating the oscillations, and the processes that produce the periodicities. In biology, insects have flight muscles, which function autonomously with wing frequencies that far exceed the animals' neural capacity; Stretch-activation of muscle contraction is the mechanism that produces the high frequency oscillation of insect flight, discussed in Section 3. The same mechanism is also invoked to explain the functioning of the cardiac muscle. In Section 4, we present a tutorial review of the cardio-vascular system, heart anatomy, and muscle cell physiology, leading up to Starling's Law of the Heart, which supports our notion that the human heart is also a nonlinear oscillator. In Section 5, we offer a broad perspective of the tenuous links between the fluid dynamical oscillators and the human heart physiology.

  16. Genomic change, retrotransposon mobilization and extensive cytosine methylation alteration in Brassica napus introgressions from two intertribal hybridizations.

    Directory of Open Access Journals (Sweden)

    Xueli Zhang

    Full Text Available Hybridization and introgression represent important means for the transfer and/or de novo origination of traits and play an important role in facilitating speciation and plant breeding. Two sets of introgression lines in Brassica napus L. were previously established by its intertribal hybridizations with two wild species and long-term selection. In this study, the methods of amplified fragment length polymorphisms (AFLP, sequence-specific amplification polymorphism (SSAP and methylation-sensitive amplified polymorphism (MSAP were used to determine their genomic change, retrotransposon mobilization and cytosine methylation alteration in these lines. The genomic change revealed by the loss or gain of AFLP bands occurred for ∼10% of the total bands amplified in the two sets of introgressions, while no bands specific for wild species were detected. The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets. MSAP analysis indicated that methylation changes were common in these lines (33.4-39.8% and the hypermethylation was more frequent than hypomethylation. Our results suggested that certain extents of genetic and epigenetic alterations were induced by hybridization and alien DNA introgression. The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed.

  17. Tye7 regulates yeast Ty1 retrotransposon sense and antisense transcription in response to adenylic nucleotides stress.

    Science.gov (United States)

    Servant, Géraldine; Pinson, Benoit; Tchalikian-Cosson, Aurélie; Coulpier, Fanny; Lemoine, Sophie; Pennetier, Carole; Bridier-Nahmias, Antoine; Todeschini, Anne Laure; Fayol, Hélène; Daignan-Fornier, Bertrand; Lesage, Pascale

    2012-07-01

    Transposable elements play a fundamental role in genome evolution. It is proposed that their mobility, activated under stress, induces mutations that could confer advantages to the host organism. Transcription of the Ty1 LTR-retrotransposon of Saccharomyces cerevisiae is activated in response to a severe deficiency in adenylic nucleotides. Here, we show that Ty2 and Ty3 are also stimulated under these stress conditions, revealing the simultaneous activation of three active Ty retrotransposon families. We demonstrate that Ty1 activation in response to adenylic nucleotide depletion requires the DNA-binding transcription factor Tye7. Ty1 is transcribed in both sense and antisense directions. We identify three Tye7 potential binding sites in the region of Ty1 DNA sequence where antisense transcription starts. We show that Tye7 binds to Ty1 DNA and regulates Ty1 antisense transcription. Altogether, our data suggest that, in response to adenylic nucleotide reduction, TYE7 is induced and activates Ty1 mRNA transcription, possibly by controlling Ty1 antisense transcription. We also provide the first evidence that Ty1 antisense transcription can be regulated by environmental stress conditions, pointing to a new level of control of Ty1 activity by stress, as Ty1 antisense RNAs play an important role in regulating Ty1 mobility at both the transcriptional and post-transcriptional stages.

  18. Virus-like attachment sites and plastic CpG islands:landmarks of diversity in plant Del retrotransposons.

    Directory of Open Access Journals (Sweden)

    Guilherme M Q Cruz

    Full Text Available Full-length Del elements from ten angiosperm genomes, 5 monocot and 5 dicot, were retrieved and putative attachment (att sites were identified. In the 2432 Del elements, two types of U5 att sites and a single conserved type of U3 att site were identified. Retroviral att sites confer specificity to the integration process, different att sites types therefore implies lineage specificity. While some features are common to all Del elements, CpG island patterns within the LTRs were particular to lineage specific clusters. All eudicot copies grouped into one single clade while the monocots harbour a more diverse collection of elements. Furthermore, full-length Del elements and truncated copies were unevenly distributed amongst chromosomes. Elements of Del lineage are organized in plants into three clusters and each cluster is composed of elements with distinct LTR features. Our results suggest that the Del lineage efficiently amplified in the monocots and that one branch is probably a newly emerging sub-lineage. Finally, sequences in all groups are under purifying selection. These results show the LTR region is dynamic and important in the evolution of LTR-retrotransposons, we speculate that it is a trigger for retrotransposon diversification.

  19. Autonomic Neuropathy in Diabetes Mellitus

    OpenAIRE

    Verrotti, Alberto; Prezioso, Giovanni; Scattoni, Raffaella; Chiarelli, Francesco

    2014-01-01

    Diabetic autonomic neuropathy (DAN) is a serious and common complication of diabetes, often overlooked and misdiagnosed. It is a systemic-wide disorder that may be asymptomatic in the early stages. The most studied and clinically important form of DAN is cardiovascular autonomic neuropathy defined as the impairment of autonomic control of the cardiovascular system in patients with diabetes after exclusion of other causes. The reported prevalence of DAN varies widely depending on inconsistent ...

  20. Autonomic Fuselet Specification and Composition

    National Research Council Canada - National Science Library

    Mills, Peter H

    2006-01-01

    A framework for autonomic fuselet business logic development was developed, using semantic web services and workflow technologies to specify fuselet information needs, to define an executable workflow...

  1. Robotics and Autonomous Systems Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — FUNCTION: Provides an environment for developing and evaluating intelligent software for both actual and simulated autonomous vehicles. Laboratory computers provide...

  2. Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L.

    Science.gov (United States)

    2013-01-01

    Background Recently, Jatropha curcas L. has attracted worldwide attention for its potential as a source of biodiesel. However, most DNA markers have demonstrated high levels of genetic similarity among and within jatropha populations around the globe. Despite promising features of copia-type retrotransposons as ideal genetic tools for gene tagging, mutagenesis, and marker-assisted selection, they have not been characterized in the jatropha genome yet. Here, we examined the diversity, evolution, and genome-wide organization of copia-type retrotransposons in the Asian, African, and Mesoamerican accessions of jatropha, then introduced a retrotransposon-based marker for this biofuel crop. Results In total, 157 PCR fragments that were amplified using the degenerate primers for the reverse transcriptase (RT) domain of copia-type retroelements were sequenced and aligned to construct the neighbor-joining tree. Phylogenetic analysis demonstrated that isolated copia RT sequences were classified into ten families, which were then grouped into three lineages. An in-depth study of the jatropha genome for the RT sequences of each family led to the characterization of full consensus sequences of the jatropha copia-type families. Estimated copy numbers of target sequences were largely different among families, as was presence of genes within 5 kb flanking regions for each family. Five copia-type families were as appealing candidates for the development of DNA marker systems. A candidate marker from family Jc7 was particularly capable of detecting genetic variation among different jatropha accessions. Fluorescence in situ hybridization (FISH) to metaphase chromosomes reveals that copia-type retrotransposons are scattered across chromosomes mainly located in the distal part regions. Conclusion This is the first report on genome-wide analysis and the cytogenetic mapping of copia-type retrotransposons of jatropha, leading to the discovery of families bearing high potential as DNA

  3. The Sinbad retrotransposon from the genome of the human blood fluke, Schistosoma mansoni, and the distribution of related Pao-like elements

    Directory of Open Access Journals (Sweden)

    Morales Maria E

    2005-02-01

    Full Text Available Abstract Background Of the major families of long terminal repeat (LTR retrotransposons, the Pao/BEL family is probably the least well studied. It is becoming apparent that numerous LTR retrotransposons and other mobile genetic elements have colonized the genome of the human blood fluke, Schistosoma mansoni. Results A proviral form of Sinbad, a new LTR retrotransposon, was identified in the genome of S. mansoni. Phylogenetic analysis indicated that Sinbad belongs to one of five discreet subfamilies of Pao/BEL like elements. BLAST searches of whole genomes and EST databases indicated that members of this clade occurred in species of the Insecta, Nematoda, Echinodermata and Chordata, as well as Platyhelminthes, but were absent from all plants, fungi and lower eukaryotes examined. Among the deuterostomes examined, only aquatic species harbored these types of elements. All four species of nematode examined were positive for Sinbad sequences, although among insect and vertebrate genomes, some were positive and some negative. The full length, consensus Sinbad retrotransposon was 6,287 bp long and was flanked at its 5'- and 3'-ends by identical LTRs of 386 bp. Sinbad displayed a triple Cys-His RNA binding motif characteristic of Gag of Pao/BEL-like elements, followed by the enzymatic domains of protease, reverse transcriptase (RT, RNAseH, and integrase, in that order. A phylogenetic tree of deduced RT sequences from 26 elements revealed that Sinbad was most closely related to an unnamed element from the zebrafish Danio rerio and to Saci-1, also from S. mansoni. It was also closely related to Pao from Bombyx mori and to Ninja of Drosophila simulans. Sinbad was only distantly related to the other schistosome LTR retrotransposons Boudicca, Gulliver, Saci-2, Saci-3, and Fugitive, which are gypsy-like. Southern hybridization and bioinformatics analyses indicated that there were about 50 copies of Sinbad in the S. mansoni genome. The presence of ESTs

  4. Morally autonomous practice?

    Science.gov (United States)

    Scott, P A

    1998-12-01

    The structures and contexts within which nurses work results in the moral agency and moral autonomy of the nurse being compromised. This claim results from a confusion of (1) the concept of autonomy with those of freedom and independence; and (2) a confusion of the notion of moral autonomy with that of autonomous professional practice. The drawing of appropriate distinctions allows clarification of the relevant concepts. It also underlines the responsibility of practitioners to recognize the moral dimension of their practice, and the moral implications of their actions, as they attempt to meet the health care needs of their patients and develop practice professionally.

  5. Autonomic epileptic seizures, autonomic effects of seizures, and SUDEP.

    Science.gov (United States)

    Moseley, Brian; Bateman, Lisa; Millichap, John J; Wirrell, Elaine; Panayiotopoulos, Chrysostomos P

    2013-03-01

    Many generalized tonic-clonic seizures are accompanied by profound autonomic changes. However, autonomic seizures and autonomic status epilepticus can also be seen with specific electroclinical syndromes (Panayiotopoulos syndrome), etiologies, and localizations. Such autonomic symptoms may impact cardiorespiratory function. While it is likely that several factors contribute to SUDEP, further study of both ictal respiratory and cardiac changes and underlying neuroanatomical mechanisms involved in autonomic seizure semiology are likely to provide important data to improve our understanding of the pathophysiology of this devastating condition. This paper will review the association between autonomic symptoms and epileptic seizures and will highlight the work of three young investigators. Drs. Lisa Bateman and Brian Moseley will review their work on cardiorespiratory effects of recorded seizures and how this assists in our understanding of SUDEP. Dr. John Millichap will review autonomic seizures and autonomic dysfunctions related to childhood epilepsy and will discuss the importance of expanded research efforts in this field. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Towards autonomous vehicular clouds

    Directory of Open Access Journals (Sweden)

    Stephan Olariu

    2011-09-01

    Full Text Available The dawn of the 21st century has seen a growing interest in vehicular networking and its myriad potential applications. The initial view of practitioners and researchers was that radio-equipped vehicles could keep the drivers informed about potential safety risks and increase their awareness of road conditions. The view then expanded to include access to the Internet and associated services. This position paper proposes and promotes a novel and more comprehensive vision namely, that advances in vehicular networks, embedded devices and cloud computing will enable the formation of autonomous clouds of vehicular computing, communication, sensing, power and physical resources. Hence, we coin the term, autonomous vehicular clouds (AVCs. A key feature distinguishing AVCs from conventional cloud computing is that mobile AVC resources can be pooled dynamically to serve authorized users and to enable autonomy in real-time service sharing and management on terrestrial, aerial, or aquatic pathways or theaters of operations. In addition to general-purpose AVCs, we also envision the emergence of specialized AVCs such as mobile analytics laboratories. Furthermore, we envision that the integration of AVCs with ubiquitous smart infrastructures including intelligent transportation systems, smart cities and smart electric power grids will have an enormous societal impact enabling ubiquitous utility cyber-physical services at the right place, right time and with right-sized resources.

  7. Autonomous Formation Flight

    Science.gov (United States)

    Schkolnik, Gerard S.; Cobleigh, Brent

    2004-01-01

    NASA's Strategic Plan for the Aerospace Technology Enterprise includes ambitious objectives focused on affordable air travel, reduced emissions, and expanded aviation-system capacity. NASA Dryden Flight Research Center, in cooperation with NASA Ames Research Center, the Boeing Company, and the University of California, Los Angeles, has embarked on an autonomous-formation-flight project that promises to make significant strides towards these goals. For millions of years, birds have taken advantage of the aerodynamic benefit of flying in formation. The traditional "V" formation flown by many species of birds (including gulls, pelicans, and geese) enables each of the trailing birds to fly in the upwash flow field that exists just outboard of the bird immediately ahead in the formation. The result for each trailing bird is a decrease in induced drag and thus a reduction in the energy needed to maintain a given speed. Hence, for migratory birds, formation flight extends the range of the system of birds over the range of birds flying solo. The Autonomous Formation Flight (AFF) Project is seeking to extend this symbiotic relationship to aircraft.

  8. Overview of the Autonomic Nervous System

    Science.gov (United States)

    ... process. Autonomic disorders may be reversible or progressive. Anatomy of the autonomic nervous system The autonomic nervous ... with acetylcholine and placed on the legs and forearm. Then, the volume of sweat is measured to ...

  9. Behavioural domain knowledge transfer for autonomous agents

    CSIR Research Space (South Africa)

    Rosman, Benjamin S

    2014-11-01

    Full Text Available , and Behavior Transfer in Autonomous Robots, AAAI 2014 Fall Symposium Series, 13-15 November 2014 Behavioural Domain Knowledge Transfer for Autonomous Agents Benjamin Rosman Mobile Intelligent Autonomous Systems Modelling and Digital Science Council...

  10. Autonomous Learner Model Resource Book

    Science.gov (United States)

    Betts, George T.; Carey, Robin J.; Kapushion, Blanche M.

    2016-01-01

    "Autonomous Learner Model Resource Book" includes activities and strategies to support the development of autonomous learners. More than 40 activities are included, all geared to the emotional, social, cognitive, and physical development of students. Teachers may use these activities and strategies with the entire class, small groups, or…

  11. Assessment of genetic diversity among Indian potato (Solanum tuberosum L.) collection using microsatellite and retrotransposon based marker systems.

    Science.gov (United States)

    Sharma, Vishakha; Nandineni, Madhusudan R

    2014-04-01

    Potato (Solanum tuberosum) is an important non-cereal crop throughout the world and is highly recommended for ensuring global food security. Owing to the complexities in genetics and inheritance pattern of potato, the conventional method of cross breeding for developing improved varieties has been difficult. Identification and tagging of desirable traits with informative molecular markers would aid in the development of improved varieties. Insertional polymorphism of copia-like and gypsy-like long terminal repeat retrotransposons (RTN) were investigated among 47 potato varieties from India using Inter-Retrotransposon Amplified Polymorphism (IRAP) and Retrotransposon Microsatellite Amplified Polymorphism (REMAP) marker techniques and were compared with the DNA profiles obtained with simple sequence repeats (SSRs). The genetic polymorphism, efficiency of polymorphism and effectiveness of marker systems were evaluated to assess the extent of genetic diversity among Indian potato varieties. A total of 139 polymorphic SSR alleles, 270 IRAP and 98 REMAP polymorphic bands, showing polymorphism of 100%, 87.9% and 68.5%, respectively, were used for detailed characterization of the genetic relationships among potato varieties by using cluster analysis and principal coordinate analysis (PCoA). IRAP analysis resulted in the highest number of polymorphic bands with an average of 15 polymorphic bands per assay unit when compared to the other two marker systems. Based on pair-wise comparison, the genetic similarity was calculated using Dice similarity coefficient. The SSRs showed a wide range in genetic similarity values (0.485-0.971) as compared to IRAP (0.69-0.911) and REMAP (0.713-0.947). A Mantel's matrix correspondence test showed a high positive correlation (r=0.6) between IRAP and REMAP, an intermediate value (r=0.58) for IRAP and SSR and the lowest value (r=0.17) for SSR and REMAP. Statistically significant cophenetic correlation coefficient values, of 0.961, 0.941 and 0

  12. Research Institute for Autonomous Precision Guided Systems

    National Research Council Canada - National Science Library

    Rogacki, John R

    2007-01-01

    ... vehicles, cooperative flight of autonomous aerial vehicles using GPS and vision information, cooperative and sharing of information in search missions involving multiple autonomous agents, multi-scale...

  13. Evolutionary Autonomous Health Monitoring System (EAHMS) Project

    Data.gov (United States)

    National Aeronautics and Space Administration — For supporting NASA's Robotics, Tele-Robotics and Autonomous Systems Roadmap, we are proposing the "Evolutionary Autonomous Health Monitoring System" (EAHMS) for...

  14. Autonomous Martian flying rover

    Science.gov (United States)

    1990-01-01

    A remotely programmable, autonomous flying rover is proposed to extensively survey the Martian surface environment. A Mach .3, solar powered, modified flying wing could cover roughly a 2000 mile range during Martian daylight hours. Multiple craft launched from an orbiting mother ship could provide near-global coverage. Each craft is envisioned to fly at about 1 km above the surface and measure atmospheric composition, pressure and temperature, map surface topography, and remotely penetrate the near subsurface looking for water (ice) and perhaps evidence of life. Data collected are relayed to Earth via the orbiting mother ship. Near surface guidance and control capability is an adaptation of current cruise missile technology. A solar powered aircraft designed to fly in the low temperature, low density, carbon dioxide Martian atmosphere near the surface appears feasible.

  15. Autonomous component carrier selection

    DEFF Research Database (Denmark)

    Garcia, Luis Guilherme Uzeda; Pedersen, Klaus; Mogensen, Preben

    2009-01-01

    management and efficient system operation. Due to the expected large number of user-deployed cells, centralized network planning becomes unpractical and new scalable alternatives must be sought. In this article, we propose a fully distributed and scalable solution to the interference management problem......Low-power base stations such as e.g. Femto-cells are one of the candidates for high data rate provisioning in local areas, such as residences, apartment complexes, business offices and outdoor hotspot scenarios. Unfortunately, the benefits are not without new challenges in terms of interference...... in local areas, basing our study case on LTE-Advanced. We present extensive network simulation results to demonstrate that a simple and robust interference management scheme, called autonomous component carrier selection allows each cell to select the most attractive frequency configuration; improving...

  16. An evaluation of a SVA retrotransposon in the FUS promoter as a transcriptional regulator and its association to ALS.

    Directory of Open Access Journals (Sweden)

    Abigail L Savage

    Full Text Available Genetic mutations of FUS have been linked to many diseases including Amyotrophic Lateral Sclerosis (ALS and Frontotemporal Lobar Degeneration. A primate specific and polymorphic retrotransposon of the SINE-VNTR-Alu (SVA family is present upstream of the FUS gene. Here we have demonstrated that this retrotransposon can act as a classical transcriptional regulatory domain in the context of a reporter gene construct both in vitro in the human SK-N-AS neuroblastoma cell line and in vivo in a chick embryo model. We have also demonstrated that the SVA is composed of multiple distinct regulatory domains, one of which is a variable number tandem repeat (VNTR. The ability of the SVA and its component parts to direct reporter gene expression supported a hypothesis that this region could direct differential FUS expression in vivo. The SVA may therefore contribute to the modulation of FUS expression exhibited in and associated with neurological disorders including ALS where FUS regulation may be an important parameter in progression of the disease. As VNTRs are often clinical associates for disease progression we determined the extent of polymorphism within the SVA. In total 2 variants of the SVA were identified based within a central VNTR. Preliminary analysis addressed the association of these SVA variants within a small sporadic ALS cohort but did not reach statistical significance, although we did not include other parameters such as SNPs within the SVA or an environmental factor in this analysis. The latter may be particularly important as the transcriptional and epigenetic properties of the SVA are likely to be directed by the environment of the cell.

  17. Cybersecurity for aerospace autonomous systems

    Science.gov (United States)

    Straub, Jeremy

    2015-05-01

    High profile breaches have occurred across numerous information systems. One area where attacks are particularly problematic is autonomous control systems. This paper considers the aerospace information system, focusing on elements that interact with autonomous control systems (e.g., onboard UAVs). It discusses the trust placed in the autonomous systems and supporting systems (e.g., navigational aids) and how this trust can be validated. Approaches to remotely detect the UAV compromise, without relying on the onboard software (on a potentially compromised system) as part of the process are discussed. How different levels of autonomy (task-based, goal-based, mission-based) impact this remote characterization is considered.

  18. Cranial Autonomic Symptoms in Migraine

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2009-11-01

    Full Text Available Cranial autonomic symptoms (CAS in patients with migraine and cluster headaches (CH were characterized and compared in a prospective study of consecutive patients attending a headache clinic at Taipei Veterans General Hospital, Taiwan.

  19. Catecholamines and diabetic autonomic neuropathy

    DEFF Research Database (Denmark)

    Hilsted, J

    1995-01-01

    of plasma catecholamine measurements is not due to changes in the clearance of catecholamines in diabetic autonomic neuropathy. The physiological responses to infused adrenaline and to noradrenaline are enhanced, for noradrenaline mainly cardiovascular responses. Adrenoceptors (alpha and beta adrenoceptors...

  20. AUTONOMOUS GAUSSIAN DECOMPOSITION

    International Nuclear Information System (INIS)

    Lindner, Robert R.; Vera-Ciro, Carlos; Murray, Claire E.; Stanimirović, Snežana; Babler, Brian; Heiles, Carl; Hennebelle, Patrick; Goss, W. M.; Dickey, John

    2015-01-01

    We present a new algorithm, named Autonomous Gaussian Decomposition (AGD), for automatically decomposing spectra into Gaussian components. AGD uses derivative spectroscopy and machine learning to provide optimized guesses for the number of Gaussian components in the data, and also their locations, widths, and amplitudes. We test AGD and find that it produces results comparable to human-derived solutions on 21 cm absorption spectra from the 21 cm SPectral line Observations of Neutral Gas with the EVLA (21-SPONGE) survey. We use AGD with Monte Carlo methods to derive the H i line completeness as a function of peak optical depth and velocity width for the 21-SPONGE data, and also show that the results of AGD are stable against varying observational noise intensity. The autonomy and computational efficiency of the method over traditional manual Gaussian fits allow for truly unbiased comparisons between observations and simulations, and for the ability to scale up and interpret the very large data volumes from the upcoming Square Kilometer Array and pathfinder telescopes

  1. Is paramecium swimming autonomic?

    Science.gov (United States)

    Bandyopadhyay, Promode R.; Toplosky, Norman; Hansen, Joshua

    2010-11-01

    We seek to explore if the swimming of paramecium has an underlying autonomic mechanism. Such robotic elements may be useful in capturing the disturbance field in an environment in real time. Experimental evidence is emerging that motion control neurons of other animals may be present in paramecium as well. The limit cycle determined using analog simulation of the coupled nonlinear oscillators of olivo-cerebellar dynamics (ieee joe 33, 563-578, 2008) agrees with the tracks of the cilium of a biological paramecium. A 4-motor apparatus has been built that reproduces the kinematics of the cilium motion. The motion of the biological cilium has been analyzed and compared with the results of the finite element modeling of forces on a cilium. The modeling equates applied torque at the base of the cilium with drag, the cilium stiffness being phase dependent. A low friction pendulum apparatus with a multiplicity of electromagnetic actuators is being built for verifying the maps of the attractor basin computed using the olivo-cerebellar dynamics for different initial conditions. Sponsored by ONR 33.

  2. Autonomous Energy Grids: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Kroposki, Benjamin D [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Dall-Anese, Emiliano [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Bernstein, Andrey [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Zhang, Yingchen [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Hodge, Brian S [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2017-10-04

    With much higher levels of distributed energy resources - variable generation, energy storage, and controllable loads just to mention a few - being deployed into power systems, the data deluge from pervasive metering of energy grids, and the shaping of multi-level ancillary-service markets, current frameworks to monitoring, controlling, and optimizing large-scale energy systems are becoming increasingly inadequate. This position paper outlines the concept of 'Autonomous Energy Grids' (AEGs) - systems that are supported by a scalable, reconfigurable, and self-organizing information and control infrastructure, can be extremely secure and resilient (self-healing), and self-optimize themselves in real-time for economic and reliable performance while systematically integrating energy in all forms. AEGs rely on scalable, self-configuring cellular building blocks that ensure that each 'cell' can self-optimize when isolated from a larger grid as well as partaking in the optimal operation of a larger grid when interconnected. To realize this vision, this paper describes the concepts and key research directions in the broad domains of optimization theory, control theory, big-data analytics, and complex system modeling that will be necessary to realize the AEG vision.

  3. [Autonomic peripheral neuropathy].

    Science.gov (United States)

    Adams, David; Cauquil, Cecile; Lozeron, Pierre

    2012-11-01

    The mechanisms of dysautonomic disturbances are varied and mostly acquired. They can result from lesions of sympathetic or parasympathetic vegetative fibers located in the peripheral contingent, or in the somatic contingent by demyelination or axonal loss; or more rarely by cellular bodies in the sympathetic or parasympathetic ganglia. Several chronic peripheral neuropathies can be associated with dysautonomia. Only some causes need to be known because they can be clinically significant. Dysautonomia may be seen during chronic acquired neuropathies but also acute or subacute ones. The most frequent cause in the world is the dysautonomia of the diabetes; it affects all the systems; the cardiovascular dysfunction has an impact on the prognosis for survival when it is severe. Hereditary autonomic neuropathies are rare; they can declare themselves very early during the Riley-Day syndrome or very late during amyloid polyneuropathies due to transthyretin gene mutation. The diagnosis can be confirmed by molecular biology. The dysautonomia is frequent and often severe. These neuropathies justify symptomatic treatment to improve quality of life. For some of them, a specific treatment can be proposed to treat the causal affection to try to stop the progression of the disease. Copyright © 2012. Published by Elsevier Masson SAS.

  4. AUTONOMOUS GAUSSIAN DECOMPOSITION

    Energy Technology Data Exchange (ETDEWEB)

    Lindner, Robert R.; Vera-Ciro, Carlos; Murray, Claire E.; Stanimirović, Snežana; Babler, Brian [Department of Astronomy, University of Wisconsin, 475 North Charter Street, Madison, WI 53706 (United States); Heiles, Carl [Radio Astronomy Lab, UC Berkeley, 601 Campbell Hall, Berkeley, CA 94720 (United States); Hennebelle, Patrick [Laboratoire AIM, Paris-Saclay, CEA/IRFU/SAp-CNRS-Université Paris Diderot, F-91191 Gif-sur Yvette Cedex (France); Goss, W. M. [National Radio Astronomy Observatory, P.O. Box O, 1003 Lopezville, Socorro, NM 87801 (United States); Dickey, John, E-mail: rlindner@astro.wisc.edu [University of Tasmania, School of Maths and Physics, Private Bag 37, Hobart, TAS 7001 (Australia)

    2015-04-15

    We present a new algorithm, named Autonomous Gaussian Decomposition (AGD), for automatically decomposing spectra into Gaussian components. AGD uses derivative spectroscopy and machine learning to provide optimized guesses for the number of Gaussian components in the data, and also their locations, widths, and amplitudes. We test AGD and find that it produces results comparable to human-derived solutions on 21 cm absorption spectra from the 21 cm SPectral line Observations of Neutral Gas with the EVLA (21-SPONGE) survey. We use AGD with Monte Carlo methods to derive the H i line completeness as a function of peak optical depth and velocity width for the 21-SPONGE data, and also show that the results of AGD are stable against varying observational noise intensity. The autonomy and computational efficiency of the method over traditional manual Gaussian fits allow for truly unbiased comparisons between observations and simulations, and for the ability to scale up and interpret the very large data volumes from the upcoming Square Kilometer Array and pathfinder telescopes.

  5. Autonomous power system: Integrated scheduling

    Science.gov (United States)

    Ringer, Mark J.

    1992-01-01

    The Autonomous Power System (APS) project at NASA Lewis Research Center is designed to demonstrate the abilities of integrated intelligent diagnosis, control and scheduling techniques to space power distribution hardware. The project consists of three elements: the Autonomous Power Expert System (APEX) for fault diagnosis, isolation, and recovery (FDIR), the Autonomous Intelligent Power Scheduler (AIPS) to determine system configuration, and power hardware (Brassboard) to simulate a space-based power system. Faults can be introduced into the Brassboard and in turn, be diagnosed and corrected by APEX and AIPS. The Autonomous Intelligent Power Scheduler controls the execution of loads attached to the Brassboard. Each load must be executed in a manner that efficiently utilizes available power and satisfies all load, resource, and temporal constraints. In the case of a fault situation on the Brassboard, AIPS dynamically modifies the existing schedule in order to resume efficient operation conditions. A database is kept of the power demand, temporal modifiers, priority of each load, and the power level of each source. AIPS uses a set of heuristic rules to assign start times and resources to each load based on load and resource constraints. A simple improvement engine based upon these heuristics is also available to improve the schedule efficiency. This paper describes the operation of the Autonomous Intelligent Power Scheduler as a single entity, as well as its integration with APEX and the Brassboard. Future plans are discussed for the growth of the Autonomous Intelligent Power Scheduler.

  6. GalEa retrotransposons from galatheid squat lobsters (Decapoda, Anomura) define a new clade of Ty1/copia-like elements restricted to aquatic species.

    Science.gov (United States)

    Terrat, Yves; Bonnivard, Eric; Higuet, Dominique

    2008-01-01

    Crustacean species have not been examined in great detail for their transposable elements content. Here we focus on galatheid crabs, which are one of the most diverse and widespread taxonomic groups of Decapoda. Ty1/copia retrotransposons are a diverse and taxonomically dispersed group. Using degenerate primers, we isolated several DNA fragments that show homology with Ty1/copia retroelements reverse transcriptase gene. We named the corresponding elements from which they originated GalEa1 to GalEa3 and analyzed one of them further by isolating various clones containing segments of GalEa1. This is the first LTR retrotransposon described in crustacean genome. Nucleotide sequencing of the clones revealed that GalEa1 has LTRs (124 bp) and that the internal sequence (4,421 bp) includes a single large ORF containing gag and pol regions. Further screening identified highly related elements in six of the nine galatheid species studied. By performing BLAST searches on genome databases, we could also identify GalEa-like elements in some fishes and Urochordata genomes. These elements define a new clade of Ty1/copia retrotransposons that differs from all other Ty1/copia elements and that seems to be restricted to aquatic species.

  7. Efficient DNA fingerprinting based on the targeted sequencing of active retrotransposon insertion sites using a bench-top high-throughput sequencing platform.

    Science.gov (United States)

    Monden, Yuki; Yamamoto, Ayaka; Shindo, Akiko; Tahara, Makoto

    2014-10-01

    In many crop species, DNA fingerprinting is required for the precise identification of cultivars to protect the rights of breeders. Many families of retrotransposons have multiple copies throughout the eukaryotic genome and their integrated copies are inherited genetically. Thus, their insertion polymorphisms among cultivars are useful for DNA fingerprinting. In this study, we conducted a DNA fingerprinting based on the insertion polymorphisms of active retrotransposon families (Rtsp-1 and LIb) in sweet potato. Using 38 cultivars, we identified 2,024 insertion sites in the two families with an Illumina MiSeq sequencing platform. Of these insertion sites, 91.4% appeared to be polymorphic among the cultivars and 376 cultivar-specific insertion sites were identified, which were converted directly into cultivar-specific sequence-characterized amplified region (SCAR) markers. A phylogenetic tree was constructed using these insertion sites, which corresponded well with known pedigree information, thereby indicating their suitability for genetic diversity studies. Thus, the genome-wide comparative analysis of active retrotransposon insertion sites using the bench-top MiSeq sequencing platform is highly effective for DNA fingerprinting without any requirement for whole genome sequence information. This approach may facilitate the development of practical polymerase chain reaction-based cultivar diagnostic system and could also be applied to the determination of genetic relationships. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  8. Long non-coding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function.

    Science.gov (United States)

    Hu, Tianxiang; Pi, Wenhu; Zhu, Xingguo; Yu, Miao; Ha, Hongseok; Shi, Huidong; Choi, Jeong-Hyeon; Tuan, Dorothy

    2017-05-05

    LTR retrotransposons are repetitive DNA elements comprising ∼10% of the human genome. However, LTR sequences are disproportionately present in human long, non-coding RNAs (lncRNAs). Whether and how the LTR lncRNAs serve biological functions are largely unknown. Here we show that in primary human erythroblasts, lncRNAs transcribed from the LTR retrotransposons of ERV-9 human endogenous retrovirus activated transcription of key erythroid genes and modulated ex vivo erythropoiesis. To dissect the functional mechanism of ERV-9 lncRNAs, we performed genome-wide RNA and ChIRP analyses before and after global knockdown or locus-specific deletion of ERV-9 lncRNAs in human erythroblasts carrying ∼4000 copies of the ERV-9 LTRs and in transgenic mouse erythroblasts carrying a single copy of the primate-specific ERV-9 LTR in the 100 kb human β-globin gene locus. We found that ERV-9 lncRNAs acted in cis to stabilize assembly of the ERV-9 LTR enhancer complex and facilitate long-range LTR enhancer function in activating transcription of downstream, cis-linked globin genes. Our findings suggested that LTR lncRNAs transcribed from many of the 4000 copies of ERV-9 LTR retrotransposons acted by a similar cis mechanism to modulate LTR enhancer function in activating transcription of downstream genes critical to cellular processes including erythropoiesis. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Autonomous Byte Stream Randomizer

    Science.gov (United States)

    Paloulian, George K.; Woo, Simon S.; Chow, Edward T.

    2013-01-01

    Net-centric networking environments are often faced with limited resources and must utilize bandwidth as efficiently as possible. In networking environments that span wide areas, the data transmission has to be efficient without any redundant or exuberant metadata. The Autonomous Byte Stream Randomizer software provides an extra level of security on top of existing data encryption methods. Randomizing the data s byte stream adds an extra layer to existing data protection methods, thus making it harder for an attacker to decrypt protected data. Based on a generated crypto-graphically secure random seed, a random sequence of numbers is used to intelligently and efficiently swap the organization of bytes in data using the unbiased and memory-efficient in-place Fisher-Yates shuffle method. Swapping bytes and reorganizing the crucial structure of the byte data renders the data file unreadable and leaves the data in a deconstructed state. This deconstruction adds an extra level of security requiring the byte stream to be reconstructed with the random seed in order to be readable. Once the data byte stream has been randomized, the software enables the data to be distributed to N nodes in an environment. Each piece of the data in randomized and distributed form is a separate entity unreadable on its own right, but when combined with all N pieces, is able to be reconstructed back to one. Reconstruction requires possession of the key used for randomizing the bytes, leading to the generation of the same cryptographically secure random sequence of numbers used to randomize the data. This software is a cornerstone capability possessing the ability to generate the same cryptographically secure sequence on different machines and time intervals, thus allowing this software to be used more heavily in net-centric environments where data transfer bandwidth is limited.

  10. Compact autonomous navigation system (CANS)

    Science.gov (United States)

    Hao, Y. C.; Ying, L.; Xiong, K.; Cheng, H. Y.; Qiao, G. D.

    2017-11-01

    Autonomous navigation of Satellite and constellation has series of benefits, such as to reduce operation cost and ground station workload, to avoid the event of crises of war and natural disaster, to increase spacecraft autonomy, and so on. Autonomous navigation satellite is independent of ground station support. Many systems are developed for autonomous navigation of satellite in the past 20 years. Along them American MANS (Microcosm Autonomous Navigation System) [1] of Microcosm Inc. and ERADS [2] [3] (Earth Reference Attitude Determination System) of Honeywell Inc. are well known. The systems anticipate a series of good features of autonomous navigation and aim low cost, integrated structure, low power consumption and compact layout. The ERADS is an integrated small 3-axis attitude sensor system with low cost and small volume. It has the Earth center measurement accuracy higher than the common IR sensor because the detected ultraviolet radiation zone of the atmosphere has a brightness gradient larger than that of the IR zone. But the ERADS is still a complex system because it has to eliminate many problems such as making of the sapphire sphere lens, birefringence effect of sapphire, high precision image transfer optical fiber flattener, ultraviolet intensifier noise, and so on. The marginal sphere FOV of the sphere lens of the ERADS is used to star imaging that may be bring some disadvantages., i.e. , the image energy and attitude measurements accuracy may be reduced due to the tilt image acceptance end of the fiber flattener in the FOV. Besides Japan, Germany and Russia developed visible earth sensor for GEO [4] [5]. Do we have a way to develop a cheaper/easier and more accurate autonomous navigation system that can be used to all LEO spacecraft, especially, to LEO small and micro satellites? To return this problem we provide a new type of the system—CANS (Compact Autonomous Navigation System) [6].

  11. Diaspora, a large family of Ty3-gypsy retrotransposons in Glycine max, is an envelope-less member of an endogenous plant retrovirus lineage.

    Science.gov (United States)

    Yano, Sho T; Panbehi, Bahman; Das, Arpita; Laten, Howard M

    2005-05-05

    The chromosomes of higher plants are littered with retrotransposons that, in many cases, constitute as much as 80% of plant genomes. Long terminal repeat retrotransposons have been especially successful colonizers of the chromosomes of higher plants and examinations of their function, evolution, and dispersal are essential to understanding the evolution of eukaryotic genomes. In soybean, several families of retrotransposons have been identified, including at least two that, by virtue of the presence of an envelope-like gene, may constitute endogenous retroviruses. However, most elements are highly degenerate and are often sequestered in regions of the genome that sequencing projects initially shun. In addition, finding potentially functional copies from genomic DNA is rare. This study provides a mechanism to surmount these issues to generate a consensus sequence that can then be functionally and phylogenetically evaluated. Diaspora is a multicopy member of the Ty3-gypsy-like family of LTR retrotransposons and comprises at least 0.5% of the soybean genome. Although the Diaspora family is highly degenerate, and with the exception of this report, is not represented in the Genbank nr database, a full-length consensus sequence was generated from short overlapping sequences using a combination of experimental and in silico methods. Diaspora is 11,737 bp in length and contains a single 1892-codon ORF that encodes a gag-pol polyprotein. Phylogenetic analysis indicates that it is closely related to Athila and Calypso retroelements from Arabidopsis and soybean, respectively. These in turn form the framework of an endogenous retrovirus lineage whose members possess an envelope-like gene. Diaspora appears to lack any trace of this coding region. A combination of empirical sequencing and retrieval of unannotated Genome Survey Sequence database entries was successfully used to construct a full-length representative of the Diaspora family in Glycine max. Diaspora is presently the

  12. Autonomous Landing on Moving Platforms

    KAUST Repository

    Mendoza Chavez, Gilberto

    2016-08-01

    This thesis investigates autonomous landing of a micro air vehicle (MAV) on a nonstationary ground platform. Unmanned aerial vehicles (UAVs) and micro air vehicles (MAVs) are becoming every day more ubiquitous. Nonetheless, many applications still require specialized human pilots or supervisors. Current research is focusing on augmenting the scope of tasks that these vehicles are able to accomplish autonomously. Precise autonomous landing on moving platforms is essential for self-deployment and recovery of MAVs, but it remains a challenging task for both autonomous and piloted vehicles. Model Predictive Control (MPC) is a widely used and effective scheme to control constrained systems. One of its variants, output-feedback tube-based MPC, ensures robust stability for systems with bounded disturbances under system state reconstruction. This thesis proposes a MAV control strategy based on this variant of MPC to perform rapid and precise autonomous landing on moving targets whose nominal (uncommitted) trajectory and velocity are slowly varying. The proposed approach is demonstrated on an experimental setup.

  13. Autonomic Function in Neurodegenerative Diseases

    DEFF Research Database (Denmark)

    Sørensen, Gertrud Laura; Jennum, Poul Jørgen

    2013-01-01

    the method by applying standardized methods to measure the autonomic function based on heart rate variability (HRV) measures. 3) Based on the results, assess the validity of autonomic dysfunction as an early marker of a neurodegenerative disease. 4) Evaluate the influence of hypocretin loss in narcolepsy...... areas, which is consistent with the Braak hypothesis. In the narcolepsy patients, it was shown that a reduced HRR to arousals was primarily predicted by hypocretin deficiency in both rapid-eye-movement (REM) and non-REM sleep, independent of cataplexy and other factors. The results confirm...... that hypocretin deficiency affects the autonomic nervous system of patients with narcolepsy and that the hypocretin system is important for proper heart rate modulation at rest.Furthermore, it was shown that hypocretin deficiency and cataplexy are associated with signs of destabilized sleep-wake and REM sleep...

  14. The Bering Autonomous Target Detection

    DEFF Research Database (Denmark)

    Jørgensen, John Leif; Denver, Troelz; Betto, Maurizio

    2003-01-01

    An autonomous asteroid target detection and tracking method has been developed. The method features near omnidirectionality and focus on high speed operations and completeness of search of the near space rather than the traditional faint object search methods, employed presently at the larger...... telescopes. The method has proven robust in operation and is well suited for use onboard spacecraft. As development target for the method and the associated instrumentation the asteroid research mission Bering has been used. Onboard a spacecraft, the autonomous detection is centered around the fully...

  15. Political accountability and autonomous weapons

    Directory of Open Access Journals (Sweden)

    James Igoe Walsh

    2015-09-01

    Full Text Available Autonomous weapons would have the capacity to select and attack targets without direct human input. One important objection to the introduction of such weapons is that they will make it more difficult to identify and hold accountable those responsible for undesirable outcomes such as mission failures and civilian casualties. I hypothesize that individuals can modify their attribution of responsibility in predicable ways to accommodate this new technology. The results of a survey experiment are consistent with this; subjects continue to find responsible and hold accountable political and military leaders when autonomous weapons are used, but also attribute responsibility to the designers and programmers of such weapons.

  16. Autonomic Regulation of Splanchnic Circulation

    Directory of Open Access Journals (Sweden)

    Kathleen A Fraser

    1991-01-01

    Full Text Available The role of the autonomic nervous system in circulatory regulation of the splanchnic organs (stomach, small intestine, colon, liver, pancreas and spleen is reviewed. In general, the sympathetic nervous system is primarily involved in vasoconstriction, while the parasympathetic contributes to vasodilation. Vasoconstriction in the splanchnic circulation appears to be mediated by alpha-2 receptors and vasodilation by activation of primary afferent nerves with subsequent release of vasodilatory peptides, or by stimulation of beta-adrenergic receptors. As well, an important function of the autonomic nervous system is to provide a mechanism by which splanchnic vascular reserve can be mobilized during stress to maintain overall cardiovascular homeostasis.

  17. Structural Discrimination and Autonomous Vehicles

    DEFF Research Database (Denmark)

    Liu, Hin-Yan

    2016-01-01

    This paper examines the potential for structural discrimination to be woven into the fabric of autonomous vehicle developments, which remain underexplored and undiscussed. The prospect for structural discrimination arises as a result of the coordinated modes of autonomous vehicle behaviour...... discrimination looms with the possibility of crash optimisation impulses in which a protective shield is cast over those individuals in which society may have a vested interest in prioritising or safeguarding. A stark dystopian scenario is introduced to sketch the contours whereby personal beacons signal...

  18. A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice

    KAUST Repository

    La, Honggui

    2011-09-06

    DNA 5-methylcytosine (5-meC) is an important epigenetic mark for transcriptional gene silencing in many eukaryotes. In Arabidopsis, 5-meC DNA glycosylase/lyases actively remove 5-meC to counter-act transcriptional gene silencing in a locus-specific manner, and have been suggested to maintain the expression of transposons. However, it is unclear whether plant DNA demethylases can promote the transposition of transposons. Here we report the functional characterization of the DNA glycosylase/lyase DNG701 in rice. DNG701 encodes a large (1,812 amino acid residues) DNA glycosylase domain protein. Recombinant DNG701 protein showed 5-meC DNA glycosylase and lyase activities in vitro. Knockout or knockdown of DNG701 in rice plants led to DNA hypermethylation and reduced expression of the retrotransposon Tos17. Tos17 showed less transposition in calli derived from dng701 knockout mutant seeds compared with that in wild-type calli. Overexpression of DNG701 in both rice calli and transgenic plants substantially reduced DNA methylation levels of Tos17 and enhanced its expression. The overexpression also led to more frequent transposition of Tos17 in calli. Our results demonstrate that rice DNG701 is a 5-meC DNA glycosylase/lyase responsible for the demethylation of Tos17 and this DNA demethylase plays a critical role in promoting Tos17 transposition in rice calli.

  19. Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 gene.

    Science.gov (United States)

    Saenko, Suzanne V; Lamichhaney, Sangeet; Martinez Barrio, Alvaro; Rafati, Nima; Andersson, Leif; Milinkovitch, Michel C

    2015-11-24

    The corn snake (Pantherophis guttatus) is a new model species particularly appropriate for investigating the processes generating colours in reptiles because numerous colour and pattern mutants have been isolated in the last five decades. Using our captive-bred colony of corn snakes, transcriptomic and genomic next-generation sequencing, exome assembly, and genotyping of SNPs in multiple families, we delimit the genomic interval bearing the causal mutation of amelanism, the oldest colour variant observed in that species. Proceeding with sequencing the candidate gene OCA2 in the uncovered genomic interval, we identify that the insertion of an LTR-retrotransposon in its 11(th) intron results in a considerable truncation of the p protein and likely constitutes the causal mutation of amelanism in corn snakes. As amelanistic snakes exhibit white, instead of black, borders around an otherwise normal pattern of dorsal orange saddles and lateral blotches, our results indicate that melanocytes lacking melanin are able to participate to the normal patterning of other colours in the skin. In combination with research in the zebrafish, this work opens the perspective of using corn snake colour and pattern variants to investigate the generative processes of skin colour patterning shared among major vertebrate lineages.

  20. Not so bad after all: retroviruses and long terminal repeat retrotransposons as a source of new genes in vertebrates.

    Science.gov (United States)

    Naville, M; Warren, I A; Haftek-Terreau, Z; Chalopin, D; Brunet, F; Levin, P; Galiana, D; Volff, J-N

    2016-04-01

    Viruses and transposable elements, once considered as purely junk and selfish sequences, have repeatedly been used as a source of novel protein-coding genes during the evolution of most eukaryotic lineages, a phenomenon called 'molecular domestication'. This is exemplified perfectly in mammals and other vertebrates, where many genes derived from long terminal repeat (LTR) retroelements (retroviruses and LTR retrotransposons) have been identified through comparative genomics and functional analyses. In particular, genes derived from gag structural protein and envelope (env) genes, as well as from the integrase-coding and protease-coding sequences, have been identified in humans and other vertebrates. Retroelement-derived genes are involved in many important biological processes including placenta formation, cognitive functions in the brain and immunity against retroelements, as well as in cell proliferation, apoptosis and cancer. These observations support an important role of retroelement-derived genes in the evolution and diversification of the vertebrate lineage. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  1. Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis.

    Science.gov (United States)

    Smýkal, Petr; Hýbl, Miroslav; Corander, Jukka; Jarkovský, Jirí; Flavell, Andrew J; Griga, Miroslav

    2008-08-01

    One hundred and sixty-four accessions representing Czech and Slovak pea (Pisum sativum L.) varieties bred over the last 50 years were evaluated for genetic diversity using morphological, simple sequence repeat (SSR) and retrotransposon-based insertion polymorphism (RBIP) markers. Polymorphic information content (PIC) values of 10 SSR loci and 31 RBIP markers were on average high at 0.89 and 0.73, respectively. The silhouette method after the Ward clustering produced the most probable cluster estimate, identifying nine clusters from molecular data and five to seven clusters from morphological characters. Principal component analysis of nine qualitative and eight quantitative morphological parameters explain over 90 and 93% of total variability, respectively, in the first three axes. Multidimensional scaling of molecular data revealed a continuous structure for the set. To enable integration and evaluation of all data types, a Bayesian method for clustering was applied. Three clusters identified using morphology data, with clear separation of fodder, dry seed and afila types, were resolved by DNA data into 17, 12 and five sub-clusters, respectively. A core collection of 34 samples was derived from the complete collection by BAPS Bayesian analysis. Values for average gene diversity and allelic richness for molecular marker loci and diversity indexes of phenotypic data were found to be similar between the two collections, showing that this is a useful approach for representative core selection.

  2. Connected and autonomous vehicles 2040 vision.

    Science.gov (United States)

    2014-07-01

    The Pennsylvania Department of Transportation (PennDOT) commissioned a one-year project, Connected and Autonomous : Vehicles 2040 Vision, with researchers at Carnegie Mellon University (CMU) to assess the implications of connected and : autonomous ve...

  3. Energy homeostasis, autonomic activity and obesity

    NARCIS (Netherlands)

    Scheurink, AJW; Balkan, B; Nyakas, C; vanDijk, G; Steffens, AB; Bohus, B

    1995-01-01

    Obesity is often accompanied by alterations in both sympathetic and parasympathetic autonomic functions. The present paper summarizes the results of a number of studies designed to investigate autonomic functioning in normal, genetically, and experimentally obese rats, Particular emphasis is given

  4. Evaluating Autonomous Ground-Robots

    Science.gov (United States)

    2012-06-14

    Evaluating Autonomous Ground-Robots 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Anthony Finn; Adam Jacoff; Mike...these metrics against the detailed choreography of the challenge to prevent teams ‘gaming’ the result (i.e. devising technical solutions that were

  5. Hazard Map for Autonomous Navigation

    DEFF Research Database (Denmark)

    Riis, Troels

    This dissertation describes the work performed in the area of using image analysis in the process of landing a spacecraft autonomously and safely on the surface of the Moon. This is suggested to be done using a Hazard Map. The correspondence problem between several Hazard Maps are investigated...

  6. Computing architecture for autonomous microgrids

    Science.gov (United States)

    Goldsmith, Steven Y.

    2015-09-29

    A computing architecture that facilitates autonomously controlling operations of a microgrid is described herein. A microgrid network includes numerous computing devices that execute intelligent agents, each of which is assigned to a particular entity (load, source, storage device, or switch) in the microgrid. The intelligent agents can execute in accordance with predefined protocols to collectively perform computations that facilitate uninterrupted control of the .

  7. Autonomous Duffing-Holmes Type Chaotic Oscillator

    DEFF Research Database (Denmark)

    Tamaševičius, A.; Bumelienė, S.; Kirvaitis, R.

    2009-01-01

    We have designed and built a novel Duffing type autonomous 3rd-order chaotic oscillator. In comparison with the common non-autonomous DuffingHolmes type oscillator the autonomous circuit has an internal positive feedback loop instead of an external periodic drive source. In addition...

  8. CAAD: Computer Architecture for Autonomous Driving

    OpenAIRE

    Liu, Shaoshan; Tang, Jie; Zhang, Zhe; Gaudiot, Jean-Luc

    2017-01-01

    We describe the computing tasks involved in autonomous driving, examine existing autonomous driving computing platform implementations. To enable autonomous driving, the computing stack needs to simultaneously provide high performance, low power consumption, and low thermal dissipation, at low cost. We discuss possible approaches to design computing platforms that will meet these needs.

  9. The treatment of autonomic dysfunction in tetanus

    African Journals Online (AJOL)

    may either be spontaneous or triggered by touch, visual, auditory or emotional stimuli.[7] Autonomic dysfunction may occur, and does not necessarily correlate with the severity of tetanus. Wassay et al.[8] reported autonomic dysfunction in a third of tetanus cases. Autonomic dysfunction presents as labile hypertension, ...

  10. Identification and characterization of mobile genetic elements LINEs from Brassica genome.

    Science.gov (United States)

    Nouroz, Faisal; Noreen, Shumaila; Khan, Muhammad Fiaz; Ahmed, Shehzad; Heslop-Harrison, J S Pat

    2017-09-05

    Among transposable elements (TEs), the LTR retrotransposons are abundant followed by non-LTR retrotransposons in plant genomes, the lateral being represented by LINEs and SINEs. Computational and molecular approaches were used for the characterization of Brassica LINEs, their diversity and phylogenetic relationships. Four autonomous and four non-autonomous LINE families were identified and characterized from Brassica. Most of the autonomous LINEs displayed two open reading frames, ORF1 and ORF2, where ORF1 is a gag protein domain, while ORF2 encodes endonuclease (EN) and a reverse transcriptase (RT). Three of four families encoded an additional RNase H (RH) domain in pol gene common to 'R' and 'I' type of LINEs. The PCR analyses based on LINEs RT fragments indicate their high diversity and widespread occurrence in tested 40 Brassica cultivars. Database searches revealed the homology in LINE sequences in closely related genera Arabidopsis indicating their origin from common ancestors predating their separation. The alignment of 58 LINEs RT sequences from Brassica, Arabidopsis and other plants depicted 4 conserved domains (domain II-V) showing similarity to previously detected domains. Based on RT alignment of Brassica and 3 known LINEs from monocots, Brassicaceae LINEs clustered in separate clade, further resolving 4 Brassica-Arabidopsis specific families in 2 sub-clades. High similarities were observed in RT sequences in the members of same family, while low homology was detected in members across the families. The investigation led to the characterization of Brassica specific LINE families and their diversity across Brassica species and their cultivars. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. PwRn1, a novel Ty3/gypsy-like retrotransposon of Paragonimus westermani: molecular characters and its differentially preserved mobile potential according to host chromosomal polyploidy

    Science.gov (United States)

    Bae, Young-An; Ahn, Jong-Sook; Kim, Seon-Hee; Rhyu, Mun-Gan; Kong, Yoon; Cho, Seung-Yull

    2008-01-01

    Background Retrotransposons have been known to involve in the remodeling and evolution of host genome. These reverse transcribing elements, which show a complex evolutionary pathway with diverse intermediate forms, have been comprehensively analyzed from a wide range of host genomes, while the information remains limited to only a few species in the phylum Platyhelminthes. Results A LTR retrotransposon and its homologs with a strong phylogenetic affinity toward CsRn1 of Clonorchis sinensis were isolated from a trematode parasite Paragonimus westermani via a degenerate PCR method and from an insect species Anopheles gambiae by in silico analysis of the whole mosquito genome, respectively. These elements, designated PwRn1 and AgCR-1 – AgCR-14 conserved unique features including a t-RNATrp primer binding site and the unusual CHCC signature of Gag proteins. Their flanking LTRs displayed >97% nucleotide identities and thus, these elements were likely to have expanded recently in the trematode and insect genomes. They evolved heterogeneous expression strategies: a single fused ORF, two separate ORFs with an identical reading frame and two ORFs overlapped by -1 frameshifting. Phylogenetic analyses suggested that the elements with the separate ORFs had evolved from an ancestral form(s) with the overlapped ORFs. The mobile potential of PwRn1 was likely to be maintained differentially in association with the karyotype of host genomes, as was examined by the presence/absence of intergenomic polymorphism and mRNA transcripts. Conclusion Our results on the structural diversity of CsRn1-like elements can provide a molecular tool to dissect a more detailed evolutionary episode of LTR retrotransposons. The PwRn1-associated genomic polymorphism, which is substantial in diploids, will also be informative in addressing genomic diversification following inter-/intra-specific hybridization in P. westermani populations. PMID:18851759

  12. PwRn1, a novel Ty3/gypsy-like retrotransposon of Paragonimus westermani: molecular characters and its differentially preserved mobile potential according to host chromosomal polyploidy

    Directory of Open Access Journals (Sweden)

    Kong Yoon

    2008-10-01

    Full Text Available Abstract Background Retrotransposons have been known to involve in the remodeling and evolution of host genome. These reverse transcribing elements, which show a complex evolutionary pathway with diverse intermediate forms, have been comprehensively analyzed from a wide range of host genomes, while the information remains limited to only a few species in the phylum Platyhelminthes. Results A LTR retrotransposon and its homologs with a strong phylogenetic affinity toward CsRn1 of Clonorchis sinensis were isolated from a trematode parasite Paragonimus westermani via a degenerate PCR method and from an insect species Anopheles gambiae by in silico analysis of the whole mosquito genome, respectively. These elements, designated PwRn1 and AgCR-1 – AgCR-14 conserved unique features including a t-RNATrp primer binding site and the unusual CHCC signature of Gag proteins. Their flanking LTRs displayed >97% nucleotide identities and thus, these elements were likely to have expanded recently in the trematode and insect genomes. They evolved heterogeneous expression strategies: a single fused ORF, two separate ORFs with an identical reading frame and two ORFs overlapped by -1 frameshifting. Phylogenetic analyses suggested that the elements with the separate ORFs had evolved from an ancestral form(s with the overlapped ORFs. The mobile potential of PwRn1 was likely to be maintained differentially in association with the karyotype of host genomes, as was examined by the presence/absence of intergenomic polymorphism and mRNA transcripts. Conclusion Our results on the structural diversity of CsRn1-like elements can provide a molecular tool to dissect a more detailed evolutionary episode of LTR retrotransposons. The PwRn1-associated genomic polymorphism, which is substantial in diploids, will also be informative in addressing genomic diversification following inter-/intra-specific hybridization in P. westermani populations.

  13. The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story.

    Science.gov (United States)

    Bousios, Alexandros; Kourmpetis, Yiannis A I; Pavlidis, Pavlos; Minga, Evangelia; Tsaftaris, Athanasios; Darzentas, Nikos

    2012-02-01

    Sireviruses are one of the three genera of Copia long terminal repeat (LTR) retrotransposons, exclusive to and highly abundant in plants, and with a unique, among retrotransposons, genome structure. Yet, perhaps due to the few references to the Sirevirus origin of some families, compounded by the difficulty in correctly assigning retrotransposon families into genera, Sireviruses have hardly featured in recent research. As a result, analysis at this key level of classification and details of their colonization and impact on plant genomes are currently lacking. Recently, however, it became possible to accurately assign elements from diverse families to this genus in one step, based on highly conserved sequence motifs. Hence, Sirevirus dynamics in the relatively obese maize genome can now be comprehensively studied. Overall, we identified >10 600 intact and approximately 28 000 degenerate Sirevirus elements from a plethora of families, some brought into the genus for the first time. Sireviruses make up approximately 90% of the Copia population and it is the only genus that has successfully infiltrated the genome, possibly by experiencing intense amplification during the last 600 000 years, while being constantly recycled by host mechanisms. They accumulate in chromosome-distal gene-rich areas, where they insert in between gene islands, mainly in preferred zones within their own genomes. Sirevirus LTRs are heavily methylated, while there is evidence for a palindromic consensus target sequence. This work brings Sireviruses in the spotlight, elucidating their lifestyle and history, and suggesting their crucial role in the current genomic make-up of maize, and possibly other plant hosts. © 2011 INA/CERTH. The Plant Journal © 2011 Blackwell Publishing Ltd.

  14. Autonomous Cryogenics Loading Operations Simulation Software: Knowledgebase Autonomous Test Engineer

    Science.gov (United States)

    Wehner, Walter S., Jr.

    2013-01-01

    Working on the ACLO (Autonomous Cryogenics Loading Operations) project I have had the opportunity to add functionality to the physics simulation software known as KATE (Knowledgebase Autonomous Test Engineer), create a new application allowing WYSIWYG (what-you-see-is-what-you-get) creation of KATE schematic files and begin a preliminary design and implementation of a new subsystem that will provide vision services on the IHM (Integrated Health Management) bus. The functionality I added to KATE over the past few months includes a dynamic visual representation of the fluid height in a pipe based on number of gallons of fluid in the pipe and implementing the IHM bus connection within KATE. I also fixed a broken feature in the system called the Browser Display, implemented many bug fixes and made changes to the GUI (Graphical User Interface).

  15. Autonomic computing enabled cooperative networked design

    CERN Document Server

    Wodczak, Michal

    2014-01-01

    This book introduces the concept of autonomic computing driven cooperative networked system design from an architectural perspective. As such it leverages and capitalises on the relevant advancements in both the realms of autonomic computing and networking by welding them closely together. In particular, a multi-faceted Autonomic Cooperative System Architectural Model is defined which incorporates the notion of Autonomic Cooperative Behaviour being orchestrated by the Autonomic Cooperative Networking Protocol of a cross-layer nature. The overall proposed solution not only advocates for the inc

  16. Morphologic Changes in Autonomic Nerves in Diabetic Autonomic Neuropathy

    Directory of Open Access Journals (Sweden)

    Heung Yong Jin

    2015-12-01

    Full Text Available Diabetic neuropathy is one of the major complications of diabetes, and it increases morbidity and mortality in patients with both type 1 diabetes mellitus (T1DM and type 2 diabetes mellitus (T2DM. Because the autonomic nervous system, for example, parasympathetic axons, has a diffuse and wide distribution, we do not know the morphological changes that occur in autonomic neural control and their exact mechanisms in diabetic patients with diabetic autonomic neuropathy (DAN. Although the prevalence of sympathetic and parasympathetic neuropathy is similar in T1DM versus T2DM patients, sympathetic nerve function correlates with parasympathetic neuropathy only in T1DM patients. The explanation for these discrepancies might be that parasympathetic nerve function was more severely affected among T2DM patients. As parasympathetic nerve damage seems to be more advanced than sympathetic nerve damage, it might be that parasympathetic neuropathy precedes sympathetic neuropathy in T2DM, which was Ewing's concept. This could be explained by the intrinsic morphologic difference. Therefore, the morphological changes in the sympathetic and parasympathetic nerves of involved organs in T1DM and T2DM patients who have DAN should be evaluated. In this review, evaluation methods for morphological changes in the epidermal nerves of skin, and the intrinsic nerves of the stomach will be discussed.

  17. Insights into the background of autonomic medicine.

    Science.gov (United States)

    Laranjo, Sérgio; Geraldes, Vera; Oliveira, Mário; Rocha, Isabel

    2017-10-01

    Knowledge of the physiology underlying the autonomic nervous system is pivotal for understanding autonomic dysfunction in clinical practice. Autonomic dysfunction may result from primary modifications of the autonomic nervous system or be secondary to a wide range of diseases that cause severe morbidity and mortality. Together with a detailed history and physical examination, laboratory assessment of autonomic function is essential for the analysis of various clinical conditions and the establishment of effective, personalized and precise therapeutic schemes. This review summarizes the main aspects of autonomic medicine that constitute the background of cardiovascular autonomic dysfunction. Copyright © 2017 Sociedade Portuguesa de Cardiologia. Publicado por Elsevier España, S.L.U. All rights reserved.

  18. Effect of heavy metals on silencing of engineered long interspersed element-1 retrotransposon in nondividing neuroblastoma cell line.

    Science.gov (United States)

    Habibi, Laleh; Shokrgozar, Mohammad Ali; Motamedi, Mahdieh; Akrami, Seyed Mohammad

    2013-01-01

    L1 retrotransposons are the most active mobile DNA elements in human genome. Unregulated L1 retrotransposition may have deleterious effect by disrupting vital genes and inducing genomic instabilities. Therefore, human cells control L1 elements by silencing their activities through epigenetic mechanisms. It has been shown that cell division and heavy metals stimulate the frequency of L1 activities. Removal of silencing by L1 motivators may restart L1 element functions. Here, we have proposed that weather neurotoxic environmental heavy metals (as L1 stimulating factors) have a role in removing L1 silencing and restating its activities in nondividing neuronal cells. L1-RP green fluorescent protein (GFP)-tagged knock-in human neuroblastoma clones were prepared. Single-cell clone was treated with mitomycin-c combined with nontoxic and toxic concentrations of iron (Fe), copper (Cu), and mercury (Hg). Silencing status of engineered L1 elements in dividing and nondividing cells was determined through measuring the amount of GFP expressing cells with flow cytometry. The cytotoxic effect of mitomycin-c combined with metals was measured by MTT assay. Hg in nondividing cells and Fe, Cu, and Hg in dividing neuroblastoma cells could significantly remove L1 silencing. Also, mitomycin-c treatment did not have any effect on metal toxicity status in neuroblastoma cells. Totally, our findings have shown that cell division has a role in removing L1 silencing as well as L1 retrotransposition induced by environmental heavy metals. It has been also indicated that Hg at all concentrations could remove silencing of engineered L1 element regardless of cell cycle state.

  19. Achilles, a New Family of Transcriptionally Active Retrotransposons from the Olive Fruit Fly, with Y Chromosome Preferential Distribution.

    Directory of Open Access Journals (Sweden)

    Konstantina T Tsoumani

    Full Text Available Sex chromosomes have many unusual features relative to autosomes. The in depth exploration of their structure will improve our understanding of their origin and divergence (degeneration as well as the evolution of genetic sex determination pathways which, most often are attributed to them. In Tephritids, the structure of Y chromosome, where the male-determining factor M is localized, is largely unexplored and limited data concerning its sequence content and evolution are available. In order to get insight into the structure and organization of the Y chromosome of the major olive insect pest, the olive fly Bactrocera oleae, we characterized sequences from a Pulse Field Gel Electrophoresis (PFGE-isolated Y chromosome. Here, we report the discovery of the first olive fly LTR retrotransposon with increased presence on the Y chromosome. The element belongs to the BEL-Pao superfamily, however, its sequence comparison with the other members of the superfamily suggests that it constitutes a new family that we termed Achilles. Its ~7.5 kb sequence consists of the 5'LTR, the 5'non-coding sequence and the open reading frame (ORF, which encodes the polyprotein Gag-Pol. In situ hybridization to the B. oleae polytene chromosomes showed that Achilles is distributed in discrete bands dispersed on all five autosomes, in all centromeric regions and in the granular heterochromatic network corresponding to the mitotic sex chromosomes. The between sexes comparison revealed a variation in Achilles copy number, with male flies possessing 5-10 copies more than female (CI range: 18-38 and 12-33 copies respectively per genome. The examination of its transcriptional activity demonstrated the presence of at least one intact active copy in the genome, showing a differential level of expression between sexes as well as during embryonic development. The higher expression was detected in male germline tissues (testes. Moreover, the presence of Achilles-like elements in

  20. Intronic L1 retrotransposons and nested genes cause transcriptional interference by inducing intron retention, exonization and cryptic polyadenylation.

    Directory of Open Access Journals (Sweden)

    Kristel Kaer

    Full Text Available Transcriptional interference has been recently recognized as an unexpectedly complex and mostly negative regulation of genes. Despite a relatively few studies that emerged in recent years, it has been demonstrated that a readthrough transcription derived from one gene can influence the transcription of another overlapping or nested gene. However, the molecular effects resulting from this interaction are largely unknown.Using in silico chromosome walking, we searched for prematurely terminated transcripts bearing signatures of intron retention or exonization of intronic sequence at their 3' ends upstream to human L1 retrotransposons, protein-coding and noncoding nested genes. We demonstrate that transcriptional interference induced by intronic L1s (or other repeated DNAs and nested genes could be characterized by intron retention, forced exonization and cryptic polyadenylation. These molecular effects were revealed from the analysis of endogenous transcripts derived from different cell lines and tissues and confirmed by the expression of three minigenes in cell culture. While intron retention and exonization were comparably observed in introns upstream to L1s, forced exonization was preferentially detected in nested genes. Transcriptional interference induced by L1 or nested genes was dependent on the presence or absence of cryptic splice sites, affected the inclusion or exclusion of the upstream exon and the use of cryptic polyadenylation signals.Our results suggest that transcriptional interference induced by intronic L1s and nested genes could influence the transcription of the large number of genes in normal as well as in tumor tissues. Therefore, this type of interference could have a major impact on the regulation of the host gene expression.

  1. Autonomous Agents as Artistic Collaborators

    DEFF Research Database (Denmark)

    Kadish, David

    In this paper, I ask whether it is possible to exert creative direction on the emergence of large scale patterns from the actions of autonomous or semi-autonomous actors. As an artist and an engineer, I undertake installations and projects with an intent to create, to make art or innovative...... structures. At the same time, one of my artistic interests is in ceding a great deal of creative control to a cluster of robotic actors, in the process interrogating the lack of control that we, as a species, exert over the world. Here, I explore this idea in the context of an ongoing project called...... which innovations at large (galactic systems) and small (DNA) scales emerged were happy accidents of physics and chemistry. This raises the fundamental questions that my work explores, interrogating the relationship between the creativity of emergent processes on the micro- and macro- scales...

  2. Health, autonomic financing and transferences

    Directory of Open Access Journals (Sweden)

    David Cantarero Prieto

    2002-01-01

    Full Text Available The present paper has as objective to study the whole relative problem to the autonomous communities and regional heath care expenditure financing in Spain. This article has a dual purpose. First, the financing of the current health care attendance is approached in the Spanish regions passing magazine to its possible variants and we observe that the balance of our system is clearly inclined towards the side of the integration in the general pattern of financing («Fiscal Room» with specific conditions («Mixed System». Secondly, we examine the new situation in the mark of health care and its corresponding financing in the new model approved in 2001, in terms of the effects of tax assignment on autonomous communities.

  3. Autonomously managed high power systems

    International Nuclear Information System (INIS)

    Weeks, D.J.; Bechtel, R.T.

    1985-01-01

    The need for autonomous power management capabilities will increase as the power levels of spacecraft increase into the multi-100 kW range. The quantity of labor intensive ground and crew support consumed by the 9 kW Skylab cannot be afforded in support of a 75-300 kW Space Station or high power earth orbital and interplanetary spacecraft. Marshall Space Flight Center is managing a program to develop necessary technologies for high power system autonomous management. To date a reference electrical power system and automation approaches have been defined. A test facility for evaluation and verification of management algorithms and hardware has been designed with the first of the three power channel capability nearing completion

  4. Autonomous Industrial Mobile Manipulation (AIMM)

    DEFF Research Database (Denmark)

    Hvilshøj, Mads; Bøgh, Simon; Nielsen, Oluf Skov

    2012-01-01

    Purpose - The purpose of this paper is to provide a review of the interdisciplinary research field Autonomous Industrial Mobile Manipulation (AIMM), with an emphasis on physical implementations and applications. Design/methodology/approach - Following an introduction to AIMM, this paper investiga......Purpose - The purpose of this paper is to provide a review of the interdisciplinary research field Autonomous Industrial Mobile Manipulation (AIMM), with an emphasis on physical implementations and applications. Design/methodology/approach - Following an introduction to AIMM, this paper......; sustainability, configuration, adaptation, autonomy, positioning, manipulation and grasping, robot-robot interaction, human-robot interaction, process quality, dependability, and physical properties. Findings - The concise yet comprehensive review provides both researchers (academia) and practitioners (industry...... Manipulation (AIMM)....

  5. Novel non-autonomous transposable elements on W chromosome ...

    Indian Academy of Sciences (India)

    2010-09-06

    Sep 6, 2010 ... 1Department of Biological Production, Faculty of Agriculture, Tokyo University of Agriculture and Technology,. Saiwai-cho 3-5-8, Fuchu, Tokyo 183-8509, Japan. 2Department of Agricultural and ...... retrotransposons occur in apple and are polymorphic between va- rieties but not sports. Theor. Appl. Genet.

  6. Autonomic computing meets SCADA security

    OpenAIRE

    Nazir, S; Patel, S; Patel, D

    2017-01-01

    © 2017 IEEE. National assets such as transportation networks, large manufacturing, business and health facilities, power generation, and distribution networks are critical infrastructures. The cyber threats to these infrastructures have increasingly become more sophisticated, extensive and numerous. Cyber security conventional measures have proved useful in the past but increasing sophistication of attacks dictates the need for newer measures. The autonomic computing paradigm mimics the auton...

  7. Autonomic neuropathy in diabetes mellitus

    Directory of Open Access Journals (Sweden)

    Alberto eVerrotti

    2014-12-01

    Full Text Available Diabetic autonomic neuropathy (DAN is a serious and common complication of diabetes, often overlooked and misdiagnosed. It is a systemic-wide disorder that may be asymptomatic in the early stages. The most studied and clinically important form of DAN is cardiovascular autonomic neuropathy (CAN defined as the impairment of autonomic control of the cardiovascular system in patients with diabetes after exclusion of other causes. The reported prevalence of DAN varies widely depending on inconsistent definition, different diagnostic method, different patient cohorts studied. The pathogenesis is still unclear and probably multifactorial. Once DAN becomes clinically evident, no form of therapy has been identified which can effectively stop or reverse it. Prevention strategies are based on strict glycemic control with intensive insulin treatment, multifactorial intervention and lifestyle modification including control of hypertension, dyslipidemia, stop smoking, weight loss and adequate physical exercise. The present review summarizes the latest knowledge regarding clinical presentation, epidemiology, pathogenesis and management of DAN, with some mention to childhood and adolescent population.

  8. Semi autonomous mine detection system

    Energy Technology Data Exchange (ETDEWEB)

    Douglas Few; Roelof Versteeg; Herman Herman

    2010-04-01

    CMMAD is a risk reduction effort for the AMDS program. As part of CMMAD, multiple instances of semi autonomous robotic mine detection systems were created. Each instance consists of a robotic vehicle equipped with sensors required for navigation and marking, a countermine sensors and a number of integrated software packages which provide for real time processing of the countermine sensor data as well as integrated control of the robotic vehicle, the sensor actuator and the sensor. These systems were used to investigate critical interest functions (CIF) related to countermine robotic systems. To address the autonomy CIF, the INL developed RIK was extended to allow for interaction with a mine sensor processing code (MSPC). In limited field testing this system performed well in detecting, marking and avoiding both AT and AP mines. Based on the results of the CMMAD investigation we conclude that autonomous robotic mine detection is feasible. In addition, CMMAD contributed critical technical advances with regard to sensing, data processing and sensor manipulation, which will advance the performance of future fieldable systems. As a result, no substantial technical barriers exist which preclude – from an autonomous robotic perspective – the rapid development and deployment of fieldable systems.

  9. Autonomous Cryogenic Load Operations: KSC Autonomous Test Engineer

    Science.gov (United States)

    Shrading, Nicholas J.

    2012-01-01

    The KSC Autonomous Test Engineer (KATE) program has a long history at KSC. Now a part of the Autonomous Cryogenic Load Operations (ACLO) mission, this software system has been sporadically developed over the past 20+ years. Originally designed to provide health and status monitoring for a simple water-based fluid system, it was proven to be a capable autonomous test engineer for determining sources of failure in. the system, As part.of a new goal to provide this same anomaly-detection capability for a complicated cryogenic fluid system, software engineers, physicists, interns and KATE experts are working to upgrade the software capabilities and graphical user interface. Much progress was made during this effort to improve KATE. A display ofthe entire cryogenic system's graph, with nodes for components and edges for their connections, was added to the KATE software. A searching functionality was added to the new graph display, so that users could easily center their screen on specific components. The GUI was also modified so that it displayed information relevant to the new project goals. In addition, work began on adding new pneumatic and electronic subsystems into the KATE knowledgebase, so that it could provide health and status monitoring for those systems. Finally, many fixes for bugs, memory leaks, and memory errors were implemented and the system was moved into a state in which it could be presented to stakeholders. Overall, the KATE system was improved and necessary additional features were added so that a presentation of the program and its functionality in the next few months would be a success.

  10. Autonomous Cryogenic Load Operations: Knowledge-Based Autonomous Test Engineer

    Science.gov (United States)

    Schrading, J. Nicolas

    2013-01-01

    The Knowledge-Based Autonomous Test Engineer (KATE) program has a long history at KSC. Now a part of the Autonomous Cryogenic Load Operations (ACLO) mission, this software system has been sporadically developed over the past 20 years. Originally designed to provide health and status monitoring for a simple water-based fluid system, it was proven to be a capable autonomous test engineer for determining sources of failure in the system. As part of a new goal to provide this same anomaly-detection capability for a complicated cryogenic fluid system, software engineers, physicists, interns and KATE experts are working to upgrade the software capabilities and graphical user interface. Much progress was made during this effort to improve KATE. A display of the entire cryogenic system's graph, with nodes for components and edges for their connections, was added to the KATE software. A searching functionality was added to the new graph display, so that users could easily center their screen on specific components. The GUI was also modified so that it displayed information relevant to the new project goals. In addition, work began on adding new pneumatic and electronic subsystems into the KATE knowledge base, so that it could provide health and status monitoring for those systems. Finally, many fixes for bugs, memory leaks, and memory errors were implemented and the system was moved into a state in which it could be presented to stakeholders. Overall, the KATE system was improved and necessary additional features were added so that a presentation of the program and its functionality in the next few months would be a success.

  11. Towards the Development of Autonomous Ferries

    OpenAIRE

    Bitar, Glenn Ivan

    2017-01-01

    Autonomous ships is at the moment a heavily researched topic in the maritime industry. Development to introduce autonomous ferries in the Norwegian fjords is under way. This thesis is a study of technical and formal challenges related to autonomous ferries. The thesis goes into topics such as industrial control systems for ships, path planning and collision avoidance algorithms, as well as automatic docking. Additionally, information and statistics regarding ferry activities in Norway are pre...

  12. The Human Element and Autonomous Ships

    OpenAIRE

    Sauli Ahvenjärvi

    2016-01-01

    The autonomous ship technology has become a “hot” topic in the discussion about more efficient, environmentally friendly and safer sea transportation solutions. The time is becoming mature for the introduction of commercially sensible solutions for unmanned and fully autonomous cargo and passenger ships. Safety will be the most interesting and important aspect in this development. The utilization of the autonomous ship technology will have many effects on the safety, both positive and negativ...

  13. Autonomous Exploration Using an Information Gain Metric

    Science.gov (United States)

    2016-03-01

    navigation goals, serving to drive an autonomous system. By continually moving to these navigation goals and taking measurements, the system works to...ARL-TR-7638 ● MAR 2016 US Army Research Laboratory Autonomous Exploration Using an Information Gain Metric by Nicholas C Fung...Laboratory Autonomous Exploration Using an Information Gain Metric by Nicholas C Fung, Jason M Gregory, and John G Rogers Computational and

  14. DARTS: Deceiving Autonomous Cars with Toxic Signs

    OpenAIRE

    Sitawarin, Chawin; Bhagoji, Arjun Nitin; Mosenia, Arsalan; Chiang, Mung; Mittal, Prateek

    2018-01-01

    Sign recognition is an integral part of autonomous cars. Any misclassification of traffic signs can potentially lead to a multitude of disastrous consequences, ranging from a life-threatening accident to a large-scale interruption of transportation services relying on autonomous cars. In this paper, we propose and examine realistic security attacks against sign recognition systems for Deceiving Autonomous caRs with Toxic Signs (we call the proposed attacks DARTS). Leveraging the concept of ad...

  15. Design of an Autonomous Forklift Using Kinect

    OpenAIRE

    Abdellatif Mohamed; Shoeir Metwali; Talaat Omar; Gabalah Mahmoud; Elbably Mohamed; Saleh Saleh

    2018-01-01

    Material handling is a necessary, but expensive activity in factories. Autonomous robot technology can help reduce the cost and relax humans from the exhaustive job of driving forklifts. In this paper, we describe the mechatronics design and implementation of an autonomous forklift. The robot can perceive the 3D dynamic world and can plan its motion autonomously to lift materials from a source to target locations. Dynamic map of the world is built using data from a Microsoft Kinect head and r...

  16. Implementing a Cloud Platform for Autonomous Driving

    OpenAIRE

    Liu, Shaoshan; Tang, Jie; Wang, Chao; Wang, Quan; Gaudiot, Jean-Luc

    2017-01-01

    Autonomous driving clouds provide essential services to support autonomous vehicles. Today these services include but not limited to distributed simulation tests for new algorithm deployment, offline deep learning model training, and High-Definition (HD) map generation. These services require infrastructure support including distributed computing, distributed storage, as well as heterogeneous computing. In this paper, we present the details of how we implement a unified autonomous driving clo...

  17. The treatment of autonomic dysfunction in tetanus

    Directory of Open Access Journals (Sweden)

    T van den Heever

    2017-07-01

    Full Text Available We report a case of generalised tetanus in a 50-year-old female patient after sustaining a wound to her right lower leg. She developed autonomic dysfunction, which included labile hypertension alternating with hypotension and sweating. The autonomic dysfunction was treated successfully with a combination of morphine sulphate infusion, magnesium sulphate, and clonidine. She also received adrenaline and phenylephrine infusions as needed for hypotension. We then discuss the pathophysiology, clinical features and treatment options of autonomic dysfunction.

  18. The genetic diversity and evolution of field pea (Pisum studied by high throughput retrotransposon based insertion polymorphism (RBIP marker analysis

    Directory of Open Access Journals (Sweden)

    Smýkal Petr

    2010-02-01

    Full Text Available Abstract Background The genetic diversity of crop species is the result of natural selection on the wild progenitor and human intervention by ancient and modern farmers and breeders. The genomes of modern cultivars, old cultivated landraces, ecotypes and wild relatives reflect the effects of these forces and provide insights into germplasm structural diversity, the geographical dimension to species diversity and the process of domestication of wild organisms. This issue is also of great practical importance for crop improvement because wild germplasm represents a rich potential source of useful under-exploited alleles or allele combinations. The aim of the present study was to analyse a major Pisum germplasm collection to gain a broad understanding of the diversity and evolution of Pisum and provide a new rational framework for designing germplasm core collections of the genus. Results 3020 Pisum germplasm samples from the John Innes Pisum germplasm collection were genotyped for 45 retrotransposon based insertion polymorphism (RBIP markers by the Tagged Array Marker (TAM method. The data set was stored in a purpose-built Germinate relational database and analysed by both principal coordinate analysis and a nested application of the Structure program which yielded substantially similar but complementary views of the diversity of the genus Pisum. Structure revealed three Groups (1-3 corresponding approximately to landrace, cultivar and wild Pisum respectively, which were resolved by nested Structure analysis into 14 Sub-Groups, many of which correlate with taxonomic sub-divisions of Pisum, domestication related phenotypic traits and/or restricted geographical locations. Genetic distances calculated between these Sub-Groups are broadly supported by principal coordinate analysis and these, together with the trait and geographical data, were used to infer a detailed model for the domestication of Pisum. Conclusions These data provide a clear picture

  19. Science Data Understanding for Autonomous Rover Exploration

    Data.gov (United States)

    National Aeronautics and Space Administration — Autonomous rover traversal speed and capabilities are rapidly increasing, but communications bandwidth for planetary exploration remains limited. In order to...

  20. A Generic Architecture for Autonomous Uninhabited Vehicles

    National Research Council Canada - National Science Library

    Barbier, Magali; Gabard, Jean-Francois; Ayreault, Herve

    2007-01-01

    ...; few solutions propose architecture adaptive to several types of platform. Autonomous vehicles that move in partially known and dynamic environments have to deal with asynchronous disruptive events...

  1. Public Health, Ethics, and Autonomous Vehicles.

    Science.gov (United States)

    Fleetwood, Janet

    2017-04-01

    With the potential to save nearly 30 000 lives per year in the United States, autonomous vehicles portend the most significant advance in auto safety history by shifting the focus from minimization of postcrash injury to collision prevention. I have delineated the important public health implications of autonomous vehicles and provided a brief analysis of a critically important ethical issue inherent in autonomous vehicle design. The broad expertise, ethical principles, and values of public health should be brought to bear on a wide range of issues pertaining to autonomous vehicles.

  2. Autonomous systems for plant protection

    DEFF Research Database (Denmark)

    Griepentrog, Hans W.; Ruckelhausen, Arno; Jørgensen, Rasmus N.

    2010-01-01

    of autonomous operations related to crop protection probably commercially available in the near future. Scouting and monitoring together with the efficient application of chemicals or mechanical treatments are operations which can be successful automated. Drawbacks are that current systems are lacking robust......Advances in automation are demanded by the market mainly as a response to high labor costs. Robotic outdoor systems are ready to allow not only economically viable operations but also increased efficiency in agriculture, horticulture and forestry. The aim of this chapter is to give examples...

  3. Autonomous quality assurance and troubleshooting

    Science.gov (United States)

    DuPlain, Ronald F.; Radziwill, Nicole M.; Shelton, Amy L.

    2006-06-01

    To improve operational availability (the proportion of time that a telescope is able to accomplish what a visiting observer wants at the time the observation is scheduled), response time to faults must be minimized. One way this can be accomplished is by characterizing the relationships and interdependencies between components in a control system, developing algorithms to identify the root cause of a problem, and capturing expert knowledge of a system to simplify the process of troubleshooting. Results from a prototype development are explained, along with deployment issues. Implications for the future, such as effective knowledge representation and management, and learning processes which integrate autonomous and interactive components, are discussed.

  4. Topological entropy of autonomous flows

    Energy Technology Data Exchange (ETDEWEB)

    Badii, R. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1997-06-01

    When studying fluid dynamics, especially in a turbulent regime, it is crucial to estimate the number of active degrees of freedom or of localized structures in the system. The topological entropy quantifies the exponential growth of the number of `distinct` orbits in a dynamical system as a function of their length, in the infinite spatial resolution limit. Here, I illustrate a novel method for its evaluation, which extends beyond maps and is applicable to any system, including autonomous flows: these are characterized by lack of a definite absolute time scale for the orbit lengths. (author) 8 refs.

  5. Autonomous sensor manager agents (ASMA)

    Science.gov (United States)

    Osadciw, Lisa A.

    2004-04-01

    Autonomous sensor manager agents are presented as an algorithm to perform sensor management within a multisensor fusion network. The design of the hybrid ant system/particle swarm agents is described in detail with some insight into their performance. Although the algorithm is designed for the general sensor management problem, a simulation example involving 2 radar systems is presented. Algorithmic parameters are determined by the size of the region covered by the sensor network, the number of sensors, and the number of parameters to be selected. With straight forward modifications, this algorithm can be adapted for most sensor management problems.

  6. Autonomously managed electrical power systems

    Science.gov (United States)

    Callis, Charles P.

    1986-01-01

    The electric power systems for future spacecraft such as the Space Station will necessarily be more sophisticated and will exhibit more nearly autonomous operation than earlier spacecraft. These new power systems will be more reliable and flexible than their predecessors offering greater utility to the users. Automation approaches implemented on various power system breadboards are investigated. These breadboards include the Hubble Space Telescope power system test bed, the Common Module Power Management and Distribution system breadboard, the Autonomusly Managed Power System (AMPS) breadboard, and the 20 kilohertz power system breadboard. Particular attention is given to the AMPS breadboard. Future plans for these breadboards including the employment of artificial intelligence techniques are addressed.

  7. The Autonomous Pathogen Detection System

    Energy Technology Data Exchange (ETDEWEB)

    Dzenitis, J M; Makarewicz, A J

    2009-01-13

    We developed, tested, and now operate a civilian biological defense capability that continuously monitors the air for biological threat agents. The Autonomous Pathogen Detection System (APDS) collects, prepares, reads, analyzes, and reports results of multiplexed immunoassays and multiplexed PCR assays using Luminex{copyright} xMAP technology and flow cytometer. The mission we conduct is particularly demanding: continuous monitoring, multiple threat agents, high sensitivity, challenging environments, and ultimately extremely low false positive rates. Here, we introduce the mission requirements and metrics, show the system engineering and analysis framework, and describe the progress to date including early development and current status.

  8. BART: The Czech Autonomous Observatory

    Czech Academy of Sciences Publication Activity Database

    Nekola, Martin; Hudec, René; Jelínek, M.; Kubánek, P.; Štrobl, Jan; Polášek, Cyril

    2010-01-01

    Roč. 2010, Spec. Is. (2010), 103986/1-103986/5 ISSN 1687-7969. [Workshop on Robotic Autonomous Observatories. Málaga, 18.05.2009-21.05.2009] R&D Projects: GA ČR GA205/08/1207 Grant - others:ESA(XE) ESA-PECS project No. 98023; Spanish Ministry of Education and Science(ES) AP2003-1407 Institutional research plan: CEZ:AV0Z10030501 Keywords : robotic telescope * BART * gamma ray bursts Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics http://www.hindawi.com/journals/aa/2010/103986.html

  9. Autonomic neuropathy in Fabry disease: a prospective study using the Autonomic Symptom Profile and cardiovascular autonomic function tests

    NARCIS (Netherlands)

    Biegstraaten, Marieke; van Schaik, Ivo N.; Wieling, Wouter; Wijburg, Frits A.; Hollak, Carla E. M.

    2010-01-01

    ABSTRACT: BACKGROUND: Fabry patients have symptoms and signs compatible with autonomic dysfunction. These symptoms and signs are considered to be due to impairment of the peripheral nervous system, but findings indicative of autonomic neuropathy in other diseases, such as orthostatic intolerance and

  10. Structured control for autonomous robots

    International Nuclear Information System (INIS)

    Simmons, R.G.

    1994-01-01

    To operate in rich, dynamic environments, autonomous robots must be able to effectively utilize and coordinate their limited physical and occupational resources. As complexity increases, it becomes necessary to impose explicit constraints on the control of planning, perception, and action to ensure that unwanted interactions between behaviors do not occur. This paper advocates developing complex robot systems by layering reactive behaviors onto deliberative components. In this structured control approach, the deliberative components handle normal situations and the reactive behaviors, which are explicitly constrained as to when and how they are activated, handle exceptional situations. The Task Control Architecture (TCA) has been developed to support this approach. TCA provides an integrated set of control constructs useful for implementing deliberative and reactive behaviors. The control constructs facilitate modular and evolutionary system development: they are used to integrate and coordinate planning, perception, and execution, and to incrementally improve the efficiency and robustness of the robot systems. To date, TCA has been used in implementing a half-dozen mobile robot systems, including an autonomous six-legged rover and indoor mobile manipulator

  11. Autonomous Robotic Inspection in Tunnels

    Science.gov (United States)

    Protopapadakis, E.; Stentoumis, C.; Doulamis, N.; Doulamis, A.; Loupos, K.; Makantasis, K.; Kopsiaftis, G.; Amditis, A.

    2016-06-01

    In this paper, an automatic robotic inspector for tunnel assessment is presented. The proposed platform is able to autonomously navigate within the civil infrastructures, grab stereo images and process/analyse them, in order to identify defect types. At first, there is the crack detection via deep learning approaches. Then, a detailed 3D model of the cracked area is created, utilizing photogrammetric methods. Finally, a laser profiling of the tunnel's lining, for a narrow region close to detected crack is performed; allowing for the deduction of potential deformations. The robotic platform consists of an autonomous mobile vehicle; a crane arm, guided by the computer vision-based crack detector, carrying ultrasound sensors, the stereo cameras and the laser scanner. Visual inspection is based on convolutional neural networks, which support the creation of high-level discriminative features for complex non-linear pattern classification. Then, real-time 3D information is accurately calculated and the crack position and orientation is passed to the robotic platform. The entire system has been evaluated in railway and road tunnels, i.e. in Egnatia Highway and London underground infrastructure.

  12. Autonomous Lawnmower using FPGA implementation.

    Science.gov (United States)

    Ahmad, Nabihah; Lokman, Nabill bin; Helmy Abd Wahab, Mohd

    2016-11-01

    Nowadays, there are various types of robot have been invented for multiple purposes. The robots have the special characteristic that surpass the human ability and could operate in extreme environment which human cannot endure. In this paper, an autonomous robot is built to imitate the characteristic of a human cutting grass. A Field Programmable Gate Array (FPGA) is used to control the movements where all data and information would be processed. Very High Speed Integrated Circuit (VHSIC) Hardware Description Language (VHDL) is used to describe the hardware using Quartus II software. This robot has the ability of avoiding obstacle using ultrasonic sensor. This robot used two DC motors for its movement. It could include moving forward, backward, and turning left and right. The movement or the path of the automatic lawn mower is based on a path planning technique. Four Global Positioning System (GPS) plot are set to create a boundary. This to ensure that the lawn mower operates within the area given by user. Every action of the lawn mower is controlled by the FPGA DE' Board Cyclone II with the help of the sensor. Furthermore, Sketch Up software was used to design the structure of the lawn mower. The autonomous lawn mower was able to operate efficiently and smoothly return to coordinated paths after passing the obstacle. It uses 25% of total pins available on the board and 31% of total Digital Signal Processing (DSP) blocks.

  13. An autonomous weeding robot for organic farming

    NARCIS (Netherlands)

    Bakker, T.; Asselt, van C.J.; Bontsema, J.; Müller, J.; Straten, van G.

    2006-01-01

    The objective of this research is the replacement of hand weeding in organic farming by a device working autonomously at ¯eld level. The autonomous weeding robot was designed using a structured design approach, giving a good overview of the total design. A vehicle was developed with a diesel engine,

  14. Autonomous Control of Space Reactor Systems

    International Nuclear Information System (INIS)

    Belle R. Upadhyaya; K. Zhao; S.R.P. Perillo; Xiaojia Xu; M.G. Na

    2007-01-01

    Autonomous and semi-autonomous control is a key element of space reactor design in order to meet the mission requirements of safety, reliability, survivability, and life expectancy. Interrestrial nuclear power plants, human operators are available to perform intelligent control functions that are necessary for both normal and abnormal operational conditions

  15. The Cardiovascular Autonomic Nervous System and Anaesthesia

    African Journals Online (AJOL)

    QuickSilver

    part of our training and practice is spent acquiring skills in averting or utilizing the autonomic nervous system effects of anaesthetic drugs or surgical procedures under a variety of pathophysiological conditions. Moreover, many of these pathophysiological condi- tions may be associated with impaired preoperative autonomic ...

  16. Blunted autonomic response in cluster headache patients

    DEFF Research Database (Denmark)

    Barloese, Mads; Brinth, Louise; Mehlsen, Jesper

    2015-01-01

    BACKGROUND: Cluster headache (CH) is a disabling headache disorder with chronobiological features. The posterior hypothalamus is involved in CH pathophysiology and is a hub for autonomic control. We studied autonomic response to the head-up tilt table test (HUT) including heart rate variability...

  17. Basic and clinical pharmacology of autonomic drugs.

    Science.gov (United States)

    Becker, Daniel E

    2012-01-01

    Autonomic drugs are used clinically to either imitate or inhibit the normal functions of the sympathetic and parasympathetic nervous systems. A large number of additional drug classes also interact with these systems to produce a stunning number of possible side effects. This article reviews the basic function of the autonomic nervous system and the various drug classes that act within these neural synapses.

  18. Safe and Autonomous Drones for Urban Flight

    Science.gov (United States)

    Krishnakumar, Kalmanje

    2016-01-01

    Autonomous vehicles are no longer futuristic technology; in fact, there are already cars with self-driving features on the road. Over the next five years, the connected vehicles will disrupt the entire automotive and UAS ecosystems. The industry will undergo fundamental change as semi-autonomous driving and flying emerges, followed by an eventual shift to full autonomy.

  19. Autonomous Control of Space Reactor Systems

    Energy Technology Data Exchange (ETDEWEB)

    Belle R. Upadhyaya; K. Zhao; S.R.P. Perillo; Xiaojia Xu; M.G. Na

    2007-11-30

    Autonomous and semi-autonomous control is a key element of space reactor design in order to meet the mission requirements of safety, reliability, survivability, and life expectancy. Interrestrial nuclear power plants, human operators are avilable to perform intelligent control functions that are necessary for both normal and abnormal operational conditions.

  20. Planning Flight Paths of Autonomous Aerobots

    Science.gov (United States)

    Kulczycki, Eric; Elfes, Alberto; Sharma, Shivanjli

    2009-01-01

    Algorithms for planning flight paths of autonomous aerobots (robotic blimps) to be deployed in scientific exploration of remote planets are undergoing development. These algorithms are also adaptable to terrestrial applications involving robotic submarines as well as aerobots and other autonomous aircraft used to acquire scientific data or to perform surveying or monitoring functions.

  1. Autonomic dysfunction in cirrhosis and portal hypertension

    DEFF Research Database (Denmark)

    Dümcke, Christine Winkler; Møller, Søren

    2008-01-01

    Liver cirrhosis and portal hypertension are frequently associated with signs of circulatory dysfunction and peripheral polyneuropathy, which includes defects of the autonomic nervous system. Autonomic dysfunction, which is seen in both alcoholic and non-alcoholic liver cirrhosis and increases wit...

  2. Intelligent autonomous systems 12. Vol. 2. Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Sukhan [Sungkyunkwan Univ., Gyeonggi-Do (Korea, Republic of). College of Information and Communication Engineering; Yoon, Kwang-Joon [Konkuk Univ., Seoul (Korea, Republic of); Cho, Hyungsuck [Daegu Gyeongbuk Institute of Science and Technology, Daegu (Korea, Republic of); Lee, Jangmyung (eds.) [Pusan National Univ. (Korea, Republic of). Dept. of Electronics Engineering

    2013-02-01

    Recent research in Intelligent and Autonomous Systems. Volume 2 of the proceedings of the 12th International Conference IAS-12, held June 26-29, 2012, jeju Island, Korea. Written by leading experts in the field. Intelligent autonomous systems are emerged as a key enabler for the creation of a new paradigm of services to humankind, as seen by the recent advancement of autonomous cars licensed for driving in our streets, of unmanned aerial and underwater vehicles carrying out hazardous tasks on-site, and of space robots engaged in scientific as well as operational missions, to list only a few. This book aims at serving the researchers and practitioners in related fields with a timely dissemination of the recent progress on intelligent autonomous systems, based on a collection of papers presented at the 12th International Conference on Intelligent Autonomous Systems, held in Jeju, Korea, June 26-29, 2012. With the theme of ''Intelligence and Autonomy for the Service to Humankind, the conference has covered such diverse areas as autonomous ground, aerial, and underwater vehicles, intelligent transportation systems, personal/domestic service robots, professional service robots for surgery/rehabilitation, rescue/security and space applications, and intelligent autonomous systems for manufacturing and healthcare. This volume 2 includes contributions devoted to Service Robotics and Human-Robot Interaction and Autonomous Multi-Agent Systems and Life Engineering.

  3. Autonomous power system intelligent diagnosis and control

    Science.gov (United States)

    Ringer, Mark J.; Quinn, Todd M.; Merolla, Anthony

    1991-01-01

    The Autonomous Power System (APS) project at NASA Lewis Research Center is designed to demonstrate the abilities of integrated intelligent diagnosis, control, and scheduling techniques to space power distribution hardware. Knowledge-based software provides a robust method of control for highly complex space-based power systems that conventional methods do not allow. The project consists of three elements: the Autonomous Power Expert System (APEX) for fault diagnosis and control, the Autonomous Intelligent Power Scheduler (AIPS) to determine system configuration, and power hardware (Brassboard) to simulate a space based power system. The operation of the Autonomous Power System as a whole is described and the responsibilities of the three elements - APEX, AIPS, and Brassboard - are characterized. A discussion of the methodologies used in each element is provided. Future plans are discussed for the growth of the Autonomous Power System.

  4. Anesthesia Management in Diabetic Cardiovascular Autonomic Neuropathy

    Directory of Open Access Journals (Sweden)

    Feride Karacaer

    2016-06-01

    Full Text Available Cardiovascular autonomic neuropathy is frequently observed in patients with diabetes mellitus and encompasses damage to the autonomic nerve fibers, resulting in abnormalities in heart rate control and vascular dynamics. There is an increased mortality and morbidity rate among these patients. A series of cardiovascular reflex tests known as Ewing's battery tests are used for diagnosis cardiac autonomic neuropathy and provide valuable information to the clinical assessment of these patients. As anesthesia has a major influence on perioperative autonomic function, the interplay between cardiovascular autonomic neuropathy and anesthesia may result in unexpected haemodynamic instability during surgery and postoperative recovery. A comprehensive preoperative assessment and perioperative cautious monitoring are necessary for successful anesthesia management. [Archives Medical Review Journal 2016; 25(2.000: 140-151

  5. Current challenges in autonomous driving

    Science.gov (United States)

    Barabás, I.; Todoruţ, A.; Cordoş, N.; Molea, A.

    2017-10-01

    Nowadays the automotive industry makes a quantum shift to a future, where the driver will have smaller and smaller role in driving his or her vehicle ending up being totally excluded. In this paper, we have investigated the different levels of driving automatization, the prospective effects of these new technologies on the environment and traffic safety, the importance of regulations and their current state, the moral aspects of introducing these technologies and the possible scenarios of deploying the autonomous vehicles. We have found that the self-driving technologies are facing many challenges: a) They must make decisions faster in very diverse conditions which can include many moral dilemmas as well; b) They have an important potential in reducing the environmental pollution by optimizing their routes, driving styles by communicating with other vehicles, infrastructures and their environment; c) There is a considerable gap between the self-drive technology level and the current regulations; fortunately, this gap shows a continuously decreasing trend; d) In case of many types of imminent accidents management there are many concerns about the ability of making the right decision. Considering that this field has an extraordinary speed of development, our study is up to date at the submission deadline. Self-driving technologies become increasingly sophisticated and technically accessible, and in some cases, they can be deployed for commercial vehicles as well. According to the current stage of research and development, it is still unclear how the self-driving technologies will be able to handle extreme and unexpected events including their moral aspects. Since most of the traffic accidents are caused by human error or omission, it is expected that the emergence of the autonomous technologies will reduce these accidents in their number and gravity, but the very few currently available test results have not been able to scientifically underpin this issue yet. The

  6. Development of microsatellite markers specific for the short arm of rye (Secale cereale L.) chromosome 1

    Czech Academy of Sciences Publication Activity Database

    Kofler, R.; Bartoš, Jan; Gong, L.; Stift, G.; Suchánková, Pavla; Šimková, Hana; Berenyi, M.; Burg, K.; Doležel, Jaroslav; Lelley, T.

    2008-01-01

    Roč. 117, č. 6 (2008), s. 915-926 ISSN 0040-5752 R&D Projects: GA ČR GA521/04/0607; GA ČR GP521/06/P412 Institutional research plan: CEZ:AV0Z50380511 Keywords : NON-LTR RETROTRANSPOSONS * ORYZA-SATIVA L. * PLANT GENOMES Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.490, year: 2008

  7. Sleep in trigeminal autonomic cephalagias

    DEFF Research Database (Denmark)

    Barløse, Mads; Lund, Nunu; Jensen, Rigmor Højland

    2014-01-01

    PURPOSE OF REVIEW: Sleep and cluster headache (CH) are believed to be interconnected but the precise relation to the other trigeminal autonomic cephalalgias (TACs) is uncertain and complex. A better understanding of these relations may eventually lead to a clarification of the underlying mechanisms...... and eventually to more effective therapeutic regimens. This review aims to evaluate the existing literature on the subject of TACs and sleep. An association between episodic CH and distinct macrostructural sleep phases, especially the relation to rapid eye movement (REM) sleep, has been described in some older...... studies but could not be confirmed in other, more recent studies. Investigations into the microstructure of sleep in these patients are lacking. Only a few case reports exist on the relation between sleep and other TACs. SUMMARY: Recent studies do not find an association between CH and REM sleep. One...

  8. Autonomous Medical Care for Exploration

    Science.gov (United States)

    Johnson-Throop, Kathy A.; Polk, J. D.; Hines, John W.; Nall, Marsha M.

    2005-01-01

    The goal of Autonomous Medical Care (AMC) is to ensure a healthy, well-performing crew which is a primary need for exploration. The end result of this effort will be the requirements and design for medical systems for the CEV, lunar operations, and Martian operations as well as a ground-based crew health optimization plan. Without such systems, we increase the risk of medical events occurring during a mission and we risk being unable to deal with contingencies of illness and injury, potentially threatening mission success. AMC has two major components: 1) pre-flight crew health optimization and 2) in-flight medical care. The goal of pre-flight crew health optimization is to reduce the risk of illness occurring during a mission by primary prevention and prophylactic measures. In-flight autonomous medical care is the capability to provide medical care during a mission with little or no real-time support from Earth. Crew medical officers or other crew members provide routine medical care as well as medical care to ill or injured crew members using resources available in their location. Ground support becomes telemedical consultation on-board systems/people collect relevant data for ground support to review. The AMC system provides capabilities to incorporate new procedures and training and advice as required. The on-board resources in an autonomous system should be as intelligent and integrated as is feasible, but autonomous does not mean that no human will be involved. The medical field is changing rapidly, and so a challenge is to determine which items to pursue now, which to leverage other efforts (e.g. military), and which to wait for commercial forces to mature. Given that what is used for the CEV or the Moon will likely be updated before going to Mars, a critical piece of the system design will be an architecture that provides for easy incorporation of new technologies into the system. Another challenge is to determine the level of care to provide for each

  9. Autonomous Infrastructure for Observatory Operations

    Science.gov (United States)

    Seaman, R.

    This is an era of rapid change from ancient human-mediated modes of astronomical practice to a vision of ever larger time domain surveys, ever bigger "big data", to increasing numbers of robotic telescopes and astronomical automation on every mountaintop. Over the past decades, facets of a new autonomous astronomical toolkit have been prototyped and deployed in support of numerous space missions. Remote and queue observing modes have gained significant market share on the ground. Archives and data-mining are becoming ubiquitous; astroinformatic techniques and virtual observatory standards and protocols are areas of active development. Astronomers and engineers, planetary and solar scientists, and researchers from communities as diverse as particle physics and exobiology are collaborating on a vast range of "multi-messenger" science. What then is missing?

  10. Design of Autonomous Underwater Vehicle

    Directory of Open Access Journals (Sweden)

    Tadahiro Hyakudome

    2011-03-01

    Full Text Available There are concerns about the impact that global warming will have on our environment, and which will inevitably result in expanding deserts and rising water levels. While a lot of underwater vehicles are utilized, AUVs (Autonomous Underwater Vehicle were considered and chosen, as the most suitable tool for conduction survey concerning these global environmental problems. AUVs can comprehensive survey because the vehicle does not have to be connected to the support vessel by tether cable. When such underwater vehicles are made, it is necessary to consider about the following things. 1 Seawater and Water Pressure Environment, 2 Sink, 3 There are no Gas or Battery Charge Stations, 4 Global Positioning System cannot use, 5 Radio waves cannot use. In the paper, outline of above and how deal about it are explained.

  11. Radar based autonomous sensor module

    Science.gov (United States)

    Styles, Tim

    2016-10-01

    Most surveillance systems combine camera sensors with other detection sensors that trigger an alert to a human operator when an object is detected. The detection sensors typically require careful installation and configuration for each application and there is a significant burden on the operator to react to each alert by viewing camera video feeds. A demonstration system known as Sensing for Asset Protection with Integrated Electronic Networked Technology (SAPIENT) has been developed to address these issues using Autonomous Sensor Modules (ASM) and a central High Level Decision Making Module (HLDMM) that can fuse the detections from multiple sensors. This paper describes the 24 GHz radar based ASM, which provides an all-weather, low power and license exempt solution to the problem of wide area surveillance. The radar module autonomously configures itself in response to tasks provided by the HLDMM, steering the transmit beam and setting range resolution and power levels for optimum performance. The results show the detection and classification performance for pedestrians and vehicles in an area of interest, which can be modified by the HLDMM without physical adjustment. The module uses range-Doppler processing for reliable detection of moving objects and combines Radar Cross Section and micro-Doppler characteristics for object classification. Objects are classified as pedestrian or vehicle, with vehicle sub classes based on size. Detections are reported only if the object is detected in a task coverage area and it is classified as an object of interest. The system was shown in a perimeter protection scenario using multiple radar ASMs, laser scanners, thermal cameras and visible band cameras. This combination of sensors enabled the HLDMM to generate reliable alerts with improved discrimination of objects and behaviours of interest.

  12. Autonomous caregiver following robotic wheelchair

    Science.gov (United States)

    Ratnam, E. Venkata; Sivaramalingam, Sethurajan; Vignesh, A. Sri; Vasanth, Elanthendral; Joans, S. Mary

    2011-12-01

    In the last decade, a variety of robotic/intelligent wheelchairs have been proposed to meet the need in aging society. Their main research topics are autonomous functions such as moving toward some goals while avoiding obstacles, or user-friendly interfaces. Although it is desirable for wheelchair users to go out alone, caregivers often accompany them. Therefore we have to consider not only autonomous functions and user interfaces but also how to reduce caregivers' load and support their activities in a communication aspect. From this point of view, we have proposed a robotic wheelchair moving with a caregiver side by side based on the MATLAB process. In this project we discussing about robotic wheel chair to follow a caregiver by using a microcontroller, Ultrasonic sensor, keypad, Motor drivers to operate robot. Using camera interfaced with the DM6437 (Davinci Code Processor) image is captured. The captured image are then processed by using image processing technique, the processed image are then converted into voltage levels through MAX 232 level converter and given it to the microcontroller unit serially and ultrasonic sensor to detect the obstacle in front of robot. In this robot we have mode selection switch Automatic and Manual control of robot, we use ultrasonic sensor in automatic mode to find obstacle, in Manual mode to use the keypad to operate wheel chair. In the microcontroller unit, c language coding is predefined, according to this coding the robot which connected to it was controlled. Robot which has several motors is activated by using the motor drivers. Motor drivers are nothing but a switch which ON/OFF the motor according to the control given by the microcontroller unit.

  13. Transcriptional analysis of the HeT-A retrotransposon in mutant and wild type stocks reveals high sequence variability at Drosophila telomeres and other unusual features

    Directory of Open Access Journals (Sweden)

    Piñeyro David

    2011-11-01

    Full Text Available Abstract Background Telomere replication in Drosophila depends on the transposition of a domesticated retroelement, the HeT-A retrotransposon. The sequence of the HeT-A retrotransposon changes rapidly resulting in differentiated subfamilies. This pattern of sequence change contrasts with the essential function with which the HeT-A is entrusted and brings about questions concerning the extent of sequence variability, the telomere contribution of different subfamilies, and whether wild type and mutant Drosophila stocks show different HeT-A scenarios. Results A detailed study on the variability of HeT-A reveals that both the level of variability and the number of subfamilies are higher than previously reported. Comparisons between GIII, a strain with longer telomeres, and its parental strain Oregon-R indicate that both strains have the same set of HeT-A subfamilies. Finally, the presence of a highly conserved splicing pattern only in its antisense transcripts indicates a putative regulatory, functional or structural role for the HeT-A RNA. Interestingly, our results also suggest that most HeT-A copies are actively expressed regardless of which telomere and where in the telomere they are located. Conclusions Our study demonstrates how the HeT-A sequence changes much faster than previously reported resulting in at least nine different subfamilies most of which could actively contribute to telomere extension in Drosophila. Interestingly, the only significant difference observed between Oregon-R and GIII resides in the nature and proportion of the antisense transcripts, suggesting a possible mechanism that would in part explain the longer telomeres of the GIII stock.

  14. Current challenges in autonomous vehicle development

    Science.gov (United States)

    Connelly, J.; Hong, W. S.; Mahoney, R. B., Jr.; Sparrow, D. A.

    2006-05-01

    The field of autonomous vehicles is a rapidly growing one, with significant interest from both government and industry sectors. Autonomous vehicles represent the intersection of artificial intelligence (AI) and robotics, combining decision-making with real-time control. Autonomous vehicles are desired for use in search and rescue, urban reconnaissance, mine detonation, supply convoys, and more. The general adage is to use robots for anything dull, dirty, dangerous or dumb. While a great deal of research has been done on autonomous systems, there are only a handful of fielded examples incorporating machine autonomy beyond the level of teleoperation, especially in outdoor/complex environments. In an attempt to assess and understand the current state of the art in autonomous vehicle development, a few areas where unsolved problems remain became clear. This paper outlines those areas and provides suggestions for the focus of science and technology research. The first step in evaluating the current state of autonomous vehicle development was to develop a definition of autonomy. A number of autonomy level classification systems were reviewed. The resulting working definitions and classification schemes used by the authors are summarized in the opening sections of the paper. The remainder of the report discusses current approaches and challenges in decision-making and real-time control for autonomous vehicles. Suggested research focus areas for near-, mid-, and long-term development are also presented.

  15. Autonomous Demand Response for Primary Frequency Regulation

    Energy Technology Data Exchange (ETDEWEB)

    Donnelly, Matt [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Trudnowski, Daniel J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mattix, S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Dagle, Jeffery E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2012-01-01

    The research documented within this report examines the use of autonomous demand response to provide primary frequency response in an interconnected power grid. The work builds on previous studies in several key areas: it uses a large realistic model (i.e., the interconnection of the western United States and Canada); it establishes a set of metrics that can be used to assess the effectiveness of autonomous demand response; and it independently adjusts various parameters associated with using autonomous demand response to assess effectiveness and to examine possible threats or vulnerabilities associated with the technology.

  16. Autonomous Bicycle: The First Self Balanced Ride

    OpenAIRE

    Ånnestad, Dag Christian

    2011-01-01

    The idea of an autonomous bicycle originates from Jens G. Balchen who wanted to make an unmanned autonomous bicycle. The idea was picked up by Amund Skavhaug who extended the idea with the concept of using an inverted pendulum to simulate a leaning rider. The previous attempts to develop a bicycle capable of performing an autonomous ride has so far all ended in failure. The main reason for the Department of Engineering Cybernetics is to develop such a bicycle is for use in recruitment and mot...

  17. Development of a Commercially Viable, Modular Autonomous Robotic Systems for Converting any Vehicle to Autonomous Control

    Science.gov (United States)

    Parish, David W.; Grabbe, Robert D.; Marzwell, Neville I.

    1994-01-01

    A Modular Autonomous Robotic System (MARS), consisting of a modular autonomous vehicle control system that can be retrofit on to any vehicle to convert it to autonomous control and support a modular payload for multiple applications is being developed. The MARS design is scalable, reconfigurable, and cost effective due to the use of modern open system architecture design methodologies, including serial control bus technology to simplify system wiring and enhance scalability. The design is augmented with modular, object oriented (C++) software implementing a hierarchy of five levels of control including teleoperated, continuous guidepath following, periodic guidepath following, absolute position autonomous navigation, and relative position autonomous navigation. The present effort is focused on producing a system that is commercially viable for routine autonomous patrolling of known, semistructured environments, like environmental monitoring of chemical and petroleum refineries, exterior physical security and surveillance, perimeter patrolling, and intrafacility transport applications.

  18. Autonomic Dysfunction in Patients with Mild to Moderate Alzheimer's Disease

    DEFF Research Database (Denmark)

    Jensen-Dahm, Christina; Waldemar, Gunhild; Staehelin Jensen, Troels

    2015-01-01

    BACKGROUND: Autonomic function has received little attention in Alzheimer's disease (AD). AD pathology has an impact on brain regions which are important for central autonomic control, but it is unclear if AD is associated with disturbance of autonomic function. OBJECTIVE: To investigate autonomic...

  19. Autonomous Operations Design Guidelines for Flight Hardware

    Data.gov (United States)

    National Aeronautics and Space Administration — SSC experimentally modified an autonomous operations flexible system suite developed for a ground application for a flight system under development by JSC. The...

  20. Autonomous Operations System: Development and Application

    Science.gov (United States)

    Toro Medina, Jaime A.; Wilkins, Kim N.; Walker, Mark; Stahl, Gerald M.

    2016-01-01

    Autonomous control systems provides the ability of self-governance beyond the conventional control system. As the complexity of mechanical and electrical systems increases, there develops a natural drive for developing robust control systems to manage complicated operations. By closing the bridge between conventional automated systems to knowledge based self-awareness systems, nominal control of operations can evolve into relying on safe critical mitigation processes to support any off-nominal behavior. Current research and development efforts lead by the Autonomous Propellant Loading (APL) group at NASA Kennedy Space Center aims to improve cryogenic propellant transfer operations by developing an automated control and health monitoring system. As an integrated systems, the center aims to produce an Autonomous Operations System (AOS) capable of integrating health management operations with automated control to produce a fully autonomous system.

  1. Cislunar Autonomous Positioning System (CAPS), Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Recent efforts led by the PI of this proposal have studied the benefits of a satellite navigation technique known as Linked Autonomous Interplanetary Satellite Orbit...

  2. Computer vision for an autonomous mobile robot

    CSIR Research Space (South Africa)

    Withey, Daniel J

    2015-10-01

    Full Text Available Computer vision systems are essential for practical, autonomous, mobile robots – machines that employ artificial intelligence and control their own motion within an environment. As with biological systems, computer vision systems include the vision...

  3. Data Provisioning Systems for Autonomous Vehicles

    National Research Council Canada - National Science Library

    Varaiya, Pravin

    1999-01-01

    This project is part of a portfolio comprising four other projects to investigate the possibility of operating a collection of intelligent autonomous agents so that the collection can undertakes complex missions...

  4. A Primer on Autonomous Aerial Vehicle Design.

    Science.gov (United States)

    Coppejans, Hugo H G; Myburgh, Herman C

    2015-12-02

    There is a large amount of research currently being done on autonomous micro-aerial vehicles (MAV), such as quadrotor helicopters or quadcopters. The ability to create a working autonomous MAV depends mainly on integrating a simultaneous localization and mapping (SLAM) solution with the rest of the system. This paper provides an introduction for creating an autonomous MAV for enclosed environments, aimed at students and professionals alike. The standard autonomous system and MAV automation are discussed, while we focus on the core concepts of SLAM systems and trajectory planning algorithms. The advantages and disadvantages of using remote processing are evaluated, and recommendations are made regarding the viability of on-board processing. Recommendations are made regarding best practices to serve as a guideline for aspirant MAV designers.

  5. Advisory and autonomous cooperative driving systems

    NARCIS (Netherlands)

    Broek, T.H.A. van den; Ploeg, J.; Netten, B.D.

    2011-01-01

    In this paper, the traffic efficiency of an advisory cooperative driving system, Advisory Acceleration Control is examined and compared to the efficiency of an autonomous cooperative driving system, Cooperative Adaptive Cruise Control. The algorithms and implementation thereof are explained. The

  6. Research Institute for Autonomous Precision Guided Systems

    National Research Council Canada - National Science Library

    Sforza, Pasquale

    2003-01-01

    The aim of this project is to leverage the manpower resources dedicated to basic research in technologies relevant to autonomous precision systems at the Air Force Research Laboratory Munitions Directorate (AFRL/MN...

  7. Autonomous Task Primitives for Complex Manipulation Operations

    Data.gov (United States)

    National Aeronautics and Space Administration — The goal of this research effort is to enable robots to autonomously perform the complex manipulation tasks that are necessary to maintain a spacecraft. Robots, like...

  8. Acupuncture Effect and Central Autonomic Regulation

    Directory of Open Access Journals (Sweden)

    Qian-Qian Li

    2013-01-01

    Full Text Available Acupuncture is a therapeutic technique and part of traditional Chinese medicine (TCM. Acupuncture has clinical efficacy on various autonomic nerve-related disorders, such as cardiovascular diseases, epilepsy, anxiety and nervousness, circadian rhythm disorders, polycystic ovary syndrome (PCOS and subfertility. An increasing number of studies have demonstrated that acupuncture can control autonomic nerve system (ANS functions including blood pressure, pupil size, skin conductance, skin temperature, muscle sympathetic nerve activities, heart rate and/or pulse rate, and heart rate variability. Emerging evidence indicates that acupuncture treatment not only activates distinct brain regions in different kinds of diseases caused by imbalance between the sympathetic and parasympathetic activities, but also modulates adaptive neurotransmitter in related brain regions to alleviate autonomic response. This review focused on the central mechanism of acupuncture in modulating various autonomic responses, which might provide neurobiological foundations for acupuncture effects.

  9. Acupuncture effect and central autonomic regulation.

    Science.gov (United States)

    Li, Qian-Qian; Shi, Guang-Xia; Xu, Qian; Wang, Jing; Liu, Cun-Zhi; Wang, Lin-Peng

    2013-01-01

    Acupuncture is a therapeutic technique and part of traditional Chinese medicine (TCM). Acupuncture has clinical efficacy on various autonomic nerve-related disorders, such as cardiovascular diseases, epilepsy, anxiety and nervousness, circadian rhythm disorders, polycystic ovary syndrome (PCOS) and subfertility. An increasing number of studies have demonstrated that acupuncture can control autonomic nerve system (ANS) functions including blood pressure, pupil size, skin conductance, skin temperature, muscle sympathetic nerve activities, heart rate and/or pulse rate, and heart rate variability. Emerging evidence indicates that acupuncture treatment not only activates distinct brain regions in different kinds of diseases caused by imbalance between the sympathetic and parasympathetic activities, but also modulates adaptive neurotransmitter in related brain regions to alleviate autonomic response. This review focused on the central mechanism of acupuncture in modulating various autonomic responses, which might provide neurobiological foundations for acupuncture effects.

  10. Framework for Autonomous Optimization, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Phoenix Integration and MIT propose to create a novel autonomous optimization tool and application programming interface (API). The API will demonstrate the ability...

  11. A Primer on Autonomous Aerial Vehicle Design

    Directory of Open Access Journals (Sweden)

    Hugo H. G. Coppejans

    2015-12-01

    Full Text Available There is a large amount of research currently being done on autonomous micro-aerial vehicles (MAV, such as quadrotor helicopters or quadcopters. The ability to create a working autonomous MAV depends mainly on integrating a simultaneous localization and mapping (SLAM solution with the rest of the system. This paper provides an introduction for creating an autonomous MAV for enclosed environments, aimed at students and professionals alike. The standard autonomous system and MAV automation are discussed, while we focus on the core concepts of SLAM systems and trajectory planning algorithms. The advantages and disadvantages of using remote processing are evaluated, and recommendations are made regarding the viability of on-board processing. Recommendations are made regarding best practices to serve as a guideline for aspirant MAV designers.

  12. Interpersonal communication and issues for autonomous vehicles.

    Science.gov (United States)

    2017-06-01

    Interpersonal roadway communication is a vital component of the transportation system. Road users communicate to coordinate movement and increase roadway safety. Future autonomous vehicle research needs to account for the role of interpersonal roadwa...

  13. Autonomic symptoms in idiopathic REM behavior disorder

    DEFF Research Database (Denmark)

    Ferini-Strambi, Luigi; Oertel, Wolfgang; Dauvilliers, Yves

    2014-01-01

    to study the disorders of the autonomic nervous system in Parkinson's disease (PD) patients, the SCOPA-AUT, was administered to all the patients and controls. The SCOPA-AUT consists of 25 items assessing the following domains: gastrointestinal, urinary, cardiovascular, thermoregulatory, pupillomotor......Patients with idiopathic REM sleep behavior disorder (iRBD) are at very high risk of developing neurodegenerative synucleinopathies, which are disorders with prominent autonomic dysfunction. Several studies have documented autonomic dysfunction in iRBD, but large-scale assessment of autonomic...... symptoms has never been systematically performed. Patients with polysomnography-confirmed iRBD (318 cases) and controls (137 healthy volunteers and 181 sleep center controls with sleep diagnoses other than RBD) were recruited from 13 neurological centers in 10 countries from 2008 to 2011. A validated scale...

  14. Adaptive Sampling in Autonomous Marine Sensor Networks

    National Research Council Canada - National Science Library

    Eickstedt, Donald P

    2006-01-01

    ... oceanographic network scenario. This architecture has three major components, an intelligent, logical sensor that provides high-level environmental state information to a behavior-based autonomous vehicle control system, a new...

  15. Autonomous Training for Long-Term Spaceflight

    Data.gov (United States)

    National Aeronautics and Space Administration — This project will develop the autonomous capability to intelligently select/generate practice scenarios in order to provide individually targeted crew training when...

  16. Future Autonomous and Automated Systems Testbed

    Data.gov (United States)

    National Aeronautics and Space Administration — Trust is the greatest obstacle to implementing greater autonomy and automation (A&A) in the human spaceflight program. The Future Autonomous and Automated...

  17. Semi-Autonomous Vehicle Project

    Science.gov (United States)

    Stewart, Christopher

    2016-01-01

    The primary objective this summer is "evaluating standards for wireless architecture for the internet of things". The Internet of Things is the network of physical objects or "things" embedded with electronics, software, sensors and network connectivity which enables these objects to collect and exchange data and make decisions based on said data. This was accomplished by creating a semi-autonomous vehicle that takes advantage of multiple sensors, cameras, and onboard computers and combined them with a mesh network which enabled communication across large distances with little to no interruption. The mesh network took advantage of what is known as DTN - Disruption Tolerant Networking which according to NASA is the new communications protocol that is "the first step towards interplanetary internet." The use of DTN comes from the fact that it will store information if an interruption in communications is detected and even forward that information via other relays within range so that the data is not lost. This translates well into the project because as the car moves further away from whatever is sending it commands (in this case a joystick), the information can still be forwarded to the car with little to no loss of information thanks to the mesh nodes around the driving area.

  18. Autonomous nutrient detection for water quality monitoring

    OpenAIRE

    Maher, Damien; Cleary, John; Cogan, Deirdre; Diamond, Dermot

    2012-01-01

    The ever increasing demand for real time environmental monitoring is currently being driven by strong legislative and societal drivers. Low cost autonomous environmental monitoring systems are required to meet this demand as current monitoring solutions are insufficient. This poster presents an autonomous nutrient analyser platform for water quality monitoring. Results from a field trial of the nutrient analyser are reported along with current work to expand the range of water quality targ...

  19. Non-autonomous bifurcation in impulsive systems

    Directory of Open Access Journals (Sweden)

    Marat Akhmet

    2013-12-01

    Full Text Available This is the first paper which considers non-autonomous bifurcations in impulsive differential equations. Impulsive generalizations of the non-autonomous pitchfork and transcritical bifurcation are discussed. We consider scalar differential equation with fixed moments of impulses. It is illustrated by means of certain systems how the idea of pullback attracting sets remains a fruitful concept in the impulsive systems. Basics of the theory are provided.

  20. Acupuncture Effect and Central Autonomic Regulation

    OpenAIRE

    Qian-Qian Li; Guang-Xia Shi; Qian Xu; Jing Wang; Cun-Zhi Liu; Lin-Peng Wang

    2013-01-01

    Acupuncture is a therapeutic technique and part of traditional Chinese medicine (TCM). Acupuncture has clinical efficacy on various autonomic nerve-related disorders, such as cardiovascular diseases, epilepsy, anxiety and nervousness, circadian rhythm disorders, polycystic ovary syndrome (PCOS) and subfertility. An increasing number of studies have demonstrated that acupuncture can control autonomic nerve system (ANS) functions including blood pressure, pupil size, skin conductance, skin temp...

  1. Autonomous Control System for Precise Orbit Maintenance

    OpenAIRE

    Aorpimai, Manop; Hashida, Yoshi; Palmer, Phil

    2000-01-01

    In this paper, we describe a closed-loop autonomous control system that enables orbit operations to be performed without the need of any ground segment. The growing availability of GPS receivers on satellites provides an excellent means for autonomous orbit determination and our work builds upon previous work on orbit determination algorithms developed here at Surrey. The orbit is described using a set of epicycle parameters which provide an analytic model of LEO orbits. The parameters in thi...

  2. The Human Element and Autonomous Ships

    Directory of Open Access Journals (Sweden)

    Sauli Ahvenjärvi

    2016-09-01

    Full Text Available The autonomous ship technology has become a “hot” topic in the discussion about more efficient, environmentally friendly and safer sea transportation solutions. The time is becoming mature for the introduction of commercially sensible solutions for unmanned and fully autonomous cargo and passenger ships. Safety will be the most interesting and important aspect in this development. The utilization of the autonomous ship technology will have many effects on the safety, both positive and negative. It has been announced that the goal is to make the safety of an unmanned ship better that the safety of a manned ship. However, it must be understood that the human element will still be present when fully unmanned ships are being used. The shore-based control of a ship contains new safety aspects and an interesting question will be the interaction of manned and unmanned ships in the same traffic area. The autonomous ship technology should therefore be taken into account on the training of seafarers. Also it should not be forgotten that every single control algorithm and rule of the internal decision making logic of the autonomously navigating ship has been designed and coded by a human software engineer. Thus the human element is present also in this point of the lifetime navigation system of the autonomous ship.

  3. Advancing Autonomous Operations for Deep Space Vehicles

    Science.gov (United States)

    Haddock, Angie T.; Stetson, Howard K.

    2014-01-01

    Starting in Jan 2012, the Advanced Exploration Systems (AES) Autonomous Mission Operations (AMO) Project began to investigate the ability to create and execute "single button" crew initiated autonomous activities [1]. NASA Marshall Space Flight Center (MSFC) designed and built a fluid transfer hardware test-bed to use as a sub-system target for the investigations of intelligent procedures that would command and control a fluid transfer test-bed, would perform self-monitoring during fluid transfers, detect anomalies and faults, isolate the fault and recover the procedures function that was being executed, all without operator intervention. In addition to the development of intelligent procedures, the team is also exploring various methods for autonomous activity execution where a planned timeline of activities are executed autonomously and also the initial analysis of crew procedure development. This paper will detail the development of intelligent procedures for the NASA MSFC Autonomous Fluid Transfer System (AFTS) as well as the autonomous plan execution capabilities being investigated. Manned deep space missions, with extreme communication delays with Earth based assets, presents significant challenges for what the on-board procedure content will encompass as well as the planned execution of the procedures.

  4. Autonomous power networks based power system

    International Nuclear Information System (INIS)

    Jokic, A.; Van den Bosch, P.P.J.

    2006-01-01

    This paper presented the concept of autonomous networks to cope with this increased complexity in power systems while enhancing market-based operation. The operation of future power systems will be more challenging and demanding than present systems because of increased uncertainties, less inertia in the system, replacement of centralized coordinating activities by decentralized parties and the reliance on dynamic markets for both power balancing and system reliability. An autonomous network includes the aggregation of networked producers and consumers in a relatively small area with respect to the overall system. The operation of an autonomous network is coordinated and controlled with one central unit acting as an interface between internal producers/consumers and the rest of the power system. In this study, the power balance problem and system reliability through provision of ancillary services was formulated as an optimization problem for the overall autonomous networks based power system. This paper described the simulation of an optimal autonomous network dispatching in day ahead markets, based on predicted spot prices for real power, and two ancillary services. It was concluded that large changes occur in a power systems structure and operation, most of them adding to the uncertainty and complexity of the system. The introduced concept of an autonomous power network-based power system was shown to be a realistic and consistent approach to formulate and operate a market-based dispatch of both power and ancillary services. 9 refs., 4 figs

  5. The role of autonomic testing in syncope.

    Science.gov (United States)

    Jones, Pearl K; Gibbons, Christopher H

    2014-09-01

    Syncope is a common presenting complaint in both the inpatient and outpatient settings. The main goals in the clinical evaluation of syncope are to identify an underlying etiology, to stratify risk and to guide plans for therapeutic intervention. Testing begins with an initial electrocardiogram to screen for any cardiac rhythm abnormalities. Heart rate variability to paced breathing provides a standard measure of cardiac parasympathetic function and offers clues towards an autonomic cause of syncope. A Valsalva maneuver is used to evaluate for parasympathetic dysfunction through the Valsalva ratio. In addition, sympathetic adrenergic function is assessed through evaluation of blood pressure response during the Valsalva maneuver. Abnormalities to the Valsalva maneuver can suggest clues towards an autonomic cause of syncope. Head-up tilt table testing is an important part of the autonomic evaluation of patients with syncope, and can be diagnostic for many disorders that result in syncope including orthostatic hypotension, neurally mediated syncope, postural tachycardia syndrome or delayed orthostatic hypotension. Autonomic function testing provides a safe and controlled environment for evaluation of patients, and plays a pivotal role in the diagnosis of syncope, particularly in challenging cases. While the initial clinical evaluation of syncope involves a detailed history and physical examination; in situations where the diagnosis is unknown, the addition of autonomic testing is complementary and can lead to identification of autonomic causes of syncope. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Cardiac autonomic dysfunction in West syndrome.

    Science.gov (United States)

    Jansen, Katrien; Vandeput, Steven; Van Huffel, Sabine; Lagae, Lieven

    2012-12-01

    West syndrome is an age-dependent epileptic encephalopathy. Autonomic changes are increasingly being recognized in patients with epilepsy: cardiac autonomic function is mediated by sympathetic and parasympathetic efferent activity to the heart and can provide information on the functional state of the autonomic nervous system. The goal of the study is to evaluate the effect of an early epileptic encephalopathy on the autonomic nervous system by measuring heart rate variability. Cardiac autonomic function was evaluated in 13 patients with West syndrome by measuring heart rate variability during 5 min epochs of ECG in wake, stage 2 and slow wave sleep. In 5 patients who developed subsequently another type of epilepsy, a second evaluation was performed after 3 years of follow-up. Results showed a lower heart rate in stage 2 sleep in patients with West syndrome. Spectral components did not show significant differences compared to age matched controls at the moment of presentation. After follow-up of 3 years we were able to demonstrate higher low frequency (LF), lower high frequency (HF) and a higher LF/HF ratio during slow wave sleep. This study shows a lower heart rate in patients presenting with West syndrome, already at the onset of the syndrome and before ACTH treatment. The epileptic encephalopathy is not sufficient to alter spectral components of heart rate at the moment of presentation. However, already after 3 years of epilepsy, chronic autonomic changes appear. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. The imprinted retrotransposon-like gene PEG11 (RTL1 is expressed as a full-length protein in skeletal muscle from Callipyge sheep.

    Directory of Open Access Journals (Sweden)

    Keren Byrne

    Full Text Available Members of the Ty3-Gypsy retrotransposon family are rare in mammalian genomes despite their abundance in invertebrates and some vertebrates. These elements contain a gag-pol-like structure characteristic of retroviruses but have lost their ability to retrotranspose into the mammalian genome and are thought to be inactive relics of ancient retrotransposition events. One of these retrotransposon-like elements, PEG11 (also called RTL1 is located at the distal end of ovine chromosome 18 within an imprinted gene cluster that is highly conserved in placental mammals. The region contains several conserved imprinted genes including BEGAIN, DLK1, DAT, GTL2 (MEG3, PEG11 (RTL1, PEG11as, MEG8, MIRG and DIO3. An intergenic point mutation between DLK1 and GTL2 causes muscle hypertrophy in callipyge sheep and is associated with large changes in expression of the genes linked in cis between DLK1 and MEG8. It has been suggested that over-expression of DLK1 is the effector of the callipyge phenotype; however, PEG11 gene expression is also strongly correlated with the emergence of the muscling phenotype as a function of genotype, muscle type and developmental stage. To date, there has been no direct evidence that PEG11 encodes a protein, especially as its anti-sense transcript (PEG11as contains six miRNA that cause cleavage of the PEG11 transcript. Using immunological and mass spectrometry approaches we have directly identified the full-length PEG11 protein from postnatal nuclear preparations of callipyge skeletal muscle and conclude that its over-expression may be involved in inducing muscle hypertrophy. The developmental expression pattern of the PEG11 gene is consistent with the callipyge mutation causing recapitulation of the normal fetal-like gene expression program during postnatal development. Analysis of the PEG11 sequence indicates strong conservation of the regions encoding the antisense microRNA and in at least two cases these correspond with structural

  8. Autonomous Vehicles: Disengagements, Accidents and Reaction Times.

    Science.gov (United States)

    Dixit, Vinayak V; Chand, Sai; Nair, Divya J

    2016-01-01

    Autonomous vehicles are being viewed with scepticism in their ability to improve safety and the driving experience. A critical issue with automated driving at this stage of its development is that it is not yet reliable and safe. When automated driving fails, or is limited, the autonomous mode disengages and the drivers are expected to resume manual driving. For this transition to occur safely, it is imperative that drivers react in an appropriate and timely manner. Recent data released from the California trials provide compelling insights into the current factors influencing disengagements of autonomous mode. Here we show that the number of accidents observed has a significantly high correlation with the autonomous miles travelled. The reaction times to take control of the vehicle in the event of a disengagement was found to have a stable distribution across different companies at 0.83 seconds on average. However, there were differences observed in reaction times based on the type of disengagements, type of roadway and autonomous miles travelled. Lack of trust caused by the exposure to automated disengagements was found to increase the likelihood to take control of the vehicle manually. Further, with increased vehicle miles travelled the reaction times were found to increase, which suggests an increased level of trust with more vehicle miles travelled. We believe that this research would provide insurers, planners, traffic management officials and engineers fundamental insights into trust and reaction times that would help them design and engineer their systems.

  9. Autonomous Vehicles: Disengagements, Accidents and Reaction Times.

    Directory of Open Access Journals (Sweden)

    Vinayak V Dixit

    Full Text Available Autonomous vehicles are being viewed with scepticism in their ability to improve safety and the driving experience. A critical issue with automated driving at this stage of its development is that it is not yet reliable and safe. When automated driving fails, or is limited, the autonomous mode disengages and the drivers are expected to resume manual driving. For this transition to occur safely, it is imperative that drivers react in an appropriate and timely manner. Recent data released from the California trials provide compelling insights into the current factors influencing disengagements of autonomous mode. Here we show that the number of accidents observed has a significantly high correlation with the autonomous miles travelled. The reaction times to take control of the vehicle in the event of a disengagement was found to have a stable distribution across different companies at 0.83 seconds on average. However, there were differences observed in reaction times based on the type of disengagements, type of roadway and autonomous miles travelled. Lack of trust caused by the exposure to automated disengagements was found to increase the likelihood to take control of the vehicle manually. Further, with increased vehicle miles travelled the reaction times were found to increase, which suggests an increased level of trust with more vehicle miles travelled. We believe that this research would provide insurers, planners, traffic management officials and engineers fundamental insights into trust and reaction times that would help them design and engineer their systems.

  10. Enabling technologies for autonomous MAV operations

    Science.gov (United States)

    Elbanhawi, M.; Mohamed, A.; Clothier, R.; Palmer, J. L.; Simic, M.; Watkins, S.

    2017-05-01

    The utility of micro air vehicles (MAVs) has expanded significantly in the last decade, and there are now numerous commercial systems available at relatively low cost. This expansion has arisen mainly due to the miniaturisation of flight control systems and advances in energy storage and propulsion technologies. Several emerging applications involve routine operation of MAVs in complex urban environments such as parcel delivery, communications relay and environmental monitoring. However, MAVs currently rely on one or more operators-in-the-loop and, whilst desirable, full autonomous operation has not yet been achieved. In this review paper, autonomous MAV operation in complex environments is explored with conceptualisation for future MAV operation in urban environments. Limitations of current technologies are systematically examined through consideration of the state-of-the-art and future trends. The main limitations challenging the realisation of fully autonomous MAVs are mainly attributed to: computational power, communication and energy storage. These limitations lead to poor sensing and planning capabilities, which are essential components of autonomous MAVs. Possible solutions are explored with goal of enabling MAVs to reliably operate autonomously in urban environments.

  11. Lessons learned from the Autonomous Power System

    Science.gov (United States)

    Ringer, Mark J.; Quinn, Todd M.; Merolla, Anthony

    1992-01-01

    The Autonomous Power System (APS) project at the NASA Lewis Research Center is designed to demonstrate the applications of integrated intelligent diagnosis, control and scheduling techniques to space power distribution systems. The project consists of three elements: the Autonomous Power Expert System (APEX) for Fault Diagnosis, Isolation, and Recovery (FDIR); the Autonomous Intelligent Power Scheduler (AIPS) to efficiently assign activities start times and resources; and power hardware (Brassboard) to emulate a space-based power system. The APS project had been through one design iteration. Each of the three elements of the APS project has been designed, tested, and integrated into a complete working system. After these three portions were completed, an evaluation period was initiated. Each piece of the system was critiqued based on individual performance as well as the ability to interact with the other portions of the APS project. These critiques were then used to determine guidelines for new and improved components of the APS system.

  12. An Expert System for Autonomous Spacecraft Control

    Science.gov (United States)

    Sherwood, Rob; Chien, Steve; Tran, Daniel; Cichy, Benjamin; Castano, Rebecca; Davies, Ashley; Rabideau, Gregg

    2005-01-01

    The Autonomous Sciencecraft Experiment (ASE), part of the New Millennium Space Technology 6 Project, is flying onboard the Earth Orbiter 1 (EO-1) mission. The ASE software enables EO-1 to autonomously detect and respond to science events such as: volcanic activity, flooding, and water freeze/thaw. ASE uses classification algorithms to analyze imagery onboard to detect chang-e and science events. Detection of these events is then used to trigger follow-up imagery. Onboard mission planning software then develops a response plan that accounts for target visibility and operations constraints. This plan is then executed using a task execution system that can deal with run-time anomalies. In this paper we describe the autonomy flight software and how it enables a new paradigm of autonomous science and mission operations. We will also describe the current experiment status and future plans.

  13. Autonomous Robot Navigation based on Visual Landmarks

    DEFF Research Database (Denmark)

    Livatino, Salvatore

    2005-01-01

    The use of landmarks for robot navigation is a popular alternative to having a geometrical model of the environment through which to navigate and monitor self-localization. If the landmarks are defined as special visual structures already in the environment then we have the possibility of fully...... autonomous navigation and self-localization using automatically selected landmarks. The thesis investigates autonomous robot navigation and proposes a new method which benefits from the potential of the visual sensor to provide accuracy and reliability to the navigation process while relying on naturally...... update of the estimated robot position while the robot is moving. In order to make the system autonomous, both acquisition and observation of landmarks have to be carried out automatically. The thesis consequently proposes a method for learning and navigation of a working environment and it explores...

  14. On-Orbit Autonomous Assembly from Nanosatellites

    Science.gov (United States)

    Murchison, Luke S.; Martinez, Andres; Petro, Andrew

    2015-01-01

    The On-Orbit Autonomous Assembly from Nanosatellites (OAAN) project will demonstrate autonomous control algorithms for rendezvous and docking maneuvers; low-power reconfigurable magnetic docking technology; and compact, lightweight and inexpensive precision relative navigation using carrier-phase differential (CD) GPS with a three-degree of freedom ground demonstration. CDGPS is a specific relative position determination method that measures the phase of the GPS carrier wave to yield relative position data accurate to.4 inch (1 centimeter). CDGPS is a technology commonly found in the surveying industry. The development and demonstration of these technologies will fill a current gap in the availability of proven autonomous rendezvous and docking systems for small satellites.

  15. Cardiovascular Autonomic Neuropathy in Systemic Lupus Erythematosus.

    Science.gov (United States)

    Alam, Md Mahboob; Das, Pinaki; Ghosh, Parasar; Zaman, Md Salim Uz; Boro, Madhusmita; Sadhu, Manika; Mazumdar, Ardhendu

    2015-01-01

    Objective is to evaluate cardiovascular autonomic function in SLE by simple non-invasive tests. A case control study was carried out involving 18-50 yrs old previously diagnosed SLE patients and same number of age and sex-matched controls. Parasympathetic function was assessed by heart rate (HR) response to Valsalva maneuver, deep breathing and standing. Sympathetic function was evaluated by blood pressure response to standing and sustained hand-grip test (HGT). There were 50 female SLE patients. They had significantly higher minimum resting HR and diastolic blood pressure (DBP). HR variation with deep breathing, expiratory inspiratory ratio, 30:15 ratio and DBP change in response to HGT were significantly lower inpatients compared to controls. Thirty patients (60%) had at least one abnormal or two borderline test results indicating autonomic impairment of which 27 had parasympathetic dysfunction and 7 had sympathetic dysfunction. Autonomic dysfunction is common in SLE with higher prevalence of parasympathetic impairment.

  16. Autonomous driving technical, legal and social aspects

    CERN Document Server

    Gerdes, J; Lenz, Barbara; Winner, Hermann

    2016-01-01

    This book takes a look at fully automated, autonomous vehicles and discusses many open questions: How can autonomous vehicles be integrated into the current transportation system with diverse users and human drivers? Where do automated vehicles fall under current legal frameworks? What risks are associated with automation and how will society respond to these risks? How will the marketplace react to automated vehicles and what changes may be necessary for companies? Experts from Germany and the United States define key societal, engineering, and mobility issues related to the automation of vehicles. They discuss the decisions programmers of automated vehicles must make to enable vehicles to perceive their environment, interact with other road users, and choose actions that may have ethical consequences. The authors further identify expectations and concerns that will form the basis for individual and societal acceptance of autonomous driving. While the safety benefits of such vehicles are tremendous, the auth...

  17. Development of an autonomous power system testbed

    International Nuclear Information System (INIS)

    Barton, J.R.; Adams, T.; Liffring, M.E.

    1985-01-01

    A power system testbed has been assembled to advance the development of large autonomous electrical power systems required for the space station, spacecraft, and aircraft. The power system for this effort was designed to simulate single- or dual-bus autonomous power systems, or autonomous systems that reconfigure from a single bus to a dual bus following a severe fault. The approach taken was to provide a flexible power system design with two computer systems for control and management. One computer operates as the control system and performs basic control functions, data and command processing, charge control, and provides status to the second computer. The second computer contains expert system software for mission planning, load management, fault identification and recovery, and sends load and configuration commands to the control system

  18. Control of autonomous robot using neural networks

    Science.gov (United States)

    Barton, Adam; Volna, Eva

    2017-07-01

    The aim of the article is to design a method of control of an autonomous robot using artificial neural networks. The introductory part describes control issues from the perspective of autonomous robot navigation and the current mobile robots controlled by neural networks. The core of the article is the design of the controlling neural network, and generation and filtration of the training set using ART1 (Adaptive Resonance Theory). The outcome of the practical part is an assembled Lego Mindstorms EV3 robot solving the problem of avoiding obstacles in space. To verify models of an autonomous robot behavior, a set of experiments was created as well as evaluation criteria. The speed of each motor was adjusted by the controlling neural network with respect to the situation in which the robot was found.

  19. Autonomous calibration of single spin qubit operations

    Science.gov (United States)

    Frank, Florian; Unden, Thomas; Zoller, Jonathan; Said, Ressa S.; Calarco, Tommaso; Montangero, Simone; Naydenov, Boris; Jelezko, Fedor

    2017-12-01

    Fully autonomous precise control of qubits is crucial for quantum information processing, quantum communication, and quantum sensing applications. It requires minimal human intervention on the ability to model, to predict, and to anticipate the quantum dynamics, as well as to precisely control and calibrate single qubit operations. Here, we demonstrate single qubit autonomous calibrations via closed-loop optimisations of electron spin quantum operations in diamond. The operations are examined by quantum state and process tomographic measurements at room temperature, and their performances against systematic errors are iteratively rectified by an optimal pulse engineering algorithm. We achieve an autonomous calibrated fidelity up to 1.00 on a time scale of minutes for a spin population inversion and up to 0.98 on a time scale of hours for a single qubit π/2 -rotation within the experimental error of 2%. These results manifest a full potential for versatile quantum technologies.

  20. Irresponsibilities, inequalities and injustice for autonomous vehicles

    DEFF Research Database (Denmark)

    Liu, Hin-Yan

    2017-01-01

    With their prospect for causing both novel and known forms of damage, harm and injury, the issue of responsibility has been a recurring theme in the debate concerning autonomous vehicles. Yet, the discussion of responsibility has obscured the finer details both between the underlying concepts...... of responsibility, and their application to the interaction between human beings and artificial decision-making entities. By developing meaningful distinctions and examining their ramifications, this article contributes to this debate by refining the underlying concepts that together inform the idea...... of responsibility. Two different approaches are offered to the question of responsibility and autonomous vehicles: targeting and risk distribution. The article then introduces a thought experiment which situates autonomous vehicles within the context of crash optimisation impulses and coordinated or networked...

  1. Blood pressure regulation in diabetic autonomic neuropathy

    DEFF Research Database (Denmark)

    Hilsted, J

    1985-01-01

    Defective blood pressure responses to standing, exercise and epinephrine infusions have been demonstrated in diabetic patients with autonomic neuropathy. The circulatory mechanisms underlying blood pressure responses to exercise and standing up in these patients are well characterized: In both...... which may contribute to exercise hypotension in these patients. During hypoglycemia, blood pressure regulation seems intact in patients with autonomic neuropathy. This is probably due to release of substantial amounts of catecholamines during these experiments. During epinephrine infusions a substantial...... blood pressure fall ensues in patients with autonomic neuropathy, probably due to excessive muscular vasodilation. It is unresolved why blood pressure regulation is intact during hypoglycemia and severely impaired--at similar catecholamine concentrations--during epinephrine infusions....

  2. Identification and characterization of REC66, a Ty1-copia-like retrotransposon in the genome of red flower of Mirabilis jalapa L.

    Directory of Open Access Journals (Sweden)

    Shunri Jiang

    2017-01-01

    Full Text Available Mirabilis jalapa Lis the most commonly grown ornamental species of Mirabilis and is available in a range of brilliant colors. However, genetic research on Mirabilis jalapa Lis limited. Using fluorescent differential display (FDD screening, we report the identification of a novel Ty1-copia-like retrotransposon in the genome of the red flower of Mirabilis jalapa L, and we named it REC66based on its sequence homology to the GAG protein from Ty1-copiaretrotransposon. Using degenerate primers based on the DNA sequence of REC66, a total of fourteen different variants in reverse transcriptase (RT sequence were recovered from the genomic DNA. These RT sequences show a high degree of heterogeneity characterized mainly by deletion mutation; they can be divided into three subfamilies, of which the majority encode defective RT. This is the first report of a Ty1-copiaretrotransposon in Mirabilis jalapa L. The finding could be helpful for the development of new molecular markers for genetic studies, particularly on the origin and evolutionary relationships of M. jalapa L, and the study of Ty1-copiaretrotransposons and plant genome evolution in the genus Mirabilisor family Nyctaginaceae.

  3. New role of LTR-retrotransposons for emergence and expansion of disease-resistance genes and high-copy gene families in plants.

    Science.gov (United States)

    Kim, Seungill; Choi, Doil

    2018-02-01

    Long terminal repeat retrotransposons (LTR-Rs) are major elements creating new genome structure for expansion of plant genomes. However, in addition to the genome expansion, the role of LTR-Rs has been unexplored. In this study, we constructed new reference genome sequences of two pepper species (Capsicum baccatum and C. chinense), and updated the reference genome of C. annuum. We focused on the study for speciation of Capsicum spp. and its driving forces. We found that chromosomal translocation, unequal amplification of LTR-Rs, and recent gene duplications in the pepper genomes as major evolutionary forces for diversification of Capsicum spp. Specifically, our analyses revealed that the nucleotide-binding and leucine-rich-repeat proteins (NLRs) were massively created by LTR-R-driven retroduplication. These retoduplicated NLRs were abundant in higher plants, and most of them were lineage-specific. The retroduplication was a main process for creation of functional disease-resistance genes in Solanaceae plants. In addition, 4-10% of whole genes including highly amplified families such as MADS-box and cytochrome P450 emerged by the retroduplication in the plants. Our study provides new insight into creation of disease-resistance genes and high-copy number gene families by retroduplication in plants. [BMB Reports 2018; 51(2): 55-56].

  4. A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla).

    Science.gov (United States)

    Gallus, S; Kumar, V; Bertelsen, M F; Janke, A; Nilsson, M A

    2015-10-25

    Ruminantia, the ruminating, hoofed mammals (cow, deer, giraffe and allies) are an unranked artiodactylan clade. Around 50-60 million years ago the BovB retrotransposon entered the ancestral ruminantian genome through horizontal gene transfer. A survey genome screen using 454-pyrosequencing of the Java mouse deer (Tragulus javanicus) and the lesser kudu (Tragelaphus imberbis) was done to investigate and to compare the landscape of transposable elements within Ruminantia. The family Tragulidae (mouse deer) is the only representative of Tragulina and phylogenetically important, because it represents the earliest divergence in Ruminantia. The data analyses show that, relative to other ruminantian species, the lesser kudu genome has seen an expansion of BovB Long INterspersed Elements (LINEs) and BovB related Short INterspersed Elements (SINEs) like BOVA2. In comparison the genome of Java mouse deer has fewer BovB elements than other ruminants, especially Bovinae, and has in addition a novel CHR-3 SINE most likely propagated by LINE-1. By contrast the other ruminants have low amounts of CHR SINEs but high numbers of actively propagating BovB-derived and BovB-propagated SINEs. The survey sequencing data suggest that the transposable element landscape in mouse deer (Tragulina) is unique among Ruminantia, suggesting a lineage specific evolutionary trajectory that does not involve BovB mediated retrotransposition. This shows that the genomic landscape of mobile genetic elements can rapidly change in any lineage. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Are Turkish University Students Autonomous or Not?

    Directory of Open Access Journals (Sweden)

    Büşra Kırtık

    2017-01-01

    Full Text Available The present study tried to determine Turkish learners’ attitudes, and the Turkish education system’s approach towards learner autonomy with regard to three main points: 1 whether Turkish university students are aware of learner autonomy or not 2 whether Turkish university students have the characteristics of autonomous learners (whether they are autonomous learners or not, and 3 if the Turkish education system is suitable for fostering learner autonomy or not from the viewpoint of the participants. Participants were 50 second grade learners in the English Language Teaching Departments of Hacettepe University (N=10, Mehmet Akif Ersoy University (N=10, and Uludag University (N=30 who had already taken courses about learner autonomy.  The data were collected by means of a questionnaire which had two Likert-scale sections and an open-ended questions section. The first Likert-scale section contained 15 characteristics of autonomous learners each of which was rated by the participants in a scale from strongly disagree to agree, from 1 to 5. In the second Likert-scale section, the participants were asked to rate the Turkish education system’s five basic elements such as school curriculums, course materials, approaches used by the teachers in classrooms, learning activities, and classroom settings. Additionally, learners’ opinions about their awareness and understanding of learner autonomy were gathered by five open ended questions. The results proposed that the participants were aware of learner autonomy, and had the characteristics of autonomous learners. On the other hand, results showed that the Turkish education system was not suitable for autonomous learners and did not foster learner autonomy. The findings suggested that the Turkish education system should be designed again in such a way to support the autonomous learners and to foster learner autonomy in all sections of the education.

  6. Autonomous execution of the Precision Immobilization Technique

    Science.gov (United States)

    Mascareñas, David D. L.; Stull, Christopher J.; Farrar, Charles R.

    2017-03-01

    Over the course of the last decade great advances have been made in autonomously driving cars. The technology has advanced to the point that driverless car technology is currently being tested on publicly accessed roadways. The introduction of these technologies onto publicly accessed roadways not only raises questions of safety, but also security. Autonomously driving cars are inherently cyber-physical systems and as such will have novel security vulnerabilities that couple both the cyber aspects of the vehicle including the on-board computing and any network data it makes use of, with the physical nature of the vehicle including its sensors, actuators, and the vehicle chassis. Widespread implementation of driverless car technology will require that both the cyber, as well as physical security concerns surrounding these vehicles are addressed. In this work, we specifically developed a control policy to autonomously execute the Precision Immobilization Technique, a.k.a. the PIT maneuver. The PIT maneuver was originally developed by law enforcement to end high-speed vehicular pursuits in a quasi-safe manner. However, there is still a risk of damage/roll-over to both the vehicle executing the PIT maneuver as well as to the vehicle subject to the PIT maneuver. In law enforcement applications, it would be preferable to execute the PIT maneuver using an autonomous vehicle, thus removing the danger to law-enforcement officers. Furthermore, it is entirely possible that unscrupulous individuals could inject code into an autonomously-driving car to use the PIT maneuver to immobilize other vehicles while maintaining anonymity. For these reasons it is useful to know how the PIT maneuver can be implemented on an autonomous car. In this work a simple control policy based on velocity pursuit was developed to autonomously execute the PIT maneuver using only a vision and range measurements that are both commonly collected by contemporary driverless cars. The ability of this

  7. Design of an autonomous exterior security robot

    Science.gov (United States)

    Myers, Scott D.

    1994-01-01

    This paper discusses the requirements and preliminary design of robotic vehicle designed for performing autonomous exterior perimeter security patrols around warehouse areas, ammunition supply depots, and industrial parks for the U.S. Department of Defense. The preliminary design allows for the operation of up to eight vehicles in a six kilometer by six kilometer zone with autonomous navigation and obstacle avoidance. In addition to detection of crawling intruders at 100 meters, the system must perform real-time inventory checking and database comparisons using a microwave tags system.

  8. Emerging Technologies for Autonomous Language Learning

    Directory of Open Access Journals (Sweden)

    Mark Warschauer

    2011-09-01

    Full Text Available Drawing on a lengthier review completed for the US National Institute for Literacy, this paper examines emerging technologies that are applicable to self-access and autonomous learning in the areas of listening and speaking, collaborative writing, reading and language structure, and online interaction. Digital media reviewed include podcasts, blogs, wikis, online writing sites, text-scaffolding software, concordancers, multiuser virtual environments, multiplayer games, and chatbots. For each of these technologies, we summarize recent research and discuss possible uses for autonomous language learning.

  9. A mission planner for an autonomous tractor

    DEFF Research Database (Denmark)

    Bochtis, Dionysis; Vougioukas, S.G.; Griepentrog, Hans W.

    2009-01-01

    In this article, a mission planner of field coverage operations for an autonomous agricultural tractor is presented. Missions for a particular autonomous tractor are defined using an XML (extendible markup language) formatted file that can be uploaded to the tractor through the user interface...... and formulated, via semantic representations, as a vehicle routing problem (VRP). By using this approach, the total non-working distance can be reduced by up to 50% compared to the conventional non-optimized method. Three sets of experiments are presented. In the first set, three fields were separately covered...

  10. Advanced control architecture for autonomous vehicles

    Science.gov (United States)

    Maurer, Markus; Dickmanns, Ernst D.

    1997-06-01

    An advanced control architecture for autonomous vehicles is presented. The hierarchical architecture consists of four levels: a vehicle level, a control level, a rule-based level and a knowledge-based level. A special focus is on forms of internal representation, which have to be chosen adequately for each level. The control scheme is applied to VaMP, a Mercedes passenger car which autonomously performs missions on German freeways. VaMP perceives the environment with its sense of vision and conventional sensors. It controls its actuators for locomotion and attention focusing. Modules for perception, cognition and action are discussed.

  11. Autonomous control of distributed storages in microgrids

    DEFF Research Database (Denmark)

    Loh, Poh Chiang; Blaabjerg, Frede

    2011-01-01

    Operation of distributed generators in microgrids has widely been discussed, but would not be fully autonomous, if distributed storages are not considered. Storages in general are important, since they provide energy buffering to load changes, energy leveling to source variations and ride......-through enhancement to the overall microgrids. Recognizing their importance, this paper presents a scheme for sharing power among multiple distributed storages, in coordination with the distributed sources and loads. The scheme prompts the storages to autonomously sense for system conditions, requesting for maximum...

  12. Autonomous operation of distributed storages in microgrids

    DEFF Research Database (Denmark)

    Loh, Poh Chiang; Chai, Yi Kai; Li, Ding

    2014-01-01

    Operation of distributed generators in microgrids has been widely discussed, but would not be fully autonomous if distributed energy storages are not considered. Storages are important since they provide energy buffering to load changes, energy levelling to source variations and ride......-through enhancement to the microgrids. Recognising their importance, this study presents a scheme for sharing power among multiple distributed storages in coordination with the distributed sources and loads. The scheme prompts the storages to autonomously sense for local operating conditions, requesting for maximum...

  13. Applying Energy Autonomous Robots for Dike Inspection

    OpenAIRE

    Dresscher, Douwe; de Vries, Theodorus J.A.; Stramigioli, Stefano

    2015-01-01

    This article presents an exploratory study of an energy-autonomous robot that can be deployed on the Dutch dykes. Based on theory in energy harvesting from sun and wind and the energy-cost of locomotion an analytic expression to determine the feasible daily operational time of such a vehicle is composed. The parameters in this expression are identified using lab results and weather statistics. After an evaluation of the “Energy autonomous robot in the Netherlands‿ case, the results are genera...

  14. On-orbit Autonomous Assembly from Nanosatellites (OAAN)

    Data.gov (United States)

    National Aeronautics and Space Administration — On-orbit Autonomous Assembly from Nanosatellites (OAAN) demonstrates the technology to autonomously dock two or more nanosatellites to form an integrated satellite...

  15. Navigation of autonomous underwater vehicle using extended kalman filter

    Digital Repository Service at National Institute of Oceanography (India)

    Ranjan, T.N.; Nherakkol, A.; Navelkar, G.S.

    To navigate the Autonomous Underwater Vehicle (AUV) accurately is one of the most important aspects in its application. A truly autonomous vehicle must determine its position which requires the optimal integration of all available attitude...

  16. Autonomous Vehicle Survey of Bicyclists and Pedestrians in Pittsburgh, 2017

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — In Pittsburgh, Autonomous Vehicle (AV) companies have been testing autonomous vehicles since September 2016. However, the tech is new, and there have been some...

  17. CSIR eNews: Mobile Intelligent Autonomous Systems

    CSIR Research Space (South Africa)

    CSIR

    2008-03-01

    Full Text Available The CSIR plans to address the challenges associated with intelligent mobile autonomous mapping of dynamic and unstructured environments through focused scientific research in the domains of intelligent autonomous localisation and dynamic scene...

  18. GPM GROUND VALIDATION AUTONOMOUS PARSIVEL UNIT (APU) NSSTC V1

    Data.gov (United States)

    National Aeronautics and Space Administration — The GPM Ground Validation Autonomous Parsivel Unit (APU) NSSTC dataset was collected by the Autonomous Parsivel Unit (APU), which is an optical disdrometer based on...

  19. GPM GROUND VALIDATION AUTONOMOUS PARSIVEL UNIT (APU) GCPEX V1

    Data.gov (United States)

    National Aeronautics and Space Administration — The GPM Ground Validation Autonomous Parsivel Unit (APU) GCPEx dataset was collected by the Autonomous Parsivel Unit (APU), which is an optical disdrometer that...

  20. GPM GROUND VALIDATION AUTONOMOUS PARSIVEL UNIT (APU) HYMEX V1

    Data.gov (United States)

    National Aeronautics and Space Administration — The GPM Ground Validation Autonomous Parsivel Unit (APU) HyMeX dataset was collected by the Autonomous Parsivel Unit (APU), which is an optical disdrometer that...

  1. Conference proceedings of the Northeast Autonomous Vehicle Summit.

    Science.gov (United States)

    2017-05-24

    The development of autonomous vehicle technology and potential adoption of autonomous vehicles is occurring at a rapid rate in the United States. As this technology evolves, there are many technical, logistical and legal issues that need to be addres...

  2. An autonomous control framework for advanced reactors

    Directory of Open Access Journals (Sweden)

    Richard T. Wood

    2017-08-01

    Full Text Available Several Generation IV nuclear reactor concepts have goals for optimizing investment recovery through phased introduction of multiple units on a common site with shared facilities and/or reconfigurable energy conversion systems. Additionally, small modular reactors are suitable for remote deployment to support highly localized microgrids in isolated, underdeveloped regions. The long-term economic viability of these advanced reactor plants depends on significant reductions in plant operations and maintenance costs. To accomplish these goals, intelligent control and diagnostic capabilities are needed to provide nearly autonomous operations with anticipatory maintenance. A nearly autonomous control system should enable automatic operation of a nuclear power plant while adapting to equipment faults and other upsets. It needs to have many intelligent capabilities, such as diagnosis, simulation, analysis, planning, reconfigurability, self-validation, and decision. These capabilities have been the subject of research for many years, but an autonomous control system for nuclear power generation remains as-yet an unrealized goal. This article describes a functional framework for intelligent, autonomous control that can facilitate the integration of control, diagnostic, and decision-making capabilities to satisfy the operational and performance goals of power plants based on multimodular advanced reactors.

  3. An autonomous control framework for advanced reactors

    Energy Technology Data Exchange (ETDEWEB)

    Wood, Richard T.; Upadhyaya, Belle R.; Floyd, Dan C. [Dept. of Nuclear Engineering, University of Tennessee, Knoxville (United States)

    2017-08-15

    Several Generation IV nuclear reactor concepts have goals for optimizing investment recovery through phased introduction of multiple units on a common site with shared facilities and/or reconfigurable energy conversion systems. Additionally, small modular reactors are suitable for remote deployment to support highly localized microgrids in isolated, underdeveloped regions. The long-term economic viability of these advanced reactor plants depends on significant reductions in plant operations and maintenance costs. To accomplish these goals, intelligent control and diagnostic capabilities are needed to provide nearly autonomous operations with anticipatory maintenance. A nearly autonomous control system should enable automatic operation of a nuclear power plant while adapting to equipment faults and other upsets. It needs to have many intelligent capabilities, such as diagnosis, simulation, analysis, planning, reconfigurability, self-validation, and decision. These capabilities have been the subject of research for many years, but an autonomous control system for nuclear power generation remains as-yet an unrealized goal. This article describes a functional framework for intelligent, autonomous control that can facilitate the integration of control, diagnostic, and decision-making capabilities to satisfy the operational and performance goals of power plants based on multimodular advanced reactors.

  4. Control algorithms for autonomous robot navigation

    International Nuclear Information System (INIS)

    Jorgensen, C.C.

    1985-01-01

    This paper examines control algorithm requirements for autonomous robot navigation outside laboratory environments. Three aspects of navigation are considered: navigation control in explored terrain, environment interactions with robot sensors, and navigation control in unanticipated situations. Major navigation methods are presented and relevance of traditional human learning theory is discussed. A new navigation technique linking graph theory and incidental learning is introduced

  5. Sleep restriction progress to cardiac autonomic imbalance ...

    African Journals Online (AJOL)

    Since it's more difficult to maintain adequate sleep duration among night watchmen during their working schedule, hence the purpose of our present study was to investigate whether mental stress or fatigue over restricted sleep period in night shift, affects HRV, in order to elucidate on cardiac autonomic modulation among ...

  6. Distributed formation control for autonomous robots

    NARCIS (Netherlands)

    Garcia de Marina Peinado, Hector Jesús

    2016-01-01

    This thesis addresses several theoretical and practical problems related to formation-control of autonomous robots. Formation-control aims to simultaneously accomplish the tasks of forming a desired shape by the robots and controlling their coordinated collective motion. This kind of robot

  7. The CASCADAS Framework for Autonomic Communications

    Science.gov (United States)

    Baresi, Luciano; Ferdinando, Antonio Di; Manzalini, Antonio; Zambonelli, Franco

    An interesting approach to the design and development of the future Internet foresees a networked service eco-system capable of seamlessly offering services for human-to-human, human-to-machine and machine-to-machine interactions. This chapter builds in this direction by describing a distributed component-ware framework for autonomic and situation-aware communication developed within the CASCADAS project. The core of this framework is the Autonomic Communication Element (ACE), an innovative software abstraction capable of providing dynamically adaptable services that can be built, composed, and let evolve according to autonomic principles. Services are capable of adapting their logic to the dynamically changing context they operate in without human intervention. As a result, whenever the need arises, ACEs can be federated autonomously and produce new services on a situation-aware basis. Systems and, in particular, eco-systems can thus be conceived as collections of ACEs. The chapter introduces the concept of ACE and its different facets. It also presents the architecture of a prototype ACE-based platform and exemplifies the different concepts through a future Pervasive Behavioral Advertisement scenario.

  8. Autonomous Control, Climate and Environmental Changes Effects ...

    African Journals Online (AJOL)

    Autonomous Control, Climate and Environmental Changes Effects on Trypanosomiasis in Sub-Saharan Africa: A Review. ... African trypanosomiasis is a parasitic disease that causes serious economic losses in livestock due to anemia, loss of condition and emaciation. The disease when neglected is lethal and untreated ...

  9. Autonomous Renewable Energy Systems | Van Voorden | Nigerian ...

    African Journals Online (AJOL)

    The problems of having many renewable sources such as wind and solar generating units in a power system are uncontrollable fluctuations in power generation and the difficulty in forecasting the power generation capability of these sources due to their stochastic nature. Therefore, autonomous electricity systems with a ...

  10. Autonomous biomorphic robots as platforms for sensors

    International Nuclear Information System (INIS)

    Tilden, M.; Hasslacher, B.; Mainieri, R.; Moses, J.

    1996-01-01

    The idea of building autonomous robots that can carry out complex and nonrepetitive tasks is an old one, so far unrealized in any meaningful hardware. Tilden has shown recently that there are simple, processor-free solutions to building autonomous mobile machines that continuously adapt to unknown and hostile environments, are designed primarily to survive, and are extremely resistant to damage. These devices use smart mechanics and simple (low component count) electronic neuron control structures having the functionality of biological organisms from simple invertebrates to sophisticated members of the insect and crab family. These devices are paradigms for the development of autonomous machines that can carry out directed goals. The machine then becomes a robust survivalist platform that can carry sensors or instruments. These autonomous roving machines, now in an early stage of development (several proof-of-concept prototype walkers have been built), can be developed so that they are inexpensive, robust, and versatile carriers for a variety of instrument packages. Applications are immediate and many, in areas as diverse as prosthetics, medicine, space, construction, nanoscience, defense, remote sensing, environmental cleanup, and biotechnology

  11. A universal projective synchronization of general autonomous ...

    Indian Academy of Sciences (India)

    This paper investigates the generalized projective synchronization in general autonomous chaotic system. A universal controller is designed and the effectiveness is verified via theoretical analysis and numerical simulations. The controller design is irrelevant to concrete system structure and initial values. It has strong ...

  12. A network of (autonomic) clock outputs

    NARCIS (Netherlands)

    Kalsbeek, A.; Perreau-Lenz, S.; Buijs, R. M.

    2006-01-01

    The circadian clock in the suprachiasmatic nuclei (SCN) is composed of thousands of oscillator neurons, each of which is dependent on the cell-autonomous action of a defined set of circadian clock genes. A major question is still how these individual oscillators are organized into a biological clock

  13. A network of (autonomic) clock outputs

    NARCIS (Netherlands)

    Kalsbeek, A.; Perreau-Lenz, S.; Buijs, R. M.

    2006-01-01

    The circadian clock in the suprachiasmatic nuclei (SCN) is composed of thousands of oscillator neurons, each dependent on the cell-autonomous action of a defined set of circadian clock genes. A major question is still how these individual oscillators are organized into a biological clock that

  14. Autonomic changes in fibromyalgia: Clinical and ...

    African Journals Online (AJOL)

    Background: Autonomic nervous system (ANS) dysfunction is one of the suggested pathophysiological mechanisms of fibromyalgia (FM). Its dysfunction may contribute to enhanced pain and other clinical problems associated with FM. Previous studies showed conflicting results regarding ANS function in FM. Some studies ...

  15. Information Engineering in Autonomous Robot Software

    NARCIS (Netherlands)

    Ziafati, P.

    2015-01-01

    In order to engage and help in our daily life, autonomous robots are to operate in dynamic and unstructured environments and interact with people. As the robot's environment and its behaviour are getting more complex, so are the robot's software and the knowledge that the robot needs to carry out

  16. Autonomous biomorphic robots as platforms for sensors

    Energy Technology Data Exchange (ETDEWEB)

    Tilden, M.; Hasslacher, B.; Mainieri, R.; Moses, J.

    1996-10-01

    The idea of building autonomous robots that can carry out complex and nonrepetitive tasks is an old one, so far unrealized in any meaningful hardware. Tilden has shown recently that there are simple, processor-free solutions to building autonomous mobile machines that continuously adapt to unknown and hostile environments, are designed primarily to survive, and are extremely resistant to damage. These devices use smart mechanics and simple (low component count) electronic neuron control structures having the functionality of biological organisms from simple invertebrates to sophisticated members of the insect and crab family. These devices are paradigms for the development of autonomous machines that can carry out directed goals. The machine then becomes a robust survivalist platform that can carry sensors or instruments. These autonomous roving machines, now in an early stage of development (several proof-of-concept prototype walkers have been built), can be developed so that they are inexpensive, robust, and versatile carriers for a variety of instrument packages. Applications are immediate and many, in areas as diverse as prosthetics, medicine, space, construction, nanoscience, defense, remote sensing, environmental cleanup, and biotechnology.

  17. Integrating the autonomous subsystems management process

    Science.gov (United States)

    Ashworth, Barry R.

    1992-01-01

    Ways in which the ranking of the Space Station Module Power Management and Distribution testbed may be achieved and an individual subsystem's internal priorities may be managed within the complete system are examined. The application of these results in the integration and performance leveling of the autonomously managed system is discussed.

  18. A universal projective synchronization of general autonomous ...

    Indian Academy of Sciences (India)

    Fuzhong Nian et al and the validity of our method was verified through theoretical analysis and numerical simulations. 2. Generalized projective synchronization controller design. Consider a general autonomous system: ˙X = AX + B. (1). Here X = [x1, x1,..., xn]T is the state vector of the drive system, B is a n × 1 constant.

  19. Autonomous Robot Navigation In Public Nature Park

    DEFF Research Database (Denmark)

    Andersen, Jens Christian; Andersen, Nils Axel; Ravn, Ole

    2005-01-01

    This extended abstract describes a project to make a robot travel autonomously across a public nature park. The challenge is to detect and follow the right path across junctions and open squares avoiding people and obstacles. The robot is equipped with a laser scanner, a (low accuracy) GPS, wheel...

  20. Control algorithms for autonomous robot navigation

    Energy Technology Data Exchange (ETDEWEB)

    Jorgensen, C.C.

    1985-09-20

    This paper examines control algorithm requirements for autonomous robot navigation outside laboratory environments. Three aspects of navigation are considered: navigation control in explored terrain, environment interactions with robot sensors, and navigation control in unanticipated situations. Major navigation methods are presented and relevance of traditional human learning theory is discussed. A new navigation technique linking graph theory and incidental learning is introduced.

  1. Monitoring aquatic environments with autonomous systems

    DEFF Research Database (Denmark)

    Christensen, Jesper Philip Aagaard

    High frequency measurements from autonomous sensors have become a widely used tool among aquatic scientists. This report focus primarily on the use of ecosystem metabolism based on high frequency oxygen measurements and relates the calculations to spatial variation, biomass of the primary produce...

  2. Autonomic dysfunction in a Jack Russell terrier

    Science.gov (United States)

    Caines, Deanne; Pinard, Chantale L.; Kruth, Stephen; Orr, Jeremy; James, Fiona

    2011-01-01

    A 4-year-old Jack Russell terrier was presented with an array of clinical signs suggestive of autonomic dysfunction. Many of the clinical signs were consistent with a diagnosis of dysautonomia; however, both chronicity and resolution of signs contradicted a diagnosis of this disease. PMID:21629424

  3. Autonomous droop scheme with reduced generation cost

    DEFF Research Database (Denmark)

    Nutkani, Inam Ullah; Loh, Poh Chiang; Blaabjerg, Frede

    2013-01-01

    DGs are usually of different types unlike synchronous generators. This paper presents an autonomous droop scheme that takes into consideration the operating cost, efficiency and emission penalty of each DG since all these factors directly or indirectly contributes to the Total Generation Cost (TGC...

  4. A polling model with an autonomous server

    NARCIS (Netherlands)

    de Haan, Roland; Boucherie, Richardus J.; van Ommeren, Jan C.W.

    2009-01-01

    This paper considers polling systems with an autonomous server that remain at a queue for an exponential amount of time before moving to a next queue incurring a generally distributed switch-over time. The server remains at a queue until the exponential visit time expires, also when the queue

  5. Diabetic cardiovascular autonomic neuropathy: clinical implications.

    Science.gov (United States)

    Karayannis, Georgios; Giamouzis, Gregory; Cokkinos, Dennis V; Skoularigis, John; Triposkiadis, Filippos

    2012-06-01

    Diabetic cardiovascular autonomic neuropathy (DCAN), the impairment of the autonomic balance of the cardiovascular system in the setting of diabetes mellitus (DM), is frequently observed in both Type 1 and 2 DM, has detrimental effects on the quality of life and portends increased mortality. Clinical manifestations include: resting heart rate disorders, exercise intolerance, intraoperative cardiovascular lability, orthostatic alterations in heart rate and blood pressure, QT-interval prolongation, abnormal diurnal and nocturnal blood pressure variation, silent myocardial ischemia and diabetic cardiomyopathy. Clinical tests for autonomic nervous system evaluation, heart rate variability analysis, autonomic innervation imaging techniques, microneurography and baroreflex analysis are the main diagnostic tools for DCAN detection. Aldose reductase inhibitors and antioxidants may be helpful in DCAN therapy, but a regular, more generalized and multifactorial approach should be adopted with inclusion of lifestyle modifications, strict glycemic control and treatment of concomitant traditional cardiovascular risk factors, in order to achieve the best therapeutic results. In the present review, the authors provide aspects of DCAN pathophysiology, clinical presentation, diagnosis and an algorithm regarding the evaluation and management of DCAN in DM patients.

  6. Applying Energy Autonomous Robots for Dike Inspection

    NARCIS (Netherlands)

    Dresscher, Douwe; de Vries, Theodorus J.A.; Stramigioli, Stefano

    2015-01-01

    This article presents an exploratory study of an energy-autonomous robot that can be deployed on the Dutch dykes. Based on theory in energy harvesting from sun and wind and the energy-cost of locomotion an analytic expression to determine the feasible daily operational time of such a vehicle is

  7. Autonomic changes in fibromyalgia: Clinical and ...

    African Journals Online (AJOL)

    Noha El-Sawy

    2012-03-14

    Mar 14, 2012 ... Fibromyalgia;. Tilt table test;. Standing and supine blood pressure and heart rate;. Sympathetic skin response. Abstract Background: Autonomic nervous ... Depression(HRSD) and 4 – functional status by Fibromyalgia impact questionnaire (FIQ). ..... may affect the sleep pattern and psychological state of the.

  8. Requirement analysis for autonomous systems and intelligent ...

    African Journals Online (AJOL)

    user

    This control architecture is based upon the requirements identified in the first part. We also present development of a software framework to test such flexible control architectures. Keywords: Electric power system, distributed control, autonomous systems, intelligent agents. 1. Introduction. Electric power systems is one of the ...

  9. A Multifunctional Coating for Autonomous Corrosion Control

    Science.gov (United States)

    Calle, Luz M.; Li, Wenyan; Buhrow, Jerry W.; Jolley, Scott t.

    2011-01-01

    Nearly all metals and their alloys are subject to corrosion that causes them to lose their structural integrity or other critical functionality. Protective coatings are the most commonly used method of corrosion control. However, progressively stricter environmental regulations have resulted in the ban of many commercially available corrosion protective coatings due to the harmful effects of their solvents or corrosion inhibitors. This work concerns the development of a multifunctional smart coating for the autonomous control of corrosion. This coating is being developed to have the inherent ability to detect the chemical changes associated with the onset of corrosion and respond autonomously to indicate it and control it. The multi-functionality of the coating is based on microencapsulation technology specifically designed for corrosion control applications. This design has, in addition to all the advantages of existing microcapsulation designs, the corrosion controlled release function that triggers the delivery of corrosion indicators and inhibitors on demand, only when and where needed. Microencapsulation of self-healing agents for autonomous repair of mechanical damage to the coating is also being pursued. Corrosion indicators, corrosion inhibitors, as well as self-healing agents, have been encapsulated and dispersed into several paint systems to test the corrosion detection, inhibition, and self-healing properties of the coating. Key words: Corrosion, coating, autonomous corrosion control, corrosion indication, corrosion inhibition, self-healing coating, smart coating, multifunctional coating, microencapsulation.

  10. A universal projective synchronization of general autonomous ...

    Indian Academy of Sciences (India)

    2015-11-27

    Home; Journals; Pramana – Journal of Physics; Volume 79; Issue 6. A universal projective synchronization of general autonomous chaotic system ... Proceedings of the International Workshop/Conference on Computational Condensed Matter Physics and Materials Science (IWCCMP-2015). Posted on November 27, 2015.

  11. Initial sensorimotor and delayed autonomic neuropathy in acute thallium poisoning.

    Science.gov (United States)

    Nordentoft, T; Andersen, E B; Mogensen, P H

    1998-06-01

    In a 27-year old male with acute thallium poisoning, signs of initially severe sensorimotor neuropathy with complete remission after two weeks were demonstrated. Signs of cardiovascular autonomic neuropathy were initially absent, but developed after a latency period of one week with marked improvement after seven months. Delayed autonomic neuropathy may be caused by a late affection of small unmyelinated autonomic nerve fibers.

  12. Nursing leadership and autonomous professional practice of registered nurses.

    Science.gov (United States)

    Ferguson-Paré, M

    1998-01-01

    Autonomous professional practice continues to be elusive for registered nurses. Autonomous professional practice implies that nurses would be free to determine the procedures for carrying out their nursing work. In other works, they would be able to make independent decisions about their own nursing practice. This article reports research that describes the nature of nursing leadership that supports autonomous professional practice of registered nurses.

  13. Simulation of Aircraft Sortie Generation Under an Autonomic Logistics System

    Science.gov (United States)

    2016-12-01

    kind of on-board artificial autonomic nervous system which is vital for AL operations. Through the use of intelligent reasoners, PHM detects, isolates...SIMULATION OF AIRCRAFT SORTIE GENERATION UNDER AN AUTONOMIC LOGISTICS SYSTEM THESIS Gunduz...Government. AFIT-ENS-MS-16-D-052 SIMULATION OF AIRCRAFT SORTIE GENERATION UNDER AN AUTONOMIC LOGISTICS SYSTEM THESIS Presented to

  14. Advanced Autonomous Systems for Space Operations

    Science.gov (United States)

    Gross, A. R.; Smith, B. D.; Muscettola, N.; Barrett, A.; Mjolssness, E.; Clancy, D. J.

    2002-01-01

    New missions of exploration and space operations will require unprecedented levels of autonomy to successfully accomplish their objectives. Inherently high levels of complexity, cost, and communication distances will preclude the degree of human involvement common to current and previous space flight missions. With exponentially increasing capabilities of computer hardware and software, including networks and communication systems, a new balance of work is being developed between humans and machines. This new balance holds the promise of not only meeting the greatly increased space exploration requirements, but simultaneously dramatically reducing the design, development, test, and operating costs. New information technologies, which take advantage of knowledge-based software, model-based reasoning, and high performance computer systems, will enable the development of a new generation of design and development tools, schedulers, and vehicle and system health management capabilities. Such tools will provide a degree of machine intelligence and associated autonomy that has previously been unavailable. These capabilities are critical to the future of advanced space operations, since the science and operational requirements specified by such missions, as well as the budgetary constraints will limit the current practice of monitoring and controlling missions by a standing army of ground-based controllers. System autonomy capabilities have made great strides in recent years, for both ground and space flight applications. Autonomous systems have flown on advanced spacecraft, providing new levels of spacecraft capability and mission safety. Such on-board systems operate by utilizing model-based reasoning that provides the capability to work from high-level mission goals, while deriving the detailed system commands internally, rather than having to have such commands transmitted from Earth. This enables missions of such complexity and communication` distances as are not

  15. Exercise and the autonomic nervous system.

    Science.gov (United States)

    Fu, Qi; Levine, Benjamin D

    2013-01-01

    The autonomic nervous system plays a crucial role in the cardiovascular response to acute (dynamic) exercise in animals and humans. During exercise, oxygen uptake is a function of the triple-product of heart rate and stroke volume (i.e., cardiac output) and arterial-mixed venous oxygen difference (the Fick principle). The degree to which each of the variables can increase determines maximal oxygen uptake (V˙O2max). Both "central command" and "the exercise pressor reflex" are important in determining the cardiovascular response and the resetting of the arterial baroreflex during exercise to precisely match systemic oxygen delivery with metabolic demand. In general, patients with autonomic disorders have low levels of V˙O2max, indicating reduced physical fitness and exercise capacity. Moreover, the vast majority of the patients have blunted or abnormal cardiovascular response to exercise, especially during maximal exercise. There is now convincing evidence that some of the protective and therapeutic effects of chronic exercise training are related to the impact on the autonomic nervous system. Additionally, training induced improvement in vascular function, blood volume expansion, cardiac remodeling, insulin resistance and renal-adrenal function may also contribute to the protection and treatment of cardiovascular, metabolic and autonomic disorders. Exercise training also improves mental health, helps to prevent depression, and promotes or maintains positive self-esteem. Moderate-intensity exercise at least 30 minutes per day and at least 5 days per week is recommended for the vast majority of people. Supervised exercise training is preferable to maximize function capacity, and may be particularly important for patients with autonomic disorders. © 2013 Elsevier B.V. All rights reserved.

  16. Research of autonomous landing control of unmanned combat air vehicle

    Science.gov (United States)

    Li, Shaoyan; Chen, Zongji

    2003-09-01

    This paper is to present a robust controller design method for developing autonomous landing systems of Unmanned Combat Air Vehicle (UCAV). We first analyze the characteristic of autonomous landing of UCAV, and put forward its landing performance specifications. Structure singular value μ| synthesis is used to develop autonomous landing systems to accurately follow the pre-designed ideal landing track or online generated optimal landing track. The robust performance of system is analyzed. The simulation results demonstrate that the designed autonomous landing system satisfies the performance requirements of autonomous landing of UCAV when there are uncertainties of UCAV aircraft model, measurement noises and exogenous disturbances.

  17. Apoptosis and Self-Destruct: A Contribution to Autonomic Agents?

    Science.gov (United States)

    Sterritt, Roy; Hinchey, Mike

    2004-01-01

    Autonomic Computing (AC), a self-managing systems initiative based on the biological metaphor of the autonomic nervous system, is increasingly gaining momentum as the way forward in designing reliable systems. Agent technologies have been identified as a key enabler for engineering autonomicity in systems, both in terms of retrofitting autonomicity into legacy systems and designing new systems. The AC initiative provides an opportunity to consider other biological systems and principles in seeking new design strategies. This paper reports on one such investigation; utilizing the apoptosis metaphor of biological systems to provide a dynamic health indicator signal between autonomic agents.

  18. Autonomous Orbit Navigator Development, Using GPS, Applied to Autonomous Orbit Control

    Science.gov (United States)

    Galski, Roberto Luiz

    2002-01-01

    The appearance of modem global positioning systems motivated the study and development of precise and robust systems for autonomous orbit determination of artificial satellites. These systems maintain, independently from human intervention from the ground, a precise knowledge of the satellite orbital state, through the processing of the information, autonomously generated on-board, by a receiver of the positioning system used. One of the major motivations for the research and development of autonomous navigators, is the availability of real time information about the position and velocity of the satellite, required, for instance, in earth observation missions, for interpretation and analysis of the generated images. The appearance of global positioning systems and the consequent development of autonomous navigators, by making available onboard space vehicles, updated orbit estimations, with good accuracy level, made feasible the research and development of orbit autonomous control procedures. It allowed the orbital maneuvers execution process to be performed in a way totally independent from ground human intervention. Whereas the satellite attitude control reached a high level of autonomy, due to the fact that the attitude measurements are, in general, naturally generated on-board the spacecraft, the orbit control is still now almost totally planned and executed from ground commanded actions. The proposed work consists of the study, development, simulation and analysis of a simplified navigator coupled to an autonomous orbit control system, applied to the China-Brazil Earth Resources Satellites (CBERS). At first, an autonomous orbit determination procedure is developed and analyzed. Its objective is to improve the coarse geometric solution provided by Global Positioning System (GPS) receivers. This will be done by directly using this solution as input (observation) for a real time Kalman filtering process. The orbital state vector will be extended in order to

  19. Chromosome 12p deletions in TEL-AML1 childhood acute lymphoblastic leukemia are associated with retrotransposon elements and occur postnatally.

    Science.gov (United States)

    Wiemels, Joseph L; Hofmann, Jerry; Kang, Michelle; Selzer, Rebecca; Green, Roland; Zhou, Mi; Zhong, Sheng; Zhang, Luoping; Smith, Martyn T; Marsit, Carmen; Loh, Mignon; Buffler, Patricia; Yeh, Ru-Fang

    2008-12-01

    TEL-AML1 (ETV6-RUNX1) is the most common translocation in the childhood leukemias, and is a prenatal mutation in most children. This translocation has been detected at a high rate among newborns ( approximately 1%); therefore, the rate-limiting event for leukemia seems to be secondary mutations. One such frequent mutation in this subtype is partial deletion of chromosome 12p, trans from the translocation. Nine del(12p) breakpoints within six leukemia cases were sequenced to explore the etiology of this genetic event, and most involved cryptic sterile translocations. Twelve of 18 del(12p) parent sequences involved in these breakpoints were located in repeat regions (8 of these in long interspersed nuclear elements). This stands in contrast with TEL-AML1, in which only 21 of 110 previously assessed breakpoints (19%) occur in DNA repeats (P=0.0001). An exploratory assessment of archived neonatal blood cards revealed significantly more long interspersed nuclear element CpG methylations in individuals at birth who were later diagnosed with TEL-AML1 leukemia, compared with individuals who did not contract leukemia (P=0.01). Nontemplate nucleotides were also more frequent in del(12p) than in TEL-AML1 junctions (P=0.004), suggesting formation by terminal deoxynucleotidyl transferase. Assessment of six archived neonatal blood cards indicated that no del(12p) rearrangements backtracked to birth, although two of these patients were previously positive for TEL-AML1 using the same assay with comparable sensitivity. These data are compatible with a two-stage natural history: TEL-AML1 occurs prenatally, and del(12p) occurs postnatally in more mature cells with a structure that suggests the involvement of retrotransposon instability.

  20. Establishment of a genome-wide and quantitative protocol for assessment of transcriptional activity at human retrotransposon L1 antisense promoters.

    Science.gov (United States)

    Ishiguro, Koichi; Higashino, Saneyuki; Hirakawa, Hideki; Sato, Shusei; Aizawa, Yasunori

    2017-04-03

    Long interspersed element 1 (L1) retrotransposon sequences are widespread in the human genome, occupying ~500,000 locations. The majority of L1s have lost their retrotransposition capability, although a significant population of human L1s maintains bidirectional transcriptional activity from the internal promoter. While the sense promoter drives transcription of the entire L1 mRNA and leads to L1 retrotransposition, the antisense promoter (ASP) transcribes L1-gene chimeric RNAs that include neighboring exon sequences. Activation mechanisms and functional impacts of L1ASP transcription are thought to vary at every L1ASP location. To explore the locus-specific regulation and function of L1ASP transcription, quantitative methodology is necessary for identifying the genomic positions of highly active L1ASPs on a genome-wide scale. Here, we employed deep-sequencing techniques and built a 3' RACE-based experimental and bioinformatics protocol, named the L1 antisense transcriptome protocol (LATRAP). In LATRAP, the PCR primer and the read mapping scheme were designed to reduce false positives and negatives, which may have been included as hits in previous cloning studies. LATRAP was here applied to the A549 human lung cancer cell line, and 313 L1ASP loci were detected to have transcriptional activity but differed in the number of mapped reads by four orders of magnitude. This indicates that transcriptional activities of the individual L1ASPs can vary greatly and that only a small population of L1ASP loci is active within a single nucleus. LATRAP is the first experimental method for ranking L1ASPs according to their transcriptional activity and will thus open a new avenue to unveiling the locus-specific biology of L1ASPs.

  1. SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints

    Science.gov (United States)

    2014-01-01

    Background Genomic disorders are caused by copy number changes that may exhibit recurrent breakpoints processed by nonallelic homologous recombination. However, region-specific disease-associated copy number changes have also been observed which exhibit non-recurrent breakpoints. The mechanisms underlying these non-recurrent copy number changes have not yet been fully elucidated. Results We analyze large NF1 deletions with non-recurrent breakpoints as a model to investigate the full spectrum of causative mechanisms, and observe that they are mediated by various DNA double strand break repair mechanisms, as well as aberrant replication. Further, two of the 17 NF1 deletions with non-recurrent breakpoints, identified in unrelated patients, occur in association with the concomitant insertion of SINE/variable number of tandem repeats/Alu (SVA) retrotransposons at the deletion breakpoints. The respective breakpoints are refractory to analysis by standard breakpoint-spanning PCRs and are only identified by means of optimized PCR protocols designed to amplify across GC-rich sequences. The SVA elements are integrated within SUZ12P intron 8 in both patients, and were mediated by target-primed reverse transcription of SVA mRNA intermediates derived from retrotranspositionally active source elements. Both SVA insertions occurred during early postzygotic development and are uniquely associated with large deletions of 1 Mb and 867 kb, respectively, at the insertion sites. Conclusions Since active SVA elements are abundant in the human genome and the retrotranspositional activity of many SVA source elements is high, SVA insertion-associated large genomic deletions encompassing many hundreds of kilobases could constitute a novel and as yet under-appreciated mechanism underlying large-scale copy number changes in the human genome. PMID:24958239

  2. Internal validation of two new retrotransposons-based kits (InnoQuant® HY and InnoTyper® 21) at a forensic lab.

    Science.gov (United States)

    Martins, Cátia; Ferreira, Paulo Miguel; Carvalho, Raquel; Costa, Sandra Cristina; Farinha, Carlos; Azevedo, Luísa; Amorim, António; Oliveira, Manuela

    2018-02-01

    Obtaining a genetic profile from pieces of evidence collected at a crime scene is the primary objective of forensic laboratories. New procedures, methods, kits, software or equipment must be carefully evaluated and validated before its implementation. The constant development of new methodologies for DNA testing leads to a steady process of validation, which consists of demonstrating that the technology is robust, reproducible, and reliable throughout a defined range of conditions. The present work aims to internally validate two new retrotransposon-based kits (InnoQuant ® HY and InnoTyper ® 21), under the working conditions of the Laboratório de Polícia Científica da Polícia Judiciária (LPC-PJ). For the internal validation of InnoQuant ® HY and InnoTyper ® 21 sensitivity, repeatability, reproducibility, and mixture tests and a concordance study between these new kits and those currently in use at LPC-PJ (Quantifiler ® Duo and GlobalFiler™) were performed. The results obtained for sensitivity, repeatability, and reproducibility tests demonstrated that both InnoQuant ® HY and InnoTyper ® 21 are robust, reproducible, and reliable. The results of the concordance studies demonstrate that InnoQuant ® HY produced quantification results in nearly 29% more than Quantifiler ® Duo (indicating that this new kit is more effective in challenging samples), while the differences observed between InnoTyper ® 21 and GlobalFiler™ are not significant. Therefore, the utility of InnoTyper ® 21 has been proven, especially by the successful amplification of a greater number of complete genetic profiles (27 vs. 21). The results herein presented allowed the internal validation of both InnoQuant ® HY and InnoTyper ® 21, and their implementation in the LPC-PJ laboratory routine for the treatment of challenging samples. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Characterization of the restriction enzyme-like endonuclease encoded by the Entamoeba histolytica non-long terminal repeat retrotransposon EhLINE1.

    Science.gov (United States)

    Yadav, Vijay Pal; Mandal, Prabhat Kumar; Rao, Desirazu N; Bhattacharya, Sudha

    2009-12-01

    The genome of the human pathogen Entamoeba histolytica, a primitive protist, contains non-long terminal repeat retrotransposable elements called EhLINEs. These encode reverse transcriptase and endonuclease required for retrotransposition. The endonuclease shows sequence similarity with bacterial restriction endonucleases. Here we report the salient enzymatic features of one such endonuclease. The kinetics of an EhLINE1-encoded endonuclease catalyzed reaction, determined under steady-state and single-turnover conditions, revealed a significant burst phase followed by a slower steady-state phase, indicating that release of product could be the slower step in this reaction. For circular supercoiled DNA the K(m) was 2.6 x 10(-8) M and the k(cat) was 1.6 x 10(-2) sec(-1). For linear E. histolytica DNA substrate the K(m) and k(cat) values were 1.3 x 10(-8) M and 2.2 x 10(-4) sec(-1) respectively. Single-turnover reaction kinetics suggested a noncooperative mode of hydrolysis. The enzyme behaved as a monomer. While Mg(2+) was required for activity, 60% activity was seen with Mn(2+) and none with other divalent metal ions. Substitution of PDX(12-14)D (a metal-binding motif) with PAX(12-14)D caused local conformational change in the protein tertiary structure, which could contribute to reduced enzyme activity in the mutated protein. The protein underwent conformational change upon the addition of DNA, which is consistent with the known behavior of restriction endonucleases. The similarities with bacterial restriction endonucleases suggest that the EhLINE1-encoded endonuclease was possibly acquired from bacteria through horizontal gene transfer. The loss of strict sequence specificity for nicking may have been subsequently selected to facilitate spread of the retrotransposon to intergenic regions of the E. histolytica genome.

  4. A Review of Cardiovascular Autonomic Control in Cluster Headache

    DEFF Research Database (Denmark)

    Barloese, Mads C J

    2016-01-01

    of the pathophysiological mechanisms behind cluster headache. Cranial autonomic features are an inherent and diagnostic feature; however, a number of studies and clinical observations support the involvement of systemic autonomic control in its pathophysiology. Further, cluster headache attacks are apparently more easily......," "autonomic nervous system," and "cardiac." References of identified articles were also searched for relevant articles. Studies were included if they contained data on cardiovascular or autonomic responses to autonomic tests, induced or spontaneous attacks. RESULTS: In total, 22 studies investigating cardiac...... autonomic control in cluster headache were identified. Three overall categories of investigations exist: (1) Those studying changes in heart rate, blood pressure, and electrocardiographic changes; (2) those employing various clinical autonomic tests; and finally (3) those using spectral and nonlinear...

  5. Longitudinal Control for Mengshi Autonomous Vehicle via Gauss Cloud Model

    Directory of Open Access Journals (Sweden)

    Hongbo Gao

    2017-12-01

    Full Text Available Dynamic robustness and stability control is a requirement for self-driving of autonomous vehicle. Longitudinal control technique of autonomous vehicle is basic theory and one key complex technique which must have the reliability and precision of vehicle controller. The longitudinal control technique is one of the foundations of the safety and stability of autonomous vehicle control. In our paper, we present a longitudinal control algorithm based on cloud model for Mengshi autonomous vehicle to ensure the dynamic stability and tracking performance of Mengshi autonomous vehicle. The longitudinal control algorithm mainly uses cloud model generator to control the acceleration of the autonomous vehicle to achieve the goal that controls the speed of Mengshi autonomous vehicle. The proposed longitudinal control algorithm based on cloud model is verified by real experiments on Highway driving scene. The experiments results of the acceleration and speed show that the algorithm is validity and stability.

  6. Autonomic dysfunction in different subtypes of multiple system atrophy.

    Science.gov (United States)

    Schmidt, Claudia; Herting, Birgit; Prieur, Silke; Junghanns, Susann; Schweitzer, Katherine; Globas, Christoph; Schöls, Ludger; Reichmann, Heinz; Berg, Daniela; Ziemssen, Tjalf

    2008-09-15

    Multiple system atrophy (MSA) can clinically be divided into the cerebellar (MSA-C) and the parkinsonian (MSA-P) variant. However, till now, it is unknown whether autonomic dysfunction in these two entities differs regarding severity and profile. We compared the pattern of autonomic dysfunction in 12 patients with MSA-C and 26 with MSA-P in comparison with 27 age- and sex-matched healthy controls using a standard battery of autonomic function tests and a structured anamnesis of the autonomic nervous system. MSA-P patients complained significantly more often about the symptoms of autonomic dysfunctions than MSA-C patients, especially regarding vasomotor, secretomotor, and gastrointestinal subsystems. However, regarding cardiovascular, sudomotor pupil, urogenital, and sleep subsystems, there were no significant quantitative or qualitative differences as analyzed by autonomic anamnesis and testing. Our results suggest that there are only minor differences in the pattern of autonomic dysfunction between the two clinical MSA phenotypes. (c) 2007 Movement Disorder Society.

  7. Forced synchronization of autonomous dynamical Boolean networks

    International Nuclear Information System (INIS)

    Rivera-Durón, R. R.; Campos-Cantón, E.; Campos-Cantón, I.; Gauthier, Daniel J.

    2015-01-01

    We present the design of an autonomous time-delay Boolean network realized with readily available electronic components. Through simulations and experiments that account for the detailed nonlinear response of each circuit element, we demonstrate that a network with five Boolean nodes displays complex behavior. Furthermore, we show that the dynamics of two identical networks display near-instantaneous synchronization to a periodic state when forced by a common periodic Boolean signal. A theoretical analysis of the network reveals the conditions under which complex behavior is expected in an individual network and the occurrence of synchronization in the forced networks. This research will enable future experiments on autonomous time-delay networks using readily available electronic components with dynamics on a slow enough time-scale so that inexpensive data collection systems can faithfully record the dynamics

  8. Grid administration: towards an autonomic approach

    CERN Document Server

    Ubeda Garcia, M; Tsaregorodtsev, A; Charpentier, P; Bernardof, V

    2012-01-01

    Within the DIRAC framework in the LHCb collaboration, we deployed an autonomous policy system acting as a central status information point for grid elements. Experts working as grid administrators have a broad and very deep knowledge about the underlying system which makes them very precious. We have attempted to formalize this knowledge in an autonomous system able to aggregate information, draw conclusions, validate them, and take actions accordingly. The DIRAC Resource Status System (RSS) is a monitoring and generic policy system that enforces managerial and operational actions automatically. As an example, the status of a grid entity can be evaluated using a number of policies, each making assessments relative to specific monitoring information. Individual results of these policies can be combined to evaluate and propose a global status for the resource. This evaluation goes through a validation step driven by a state machine and an external validation system. Once validated, actions can be triggered acco...

  9. 13th International Conference Intelligent Autonomous Systems

    CERN Document Server

    Michael, Nathan; Berns, Karsten; Yamaguchi, Hiroaki

    2016-01-01

    This book describes the latest research accomplishments, innovations, and visions in the field of robotics as presented at the 13th International Conference on Intelligent Autonomous Systems (IAS), held in Padua in July 2014, by leading researchers, engineers, and practitioners from across the world. The contents amply confirm that robots, machines, and systems are rapidly achieving intelligence and autonomy, mastering more and more capabilities such as mobility and manipulation, sensing and perception, reasoning, and decision making. A wide range of research results and applications are covered, and particular attention is paid to the emerging role of autonomous robots and intelligent systems in industrial production, which reflects their maturity and robustness. The contributions have been selected through a rigorous peer-review process and contain many exciting and visionary ideas that will further galvanize the research community, spurring novel research directions. The series of biennial IAS conferences ...

  10. Elements of Autonomous Self-Reconfigurable Robots

    DEFF Research Database (Denmark)

    Christensen, David Johan

    In this thesis, we study several central elements of autonomous self-reconfigurable modular robots. Unlike conventional robots such robots are: i) Modular, since robots are assembled from numerous robotic modules. ii) Reconfigurable, since the modules can be combined in a variety of ways. iii) Self......-reconfigurable, since the modules themselves are able to change how they are combined. iv) Autonomous, since robots control themselves without human guidance. Such robots are attractive to study since they in theory have several desirable characteristics, such as versatility, reliability and cheapness. In practice...... robots: design, scalability, self-reconfiguration and adaptation. The first element we consider is the design of systems, modules, robots, and behaviors. We introduce a number of design principles that will guide our designs throughout the thesis. The design principles advocate simple, extendable...

  11. Fuzzy logic in autonomous orbital operations

    Science.gov (United States)

    Lea, Robert N.; Jani, Yashvant

    1991-01-01

    Fuzzy logic can be used advantageously in autonomous orbital operations that require the capability of handling imprecise measurements from sensors. Several applications are underway to investigate fuzzy logic approaches and develop guidance and control algorithms for autonomous orbital operations. Translational as well as rotational control of a spacecraft have been demonstrated using space shuttle simulations. An approach to a camera tracking system has been developed to support proximity operations and traffic management around the Space Station Freedom. Pattern recognition and object identification algorithms currently under development will become part of this camera system at an appropriate level in the future. A concept to control environment and life support systems for large Lunar based crew quarters is also under development. Investigations in the area of reinforcement learning, utilizing neural networks, combined with a fuzzy logic controller, are planned as a joint project with the Ames Research Center.

  12. Mobile Robot Designed with Autonomous Navigation System

    Science.gov (United States)

    An, Feng; Chen, Qiang; Zha, Yanfang; Tao, Wenyin

    2017-10-01

    With the rapid development of robot technology, robots appear more and more in all aspects of life and social production, people also ask more requirements for the robot, one is that robot capable of autonomous navigation, can recognize the road. Take the common household sweeping robot as an example, which could avoid obstacles, clean the ground and automatically find the charging place; Another example is AGV tracking car, which can following the route and reach the destination successfully. This paper introduces a new type of robot navigation scheme: SLAM, which can build the environment map in a totally strange environment, and at the same time, locate its own position, so as to achieve autonomous navigation function.

  13. Wavefront Propagation and Fuzzy Based Autonomous Navigation

    Directory of Open Access Journals (Sweden)

    Adel Al-Jumaily

    2005-06-01

    Full Text Available Path planning and obstacle avoidance are the two major issues in any navigation system. Wavefront propagation algorithm, as a good path planner, can be used to determine an optimal path. Obstacle avoidance can be achieved using possibility theory. Combining these two functions enable a robot to autonomously navigate to its destination. This paper presents the approach and results in implementing an autonomous navigation system for an indoor mobile robot. The system developed is based on a laser sensor used to retrieve data to update a two dimensional world model of therobot environment. Waypoints in the path are incorporated into the obstacle avoidance. Features such as ageing of objects and smooth motion planning are implemented to enhance efficiency and also to cater for dynamic environments.

  14. Promotion of autonomous employment among unemployed youth

    Directory of Open Access Journals (Sweden)

    Olga González Morales

    2004-01-01

    Full Text Available The promotion of the enterprising spirit and the support to the entrepreneurship and to self-employed are lines of performance that the European Commission recommends to the members states to help the young men and unemployed adults to look for a professional exit in the field of the autonomous employment. This work analyzes one of the lines of performance as for support to the creation of employment: the evolution of the number of beneficiaries taken refuge in the program of support to the autonomous Spanish employment during the period of 1998-2002, with special reference to the implication of the 25-year-old minor young men in the same one.

  15. Forced synchronization of autonomous dynamical Boolean networks

    Energy Technology Data Exchange (ETDEWEB)

    Rivera-Durón, R. R., E-mail: roberto.rivera@ipicyt.edu.mx; Campos-Cantón, E., E-mail: eric.campos@ipicyt.edu.mx [División de Matemáticas Aplicadas, Instituto Potosino de Investigación Científica y Tecnológica A. C., Camino a la Presa San José 2055, Col. Lomas 4 Sección, C.P. 78216, San Luis Potosí, S.L.P. (Mexico); Campos-Cantón, I. [Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, C.P. 78000, San Luis Potosí, S.L.P. (Mexico); Gauthier, Daniel J. [Department of Physics and Center for Nonlinear and Complex Systems, Duke University, Box 90305, Durham, North Carolina 27708 (United States)

    2015-08-15

    We present the design of an autonomous time-delay Boolean network realized with readily available electronic components. Through simulations and experiments that account for the detailed nonlinear response of each circuit element, we demonstrate that a network with five Boolean nodes displays complex behavior. Furthermore, we show that the dynamics of two identical networks display near-instantaneous synchronization to a periodic state when forced by a common periodic Boolean signal. A theoretical analysis of the network reveals the conditions under which complex behavior is expected in an individual network and the occurrence of synchronization in the forced networks. This research will enable future experiments on autonomous time-delay networks using readily available electronic components with dynamics on a slow enough time-scale so that inexpensive data collection systems can faithfully record the dynamics.

  16. Autonomous Sea-Ice Thickness Survey

    Science.gov (United States)

    2016-06-01

    reflects real variations in ice thickness of about ±0.1 m while the higher-frequency variations probably resulted from movement of the arms of the...E Ray, E. Trautmann, L. A. Barna, and A. M Burzynski. 2013. Autonomous GPR Surveys Using Polar Rover Yeti. Journal of Field Robotics 30 (2): 194...215. Lever, J. H., Z. Courville, and D. Punt. 2016. Robotic Ground-Penetrating-Radar (GPR) Surveys to Support the 2014 Greenland Inland Traverse

  17. Autonomic dysfunction in primary Raynaud's phenomenon.

    Science.gov (United States)

    Koszewicz, M; Gosk-Bierska, I; Bilińska, M; Podemski, R; Budrewicz, S; Adamiec, R; Słotwiński, K

    2009-04-01

    The pathogenesis of Raynaud's phenomenon is still unclear. Neural and intravascular mechanisms are thought to be involved in the pathological process. The role of the autonomic nervous system is continually discussed, with particular attention to over-reactivity of the sympathetic part. The aim of this study was the clinical and electrophysiological analysis of autonomic nervous system function in patients with primary Raynaud's phenomenon. Thirty four patients with primary Raynaud's phenomenon and 31 sex and age-matched controls were examined. Neurological examination, modified Low's Questionnaire, orthostatic and sustained handgrip tests, conduction velocity study in three nerves, sympathetic skin response (SSR), and heart rate variability (HRV) during deep breathing and at rest with the fast Fourier transform were performed. In the clinical examinations, 35.3% of the primary Raynaud's patients presented sensory neuropathy, but this was not confirmed in the standard conduction velocity tests. The modified Low's Questionnaire revealed dysautonomy in 82% of the patients. Autonomic regulation during the orthostatic and handgrip tests were within the normal limits. HRV at rest and the E/I ratio were significantly lower in the patient group than in the controls, while HRV spectrum analysis revealed the predominance of the low-frequency band in the patients. These results indicate the presence of sympathetic dysregulation and impairment of parasympathetic modulation of heart function in primary Raynaud's patients. The different cardiovascular and sudomotor functions are not affected to the same degree. These observations might support the theory of a central impairment of autonomic function in primary Raynaud's phenomenon. Peripheral nerve lesion as a coexisting cause of the observed dysautonomy remains uncertain.

  18. The Emerging Threats From Autonomous Systems [video

    OpenAIRE

    Center for Homeland Defense and Security Naval Postgraduate School

    2017-01-01

    Video presentation at the 2017 APEX workshop (Alumni Professional Exchange). Rob Sen. Self-described “serial entrepreneur” Robi Sen, Chief Technology Officer with the company Department 13, offered attendees a glimpse into the future and implications of autonomous systems and artificial intelligence. Sen traces the history and the future prospects of these systems. Benefits could include fewer accidents, finely tailored personalized medicine, reduced natural resource use, opening of areas for...

  19. A universal projective synchronization of general autonomous ...

    Indian Academy of Sciences (India)

    Generalized projective synchronization controller design. Consider a general autonomous system: ˙X = AX + B. (1). Here X = [x1, x1,..., xn]T is the state vector of the drive system, B is a n × 1 constant vector, and A is a n × n square matrix: A = ⎛. ⎜. ⎝ a11(X) ... a1n(X) ... ... ... an1(X) ··· ann(X). ⎞. ⎟. ⎠ . Here, aij (X) is a function ...

  20. Somatic DNA Damages in Cardiovascular Autonomic Neuropathy

    OpenAIRE

    Supriya Simon, A.; Dinesh Roy, D.; Jayapal, V.; Vijayakumar, T.

    2010-01-01

    Cardiovascular autonomic neuropathy (CAN) is one of the most clinically significant complications of diabetes mellitus. Even though many ethological factors have been attributed for the pathogenesis of this disease no attempts were made to correlate DNA damage as a causative factor. Hence the present study was undertaken to asses the extent of somatic DNA damages by cytokinesis-block micronuclei assay (CBMN). An attempt is also being made to correlate the habits and/or risk factors and socioe...

  1. Autonomous Robot Control via Autonomy Levels (ARCAL)

    Science.gov (United States)

    2015-08-21

    10 LINCOLN LABORATORY JOURNAL ■ VOLUME 22, 2015 Autonomous Robot Control via Autonomy Levels (ARCAL) Lawrence A.M. Bush and Andrew Wang In the...Adjustable autonomy technolo- gies, concepts, and simulation environments to evaluate teaming behaviors will enable researchers to develop these systems...A damaged nuclear energy facility also Unmanned aircraft systems (UAS) need to handle more autonomy and perform more intelligent behaviors. These

  2. Feasible Path Planning for Autonomous Vehicles

    Directory of Open Access Journals (Sweden)

    Vu Trieu Minh

    2014-01-01

    Full Text Available The objective of this paper is to find feasible path planning algorithms for nonholonomic vehicles including flatness, polynomial, and symmetric polynomial trajectories subject to the real vehicle dynamical constraints. Performances of these path planning methods are simulated and compared to evaluate the more realistic and smoother generated trajectories. Results show that the symmetric polynomial algorithm provides the smoothest trajectory. Therefore, this algorithm is recommended for the development of an automatic control for autonomous vehicles.

  3. A Generic Architecture for Autonomous Uninhabited Vehicles

    Science.gov (United States)

    2007-11-01

    RTO-MP-AVT-146 20 - 1 UNCLASSIFIED/UNLIMITED UNCLASSIFIED/UNLIMITED A Generic Architecture for Autonomous Uninhabited Vehicles Magali BARBIER ...it fires the event- triggered transitions of the Petri nets and runs actions associated to transitions; Barbier , M.; Gabard, J.-F.; Ayreault, H...affect the mission; a reaction is specified for each one: • in case of an engine failure, transit to the nearest emergency site; • in case of a

  4. Menopause and autonomic control of heart

    OpenAIRE

    Arunima Chaudhuri; Nirmala G Borade

    2012-01-01

    Menopause is associated with decreased heart rate variability, which is due to reduced parasympathetic or increased sympathetic outflow to the heart. Acute myocardial infarction may be accompanied by decreased heart rate variability. The causes of autonomic dysfunction in postmenopausal women may be multi-factorial i.e., dyslipidemia, increased body fat percentage, aging and loss of female sex hormones. The cardiac vagotonic and sympatholytic effects of estrogen can explain, at least in part,...

  5. Integrating autonomous Problem Resolution Models with Remedy

    OpenAIRE

    Marquina, M A; Padilla, J; Ramos, R

    2000-01-01

    This paper briefly defines the concept of Problem Resolution Model and shows possible approaches to the issues which may arise when integrating various PRMs to present a consistent view to the end user, despite of the peculiarities of each physical implementation. Integration refers to various autonomous PRMs having to interact as problems pass from one to another in the resolution flow. This process should be transparent to the user and internally there must be a way to track in which stage ...

  6. Development of autonomous vehicles’ testing system

    Science.gov (United States)

    Ivanov, A. M.; Shadrin, S. S.

    2018-02-01

    This article describes overview of automated and, in perspective, autonomous vehicles’ (AV) implementation risks. Set of activities, actual before the use of AVs on public roads, minimizing negative technical and social problems of AVs’ implementation is presented. Classification of vehicle’s automated control systems operating conditions is formulated. Groups of tests for AVs are developed and justified, sequence of AVs’ testing system formation is proposed.

  7. Autonomic nervous system function in Huntington's disease.

    Science.gov (United States)

    Andrich, J; Schmitz, T; Saft, C; Postert, T; Kraus, P; Epplen, J T; Przuntek, H; Agelink, M W

    2002-06-01

    To investigate whether Huntington's disease (HD) affects autonomic nervous system (ANS) functioning. Twenty patients with HD who had positive genetic test results underwent standardised ANS function tests including sympathetic skin responses (SSRs) of the hands and feet, measurements of heart rate variability (HRV), both during five minutes of resting and deep respiration, and an orthostatic blood pressure test. Patients were classified according to the motor subscale of the unified Huntington's disease rating scale (UHDRS; mean (SD) score 26.4 (13.6)) and divided into two subgroups: UHDRS or =25 points (mid stages, M-HD). Autonomic indices were compared with those obtained for a group of well matched healthy controls (n=60). Overall, patients showed lower HRV indices than controls. Multivariate analysis with the independent factor of "group" (controls, E-HD, M-HD) showed a significant group effect on both the high frequency power (F=4.32, p=0.017) and the coefficient of variation (F=4.23, p=0.018), indicating a significant reduction in vagal modulation in the M-HD group. There was a shift in autonomic neurocardiac balance towards sympathetic predominance in the M-HD group compared with controls (F=2.89, p=0.062). Moreover, we found an inverse correlation between the severity of clinical HD symptoms (assessed by the UHDRS) and the modulation of cardiovagal activity (p=0.028). Vagal dysregulation was present in two patients; one of them also showed a pathological blood pressure test and a latency prolongation in the SSRs of the hands. Two other patients had pathologically reduced SSR amplitudes. Only patients of the M-HD group were affected. Autonomic dysfunction is present even in the middle stages of HD and affects both the sympathetic and parasympathetic branch of the ANS.

  8. Task sequencing for autonomous robotic vacuum cleaners

    Science.gov (United States)

    Gorbenko, Anna; Popov, Vladimir

    2017-07-01

    Various planning problems for robotic systems are of considerable interest. One of such problems is the problem of task sequencing. In this paper, we consider the problem of task sequencing for autonomous vacuum floor cleaning robots. We consider a graph model for the problem. We propose an efficient approach to solve the problem. In particular, we use an explicit reduction from the decision version of the problem to the satisfiability problem. We present the results of computational experiments for different satisfiability algorithms.

  9. Flocking algorithm for autonomous flying robots.

    Science.gov (United States)

    Virágh, Csaba; Vásárhelyi, Gábor; Tarcai, Norbert; Szörényi, Tamás; Somorjai, Gergő; Nepusz, Tamás; Vicsek, Tamás

    2014-06-01

    Animal swarms displaying a variety of typical flocking patterns would not exist without the underlying safe, optimal and stable dynamics of the individuals. The emergence of these universal patterns can be efficiently reconstructed with agent-based models. If we want to reproduce these patterns with artificial systems, such as autonomous aerial robots, agent-based models can also be used in their control algorithms. However, finding the proper algorithms and thus understanding the essential characteristics of the emergent collective behaviour requires thorough and realistic modeling of the robot and also the environment. In this paper, we first present an abstract mathematical model of an autonomous flying robot. The model takes into account several realistic features, such as time delay and locality of communication, inaccuracy of the on-board sensors and inertial effects. We present two decentralized control algorithms. One is based on a simple self-propelled flocking model of animal collective motion, the other is a collective target tracking algorithm. Both algorithms contain a viscous friction-like term, which aligns the velocities of neighbouring agents parallel to each other. We show that this term can be essential for reducing the inherent instabilities of such a noisy and delayed realistic system. We discuss simulation results on the stability of the control algorithms, and perform real experiments to show the applicability of the algorithms on a group of autonomous quadcopters. In our case, bio-inspiration works in two ways. On the one hand, the whole idea of trying to build and control a swarm of robots comes from the observation that birds tend to flock to optimize their behaviour as a group. On the other hand, by using a realistic simulation framework and studying the group behaviour of autonomous robots we can learn about the major factors influencing the flight of bird flocks.

  10. Autonomous Aeromagnetic Surveys Using a Fluxgate Magnetometer

    Directory of Open Access Journals (Sweden)

    Douglas G. Macharet

    2016-12-01

    Full Text Available Recent advances in the research of autonomous vehicles have showed a vast range of applications, such as exploration, surveillance and environmental monitoring. Considering the mining industry, it is possible to use such vehicles in the prospection of minerals of commercial interest beneath the ground. However, tasks such as geophysical surveys are highly dependent on specific sensors, which mostly are not designed to be used in these new range of autonomous vehicles. In this work, we propose a novel magnetic survey pipeline that aims to increase versatility, speed and robustness by using autonomous rotary-wing Unmanned Aerial Vehicles (UAVs. We also discuss the development of a state-of-the-art three-axis fluxgate, where our goal in this work was to refine and adjust the sensor topology and coupled electronics specifically for this type of vehicle and application. The sensor was built with two ring-cores using a specially developed stress-annealed CoFeSiB amorphous ribbon, in order to get sufficient resolution to detect concentrations of small ferrous minerals. Finally, we report on the results of experiments performed with a real UAV in an outdoor environment, showing the efficacy of the methodology in detecting an artificial ferrous anomaly.

  11. Safety performance monitoring of autonomous marine systems

    International Nuclear Information System (INIS)

    Thieme, Christoph A.; Utne, Ingrid B.

    2017-01-01

    The marine environment is vast, harsh, and challenging. Unanticipated faults and events might lead to loss of vessels, transported goods, collected scientific data, and business reputation. Hence, systems have to be in place that monitor the safety performance of operation and indicate if it drifts into an intolerable safety level. This article proposes a process for developing safety indicators for the operation of autonomous marine systems (AMS). The condition of safety barriers and resilience engineering form the basis for the development of safety indicators, synthesizing and further adjusting the dual assurance and the resilience based early warning indicator (REWI) approaches. The article locates the process for developing safety indicators in the system life cycle emphasizing a timely implementation of the safety indicators. The resulting safety indicators reflect safety in AMS operation and can assist in planning of operations, in daily operational decision-making, and identification of improvements. Operation of an autonomous underwater vehicle (AUV) exemplifies the process for developing safety indicators and their implementation. The case study shows that the proposed process leads to a comprehensive set of safety indicators. It is expected that application of the resulting safety indicators consequently will contribute to safer operation of current and future AMS. - Highlights: • Process for developing safety indicators for autonomous marine systems. • Safety indicators based on safety barriers and resilience thinking. • Location of the development process in the system lifecycle. • Case study on AUV demonstrating applicability of the process.

  12. Autonomous Aeromagnetic Surveys Using a Fluxgate Magnetometer.

    Science.gov (United States)

    Macharet, Douglas G; Perez-Imaz, Héctor I A; Rezeck, Paulo A F; Potje, Guilherme A; Benyosef, Luiz C C; Wiermann, André; Freitas, Gustavo M; Garcia, Luis G U; Campos, Mario F M

    2016-12-17

    Recent advances in the research of autonomous vehicles have showed a vast range of applications, such as exploration, surveillance and environmental monitoring. Considering the mining industry, it is possible to use such vehicles in the prospection of minerals of commercial interest beneath the ground. However, tasks such as geophysical surveys are highly dependent on specific sensors, which mostly are not designed to be used in these new range of autonomous vehicles. In this work, we propose a novel magnetic survey pipeline that aims to increase versatility, speed and robustness by using autonomous rotary-wing Unmanned Aerial Vehicles (UAVs). We also discuss the development of a state-of-the-art three-axis fluxgate, where our goal in this work was to refine and adjust the sensor topology and coupled electronics specifically for this type of vehicle and application. The sensor was built with two ring-cores using a specially developed stress-annealed CoFeSiB amorphous ribbon, in order to get sufficient resolution to detect concentrations of small ferrous minerals. Finally, we report on the results of experiments performed with a real UAV in an outdoor environment, showing the efficacy of the methodology in detecting an artificial ferrous anomaly.

  13. Autonomous authority in relation to the staff regulations of autonomous parliaments

    Directory of Open Access Journals (Sweden)

    Rafael Cano Silva

    2018-04-01

    Full Text Available The statutes of Autonomous Parliaments are parliamentary administrative norms approved by each legislative chamber by virtue of their parliamentary autonomy. However, the parliamentary autonomy of each autonomous parliament does not have the same normative aspect for these purposes. It is studied in this article as despite having the Constitution as a common element, it is essential the special attribution that each autonomous chamber has and that the jurisprudence, both of the Constitutional Court, and that of the Supreme Court, has put in value, question that is included in the section related to the jurisprudence. In conclusion, the bureaucratic organization, in what refers to personal media, may be substantially different in each one of the legislative assemblies, as analyzed in the conclusions of this study.

  14. Dynamics control of autonomous vehicle at driving limits and experiment on an autonomous formula racing car

    Science.gov (United States)

    Ni, Jun; Hu, Jibin

    2017-06-01

    In this paper, a novel dynamics controller for autonomous vehicle to simultaneously control it to the driving limits and follow the desired path is proposed. The dynamics controller consists of longitudinal and lateral controllers. In longitudinal controller, the G-G diagram is utilized to describe the driving and handling limits of the vehicle. The accurate G-G diagram is obtained based on phase plane approach and a nonlinear vehicle dynamic model with accurate tyre model. In lateral controller, the tyre cornering stiffness is estimated to improve the robustness of the controller. The stability analysis of the closed-looped error dynamics shows that the controller remains stable against parameters uncertainties in extreme condition such as tyre saturation. Finally, an electric autonomous Formula race car developed by the authors is used to validate the proposed controller. The autonomous driving experiment on an oval race track shows the efficiency and robustness of the proposed controller.

  15. A Priori User Acceptance and the Perceived Driving Pleasure in Semi-autonomous and Autonomous Vehicles

    DEFF Research Database (Denmark)

    Bjørner, Thomas

    The aim of this minor pilot study is, from a sociological user perspective, to explore a priori user acceptance and the perceived driving pleasure in semi- autonomous and autonomous vehicles. The methods used were 13 in-depth interviews while having participants watch video examples within four...... concerns about trust, user interactions and legislation, as well as the use of technology when driving on highways. Future studies should use a more substantial theoretical framework and real-life tests for a better understanding of user acceptance of driving automation....

  16. Knowledge of autonomic dysreflexia in the emergency department.

    Science.gov (United States)

    Jackson, Caroline R; Acland, Rick

    2011-10-01

    To determine the level of knowledge that medical staff in the emergency department and spinal unit have of autonomic dysreflexia, its causes, symptoms, treatment and complications; and to educate the participating staff about autonomic dysreflexia. The study design was a prospective questionnaire, which was completed by 91 staff in the spinal unit and emergency department in Christchurch, who then undertook a teaching session on autonomic dysreflexia. 29 of 70 staff in emergency department could not answer any questions. The average mark out of 29 was 2 for the emergency department and 12 for the spinal unit. Only 16 staff in the emergency department had had teaching on autonomic dysreflexia previously. Due to the potentially serious complications of autonomic dysreflexia, staff require teaching on autonomic dysreflexia accompanied by permanent reminders in the form of posters.

  17. Creation of a novel telomere-cutting endonuclease based on the EN domain of telomere-specific non-long terminal repeat retrotransposon, TRAS1

    Directory of Open Access Journals (Sweden)

    Yoshitake Kazutoshi

    2010-04-01

    Full Text Available Abstract Background The ends of chromosomes, termed telomeres consist of repetitive DNA. The telomeric sequences shorten with cell division and, when telomeres are critically abbreviated, cells stop proliferating. However, in cancer cells, by the expression of telomerase which elongates telomeres, the cells can continue proliferating. Many approaches for telomere shortening have been pursued in the past, but to our knowledge, cutting telomeres in vivo has not so far been demonstrated. In addition, there is lack of information on the cellular effects of telomere shortening in human cells. Results Here, we created novel chimeric endonucleases to cut telomeres by fusing the endonuclease domain (TRAS1EN of the silkworm's telomere specific non-long terminal repeat retrotransposon TRAS1 to the human telomere-binding protein, TRF1. An in vitro assay demonstrated that the TRAS1EN-TRF1 chimeric endonucleases (T-EN and EN-T cut the human (TTAGGGn repeats specifically. The concentration of TRAS1EN-TRF1 chimeric endonucleases necessary for the cleavage of (TTAGGGn repeats was about 40-fold lower than that of TRAS1EN alone. When TRAS1EN-TRF1 endonucleases were introduced into human U2OS cancer cells using adenovirus vectors, the enzymes localized at telomeres of nuclei, cleaved and shortened the telomeric DNA by double-strand breaks. When human U2OS and HFL-1 fibroblast cells were infected with EN-T recombinant adenovirus, their cellular proliferation was suppressed for about 2 weeks after infection. In contrast, the TRAS1EN mutant (H258A chimeric endonuclease fused with TRF1 (ENmut-T did not show the suppression effect. The EN-T recombinant adenovirus induced telomere shortening in U2OS cells, activated the p53-dependent pathway and caused the senescence associated cellular responses, while the ENmut-T construct did not show such effects. Conclusions A novel TRAS1EN-TRF1 chimeric endonuclease (EN-T cuts the human telomeric repeats (TTAGGGn specifically in

  18. Autonomic reactivity in muscle pain : clinical and experimental assessment

    OpenAIRE

    Kalezic, Nebojsa

    2006-01-01

    There are numerous indications of possible involvement of the autonomic nervous system in the genesis of chronic pain. The possibility exists that sympathetic activation is related to motor dysfunction and changes in sensory processing, which have otherwise been implicated in musculoskeletal disorders. The primary aim of the thesis has been to investigate autonomic regulation at rest and in response to laboratory tests of autonomic function in subjects suffering from chronic pain in different...

  19. Control of autonomous ground vehicles: a brief technical review

    Science.gov (United States)

    Babak, Shahian-Jahromi; Hussain, Syed A.; Karakas, Burak; Cetin, Sabri

    2017-07-01

    This paper presents a brief review of the developments achieved in autonomous vehicle systems technology. A concise history of autonomous driver assistance systems is presented, followed by a review of current state of the art sensor technology used in autonomous vehicles. Standard sensor fusion method that has been recently explored is discussed. Finally, advances in embedded software methodologies that define the logic between sensory information and actuation decisions are reviewed.

  20. Research on Operational Aspects of Large Autonomous Underwater Glider Fleets

    National Research Council Canada - National Science Library

    Fratantoni, David M

    2007-01-01

    This program supported research on the operational and management issues stemming from application of large fleets of autonomous underwater gliders to oceanographic research and rapid environmental...

  1. GPM Ground Validation Autonomous Parsivel Unit (APU) OLYMPEX V1

    Data.gov (United States)

    National Aeronautics and Space Administration — The GPM Ground Validation Autonomous Parsivel Unit (APU) OLYMPEX dataset was collected during the OLYMPEX field campaign held at Washington's Olympic Peninsula...

  2. Autonomous Contingency Detection and Reaction for Unmanned Aircraft, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Unmanned aircraft systems (UAS) and, in particular, intelligent, autonomous aircraft operating in the national airspace system (NAS) have the potential to...

  3. Longitudinal Control for Mengshi Autonomous Vehicle via Cloud Model

    Science.gov (United States)

    Gao, H. B.; Zhang, X. Y.; Li, D. Y.; Liu, Y. C.

    2018-03-01

    Dynamic robustness and stability control is a requirement for self-driving of autonomous vehicle. Longitudinal control method of autonomous is a key technique which has drawn the attention of industry and academe. In this paper, we present a longitudinal control algorithm based on cloud model for Mengshi autonomous vehicle to ensure the dynamic stability and tracking performance of Mengshi autonomous vehicle. An experiments is applied to test the implementation of the longitudinal control algorithm. Empirical results show that if the longitudinal control algorithm based Gauss cloud model are applied to calculate the acceleration, and the vehicles drive at different speeds, a stable longitudinal control effect is achieved.

  4. Adaptive Supervisory Engine for Autonomous Formation Flying GNC, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Autonomous multiple spacecraft formation flying represents a critical enabling technology for future space missions, including NASA's Space and Earth Science...

  5. Impact of malnutrition on cardiac autonomic modulation in children

    Directory of Open Access Journals (Sweden)

    Gláucia Siqueira Carvalho Barreto

    2016-11-01

    Conclusion: Malnourished children present changes in cardiac autonomic modulation, characterized by reductions in both sympathetic and parasympathetic activity, as well as increased heart rate and decreased blood pressure.

  6. Intelligent Autonomous Aerial Vehicles in the National Airspace, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Unmanned aerial systems (UAS) and, in particular, intelligent, autonomous aircraft operating in the National Airspace (NAS) have the potential to significantly...

  7. Contour Tracking Control for the REMUS Autonomous Underwater Vehicle

    National Research Council Canada - National Science Library

    Van Reet, Alan R

    2005-01-01

    In the interest of enhancing the capabilities of autonomous underwater vehicles used in US Naval Operations, controlling vehicle position to follow depth contours presents exciting potential for navigation...

  8. Distributed Autonomous Control of Multiple Spacecraft During Close Proximity Operations

    National Research Council Canada - National Science Library

    McCamish, Shawn B

    2007-01-01

    This research contributes to multiple spacecraft control by developing an autonomous distributed control algorithm for close proximity operations of multiple spacecraft systems, including rendezvous...

  9. Amplifying human ability through autonomics and machine learning in IMPACT

    Science.gov (United States)

    Dzieciuch, Iryna; Reeder, John; Gutzwiller, Robert; Gustafson, Eric; Coronado, Braulio; Martinez, Luis; Croft, Bryan; Lange, Douglas S.

    2017-05-01

    Amplifying human ability for controlling complex environments featuring autonomous units can be aided by learned models of human and system performance. In developing a command and control system that allows a small number of people to control a large number of autonomous teams, we employ an autonomics framework to manage the networks that represent mission plans and the networks that are composed of human controllers and their autonomous assistants. Machine learning allows us to build models of human and system performance useful for monitoring plans and managing human attention and task loads. Machine learning also aids in the development of tactics that human supervisors can successfully monitor through the command and control system.

  10. Logistics Reduction: RFID Enabled Autonomous Logistics Management (REALM)

    Data.gov (United States)

    National Aeronautics and Space Administration — The Advanced Exploration Systems (AES) Logistics Reduction (LR) project Radio-frequency identification (RFID) Enabled Autonomous Logistics Management (REALM) task...

  11. Throughput Evaluation of an Autonomous Sustainment Cargo Container System

    National Research Council Canada - National Science Library

    Yeh, Mingtze

    2007-01-01

    .... Autonomous containers will play an essential role in the ability to deliver logistical supplies to waterborne littoral vessels enabling them to maintain station and complete there military operations...

  12. GPM GROUND VALIDATION AUTONOMOUS PARSIVEL UNIT (APU) LPVEX V1

    Data.gov (United States)

    National Aeronautics and Space Administration — The GPM Ground Validation Autonomous Parsivel Unit (APU) LPVEx dataset provides rainfall data for the Global Precipitation Measurement (GPM) Misson Ground Validation...

  13. Maritime Training Serbian Autonomous Vessel Protection Detachment

    Directory of Open Access Journals (Sweden)

    Šoškić Svetislav D.

    2014-06-01

    Full Text Available The crisis in Somalia has caused appearance of piracy at sea in the Gulf of Aden and the Western Indian Ocean. Somali pirates have become a threat to economic security of the world because almost 30 percent of world oil and 20 percent of global trade passes through the Gulf of Aden. Solving the problem of piracy in this part of the world have included international organizations, institutions, military alliances and the states, acting in accordance with international law and UN Security Council resolutions. The European Union will demonstrate the application of a comprehensive approach to solving the problem of piracy at sea and the crisis in Somalia conducting naval operation — EU NAVFOR Atalanta and operation EUTM under the Common Security and Defense Policy. The paper discusses approaches to solving the problem of piracy in the Gulf of Aden and the crisis in Somalia. Also, the paper points to the complexity of the crisis in Somalia and dilemmas correctness principles that are applied to solve the problem piracy at sea. One of goals is protections of vessels of the World Food Programme (WFP delivering food aid to displaced persons in Somalia. Republic of Serbia joined in this mission and trained and sent one a autonomous team in this military operation for protection WFP. This paper consist the problem of modern piracy, particularly in the area of the Horn of Africa became a real threat for the safety of maritime ships and educational process of Serbian Autonomous vessel protection detachment. Serbian Military Academy adopted and developed educational a training program against piracy applying all the provisions and recommendations of the IMO conventions and IMO model courses for Serbian Autonomous vessel protection detachment.

  14. Autonomous vehicles: from paradigms to technology

    Science.gov (United States)

    Ionita, Silviu

    2017-10-01

    Mobility is a basic necessity of contemporary society and it is a key factor in global economic development. The basic requirements for the transport of people and goods are: safety and duration of travel, but also a number of additional criteria are very important: energy saving, pollution, passenger comfort. Due to advances in hardware and software, automation has penetrated massively in transport systems both on infrastructure and on vehicles, but man is still the key element in vehicle driving. However, the classic concept of ‘human-in-the-loop’ in terms of ‘hands on’ in driving the cars is competing aside from the self-driving startups working towards so-called ‘Level 4 autonomy’, which is defined as “a self-driving system that does not requires human intervention in most scenarios”. In this paper, a conceptual synthesis of the autonomous vehicle issue is made in connection with the artificial intelligence paradigm. It presents a classification of the tasks that take place during the driving of the vehicle and its modeling from the perspective of traditional control engineering and artificial intelligence. The issue of autonomous vehicle management is addressed on three levels: navigation, movement in traffic, respectively effective maneuver and vehicle dynamics control. Each level is then described in terms of specific tasks, such as: route selection, planning and reconfiguration, recognition of traffic signs and reaction to signaling and traffic events, as well as control of effective speed, distance and direction. The approach will lead to a better understanding of the way technology is moving when talking about autonomous cars, smart/intelligent cars or intelligent transport systems. Keywords: self-driving vehicle, artificial intelligence, deep learning, intelligent transport systems.

  15. Smartphones Promote Autonomous Learning in ESL Classrooms

    Directory of Open Access Journals (Sweden)

    Viji Ramamuruthy

    2015-10-01

    Full Text Available The rapid development of high-technology has caused new inventions of gadgets for all walks of life regardless age. In this rapidly advancing technology era many individuals possess hi-tech gadgets such as laptops, tablets, iPad, android phones and smart phones. Adult learners in higher learning institution especially are fond of using smart phones. Students become passive in the classrooms as they are glued to their smart phones. This situation triggers the question of whether learning really takes place while the students are too engaged with their smart phones in the ESL classroom. In this context, the following questions are framed to investigate this issue: What type of learning skills are gained by using smartphones in ESL classrooms? Does smartphone use promote the autonomous learning process? To what extent do learners rely on the lecturers in addition to the usage of smartphones? What are the learning satisfactions gained by ESL learners using smartphones? A total of 70 smartphone users in the age range 18 to 26 years participated in this quantitative study. Questionnaires eliciting demographic details of the respondents, learning skills, learning satisfaction, students' perception on teacher's role in the ESL classroom and autonomous learning were distributed to all the randomly chosen samples. The data were then analyzed by using SPSS version 16. The findings revealed that smartphone use boosted learners’ critical thinking, creative thinking, communication and collaboration skills. In fact, learners gain great satisfaction in the learning process through smartphones. Although learners have moved toward autonomous learning, they are still reliant on the teachers to achieve their learning goals.

  16. Multi-Spacecraft Autonomous Positioning System

    Science.gov (United States)

    Anzalone, Evan

    2015-01-01

    As the number of spacecraft in simultaneous operation continues to grow, there is an increased dependency on ground-based navigation support. The current baseline system for deep space navigation utilizes Earth-based radiometric tracking, requiring long-duration observations to perform orbit determination and generate a state update. The age, complexity, and high utilization of the ground assets pose a risk to spacecraft navigation performance. In order to perform complex operations at large distances from Earth, such as extraterrestrial landing and proximity operations, autonomous systems are required. With increasingly complex mission operations, the need for frequent and Earth-independent navigation capabilities is further reinforced. The Multi-spacecraft Autonomous Positioning System (MAPS) takes advantage of the growing interspacecraft communication network and infrastructure to allow for Earth-autonomous state measurements to enable network-based space navigation. A notional concept of operations is given in figure 1. This network is already being implemented and routinely used in Martian communications through the use of the Mars Reconnaissance Orbiter and Mars Odyssey spacecraft as relays for surface assets. The growth of this communications architecture is continued through MAVEN, and future potential commercial Mars telecom orbiters. This growing network provides an initial Marslocal capability for inter-spacecraft communication and navigation. These navigation updates are enabled by cross-communication between assets in the network, coupled with onboard navigation estimation routines to integrate packet travel time to generate ranging measurements. Inter-spacecraft communication allows for frequent state broadcasts and time updates from trusted references. The architecture is a software-based solution, enabling its implementation on a wide variety of current assets, with the operational constraints and measurement accuracy determined by onboard systems.

  17. Malicious Hubs: Detecting Abnormally Malicious Autonomous Systems

    Energy Technology Data Exchange (ETDEWEB)

    Kalafut, Andrew J. [Indiana University; Shue, Craig A [ORNL; Gupta, Prof. Minaxi [Indiana University

    2010-01-01

    While many attacks are distributed across botnets, investigators and network operators have recently targeted malicious networks through high profile autonomous system (AS) de-peerings and network shut-downs. In this paper, we explore whether some ASes indeed are safe havens for malicious activity. We look for ISPs and ASes that exhibit disproportionately high malicious behavior using 12 popular blacklists. We find that some ASes have over 80% of their routable IP address space blacklisted and others account for large fractions of blacklisted IPs. Overall, we conclude that examining malicious activity at the AS granularity can unearth networks with lax security or those that harbor cybercrime.

  18. Autonomous valve for detection of biopolymer degradation

    DEFF Research Database (Denmark)

    Keller, Stephan Urs; Noeth, Nadine-Nicole; Fetz, Stefanie

    2009-01-01

    We present a polymer microvalve that allows the detection of biopolymer degradation without the need of external energy. The valve is based on a polymer container filled with a colored marker solution and closed by a thin lid. This structure is covered by a film of poly(L-lactide) and degradation...... of the biopolymer triggers the release of the color which is detected visually. The autonomous valve has potential for the fast testing of biopolymer degradation under various environmental conditions or by specific enzymes....

  19. Menopause and autonomic control of heart

    Directory of Open Access Journals (Sweden)

    Arunima Chaudhuri

    2012-01-01

    Full Text Available Menopause is associated with decreased heart rate variability, which is due to reduced parasympathetic or increased sympathetic outflow to the heart. Acute myocardial infarction may be accompanied by decreased heart rate variability. The causes of autonomic dysfunction in postmenopausal women may be multi-factorial i.e., dyslipidemia, increased body fat percentage, aging and loss of female sex hormones. The cardiac vagotonic and sympatholytic effects of estrogen can explain, at least in part, why premenopausal women compared with postmenopausal women have a lower coronary heart disease incidence and mortality rate.

  20. Rational decision making in autonomous agents

    OpenAIRE

    Simari, Gerardo I.; Parsons, Simon D.

    2004-01-01

    Making rational decisions is one of the key elements in the design of autonomous agents with successful behavior. Even though there have been many proposals for the support of decision making, most of them can be described either as descriptive or prescriptive. The main goal of our work is to establish the relationship between two of these models, namely bdi and mdps, in order to gain further understanding of how decisions in one model are viewed from the point of view of the other. This goal...

  1. Developments and challenges for autonomous unmanned vehicles

    CERN Document Server

    Finn, Anthony

    2010-01-01

    It is widely anticipated that autonomous vehicles will have a transformational impact on military forces and will play a key role in many future force structures. As a result, many tasks have already been identified that unmanned systems could undertake more readily than humans. However, for this to occur, such systems will need to be agile, versatile, persistent, reliable, survivable and lethal. This will require many of the vehicles 'cognitive' or higher order functions to be more fully developed, whereas to date only the 'component' or physical functions have been successfully automated and

  2. Sleep restriction progress to cardiac autonomic imbalance

    Directory of Open Access Journals (Sweden)

    Arbind Kumar Choudhary

    2018-06-01

    Full Text Available Previous studies have shown that night shift work is thought to be a risk factor for cardiovascular disease and inadequate sleep is a common feature of night shift work. Since it’s more difficult to maintain adequate sleep duration among night watchmen during their working schedule, hence the purpose of our present study was to investigate whether mental stress or fatigue over restricted sleep period in night shift, affects HRV, in order to elucidate on cardiac autonomic modulation among nigh watchmen. With the purpose of this, autonomic activity determined from the levels of the heart rate variability (HRV, and also measured, body mass index (BMI, body fat percentage from skin fold thickness (biceps, triceps, and sub-scapular, supra-iliac among normal sleep watchmen (n = 28 and restricted sleep watchmen (n = 28 at first (1st day, fourth (4th day and seventh (7th day of restricted sleep period. We observed that among restricted sleep individuals, sleepiness was significant increase at 4th day and 7th day when compare to normal sleep individuals, and, there was significant increase in, mean NN, VLF, LF, LF(nu, LF/HF AND significant decrease in SDNN, RMSSD, TSP, HF, and HF(nu at 4th and 7th day of restricted sleep period. In addition to, this variable was more significant increase on 7th day, when compare with 4th day. As well as there was significant negative correlation between LF(nu and HF(nu at subsequent 4th day [r (48 = −0.84; P = 0.01] and 7th day[r (48 = −0.95; P = 0.01] of restricted sleep period. However we didn’t observe any significant variation in BMI, and body fat percentage among restricted sleep individuals when compare to normal sleep individuals with in this restricted sleep periods. Hence we concluded that partial sleep loss may cause autonomic imbalance represented by increased sympathetic and decreased parasympathetic activity; as revealed by altered HRV indices observed in this study. Keywords: Sleep

  3. [Dirofilariasis in the Autonomous Republic of Crimea].

    Science.gov (United States)

    Korolev, V A; Romashova, M F

    2005-01-01

    The paper presents data on the prevalence of dirofilariasis in the Autonomous Republic of Crimea during 5 years from 1999 to 2003. The nematode Dirofilaria repens is a causative agent of the disease. Sporadic cases of helminthiasis are annually registered in some urban and rural areas on the plain of the peninsula. The disease is absent on the foothills and Black sea coast of the southern and eastern parts of Crimea. The localization of the parasite is typical of this helminthiasis. Dirofilariasis in Crimea may be regarded as a transmissible helminthiasis with natural focal trends.

  4. Topological equivalence of nonlinear autonomous dynamical systems

    International Nuclear Information System (INIS)

    Nguyen Huynh Phan; Tran Van Nhung

    1995-12-01

    We show in this paper that the autonomous nonlinear dynamical system Σ(A,B,F): x' = Ax+Bu+F(x) is topologically equivalent to the linear dynamical system Σ(A,B,O): x' = Ax+Bu if the projection of A on the complement in R n of the controllable vectorial subspace is hyperbolic and if lipschitz constant of F is sufficiently small ( * ) and F(x) = 0 when parallel x parallel is sufficiently large ( ** ). In particular, if Σ(A,B,O) is controllable, it is topologically equivalent to Σ(A,B,F) when it is only that F satisfy ( ** ). (author). 18 refs

  5. A Diversified Investment Strategy Using Autonomous Agents

    Science.gov (United States)

    Barbosa, Rui Pedro; Belo, Orlando

    In a previously published article, we presented an architecture for implementing agents with the ability to trade autonomously in the Forex market. At the core of this architecture is an ensemble of classification and regression models that is used to predict the direction of the price of a currency pair. In this paper, we will describe a diversified investment strategy consisting of five agents which were implemented using that architecture. By simulating trades with 18 months of out-of-sample data, we will demonstrate that data mining models can produce profitable predictions, and that the trading risk can be diminished through investment diversification.

  6. ROBERT autonomous navigation robot with artificial vision

    International Nuclear Information System (INIS)

    Cipollini, A.; Meo, G.B.; Nanni, V.; Rossi, L.; Taraglio, S.; Ferjancic, C.

    1993-01-01

    This work, a joint research between ENEA (the Italian National Agency for Energy, New Technologies and the Environment) and DIGlTAL, presents the layout of the ROBERT project, ROBot with Environmental Recognizing Tools, under development in ENEA laboratories. This project aims at the development of an autonomous mobile vehicle able to navigate in a known indoor environment through the use of artificial vision. The general architecture of the robot is shown together with the data and control flow among the various subsystems. Also the inner structure of the latter complete with the functionalities are given in detail

  7. Enhanced mission performance from autonomous instrument guidance

    DEFF Research Database (Denmark)

    Jørgensen, John Leif; Jørgensen, Peter Siegbjørn; Betto, Maurizio

    2006-01-01

    During the last decade improvements in electronics, on-board processing power and software design has lead to significant advances in the development of autonomous instrumentation for spacecraft use. The Advanced Stellar Compass (ASC) and the newly developed micro-ASC (mu ASC) are excellent...... and power consumption makes the mu ASC an ideal instrument for small, high yielding satellite missions. The ASC has hitherto been used by the satellite AOCS and the high accuracy scientific instrument for attitude recovery (among others onboard ORSTED, CHAMP, and GRACE), and satellite high accuracy target...

  8. Autonomous Droop Scheme With Reduced Generation Cost

    DEFF Research Database (Denmark)

    Nutkani, Inam Ullah; Loh, Poh Chiang; Wang, Peng

    2014-01-01

    ) of the microgrid. To reduce this TGC without relying on fast communication links, an autonomous droop scheme is proposed here, whose resulting power sharing is decided by the individual DG generation costs. Comparing it with the traditional scheme, the proposed scheme retains its simplicity and it is hence more....... This objective might, however, not suit microgrids well since DGs are usually of different types, unlike synchronous generators. Other factors like cost, efficiency, and emission penalty of each DG at different loading must be considered since they contribute directly to the total generation cost (TGC...

  9. Intelligent control for autonomous aircraft missions

    Science.gov (United States)

    Neidhoefer, James Christian

    The focus of this dissertation is the design and implementation of a full-envelope, nonlinear aircraft controller that includes stability augmentation, tracking control, and autonomous path generation. The control system was demonstrated by using a 6 degree of freedom high performance aircraft model with nonlinear kinematics, full-envelope nonlinear aerodynamics, and first-order thrust and actuator dynamics. Ideas from the emerging field of intelligent control were used in the definition of the controller architecture. More specifically, "Levels of Intelligent Control" were used to provide a systematic structure for the architecture. Several ideas from the field of Artificial Intelligence were also used, including Neural Networks, Genetic Algorithms, and Adaptive Critics.

  10. Autonomous Dome for a Robotic Telescope

    Science.gov (United States)

    Kumar, A.; Sengupta, A.; Ganesh, S.

    2016-12-01

    The Physical Research Laboratory operates a 50 cm robotic observatory at Mount Abu (Rajsthan, India). This Automated Telescope for Variability Studies (ATVS) makes use of the Remote Telescope System 2 (RTS2) for autonomous operations. The observatory uses a 3.5 m dome from Sirius Observatories. We have developed electronics using Arduino electronic circuit boards with home grown logic and software to control the dome operations. We are in the process of completing the drivers to link our Arduino based dome controller with RTS2. This document is a short description of the various phases of the development and their integration to achieve the required objective.

  11. Physics Simulation Software for Autonomous Propellant Loading and Gas House Autonomous System Monitoring

    Science.gov (United States)

    Regalado Reyes, Bjorn Constant

    2015-01-01

    1. Kennedy Space Center (KSC) is developing a mobile launching system with autonomous propellant loading capabilities for liquid-fueled rockets. An autonomous system will be responsible for monitoring and controlling the storage, loading and transferring of cryogenic propellants. The Physics Simulation Software will reproduce the sensor data seen during the delivery of cryogenic fluids including valve positions, pressures, temperatures and flow rates. The simulator will provide insight into the functionality of the propellant systems and demonstrate the effects of potential faults. This will provide verification of the communications protocols and the autonomous system control. 2. The High Pressure Gas Facility (HPGF) stores and distributes hydrogen, nitrogen, helium and high pressure air. The hydrogen and nitrogen are stored in cryogenic liquid state. The cryogenic fluids pose several hazards to operators and the storage and transfer equipment. Constant monitoring of pressures, temperatures and flow rates are required in order to maintain the safety of personnel and equipment during the handling and storage of these commodities. The Gas House Autonomous System Monitoring software will be responsible for constantly observing and recording sensor data, identifying and predicting faults and relaying hazard and operational information to the operators.

  12. Shh-mediated degradation of Hhip allows cell autonomous and non-cell autonomous Shh signalling

    NARCIS (Netherlands)

    Kwong, Lina; Bijlsma, Maarten F.; Roelink, Henk

    2014-01-01

    The distribution of Sonic Hedgehog (Shh) is a highly regulated and critical process for development. Several negative feedback mechanisms are in place, including the Shh-induced upregulation of Hedgehog-interacting protein (Hhip). Hhip sequesters Shh, leading to a non-cell autonomous inhibition of

  13. Tethered Operation of Autonomous Aerial Vehicles to Provide Extended Field of View for Autonomous Ground Vehicles

    Science.gov (United States)

    2006-12-01

    competition that started in the late 1970s, with small robot mice solving a 16 x 16 maze autonomously. Seydou SOUMARE in [2] has discussed, in depth, the...1915, San Jose, CA, Feb. 1993. 11. Eva Pärt-Enander, Anders Sjöberg, Bo Melin, and Pernilla Isaksson, “The MATLAB Handbook,”Addison-Wesley, 1998

  14. Safety analysis of autonomous excavator functionality

    International Nuclear Information System (INIS)

    Seward, D.; Pace, C.; Morrey, R.; Sommerville, I.

    2000-01-01

    This paper presents an account of carrying out a hazard analysis to define the safety requirements for an autonomous robotic excavator. The work is also relevant to the growing generic class of heavy automated mobile machinery. An overview of the excavator design is provided and the concept of a safety manager is introduced. The safety manager is an autonomous module responsible for all aspects of system operational safety, and is central to the control system's architecture. Each stage of the hazard analysis is described, i.e. system model creation, hazard definition and hazard analysis. Analysis at an early stage of the design process, and on a system that interfaces directly to an unstructured environment, exposes certain issues relevant to the application of current hazard analysis methods. The approach taken in the analysis is described. Finally, it is explained how the results of the hazard analysis have influenced system design, in particular, safety manager specifications. Conclusions are then drawn about the applicability of hazard analysis of requirements in general, and suggestions are made as to how the approach can be taken further

  15. Kinodynamic Motion Planning for Autonomous Vehicles

    Directory of Open Access Journals (Sweden)

    Jiwung Choi

    2014-06-01

    Full Text Available This article proposes a computationally effective motion planning algorithm for autonomous ground vehicles operating in a semi-structured environment with a mission specified by waypoints, corridor widths and obstacles. The algorithm switches between two kinds of planners, (i static planners and (ii moving obstacle avoidance manoeuvre planners, depending on the mobility of any detected obstacles. While the first is broken down into a path planner and a controller, the second generates a sequence of controls without global path planning. Each subsystem is implemented as follows. The path planner produces an optimal piecewise linear path by applying a variant of cell decomposition and dynamic programming. The piecewise linear path is smoothed by Bézier curves such that the maximum curvatures of the curves are minimized. The controller calculates the highest allowable velocity profile along the path, consistent with the limits on both tangential and radial acceleration and the steering command for the vehicle to track the trajectory using a pure pursuit method. The moving obstacle avoidance manoeuvre produces a sequence of time-optimal local velocities, by minimizing the cost as determined by the safety of the current velocity against obstacles in the velocity obstacle paradigm and the deviation of the current velocity relative to the desired velocity, to satisfy the waypoint constraint. The algorithms are shown to be robust and computationally efficient, and to demonstrate a viable methodology for autonomous vehicle control in the presence of unknown obstacles.

  16. Perspective: Autonomic care systems for hospitalized patients.

    Science.gov (United States)

    Goldschmidt-Clermont, Pascal J; Dong, Chunming; Rhodes, Nancy M; McNeill, Diana B; Adams, Martha B; Gilliss, Catherine L; Cuffe, Michael S; Califf, Robert M; Peterson, Eric D; Lubarsky, David A

    2009-12-01

    With advancements of medical technology and improved diagnostic and treatment options, children with severe birth defects who would otherwise have no chance of surviving post birth survive to go home every day. The average lifespan in the United States has increased substantially over the last century. These successes and many other medical breakthroughs in managing complex illnesses, particularly in frail, elderly patients, have resulted in an increasing percentage of patients with comorbidities. This, coupled with a policy change by Medicare (i.e., Medicare will no longer reimburse hospitals for costs associated with treating preventable errors and injuries that a patient acquires while in the hospital), creates an enormous challenge to health care providers. To meet the challenge, the authors propose a new model of health care--the autonomic care system (ACS)--a concept derived from the intensive care unit and the autonomic computing initiative in the computer industry. Using wound care as an example, the authors examine the necessity, feasibility, design, and challenges related to ACS. Specifically, they discuss the role of the human operator, the potential combination of ACS and existing hospital information technology (e.g., electronic medical records and computerized provider order entry), and the costs associated with ACS. ACS may serve as a roadmap to revamp the health care system, bringing down the barriers among different specialties and improving the quality of care for each problem for all hospitalized patients.

  17. A Multifunctional Coating for Autonomous Corrosion Control

    Science.gov (United States)

    Calle, Luz M.; Hintze, Paul E.; Li, Wenyan; Buhrow, Jerry W.; Jolley, Scott T.

    2010-01-01

    Corrosion is a destructive process that often causes failure in metallic components and structures. Protective coatings are the most commonly used method of corrosion control. However, progressively stricter environmental regulations have resulted in the ban of many commercially available corrosion protective coatings due to the harmful effects of their solvents or corrosion inhibitors. This work concerns the development of a multifunctional, smart coating for the autonomous control of corrosion. This coating is being developed to have the inherent ability to detect the chemical changes associated with the onset of corrosion and respond autonomously to control it. The multi-functionality of the coating is based on microencapsulation technology specifically designed for corrosion control applications. This design has, in addition to all the advantages of other existing microcapsules designs, the corrosion controlled release function that allows the delivery of corrosion indicators and inhibitors on demand only when and where they are needed. Corrosion indicators as well as corrosion inhibitors have been incorporated into the microcapsules, blended into several paint systems, and tested for corrosion detection and protection efficacy.

  18. An Experimental Platform for Autonomous Bus Development

    Directory of Open Access Journals (Sweden)

    Héctor Montes

    2017-11-01

    Full Text Available Nowadays, with highly developed instrumentation, sensing and actuation technologies, it is possible to foresee an important advance in the field of autonomous and/or semi-autonomous transportation systems. Intelligent Transport Systems (ITS have been subjected to very active research for many years, and Bus Rapid Transit (BRT is one area of major interest. Among the most promising transport infrastructures, the articulated bus is an interesting, low cost, high occupancy capacity and friendly option. In this paper, an experimental platform for research on the automatic control of an articulated bus is presented. The aim of the platform is to allow full experimentation in real conditions for testing technological developments and control algorithms. The experimental platform consists of a mobile component (a commercial articulated bus fully instrumented and a ground test area composed of asphalt roads inside the Consejo Superior de Investigaciones Científicas (CSIC premises. This paper focuses also on the development of a human machine interface to ease progress in control system evaluation. Some experimental results are presented in order to show the potential of the proposed platform.

  19. Autonomous mobile robot localization using Kalman filter

    Directory of Open Access Journals (Sweden)

    Mohd Nasir Nabil Zhafri

    2017-01-01

    Full Text Available Autonomous mobile robot field has gain interest among researchers in recent years. The ability of a mobile robot to locate its current position and surrounding environment is the fundamental in order for it to operate autonomously, which commonly known as localization. Localization of mobile robot are commonly affected by the inaccuracy of the sensors. These inaccuracies are caused by various factors which includes internal interferences of the sensor and external environment noises. In order to overcome these noises, a filtering method is required in order to improve the mobile robot’s localization. In this research, a 2- wheeled-drive (2WD mobile robot will be used as platform. The odometers, inertial measurement unit (IMU, and ultrasonic sensors are used for data collection. Data collected is processed using Kalman filter to predict and correct the error from these sensors reading. The differential drive model and measurement model which estimates the environmental noises and predict a correction are used in this research. Based on the simulation and experimental results, the x, y and heading was corrected by converging the error to10 mm, 10 mm and 0.06 rad respectively.

  20. Sensor study for high speed autonomous operations

    Science.gov (United States)

    Schneider, Anne; La Celle, Zachary; Lacaze, Alberto; Murphy, Karl; Del Giorno, Mark; Close, Ryan

    2015-06-01

    As robotic ground systems advance in capabilities and begin to fulfill new roles in both civilian and military life, the limitation of slow operational speed has become a hindrance to the wide-spread adoption of these systems. For example, military convoys are reluctant to employ autonomous vehicles when these systems slow their movement from 60 miles per hour down to 40. However, these autonomous systems must operate at these lower speeds due to the limitations of the sensors they employ. Robotic Research, with its extensive experience in ground autonomy and associated problems therein, in conjunction with CERDEC/Night Vision and Electronic Sensors Directorate (NVESD), has performed a study to specify system and detection requirements; determined how current autonomy sensors perform in various scenarios; and analyzed how sensors should be employed to increase operational speeds of ground vehicles. The sensors evaluated in this study include the state of the art in LADAR/LIDAR, Radar, Electro-Optical, and Infrared sensors, and have been analyzed at high speeds to study their effectiveness in detecting and accounting for obstacles and other perception challenges. By creating a common set of testing benchmarks, and by testing in a wide range of real-world conditions, Robotic Research has evaluated where sensors can be successfully employed today; where sensors fall short; and which technologies should be examined and developed further. This study is the first step to achieve the overarching goal of doubling ground vehicle speeds on any given terrain.

  1. [Learning strategies of autonomous medical students].

    Science.gov (United States)

    Márquez U, Carolina; Fasce H, Eduardo; Ortega B, Javiera; Bustamante D, Carolina; Pérez V, Cristhian; Ibáñez G, Pilar; Ortiz M, Liliana; Espinoza P, Camila; Bastías V, Nancy

    2015-12-01

    Understanding how autonomous students are capable of regulating their own learning process is essential to develop self-directed teaching methods. To understand how self-directed medical students approach learning in medical schools at University of Concepción, Chile. A qualitative and descriptive study, performed according to Grounded Theory guidelines, following Strauss & Corbin was performed. Twenty medical students were selected by the maximum variation sampling method. The data collection technique was carried out by a semi-structured thematic interview. Students were interviewed by researchers after an informed consent procedure. Data were analyzed by the open coding method using Atlas-ti 7.5.2 software. Self-directed learners were characterized by being good planners and managing their time correctly. Students performed a diligent selection of contents to study based on reliable literature sources, theoretical relevance and type of evaluation. They also emphasized the discussion of clinical cases, where theoretical contents can be applied. This modality allows them to gain a global view of theoretical contents, to verbalize knowledge and to obtain a learning feedback. The learning process of autonomous students is intentional and planned.

  2. Autonomic function in manganese alloy workers

    Energy Technology Data Exchange (ETDEWEB)

    Barrington, W.W.; Angle, C.R.; Willcockson, N.K.; Padula, M.A. [Univ. of Nebraska Medical Center, Omaha, NE (United States); Korn, T.

    1998-07-01

    The observation of orthostatic hypotension in an index case of manganese toxicity lead to this prospective attempt to evaluate cardiovascular autonomic function and cognitive and emotional neurotoxicity in eight manganese alloy welders and machinists. The subjects consisted of a convenience sample consisting of an index case of manganese dementia, his four co-workers in a frog shop for gouging, welding, and grinding repair of high manganese railway track and a convenience sample of three mild steel welders with lesser manganese exposure also referred because of cognitive or autonomic symptoms. Frog shop air manganese samples 9.6--10 years before and 1.2--3.4 years after the diagnosis of the index case exceeded 1.0 mg/m{sup 3} in 29% and 0.2 mg/m{sup 3} in 62%. Twenty-four-hour electrocardiographic (Holter) monitoring was used to determine the temporal variability of the heartrate (RR{prime} interval) and the rates of change at low frequency and high frequency. MMPI and MCMI personality assessment and short-term memory, figure copy, controlled oral word association, and symbol digit tests were used.

  3. Autonomic Context-Aware Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Nídia G. S. Campos

    2015-01-01

    Full Text Available Autonomic Computing allows systems like wireless sensor networks (WSN to self-manage computing resources in order to extend their autonomy as much as possible. In addition, contextualization tasks can fuse two or more different sensor data into a more meaningful information. Since these tasks usually run in a single centralized context server (e.g., sink node, the massive volume of data generated by the wireless sensors can lead to a huge information overload in such server. Here we propose DAIM, a distributed autonomic inference machine distributed which allows the sensor nodes to do self-management and contextualization tasks based on fuzzy logic. We have evaluated DAIM in a real sensor network taking into account other inference machines. Experimental results illustrate that DAIM is an energy-efficient contextualization method for WSN, reducing 48.8% of the number of messages sent to the context servers while saving 19.5% of the total amount of energy spent in the network.

  4. Security-Enhanced Autonomous Network Management

    Science.gov (United States)

    Zeng, Hui

    2015-01-01

    Ensuring reliable communication in next-generation space networks requires a novel network management system to support greater levels of autonomy and greater awareness of the environment and assets. Intelligent Automation, Inc., has developed a security-enhanced autonomous network management (SEANM) approach for space networks through cross-layer negotiation and network monitoring, analysis, and adaptation. The underlying technology is bundle-based delay/disruption-tolerant networking (DTN). The SEANM scheme allows a system to adaptively reconfigure its network elements based on awareness of network conditions, policies, and mission requirements. Although SEANM is generically applicable to any radio network, for validation purposes it has been prototyped and evaluated on two specific networks: a commercial off-the-shelf hardware test-bed using Institute of Electrical Engineers (IEEE) 802.11 Wi-Fi devices and a military hardware test-bed using AN/PRC-154 Rifleman Radio platforms. Testing has demonstrated that SEANM provides autonomous network management resulting in reliable communications in delay/disruptive-prone environments.

  5. Small Autonomous Aircraft Servo Health Monitoring

    Science.gov (United States)

    Quintero, Steven

    2008-01-01

    Small air vehicles offer challenging power, weight, and volume constraints when considering implementation of system health monitoring technologies. In order to develop a testbed for monitoring the health and integrity of control surface servos and linkages, the Autonomous Aircraft Servo Health Monitoring system has been designed for small Uninhabited Aerial Vehicle (UAV) platforms to detect problematic behavior from servos and the air craft structures they control, This system will serve to verify the structural integrity of an aircraft's servos and linkages and thereby, through early detection of a problematic situation, minimize the chances of an aircraft accident. Embry-Riddle Aeronautical University's rotary-winged UAV has an Airborne Power management unit that is responsible for regulating, distributing, and monitoring the power supplied to the UAV's avionics. The current sensing technology utilized by the Airborne Power Management system is also the basis for the Servo Health system. The Servo Health system measures the current draw of the servos while the servos are in Motion in order to quantify the servo health. During a preflight check, deviations from a known baseline behavior can be logged and their causes found upon closer inspection of the aircraft. The erratic behavior nay include binding as a result of dirt buildup or backlash caused by looseness in the mechanical linkages. Moreover, the Servo Health system will allow elusive problems to be identified and preventative measures taken to avoid unnecessary hazardous conditions in small autonomous aircraft.

  6. The MAP Autonomous Mission Control System

    Science.gov (United States)

    Breed, Juile; Coyle, Steven; Blahut, Kevin; Dent, Carolyn; Shendock, Robert; Rowe, Roger

    2000-01-01

    The Microwave Anisotropy Probe (MAP) mission is the second mission in NASA's Office of Space Science low-cost, Medium-class Explorers (MIDEX) program. The Explorers Program is designed to accomplish frequent, low cost, high quality space science investigations utilizing innovative, streamlined, efficient management, design and operations approaches. The MAP spacecraft will produce an accurate full-sky map of the cosmic microwave background temperature fluctuations with high sensitivity and angular resolution. The MAP spacecraft is planned for launch in early 2001, and will be staffed by only single-shift operations. During the rest of the time the spacecraft must be operated autonomously, with personnel available only on an on-call basis. Four (4) innovations will work cooperatively to enable a significant reduction in operations costs for the MAP spacecraft. First, the use of a common ground system for Spacecraft Integration and Test (I&T) as well as Operations. Second, the use of Finite State Modeling for intelligent autonomy. Third, the integration of a graphical planning engine to drive the autonomous systems without an intermediate manual step. And fourth, the ability for distributed operations via Web and pager access.

  7. Autonomic dysfunction and neuropeptide Y in fibromyalgia.

    Science.gov (United States)

    Di Franco, M; Iannuccelli, C; Alessandri, C; Paradiso, M; Riccieri, V; Libri, F; Valesini, G

    2009-01-01

    Fibromyalgia (FM) is a syndrome associated with widespread pain and various other signs and symptoms. Several of these multisystem features could be explained on the basis of autonomic nervous system (ANS) dysfunction. The aim of the present study was to evaluate ANS dysfunction in FM based on time-domain heart rate variability (HRV) analysis and serum neuropeptide Y (NPY) levels in 51 patients with FM, 25 patients with systemic sclerosis (SSc), and 15 healthy controls (NHS). Compared with the SSc and NHS groups, the FM group had significantly higher NPY levels, and in the FM subgroup subjected to HRV analysis (25/51 patients, 49%), certain HRV indices were significantly reduced. In this subgroup, NPY was significantly correlated with the SDANN index and the NN50, but neither NPY or HRV parameters showed any significant correlation with clinical aspects of the FM. These findings suggest that autonomic dysfunction and NPY are crucial elements in the pathophysiology of FM. Additional studies are necessary to define the complex roles played by NPY and ANS in modulating pain and immunological functions of different diseases.

  8. The usual treatment of trigeminal autonomic cephalalgias.

    Science.gov (United States)

    Pareja, Juan A; Álvarez, Mónica

    2013-10-01

    Trigeminal autonomic cephalalgias include cluster headache, paroxysmal hemicrania, and short-lasting unilateral neuralgiform headache attacks with conjunctival injection, tearing, and rhinorrhea (SUNCT). Conventional pharmacological therapy can be successful in the majority of trigeminal autonomic cephalalgias patients. Most cluster headache attacks respond to 100% oxygen inhalation, or 6 mg subcutaneous sumatriptan. Nasal spray of sumatriptan (20 mg) or zolmitriptan (5 mg) are recommended as second choice. The bouts can be brought under control by a short course of corticosteroids (oral prednisone: 60-100 mg/day, or intravenous methylprednisolone: 250-500 mg/day, for 5 days, followed by tapering off the dosage), or by long-term prophylaxis with verapamil (at least 240 mg/day). Alternative long-term preventive medications include lithium carbonate (800-1600 mg/day), methylergonovine (0.4-1.2 mg/day), and topiramate (100-200 mg/day). As a rule, paroxysmal hemicrania responds to preventive treatment with indomethacin (75-150 mg/day). A short course of intravenous lidocaine (1-4 mg/kg/hour) can reduce the flow of attacks during exacerbations of SUNCT. Lamotrigine (100-300 mg/day) is the preventive drug of choice for SUNCT. Gabapentin (800-2700 mg/day), topiramate (50-300 mg/day), and carbamazepine (200-1600 mg/day) may be of help. © 2013 American Headache Society.

  9. Stimulating autonomous motivation in the classroom: The role of interpersonal teacher agency and communion

    NARCIS (Netherlands)

    Wijsman, Lindy; Mainhard, Tim; Brekelmans, Mieke

    2014-01-01

    Self Determination Theory (SDT) distinguishes the quality of motivation from its quantity or intensity (Vansteenkiste, Sierens, Soetens, Luyckx, & Lens, 2009). A sequence from controlled to autonomous motivation is adopted; autonomous motivation is seen as the best quality type. Being autonomously

  10. Cardiac Autonomic Dysfunction in Children and Adolescents with ...

    African Journals Online (AJOL)

    Introduction: Autonomic neuropathy is less well documented in children with type 1 diabetes mellitus and has received less attention than other diabetic complications. Sudden death and cardio-respiratory arrest in patients with type 1 and type 2 diabetes mellitus have been attributed to cardiac autonomic dysfunction.

  11. Increasing Road Infrastructure Capacity Through the Use of Autonomous Vehicles

    Science.gov (United States)

    2016-12-01

    Simultaneously, the millennial generation has eschewed ownership of modes of transportation, and technology has facilitated the entrance of the...capacity increases to roadways enabled by autonomous vehicle technology . Public policy can enhance the adoption rate of autonomous vehicles to...maximize the benefit of this emergent technology on the roadway system. A policy analysis provides a comparison of options and outlines regulations that

  12. Autonomic response to exercise as measured by cardio- vascular ...

    African Journals Online (AJOL)

    Motivation. There is growing interest in the use of cardiovas- cular variability indicators as measures of autonomic activity, even though reported results are not always comparable or as expected. This review aims to determine the consistency of re- sults reported on the autonomic response to physical exercise as measured ...

  13. Autonomic Impairment in Borderline Personality Disorder: A Laboratory Investigation

    Science.gov (United States)

    Weinberg, Anna; Klonsky, E. David; Hajcak, Greg

    2009-01-01

    Recent research suggests that emotional dysfunction in psychiatric disorders can be reflected in autonomic abnormalities. The present study examines sympathetic and parasympathetic autonomic nervous system activity in individuals with Borderline Personality Disorder (BPD) before, during, and following a social stressor task. Data were obtained…

  14. Autonomous metacommunicative lexicon and its specifics in manipulative discourse

    Directory of Open Access Journals (Sweden)

    Gnezdilova Yaroslava

    2017-06-01

    Full Text Available The article focuses on the study of metacommunicative means, and a unified approach to their classification is implemented. Special attention is drawn to distinguishing the main types of autonomous metacommunicative means and their functioning in manipulative discourse. The results show that the group of autonomous metacommunicative units comprises all those means, which preserve their metacommunicative functions even when other functions dominate.

  15. Cardiac autonomic control in the obstructive sleep apnea ...

    African Journals Online (AJOL)

    However, only a few studies tackled the dynamics of the autonomic nervous system during sleep in patients having OSA. Aims: To analyze the HRVover sleep stages and across sleep periods in order to clarify the impact of OSA on cardiac autonomic modulation. The second objective is to examine the nocturnal HRV of ...

  16. Biologically Inspired Waveform Diversity for Synthetic Autonomous Navigation Sensing

    Science.gov (United States)

    2009-11-01

    navigation, collision avoidance, ambiguity SUMMARY Echolocating mammals such as bats , whales and dolphins have been using waveform diversity for...we have adopted. Mammals such as bats use echolocation to perform autonomous navigation (or more strictly orientation), detection and classification...understand how bats exploit echolocation for autonomous navigation and collision avoidance we can then begin to build this into synthetic systems

  17. Equipment Proposal for the Autonomous Vehicle Systems Laboratory at UIW

    Science.gov (United States)

    2015-04-29

    testing, 5) 38 Lego Mindstorm EV3 and Hitechnic Sensors for use in feedback control and autonomous systems for STEM undergraduate and High School...autonomous robots using the Lego Mindstorm EV3. This robotics workshop will be used as a pilot study for next summer when more High School students

  18. Application of laser radar to autonomous spacecraft landing

    Science.gov (United States)

    Gleichman, Kurt; Tchoryk, Peter, Jr.; Sampson, Robert E.

    1991-01-01

    This paper discusses the scenario of an autonomous landing like that required for the Mars Rover Sample Return Mission. An application of laser radar for conducting autonomous hazard detection and avoidance is discussed. A trade-study is performed to identify operational and implementation constraints as well as the state of the art in component technology.

  19. Systematic design of an autonomous platform for robotic weeding

    NARCIS (Netherlands)

    Bakker, T.; Asselt, van C.J.; Bontsema, J.; Müller, J.; Straten, van G.

    2010-01-01

    The systematic design of an autonomous platform for robotic weeding research in arable farming is described. The long term objective of the project is the replacement of hand weeding in organic farming by a device working autonomously at field level. The distinguishing feature of the described

  20. Cardiovascular autonomic dysfunction due to diabetes mellitus: An ...

    African Journals Online (AJOL)

    Cardiovascular autonomic neuropathy (CAN) is a common form of diabetes autonomic neuropathy, causes abnormalities in heart rate control as well as central and peripheral vascular dynamics, and may carry an increased risk of mortality. The aim of this article was to review the importance of identifying CAN and ...

  1. Theoretical foundations for the responsibility of autonomous agents

    NARCIS (Netherlands)

    Hage, Jaap

    This article argues that it is possible to hold autonomous agents themselves, and not only their makers, users or owners, responsible for the acts of these agents. In this connection autonomous systems are computer programs that interact with the outside world without human interference. They

  2. Modeling of an autonomous microgrid for renewable energy sources integration

    DEFF Research Database (Denmark)

    Serban, I.; Teodorescu, Remus; Guerrero, Josep M.

    2009-01-01

    The frequency stability analysis in an autonomous microgrid (MG) with renewable energy sources (RES) is a continuously studied issue. This paper presents an original method for modeling an autonomous MG with a battery energy storage system (BESS) and a wind power plant (WPP), with the purpose...

  3. Perioperative implications of the patient with autonomic dysfunction.

    Science.gov (United States)

    McGrane, Stuart; Atria, Nicklaus P; Barwise, John A

    2014-06-01

    The autonomic nervous system functions to control heart rate, blood pressure, respiratory rate, gastrointestinal motility, hormone release, and body temperature on a second-to-second basis. Here we summarize some of the latest literature on autonomic dysfunction, focusing primarily on the perioperative implications. The variety of autonomic dysfunction now extends to a large number of clinical conditions in which the cause or effect of the autonomic component is blurred. Methods for detecting dysautonomia can be as simple as performing a history and physical examination that includes orthostatic vital signs measured in both recumbent and vertical positions; however, specialized laboratories are required for definitive diagnosis. Heart rate variability monitoring is becoming more commonplace in the assessment and understanding of autonomic instability. Degenerative diseases of the autonomic nervous system include Parkinson's disease and multiple system atrophy, with the most serious manifestations being postural hypotension and paradoxical supine hypertension. Other conditions occur in which the autonomic dysfunction is only part of a larger disease process, such as diabetic autonomic neuropathy, traumatic brain injury, and spinal cord injury. Patients with dysautonomia often have unpredictable and paradoxical physiological responses to various perioperative stimuli. Knowledge of the underlying pathophysiology of their condition is required in order to reduce symptom exacerbation and limit morbidity and mortality during the perioperative period.

  4. The treatment of autonomic dysfunction in tetanus | Maryke Spruyt ...

    African Journals Online (AJOL)

    We report a case of generalised tetanus in a 50-year-old female patient after sustaining a wound to her right lower leg. She developed autonomic dysfunction, which included labile hypertension alternating with hypotension and sweating. The autonomic dysfunction was treated successfully with a combination of morphine ...

  5. Autonomic manifestations of epilepsy | Asindi | Nigerian Journal of ...

    African Journals Online (AJOL)

    Abstract: An epileptic fit does not only manifest as bizarre motor activity but can destabilize autonomic functions. Abnormal electrical discharge originating from the cerebral cortex can spreads to involve the autonomic system thus creating a dysfunction of the sympathetic and the parasympathetic which modulate the ...

  6. Learner Behaviors and Perceptions of Autonomous Language Learning

    Science.gov (United States)

    Bekleyen, Nilüfer; Selimoglu, Figen

    2016-01-01

    The purpose of the present study was to investigate the learners' behaviors and perceptions about autonomous language learning at the university level in Turkey. It attempts to reveal what type of perceptions learners held regarding teachers' and their own responsibilities in the language learning process. Their autonomous language learning…

  7. Socially intelligent autonomous agents that learn from human reward

    NARCIS (Netherlands)

    Li, Guangliang

    2016-01-01

    In the future, autonomous agents will operate in human inhabited environments in many real world applications and become an integral part of human’s daily lives. Therefore, when autonomous agents enter into the real world, they need to adapt to many novel, dynamic and complex situations that cannot

  8. Review article: Autonomous neural inflammatory reflex and control of

    African Journals Online (AJOL)

    ... and neural autonomic pathway through vagus nerve monitor inflammatory status and coordinate appropriate host defences. Immunomodulatory stimulation of vagus nerve, acetylcholinesterase inhibitory mechanism and 7 nAChR receptor expressed on immune cells plays a role on autonomous neural inflammatory reflex.

  9. Evaluating the autonomic nervous system in patients with laryngopharyngeal reflux.

    Science.gov (United States)

    Huang, Wan-Ju; Shu, Chih-Hung; Chou, Kun-Ta; Wang, Yi-Fen; Hsu, Yen-Bin; Ho, Ching-Yin; Lan, Ming-Ying

    2013-06-01

    The pathogenesis of laryngopharyngeal reflux (LPR) remains unclear. It is linked to but distinct from gastroesophageal reflux disease (GERD), which has been shown to be related to disturbed autonomic regulation. The aim of this study is to investigate whether autonomic dysfunction also plays a role in the pathogenesis of LPR. Case-control study. Tertiary care center. Seventeen patients with LPR and 19 healthy controls, aged between 19 and 50 years, were enrolled in the study. The patients were diagnosed with LPR if they had a reflux symptom index (RSI) ≥ 13 and a reflux finding score (RFS) ≥ 7. Spectral analysis of heart rate variability (HRV) analysis was used to assess autonomic function. Anxiety and depression levels measured by the Beck Anxiety Inventory (BAI) and Beck Depression Inventory II (BDI-II) were also conducted. In HRV analysis, high frequency (HF) represents the parasympathetic activity of the autonomic nervous system, whereas low frequency (LF) represents the total autonomic activity. There were no significant differences in the LF power and HF power between the 2 groups. However, significantly lower HF% (P = .003) and a higher LF/HF ratio (P = .012) were found in patients with LPR, who demonstrated poor autonomic modulation and higher sympathetic activity. Anxiety was also frequently observed in the patient group. The study suggests that autonomic dysfunction seems to be involved in the pathogenesis of LPR. The potential beneficial effect of autonomic nervous system modulation as a therapeutic modality for LPR merits further investigation.

  10. Should autonomous agents be liable for what they do?

    NARCIS (Netherlands)

    Hage, Jaap; Keirse, A.; Loos, M.

    2017-01-01

    This article argues that it may be useful to sometimes hold autonomous agents, and not only their users, responsible for their acts. In this connection autonomous systems can be computer programs that interact with the outside world without human interference, including ‘intelligent’ weapons and

  11. Examining accident reports involving autonomous vehicles in California

    Science.gov (United States)

    Nader, Nazanin; Eurich, Sky O.; Tripp, Michelle; Varadaraju, Naresh

    2017-01-01

    Autonomous Vehicle technology is quickly expanding its market and has found in Silicon Valley, California, a strong foothold for preliminary testing on public roads. In an effort to promote safety and transparency to consumers, the California Department of Motor Vehicles has mandated that reports of accidents involving autonomous vehicles be drafted and made available to the public. The present work shows an in-depth analysis of the accident reports filed by different manufacturers that are testing autonomous vehicles in California (testing data from September 2014 to March 2017). The data provides important information on autonomous vehicles accidents’ dynamics, related to the most frequent types of collisions and impacts, accident frequencies, and other contributing factors. The study also explores important implications related to future testing and validation of semi-autonomous vehicles, tracing the investigation back to current literature as well as to the current regulatory panorama. PMID:28931022

  12. Examining accident reports involving autonomous vehicles in California.

    Science.gov (United States)

    Favarò, Francesca M; Nader, Nazanin; Eurich, Sky O; Tripp, Michelle; Varadaraju, Naresh

    2017-01-01

    Autonomous Vehicle technology is quickly expanding its market and has found in Silicon Valley, California, a strong foothold for preliminary testing on public roads. In an effort to promote safety and transparency to consumers, the California Department of Motor Vehicles has mandated that reports of accidents involving autonomous vehicles be drafted and made available to the public. The present work shows an in-depth analysis of the accident reports filed by different manufacturers that are testing autonomous vehicles in California (testing data from September 2014 to March 2017). The data provides important information on autonomous vehicles accidents' dynamics, related to the most frequent types of collisions and impacts, accident frequencies, and other contributing factors. The study also explores important implications related to future testing and validation of semi-autonomous vehicles, tracing the investigation back to current literature as well as to the current regulatory panorama.

  13. Examining accident reports involving autonomous vehicles in California.

    Directory of Open Access Journals (Sweden)

    Francesca M Favarò

    Full Text Available Autonomous Vehicle technology is quickly expanding its market and has found in Silicon Valley, California, a strong foothold for preliminary testing on public roads. In an effort to promote safety and transparency to consumers, the California Department of Motor Vehicles has mandated that reports of accidents involving autonomous vehicles be drafted and made available to the public. The present work shows an in-depth analysis of the accident reports filed by different manufacturers that are testing autonomous vehicles in California (testing data from September 2014 to March 2017. The data provides important information on autonomous vehicles accidents' dynamics, related to the most frequent types of collisions and impacts, accident frequencies, and other contributing factors. The study also explores important implications related to future testing and validation of semi-autonomous vehicles, tracing the investigation back to current literature as well as to the current regulatory panorama.

  14. Design of an Autonomous Transport System for Coastal Areas

    Directory of Open Access Journals (Sweden)

    Andrzej Lebkowski

    2018-03-01

    Full Text Available The article presents a project of an autonomous transport system that can be deployed in coastal waters, bays or between islands. Presented solutions and development trends in the transport of autonomous and unmanned units (ghost ships are presented. The structure of the control system of autonomous units is discussed together with the presentation of applied solutions in the field of artificial intelligence. The paper presents the concept of a transport system consisting of autonomous electric powered vessels designed to carry passengers, bikes, mopeds, motorcycles or passenger cars. The transport task is to be implemented in an optimal way, that is, most economically and at the same time as safe as possible. For this reason, the structure of the electric propulsion system that can be found on such units is shown. The results of simulation studies of autonomous system operation using simulator of marine navigational environment are presented.

  15. 12th International Conference on Intelligent Autonomous Systems (IAS-12)

    CERN Document Server

    Yoon, Kwang-Joon; Lee, Jangmyung; Frontiers of Intelligent Autonomous Systems

    2013-01-01

    This carefully edited volume aims at providing readers with the most recent progress on intelligent autonomous systems, with its particular emphasis on intelligent autonomous ground, aerial and underwater vehicles as well as service robots for home and healthcare under the context of the aforementioned convergence. “Frontiers of Intelligent Autonomous Systems” includes thoroughly revised and extended papers selected from the 12th International Conference on Intelligent Autonomous Systems (IAS-12), held in Jeju, Korea, June 26-29, 2012. The editors chose 35 papers out of the 202 papers presented at IAS-12 which are organized into three chapters: Chapter 1 is dedicated to autonomous navigation and mobile manipulation, Chapter 2 to unmanned aerial and underwater vehicles and Chapter 3 to service robots for home and healthcare. To help the readers to easily access this volume, each chapter starts with a chapter summary introduced by one of the editors: Chapter 1 by Sukhan Lee, Chapter 2 by Kwang Joon Yoon and...

  16. 12th International Conference on Intelligent Autonomous Systems

    CERN Document Server

    Cho, Hyungsuck; Yoon, Kwang-Joon; Lee, Jangmyung

    2013-01-01

    Intelligent autonomous systems are emerged as a key enabler for the creation of a new paradigm of services to humankind, as seen by the recent advancement of autonomous cars licensed for driving in our streets, of unmanned aerial and underwater vehicles carrying out hazardous tasks on-site, and of space robots engaged in scientific as well as operational missions, to list only a few. This book aims at serving the researchers and practitioners in related fields with a timely dissemination of the recent progress on intelligent autonomous systems, based on a collection of papers presented at the 12th International Conference on Intelligent Autonomous Systems, held in Jeju, Korea, June 26-29, 2012. With the theme of “Intelligence and Autonomy for the Service to Humankind, the conference has covered such diverse areas as autonomous ground, aerial, and underwater vehicles, intelligent transportation systems, personal/domestic service robots, professional service robots for surgery/rehabilitation, rescue/security ...

  17. Autonomous Underwater Vehicle Magnetic Mapping System

    Science.gov (United States)

    Steigerwalt, R.; Johnson, R. M.; Trembanis, A. C.; Schmidt, V. E.; Tait, G.

    2012-12-01

    An Autonomous Underwater Vehicle (AUV) Magnetic Mapping (MM) System has been developed and tested for military munitions detection as well as pipeline locating, wreck searches, and geologic surveys in underwater environments. The system is comprised of a high sensitivity Geometrics G-880AUV cesium vapor magnetometer integrated with a Teledyne-Gavia AUV and associated Doppler enabled inertial navigation further utilizing traditional acoustic bathymetric and side scan imaging. All onboard sensors and associated electronics are managed through customized crew members to autonomously operate through the vehicles primary control module. Total field magnetic measurements are recorded with asynchronous time-stamped data logs which include position, altitude, heading, pitch, roll, and electrical current usage. Pre-planned mission information can be uploaded to the system operators to define data collection metrics including speed, height above seafloor, and lane or transect spacing specifically designed to meet data quality objectives for the survey. As a result of the AUVs modular design, autonomous navigation and rapid deployment capabilities, the AUV MM System provides cost savings over current surface vessel surveys by reducing the mobilization/demobilization effort, thus requiring less manpower for operation and reducing or eliminating the need for a surface support vessel altogether. When the system completes its mission, data can be remotely downloaded via W-LAN and exported for use in advanced signal processing platforms. Magnetic compensation software has been concurrently developed to accept electrical current measurements directly from the AUV to address distortions from permanent and induced magnetization effects on the magnetometer. Maneuver and electrical current compensation terms can be extracted from the magnetic survey missions to perform automated post-process corrections. Considerable suppression of system noise has been observed over traditional

  18. Transitioning Submersible Chemical Analyzer Technologies for Sustained, Autonomous Observations From Profiling Moorings, Gliders and other AUVs

    National Research Council Canada - National Science Library

    Hanson, Alfred K; Donaghay, Percy L; Moore, Casey; Arrieta, Richard

    2006-01-01

    The long term goal is to transition existing prototype autonomous profiling nutrient analyzers into commercial products that can be readily deployed on autonomous profiling moorings, coastal gliders...

  19. Transitioning Submersible Chemical Analyzer Technologies for Sustained, Autonomous Observations from Profiling Moorings, Gliders and other AUVs

    National Research Council Canada - National Science Library

    Hanson, Alfred K; Donaghay, Percy L; Moore, Casey; Arrieta, Richard

    2005-01-01

    The long term goal is to transition existing prototype autonomous profiling nutrient analyzers into commercial products that can be readily deployed on autonomous profiling moorings, coastal gliders...

  20. Autonomic Cluster Management System (ACMS): A Demonstration of Autonomic Principles at Work

    Science.gov (United States)

    Baldassari, James D.; Kopec, Christopher L.; Leshay, Eric S.; Truszkowski, Walt; Finkel, David

    2005-01-01

    Cluster computing, whereby a large number of simple processors or nodes are combined together to apparently function as a single powerful computer, has emerged as a research area in its own right. The approach offers a relatively inexpensive means of achieving significant computational capabilities for high-performance computing applications, while simultaneously affording the ability to. increase that capability simply by adding more (inexpensive) processors. However, the task of manually managing and con.guring a cluster quickly becomes impossible as the cluster grows in size. Autonomic computing is a relatively new approach to managing complex systems that can potentially solve many of the problems inherent in cluster management. We describe the development of a prototype Automatic Cluster Management System (ACMS) that exploits autonomic properties in automating cluster management.