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Sample records for autonomous non-ltr retrotransposons

  1. The evolutionary dynamics of autonomous non-LTR retrotransposons in the lizard Anolis carolinensis shows more similarity to fish than mammals.

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    Novick, Peter A; Basta, Holly; Floumanhaft, Mark; McClure, Marcella A; Boissinot, Stéphane

    2009-08-01

    The genome of the lizard Anolis carolinensis (the green anole) is the first nonavian reptilian genome sequenced. It offers a unique opportunity to comparatively examine the evolution of amniote genomes. We analyzed the abundance and diversity of non-LTR (long terminal repeat) retrotransposons in the anole using the Genome Parsing Suite. We found that the anole genome contains an extraordinary diversity of elements. We identified 46 families of elements representing five clades (L1, L2, CR1, RTE, and R4). Within most families, elements are very similar to each other suggesting that they have been inserted recently. The rarity of old elements suggests a high rate of turnover, the insertion of new elements being offset by the loss of element-containing loci. Consequently, non-LTR retrotransposons accumulate in the anole at a low rate and are found in low copy number. This pattern of diversity shows some striking similarity with the genome of teleostean fish but contrasts greatly with the low diversity and high copy number of mammalian L1 elements, suggesting a fundamental difference in the way mammals and nonmammalian vertebrates interact with their genomic parasites. The scarcity of divergent elements in anoles suggests that insertions have a deleterious effect and are eliminated by natural selection. We propose that the low abundance of non-LTR retrotransposons in the anole is related directly or indirectly to a higher rate of ectopic recombination in the anole relative to mammals.

  2. Recent CR1 non-LTR retrotransposon activity in coscoroba reveals an insertion site preference

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    Quinn Thomas W

    2008-11-01

    Full Text Available Abstract Background Chicken repeat 1 (CR1 is a taxonomically widespread non-LTR retrotransposon. Insertion site bias, or lack thereof, has not been demonstrated for CR1. Recent CR1 retrotranspositions were used to examine flanking regions for GC content and nucleotide bias at the insertion site. Results Elucidation of the exact octomer repeat sequence (TTCTGTGA allowed for the identification of younger insertion events. The number of octomer repeats associated with a CR1 element increases after insertion with CR1s having one octomer being youngest. These young CR1s are flanked by regions of low GC content (38%. Furthermore, a bias for specific bases within the first four positions at the site of insertion was revealed. Conclusion This study focused on those loci where the insertion event has been most recent, as this would tend to minimize noise introduced by post-integration mutational events. Our data suggest that CR1 is not inserting into regions of higher GC content within the coscoroba genome; but rather, preferentially inserting into regions of lower GC content. Furthermore, there appears to be a base preference (TTCT for the insertion site. The results of this study increase the current level of understanding regarding the elusive CR1 non-LTR retrotransposon.

  3. An abundant and heavily truncated non-LTR retrotransposon (LINE) family in Beta vulgaris.

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    Wenke, Torsten; Holtgräwe, Daniela; Horn, Axel V; Weisshaar, Bernd; Schmidt, Thomas

    2009-12-01

    We describe a non-LTR retrotransposon family,BvL, of the long interspersed nuclear elements L1 clade isolated from sugar beet (Beta vulgaris). Characteristic molecular domains of three full-length BvL elements were determined in detail, showing that coding sequences are interrupted and most likely non-functionally. In addition,eight highly conserved endonuclease regions were defined by comparison with other plant LINEs. The abundant BvL family is widespread within the genus Beta, however, the vast majority of BvL copies are extremely 50 truncated indicating an error-prone reverse transcriptase activity. The dispersed distribution of BvL copies on all sugar beet chromosomes with exclusion of most heterochromatic regions was shown by fluorescent in situ hybridization. The analysis of BvL 30 end sequences and corresponding flanking regions, respectively, revealed the preferred integration of BvL into A/T-rich regions of the sugar beet genome, but no specific target sequences.

  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. The Juan non-LTR retrotransposon in mosquitoes: genomic impact, vertical transmission and indications of recent and widespread activity

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    Tu Zhijian

    2007-07-01

    Full Text Available Abstract Background In contrast to DNA-mediated transposable elements (TEs, retrotransposons, particularly non-long terminal repeat retrotransposons (non-LTRs, are generally considered to have a much lower propensity towards horizontal transfer. Detailed studies on site-specific non-LTR families have demonstrated strict vertical transmission. More studies are needed with non-site-specific non-LTR families to determine whether strict vertical transmission is a phenomenon related to site specificity or a more general characteristic of all non-LTRs. Juan is a Jockey clade non-LTR retrotransposon first discovered in mosquitoes that is widely distributed in the mosquito family Culicidae. Being a non-site specific non-LTR, Juan offers an opportunity to further investigate the hypothesis that non-LTRs are genomic elements that are primarily vertically transmitted. Results Systematic analysis of the ~1.3 Gbp Aedes aegypti (Ae. aegypti genome sequence suggests that Juan-A is the only Juan-type non-LTR in Aedes aegypti. Juan-A is highly reiterated and comprises approximately 3% of the genome. Using minimum cutoffs of 90% length and 70% nucleotide (nt identity, 663 copies were found by BLAST using the published Juan-A sequence as the query. All 663 copies are at least 95% identical to Juan-A, while 378 of these copies are 99% identical to Juan-A, indicating that the Juan-A family has been transposing recently in evolutionary history. Using the 0.34 Kb 5' UTR as the query, over 2000 copies were identified that may contain internal promoters, leading to questions on the genomic impact of Juan-A. Juan sequences were obtained by PCR, library screening, and database searches for 18 mosquito species of six genera including Aedes, Ochlerotatus, Psorophora, Culex, Deinocerites, and Wyeomyia. Comparison of host and Juan phylogenies shows overall congruence with few exceptions. Conclusion Juan-A is a major genomic component in Ae. aegypti and it has been

  6. Vertical evolution and horizontal transfer of CR1 non-LTR retrotransposons and Tc1/mariner DNA transposons in Lepidoptera species.

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    Sormacheva, Irina; Smyshlyaev, Georgiy; Mayorov, Vladimir; Blinov, Alexander; Novikov, Anton; Novikova, Olga

    2012-12-01

    Horizontal transfer (HT) is a complex phenomenon usually used as an explanation of phylogenetic inconsistence, which cannot be interpreted in terms of vertical evolution. Most examples of HT of eukaryotic genes involve transposable elements. An intriguing feature of HT is that its frequency differs among transposable elements classes. Although HT is well known for DNA transposons and long terminal repeat (LTR) retrotransposons, non-LTR retrotransposons rarely undergo HT, and their phylogenies are largely congruent to those of their hosts. Previously, we described HT of CR1-like non-LTR retrotransposons between butterflies (Maculinea) and moths (Bombyx), which occurred less than 5 million years ago (Novikova O, Sliwinska E, Fet V, Settele J, Blinov A, Woyciechowski M. 2007. CR1 clade of non-LTR retrotransposons from Maculinea butterflies (Lepidoptera: Lycaenidae): evidence for recent horizontal transmission. BMC Evol Biol. 7:93). In this study, we continued to explore the diversity of CR1 non-LTR retrotransposons among lepidopterans providing additional evidences to support HT hypothesis. We also hypothesized that DNA transposons could be involved in HT of non-LTR retrotransposons. Thus, we performed analysis of one of the groups of DNA transposons, mariner-like DNA elements, as potential vectors for HT of non-LTR retrotransposons. Our results demonstrate multiple HTs between Maculinea and Bombyx genera. Although we did not find strong evidence for our hypothesis of the involvement of DNA transposons in HT of non-LTR retrotransposons, we demonstrated that recurrent and/or simultaneous flow of TEs took place between distantly related moths and butterflies.

  7. Characterization of SR3 reveals abundance of non-LTR retrotransposons of the RTE clade in the genome of the human blood fluke, Schistosoma mansoni

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    Brindley Paul J

    2005-11-01

    Full Text Available Abstract Background It is becoming apparent that perhaps as much as half of the genome of the human blood fluke Schistosoma mansoni is constituted of mobile genetic element-related sequences. Non-long terminal repeat (LTR retrotransposons, related to the LINE elements of mammals, comprise much of this repetitive component of the schistosome genome. Of more than 12 recognized clades of non-LTR retrotransposons, only members of the CR1, RTE, and R2 clades have been reported from the schistosome genome. Results Inspection of the nucleotide sequence of bacterial artificial chromosome number 49_J_14 from chromosome 1 of the genome of Schistosoma mansoni (GenBank AC093105 revealed the likely presence of several RTE-like retrotransposons. Among these, a new non-LTR retrotransposon designated SR3 was identified and is characterized here. Analysis of gene structure and phylogenetic analysis of both the reverse transcriptase and endonuclease domains of the mobile element indicated that SR3 represented a new family of RTE-like non-LTR retrotransposons. Remarkably, two full-length copies of SR3-like elements were present in BAC 49-J-14, and one of 3,211 bp in length appeared to be intact, indicating SR3 to be an active non-LTR retrotransposon. Both were flanked by target site duplications of 10–12 bp. Southern hybridization and bioinformatics analyses indicated the presence of numerous copies (probably >1,000 of SR3 interspersed throughout the genome of S. mansoni. Bioinformatics analyses also revealed SR3 to be transcribed in both larval and adult developmental stages of S. mansoni and to be also present in the genomes of the other major schistosome parasites of humans, Schistosoma haematobium and S. japonicum. Conclusion Numerous copies of SR3, a novel non-LTR retrotransposon of the RTE clade are present in the genome of S. mansoni. Non-LTR retrotransposons of the RTE clade including SR3 appear to have been remarkably successful in colonizing, and

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

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    Seto, Yosuke; Fujiwara, Haruhiko

    2016-01-01

    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. PMID:27662593

  9. 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

  10. Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons

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    Pagano, Johanna F.B.; Ensink, Wim A.; van Olst, Marina; van Leeuwen, Selina; Nehrdich, Ulrike; Zhu, Kongju; Spaink, Herman P.; Girard, Geneviève; Rauwerda, Han; Jonker, Martijs J.; Dekker, Rob J.

    2017-01-01

    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 identified maternal-type 5S rRNA that is exclusively accumulated during oogenesis, replaced throughout the embryogenesis by a somatic-type, and thus virtually absent in adult somatic tissue. The maternal-type 5S rDNA contains several thousands of gene copies on chromosome 4 in tandem repeats with small intergenic regions, whereas the somatic-type is present in only 12 gene copies on chromosome 18 with large intergenic regions. The nine-nucleotide variation between the two 5S rRNA types likely affects TFIII binding and riboprotein L5 binding, probably leading to storage of maternal-type rRNA. Remarkably, these sequence differences are located exactly at the sequence-specific target site for genome integration by the 5S rRNA-specific Mutsu retrotransposon family. Thus, we could define maternal- and somatic-type MutsuDr subfamilies. Furthermore, we identified four additional maternal-type and two new somatic-type MutsuDr subfamilies, each with their own target sequence. This target-site specificity, frequently intact maternal-type retrotransposon elements, plus specific presence of Mutsu retrotransposon RNA and piRNA in egg and adult tissue, suggest an involvement of retrotransposons in achieving the differential copy number of the two types of 5S rDNA loci. PMID:28003516

  11. A yeast model for target-primed (non-LTR retrotransposition

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    Busby Jason N

    2007-08-01

    Full Text Available Abstract Background Target-primed (non-LTR retrotransposons, such as the human L1 element, are mobile genetic elements found in many eukaryotic genomes. They are often present in large numbers and their retrotransposition can cause mutations and genomic rearrangements. Despite their importance, many aspects of their replication are not well understood. Results We have developed a yeast model system for studying target-primed retrotransposons. This system uses the Zorro3 element from Candida albicans. A cloned copy of Zorro3, tagged with a retrotransposition indicator gene, retrotransposes at a high frequency when introduced into an appropriate C. albicans host strain. Retrotransposed copies of the tagged element exhibit similar features to the native copies, indicating that the natural retrotransposition pathway is being used. Retrotransposition is dependent on the products of the tagged element's own genes and is highly temperature-regulated. The new assay permits the analysis of the effects of specific mutations introduced into the cloned element. Conclusion This Zorro3 retrotransposition assay system complements previously available target-primed retrotransposition assays. Due to the relative simplicity of the growth, manipulation and analysis of yeast cells, the system should advance our understanding of target-primed retrotransposition.

  12. Retrotransposon OV-RTE-1 from the carcinogenic liver fluke Opisthorchis viverrini: potential target for DNA-based diagnosis.

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    Thi Phung, Luyen; Loukas, Alex; Brindley, Paul J; Sripa, Banchob; Laha, Thewarach

    2014-01-01

    Infections by the fish-borne liver flukes Opisthorchis viverrini and Clonorchis sinensis can lead to bile duct cancer. These neglected tropical disease pathogens occur in East Asia, with O. viverrini primarily in Thailand and Laos and C. sinensis in Cambodia, Vietnam, and China. Genomic information about these pathogens holds the potential to improve disease treatment and control. Transcriptome analysis indicates that mobile genetic elements are active in O. viverrini, including a novel non-Long Terminal Repeat (LTR) retrotransposon. A consensus sequence of this element, termed OV-RTE-1, was assembled from expressed sequence tags and PCR amplified genomic DNA. OV-RTE-1 was 3330 bp in length, encoded 1101 amino acid residues and exhibited hallmark structures and sequences of non-LTR retrotransposons including a single open reading frame encoding apurinic-apyrimidinic endonuclease (EN) and reverse transcriptase (RT). Phylogenetic analyses confirmed that OV-RTE-1 was member of the RTE clade of non-LTR retrotransposons. OV-RTE-1 is the first non-LTR retrotransposon characterized from the trematode family Opisthorchiidae. Sequences of OV-RTE-1 were targeted to develop a diagnostic tool for detection of infection by O. viverrini. PCR specific primers for detection of O. viverrini DNA showed 100% specificity and sensitivity for detection of as little as 5 fg of O. viverrini DNA whereas the PCR based approach showed 62% sensitivity and 100% specificity with clinical stool samples. The OV-RTE-1 specific PCR could be developed as a molecular diagnostic for Opisthorchis infection targeting parasite eggs in stool samples, especially in regions of mixed infection of O. viverrini and/or C. sinensis and minute intestinal flukes.

  13. Novel non-autonomous transposable elements onWchromosome of the silkworm, Bombyx mori

    Indian Academy of Sciences (India)

    Hiroaki Abe; Tsuguru Fujii; Toru Shimada; Kazuei Mita

    2010-09-01

    The sex chromosomes of the silkworm Bombyx mori are designated ZW(XY) for females and ZZ (XX) for males. Numerous long terminal repeat (LTR) and non-LTR retrotransposons, retroposons and DNA transposons have accumulated as strata on the W chromosome. However, there are nucleotide sequences that do not show the characteristics of typical transposable elements on the W chromosome. To analyse these uncharacterized nucleotide sequences on the W chromosome, we used whole-genome shotgun (WGS) data and assembled data that was obtained using male genome DNA. Through these analyses, we found that almost all of these uncharacterized sequences were non-autonomous transposable elements that do not fit into the conventional classification. It is notable that some of these transposable elements contained the Bombyx short interspersed element (Bm1) sequences in the elements. We designated them as secondary-Bm1 transposable elements (SBTEs). Because putative ancestral SBTE nucleotide sequences without Bm1 do not occur in theWGS data, we suggest that the Bm1 sequences of SBTEs are not carried on each element merely as a package but are components of each element. Therefore, we confirmed that SBTEs should be classified as a new group of transposable elements.

  14. 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.

  15. How retrotransposons shape genome regulation.

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    Mita, Paolo; Boeke, Jef D

    2016-04-01

    Retrotransposons are mutagenic units able to move within the genome. Despite many defenses deployed by the host to suppress potentially harmful activities of retrotransposons, these genetic units have found ways to meld with normal cellular functions through processes of exaptation and domestication. The same host mechanisms targeting transposon mobility allow for expansion and rewiring of gene regulatory networks on an evolutionary time scale. Recent works demonstrating retrotransposon activity during development, cell differentiation and neurogenesis shed new light on unexpected activities of transposable elements. Moreover, new technological advances illuminated subtler nuances of the complex relationship between retrotransposons and the host genome, clarifying the role of retroelements in evolution, development and impact on human disease.

  16. 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.

  17. The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution.

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    Estep, M C; DeBarry, J D; Bennetzen, J L

    2013-02-01

    Sample sequence analysis was employed to investigate the repetitive DNAs that were most responsible for the evolved variation in genome content across seven panicoid grasses with >5-fold variation in genome size and different histories of polyploidy. In all cases, the most abundant repeats were LTR retrotransposons, but the particular families that had become dominant were found to be different in the Pennisetum, Saccharum, Sorghum and Zea lineages. One element family, Huck, has been very active in all of the studied species over the last few million years. This suggests the transmittal of an active or quiescent autonomous set of Huck elements to this lineage at the founding of the panicoids. Similarly, independent recent activity of Ji and Opie elements in Zea and of Leviathan elements in Sorghum and Saccharum species suggests that members of these families with exceptional activation potential were present in the genome(s) of the founders of these lineages. In a detailed analysis of the Zea lineage, the combined action of several families of LTR retrotransposons were observed to have approximately doubled the genome size of Zea luxurians relative to Zea mays and Zea diploperennis in just the last few million years. One of the LTR retrotransposon amplification bursts in Zea may have been initiated by polyploidy, but the great majority of transposable element activations are not. Instead, the results suggest random activation of a few or many LTR retrotransposons families in particular lineages over evolutionary time, with some families especially prone to future activation and hyper-amplification.

  18. 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.

  19. Microarray analysis of LTR retrotransposon silencing identifies Hdac1 as a regulator of retrotransposon expression in mouse embryonic stem cells.

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    Judith Reichmann

    Full Text Available Retrotransposons are highly prevalent in mammalian genomes due to their ability to amplify in pluripotent cells or developing germ cells. Host mechanisms that silence retrotransposons in germ cells and pluripotent cells are important for limiting the accumulation of the repetitive elements in the genome during evolution. However, although silencing of selected individual retrotransposons can be relatively well-studied, many mammalian retrotransposons are seldom analysed and their silencing in germ cells, pluripotent cells or somatic cells remains poorly understood. Here we show, and experimentally verify, that cryptic repetitive element probes present in Illumina and Affymetrix gene expression microarray platforms can accurately and sensitively monitor repetitive element expression data. This computational approach to genome-wide retrotransposon expression has allowed us to identify the histone deacetylase Hdac1 as a component of the retrotransposon silencing machinery in mouse embryonic stem cells, and to determine the retrotransposon targets of Hdac1 in these cells. We also identify retrotransposons that are targets of other retrotransposon silencing mechanisms such as DNA methylation, Eset-mediated histone modification, and Ring1B/Eed-containing polycomb repressive complexes in mouse embryonic stem cells. Furthermore, our computational analysis of retrotransposon silencing suggests that multiple silencing mechanisms are independently targeted to retrotransposons in embryonic stem cells, that different genomic copies of the same retrotransposon can be differentially sensitive to these silencing mechanisms, and helps define retrotransposon sequence elements that are targeted by silencing machineries. Thus repeat annotation of gene expression microarray data suggests that a complex interplay between silencing mechanisms represses retrotransposon loci in germ cells and embryonic stem cells.

  20. Domesticated DNA transposon proteins mediate retrotransposon control

    Institute of Scientific and Technical Information of China (English)

    Kathryn A O'Donnell; Jef D Boeke

    2008-01-01

    @@ The Schizosaccharomyces pontbe genome, like those of many eukaryotes, contains a number of retrotransposable repeat sequences. The pombe elements, termed Tfl (transposon of fission yeast 1) and Tf2 possess long terminal repeats (LTRs) and belong to the gypsy family of retrotransposons [1].

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

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    Sinibaldi-Vallebona, Paola; Matteucci, Claudia [Department of Experimental Medicine and Biochemical Sciences, University ‘Tor Vergata’, Rome (Italy); Spadafora, Corrado, E-mail: cspadaf@tin.it [Italian National Institute of Health (ISS), Rome (Italy)

    2011-03-07

    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.

  2. Evolution of Centromeric Retrotransposons in Grasses

    Science.gov (United States)

    Sharma, Anupma; Presting, Gernot G.

    2014-01-01

    Centromeric retrotransposons (CRs) constitute a family of plant retroelements, some of which have the ability to target their insertion almost exclusively to the functional centromeres. Our exhaustive analysis of CR family members in four grass genomes revealed not only horizontal transfer (HT) of CR elements between the oryzoid and panicoid grass lineages but also their subsequent recombination with endogenous elements that in some cases created prolific recombinants in foxtail millet and sorghum. HT events are easily identifiable only in cases where host genome divergence significantly predates HT, thus documented HT events likely represent only a fraction of the total. If the more difficult to detect ancient HT events occurred at frequencies similar to those observable in present day grasses, the extant long terminal repeat retrotransposons represent the mosaic products of HT and recombination that are optimized for retrotransposition in their host genomes. This complicates not only phylogenetic analysis but also the establishment of a meaningful retrotransposon nomenclature, which we have nevertheless attempted to implement here. In contrast to the plant-centric naming convention used currently for CR elements, we classify elements primarily based on their phylogenetic relationships regardless of host plant, using the exhaustively studied maize elements assigned to six different subfamilies as a standard. The CR2 subfamily is the most widely distributed of the six CR subfamilies discovered in grass genomes to date and thus the most likely to play a functional role at grass centromeres. PMID:24814286

  3. Retrotransposon vectors for gene delivery in plants

    Directory of Open Access Journals (Sweden)

    Hou Yi

    2010-08-01

    Full Text Available Abstract Background Retrotransposons are abundant components of plant genomes, and although some plant retrotransposons have been used as insertional mutagens, these mobile genetic elements have not been widely exploited for plant genome manipulation. In vertebrates and yeast, retrotransposons and retroviruses are routinely altered to carry additional genes that are copied into complementary (cDNA through reverse transcription. Integration of cDNA results in gene delivery; recombination of cDNA with homologous chromosomal sequences can create targeted gene modifications. Plant retrotransposon-based vectors, therefore, may provide new opportunities for plant genome engineering. Results A retrotransposon vector system was developed for gene delivery in plants based on the Tnt1 element from Nicotiana tabacum. Mini-Tnt1 transfer vectors were constructed that lack coding sequences yet retain the 5' and 3' long terminal repeats (LTRs and adjacent cis sequences required for reverse transcription. The internal coding region of Tnt1 was replaced with a neomycin phosphotransferase gene to monitor replication by reverse transcription. Two different mini-Tnt1 s were developed: one with the native 5' LTR and the other with a chimeric 5' LTR that had the first 233 bp replaced by the CaMV 35 S promoter. After transfer into tobacco protoplasts, both vectors undergo retrotransposition using GAG and POL proteins provided in trans by endogenous Tnt1 elements. The transposition frequencies of mini-Tnt1 vectors are comparable with native Tnt1 elements, and like the native elements, insertion sites are within or near coding sequences. In this paper, we provide evidence that template switching occurs during mini-Tnt1 reverse transcription, indicating that multiple copies of Tnt1 mRNA are packaged into virus-like particles. Conclusions Our data demonstrate that mini-Tnt1 vectors can replicate efficiently in tobacco cells using GAG and POL proteins provided in trans by

  4. Differential regulation of genes by retrotransposons in rice promoters.

    Science.gov (United States)

    Dhadi, Surendar Reddy; Xu, Zijun; Shaik, Rafi; Driscoll, Kyle; Ramakrishna, Wusirika

    2015-04-01

    Rice genome harbors genes and promoters with retrotransposon insertions. There is very little information about their function. The effect of retrotransposon insertions in four rice promoter regions on gene regulation, was investigated using promoter-reporter gene constructs with and without retrotransposons. Differences in expression levels of gus and egfp reporter genes in forward orientation and rfp in reverse orientation were evaluated in rice plants with transient expression employing quantitative RT-PCR analysis, histochemical GUS staining, and eGFP and RFP fluorescent microscopy. The presence of SINE in the promoter 1 (P1) resulted in higher expression levels of the reporter genes, whereas the presence of LINE in P2 or gypsy LTR retrotransposon in P3 reduced expression of the reporter genes. Furthermore, the SINE in P1 acts as an enhancer in contrast with the LINE in P2 and the gypsy LTR retrotransposon in P3 which act as silencers. CTAA and CGG motifs in these retrotransposons are the likely candidates for the downregulation compared to TCTT motif (SINE) which is a candidate for the upregulation of gene expression. The effect of retrotransposons on gene regulation correlated with the earlier investigation of conservation patterns of these four retrotransposon insertions in several rice accessions implying their evolutionary significance.

  5. Isolation and characterization of putative functional long terminal repeat retrotransposons in the Pyrus genome

    OpenAIRE

    Jiang, Shuang; Cai, Danying; Sun, Yongwang; Teng, Yuanwen

    2016-01-01

    Background Long terminal repeat (LTR)-retrotransposons constitute 42.4 % of the genome of the ‘Suli’ pear (Pyrus pyrifolia white pear group), implying that retrotransposons have played important roles in Pyrus evolution. Therefore, further analysis of retrotransposons will enhance our understanding of the evolutionary history of Pyrus. Results We identified 1836 LTR-retrotransposons in the ‘Suli’ pear genome, of which 440 LTR-retrotransposons were predicted to contain at least two of three ge...

  6. The evolution of Ty1-copia group retrotransposons in gymnosperms.

    Science.gov (United States)

    Stuart-Rogers, C; Flavell, A J

    2001-02-01

    A diverse collection of Ty1-copia group retrotransposons has been characterized from the genome of Picea abies (Norway spruce) by degenerate PCR amplification of a region of the reverse transcriptase gene. The occurrence of these retrotransposable elements in the gymnosperms was investigated by Southern blot hybridization analysis. The distribution of the different retrotransposons across the gymnosperms varies greatly. All of the retrotransposon clones isolated are highly conserved within the Picea (spruce) genus, many are also present in Pinus (pine) and/or Abies (fir) genera, and some share strongly homologous sequences with one or more of cedar, larch, Sequoia, cypress, and Ginkgo. Further subclones of one of the most strongly conserved retrotransposon sequences, Tpa28, were obtained from Ginkgo and P. abies. Comparisons of individual sequence pairs between the two species show nucleotide cross-homologies of around 80%-85%, corresponding to nucleotide substitution rates similar to those of nuclear protein-coding genes. Analysis of Tpa28 consensus sequences reveals that strong purifying selection has acted on this retrotransposon in the lineages connecting Ginkgo and Picea. Collectively, these data suggest, first, that the evolution of the Ty1-copia retrotransposon group in the gymnosperms is dominated by germ line vertical transmission, with strong selection for reverse transcriptase sequence, and, second, that extinction of individual retrotransposon types has been comparatively rare in gymnosperm species lineages compared with angiosperms. If this very high level of sequence conservation is a general property of the retrotransposons, then their extreme sequence diversity implies that they are extremely ancient, and the major element lineages seen today may have arisen early in eukaryote evolution. The data are also consistent with horizontal transmission of particular retrotransposons between species, but such a mechanism is unnecessary to explain the results.

  7. BEL/Pao retrotransposons in metazoan genomes

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    de la Chaux Nicole

    2011-06-01

    Full Text Available Abstract Background Long terminal repeat (LTR retrotransposons are a widespread kind of transposable element present in eukaryotic genomes. They are a major factor in genome evolution due to their ability to create large scale mutations and genome rearrangements. Compared to other transposable elements, little attention has been paid to elements belonging to the metazoan BEL/Pao subclass of LTR retrotransposons. No comprehensive characterization of these elements is available so far. The aim of this study was to describe all BEL/Pao elements in a set of 62 sequenced metazoan genomes, and to analyze their phylogenetic relationship. Results We identified a total of 7,861 BEL/Pao elements in 53 of our 62 study genomes. We identified BEL/Pao elements in 20 genomes where such elements had not been found so far. Our analysis shows that BEL/Pao elements are the second-most abundant class of LTR retrotransposons in the genomes we study, more abundant than Ty1/Copia elements, and second only to Ty3/Gypsy elements. They occur in multiple phyla, including basal metazoan phyla, suggesting that BEL/Pao elements arose early in animal evolution. We confirm findings from previous studies that BEL/Pao elements do not occur in mammals. The elements we found can be grouped into more than 1725 families, 1623 of which are new, previously unknown families. These families fall into seven superfamilies, only five of which have been characterized so far. One new superfamily is a major subdivision of the Pao superfamily which we propose to call Dan, because it is restricted to the genome of the zebrafish Danio rerio. The other new superfamily comprises 83 elements and is restricted to lower aquatic eumetazoans. We propose to call this superfamily Flow. BEL/Pao elements do not show any signs of recent horizontal gene transfer between distantly related species. Conclusions In sum, our analysis identifies thousands of new BEL/Pao elements and provides new insights into

  8. Atrx promotes heterochromatin formation at retrotransposons.

    Science.gov (United States)

    Sadic, Dennis; Schmidt, Katharina; Groh, Sophia; Kondofersky, Ivan; Ellwart, Joachim; Fuchs, Christiane; Theis, Fabian J; Schotta, Gunnar

    2015-07-01

    More than 50% of mammalian genomes consist of retrotransposon sequences. Silencing of retrotransposons by heterochromatin is essential to ensure genomic stability and transcriptional integrity. Here, we identified a short sequence element in intracisternal A particle (IAP) retrotransposons that is sufficient to trigger heterochromatin formation. We used this sequence in a genome-wide shRNA screen and identified the chromatin remodeler Atrx as a novel regulator of IAP silencing. Atrx binds to IAP elements and is necessary for efficient heterochromatin formation. In addition, Atrx facilitates a robust and largely inaccessible heterochromatin structure as Atrx knockout cells display increased chromatin accessibility at retrotransposons and non-repetitive heterochromatic loci. In summary, we demonstrate a direct role of Atrx in the establishment and robust maintenance of heterochromatin.

  9. 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 (...

  10. The nuage mediates retrotransposon silencing in mouse primordial ovarian follicles

    Science.gov (United States)

    Lim, Ai Khim; Lorthongpanich, Chanchao; Chew, Ting Gang; Tan, Chin Wee Godwin; Shue, Yan Ting; Balu, Sathish; Gounko, Natalia; Kuramochi-Miyagawa, Satomi; Matzuk, Martin M.; Chuma, Shinichiro; Messerschmidt, Daniel M.; Solter, Davor; Knowles, Barbara B.

    2013-01-01

    Mobilization of endogenous retrotransposons can destabilize the genome, an imminent danger during epigenetic reprogramming of cells in the germline. The P-element-induced wimpy testis (PIWI)-interacting RNA (piRNA) pathway is known to silence retrotransposons in the mouse testes. Several piRNA pathway components localize to the unique, germline structure known as the nuage. In this study, we surveyed mouse ovaries and found, for the first time, transient appearance of nuage-like structures in oocytes of primordial follicles. Mouse vasa homolog (MVH), Piwi-like 2 (PIWIL2/MILI) and tudor domain-containing 9 (TDRD9) are present in these structures, whereas aggregates of germ cell protein with ankyrin repeats, sterile alpha motif and leucine zipper (GASZ) localize separately in the cytoplasm. Retrotransposons are silenced in primordial ovarian follicles, and de-repressed upon reduction of piRNA expression in Mvh, Mili or Gasz mutants. However, these null-mutant females, unlike their male counterparts, are fertile, uncoupling retrotransposon activation from sterility. PMID:23924633

  11. 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.

  12. Presence of env-like sequences in Quercus suber retrotransposons.

    Science.gov (United States)

    Carvalho, M; Ribeiro, T; Viegas, W; Morais-Cecilio, L; Rocheta, M

    2010-01-01

    The main difference between LTR retrotransposons and retroviruses is the presence of the envelope (env) gene in the latter, downstream of the pol gene. The env gene is involved in their infectious capacity. Here we report the presence of env-like sequences in the genome of Quercus suber (cork oak), one of the most economically important Portuguese species. These gene sequences were isolated through DNA amplification between RNaseH conserved motifs and 3' LTR, based on the structure of copia retrotransposons. Phylogenetic analysis revealed that almost all the clones isolated are clustered with Cyclops-2, a Ty3-gypsy element identified in Pisum sativum, except one clustered with gypsy and copia retroelements found in different species. This suggests the existence of a potential ancestral sequence of the env gene, prior to the separation of Ty3-gypsy and Ty1-copia retrotransposons. Additionally, the isolated env-like sequences showed 26-39% of homology with env-like sequences characterized in viruses. The origin of env-like sequences in retrotransposons from host plant taxa is discussed.

  13. Ty1-copia group retrotransposons in persimmon (Diospyros kaki Thunb.).

    Science.gov (United States)

    Nakatsuka, Akira; Iwami, Naoko; Matsumoto, Shigehito; Itamura, Hiroyuki; Yamagishi, Masumi

    2002-04-01

    We cloned and characterized Ty1-copia group retrotransposons in persimmon (Diospyros kaki Thunb.). Genomic DNA or methyl jasmonate (MJA)-treated cDNA were used as templates to amplify the reverse transcriptase region of Ty1-copia group retrotransposons. About 280 bp fragments were amplified and cloned, and 97 clones were sequenced. Forty-nine clones included frameshift or the stop codon, or both. Among 48 clones containing complete reading frames, 42 clones had unique nucleotide sequences. Alignment and phylogenetic analysis of putative amino acid sequences in the 42 clones indicated that these clones (named Tdk; retroTransposon in Diospyros kaki) fell into seven subgroups and six ungrouped sequences, indicating high sequence heterogeneity in Tdk clones. Phylogenetic analysis comparing unrelated plant species shows that some Tdk clones are more closely related to Ty1-copia group retrotransposons in the orders Solanales and Sapindales rather than to other Tdk clones. Southern blot analysis using Tdk2B, Tdk4c, Tdk6Ac, Tdk12K and Tdk13G clones as probes showed that persimmon and its related species, D. lotus, D. lotus var. glabba, D. oleifera, D. rhombifolia and D. virginiana, contained multiple Tdk-like sequences, indicating that homologous elements exist in other Diospyros species.

  14. Modeling the amplification dynamics of human Alu retrotransposons.

    Directory of Open Access Journals (Sweden)

    Dale J Hedges

    2005-09-01

    Full Text Available Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed a computer simulation that incorporates several known aspects of primate Alu retrotransposon biology and accommodates sampling effects resulting from the methods by which mobile elements are typically discovered and characterized. By modeling a number of amplification scenarios and comparing simulation-generated expectations to empirical data gathered from existing Alu subfamilies, we were able to statistically reject a number of amplification scenarios for individual subfamilies, including that of a rapid expansion or explosion of Alu amplification at the time of human-chimpanzee divergence.

  15. [Autonomic neuropathies].

    Science.gov (United States)

    Siepmann, T; Penzlin, A I; Illigens, B M W

    2013-07-01

    Autonomic neuropathies are a heterogeneous group of diseases that involve damage of small peripheral autonomic Aδ- and C-fibers. Causes of autonomic nerve fiber damage are disorders such as diabetes mellitus and HIV-infection. Predominant symptoms of autonomic neuropathy are orthostatic hypotension, gastro-intestinal problems, urogenital dysfunction, and cardiac arrhythmia, which can severely impair the quality of life in affected patients. Furthermore, autonomic neuropathies can be induced by autoimmune diseases such as acute inflammatory demyelinating polyneuropathy, hereditary disorders such as the lysosomal storage disorder Fabry disease and hereditary sensory and autonomic neuropathies, as well as certain toxins and drugs.

  16. Condensin II subunit dCAP-D3 restricts retrotransposon mobilization in Drosophila somatic cells.

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    Andrew T Schuster

    2013-10-01

    Full Text Available Retrotransposon sequences are positioned throughout the genome of almost every eukaryote that has been sequenced. As mobilization of these elements can have detrimental effects on the transcriptional regulation and stability of an organism's genome, most organisms have evolved mechanisms to repress their movement. Here, we identify a novel role for the Drosophila melanogaster Condensin II subunit, dCAP-D3 in preventing the mobilization of retrotransposons located in somatic cell euchromatin. dCAP-D3 regulates transcription of euchromatic gene clusters which contain or are proximal to retrotransposon sequence. ChIP experiments demonstrate that dCAP-D3 binds to these loci and is important for maintaining a repressed chromatin structure within the boundaries of the retrotransposon and for repressing retrotransposon transcription. We show that dCAP-D3 prevents accumulation of double stranded DNA breaks within retrotransposon sequence, and decreased dCAP-D3 levels leads to a precise loss of retrotransposon sequence at some dCAP-D3 regulated gene clusters and a gain of sequence elsewhere in the genome. Homologous chromosomes exhibit high levels of pairing in Drosophila somatic cells, and our FISH analyses demonstrate that retrotransposon-containing euchromatic loci are regions which are actually less paired than euchromatic regions devoid of retrotransposon sequences. Decreased dCAP-D3 expression increases pairing of homologous retrotransposon-containing loci in tissue culture cells. We propose that the combined effects of dCAP-D3 deficiency on double strand break levels, chromatin structure, transcription and pairing at retrotransposon-containing loci may lead to 1 higher levels of homologous recombination between repeats flanking retrotransposons in dCAP-D3 deficient cells and 2 increased retrotransposition. These findings identify a novel role for the anti-pairing activities of dCAP-D3/Condensin II and uncover a new way in which dCAP-D3/Condensin

  17. Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences

    Directory of Open Access Journals (Sweden)

    Ganko Eric W

    2004-03-01

    Full Text Available Abstract Background LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes thus far examined. Plant genomes, in particular, have been found to be comprised of a remarkably high number of LTR retrotransposons. There is a significant body of direct and indirect evidence that LTR retrotransposons have contributed to gene and genome evolution in plants. Results To explore the evolutionary history of long terminal repeat (LTR retrotransposons and their impact on the genome of Oryza sativa, we have extended an earlier computer-based survey to include all identifiable full-length, fragmented and solo LTR elements in the rice genome database as of April 2002. A total of 1,219 retroelement sequences were identified, including 217 full-length elements, 822 fragmented elements, and 180 solo LTRs. In order to gain insight into the chromosomal distribution of LTR-retrotransposons in the rice genome, a detailed examination of LTR-retrotransposon sequences on Chromosome 10 was carried out. An average of 22.3 LTR-retrotransposons per Mb were detected in Chromosome 10. Conclusions Gypsy-like elements were found to be >4 × more abundant than copia-like elements. Eleven of the thirty-eight investigated LTR-retrotransposon families displayed significant subfamily structure. We estimate that at least 46.5% of LTR-retrotransposons in the rice genome are older than the age of the species (

  18. The application of LTR retrotransposons as molecular markers in plants.

    Science.gov (United States)

    Schulman, Alan H; Flavell, Andrew J; Paux, Etienne; Ellis, T H Noel

    2012-01-01

    Retrotransposons are a major agent of genome evolution. Various molecular marker systems have been developed that exploit the ubiquitous nature of these genetic elements and their property of stable integration into dispersed chromosomal loci that are polymorphic within species. The key methods, SSAP, IRAP, REMAP, RBIP, and ISBP, all detect the sites at which the retrotransposon DNA, which is conserved between families of elements, is integrated into the genome. Marker systems exploiting these methods can be easily developed and inexpensively deployed in the absence of extensive genome sequence data. They offer access to the dynamic and polymorphic, nongenic portion of the genome and thereby complement methods, such as gene-derived SNPs, that target primarily the genic fraction.

  19. The Microprocessor controls the activity of mammalian retrotransposons.

    Science.gov (United States)

    Heras, Sara R; Macias, Sara; Plass, Mireya; Fernandez, Noemí; Cano, David; Eyras, Eduardo; Garcia-Perez, José L; Cáceres, Javier F

    2013-10-01

    More than half of the human genome is made of transposable elements whose ongoing mobilization is a driving force in genetic diversity; however, little is known about how the host regulates their activity. Here, we show that the Microprocessor (Drosha-DGCR8), which is required for microRNA biogenesis, also recognizes and binds RNAs derived from human long interspersed element 1 (LINE-1), Alu and SVA retrotransposons. Expression analyses demonstrate that cells lacking a functional Microprocessor accumulate LINE-1 mRNA and encoded proteins. Furthermore, we show that structured regions of the LINE-1 mRNA can be cleaved in vitro by Drosha. Additionally, we used a cell culture-based assay to show that the Microprocessor negatively regulates LINE-1 and Alu retrotransposition in vivo. Altogether, these data reveal a new role for the Microprocessor as a post-transcriptional repressor of mammalian retrotransposons and a defender of human genome integrity.

  20. Meiosis and retrotransposon silencing during germ cell development in mice.

    Science.gov (United States)

    Ollinger, Rupert; Reichmann, Judith; Adams, Ian R

    2010-03-01

    In mammals, germ cells derive from the pluripotent cells that are present early in embryogenesis, and then differentiate into male sperm or female eggs as development proceeds. Fusion between an egg and a sperm at fertilization allows genetic information from both parents to be transmitted to the next generation, and produces a pluripotent zygote to initiate the next round of embryogenesis. Meiosis is a central event in this self-perpetuating cycle that creates genetic diversity by generating new combinations of existing genetic alleles, and halves the number of chromosomes in the developing male and female germ cells to allow chromosome number to be maintained through successive generations. The developing germ cells also help to maintain genetic and chromosomal stability through the generations by protecting the genome from excessive de novo mutation. Several mouse mutants have recently been characterised whose germ cells exhibit defects in silencing the potentially mutagenic endogenous retroviruses and other retrotransposons that are prevalent in mammalian genomes, and these germ cells also exhibit defects in progression through meiosis. Here we review how mouse germ cells develop and proceed through meiosis, how mouse germ cells silence endogenous retroviruses and other retrotransposons, and discuss why silencing of endogenous retroviruses and other retrotransposons may be required for meiotic progression in mice.

  1. Identification and characterization of a LTR retrotransposon from the genome of Cyprinus carpio var. Jian.

    Science.gov (United States)

    Cao, Liping; Yin, Guojun; Cao, Zheming; Bing, Xuwen; Ding, Weidong

    2016-06-01

    A Ty3/gypsy-retrotransposon-type transposon was found in the genome of the Jian carp (Cyprinus carpio var. Jian) in a previous study (unpublished), and was designated a JRE retrotransposon (Jian retrotransposon). The full-length JRE retrotransposon is 5126 bp, which includes two long terminal repeats of 470 bp at the 5' end and 453 bp at the 3' end, and two open reading frames between them: 4203 bp encoding the group-specific antigen (GAG) and polyprotein (POL). The pol gene has a typical Ty3/gypsy retrotransposon structure, and the gene order is protease, reverse transcriptase, RNase H, and integrase (PR-RT-RH-IN). A phylogenetic analysis of the pol gene showed that it has similarities of 40.7, 40, and 32.8 %, to retrotransposons of Azumapecten farreri, Mizuhopecten yessoensis, and Xiphophorus maculatus, respectively. Therefore, JRE might belong to the JULE retrotransposon family. The copy number of the JRE transposon in the genome of the Jian carp is 124, determined with real-time quantitative PCR. The mRNA of the JRE retrotransposon is expressed in five Jian carp tissues, the liver, kidney, blood, muscle, and gonad, and slightly higher in the kidney and liver than in the other tissues.

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

    DEFF Research Database (Denmark)

    Mourier, Tobias; Willerslev, Eske

    2010-01-01

    transcriptional activity from Long Terminal Repeat (LTR) retrotransposons. LTR retrotransposons are normally flanked by two LTR sequences. However, the majority of LTR sequences in S. pombe exist as solitary LTRs, i.e. as single terminal repeat sequences not flanking a retrotransposon. Transcriptional activity...... of transcriptional activity are observed from both strands of solitary LTR sequences. Transcriptome data collected during meiosis suggests that transcription of solitary LTRs is correlated with the transcription of nearby protein-coding genes. CONCLUSIONS: Presumably, the host organism negatively regulates...... proliferation of LTR retrotransposons. The finding of considerable transcriptional activity of retrotransposons suggests that part of this regulation is likely to take place at a posttranscriptional level. Alternatively, the transcriptional activity may signify a hitherto unrecognized activity level...

  3. CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome.

    Science.gov (United States)

    Göke, Jonathan; Ng, Huck Hui

    2016-08-01

    The human genome contains millions of fragments from retrotransposons-highly repetitive DNA sequences that were once able to "copy and paste" themselves to other regions in the genome. However, the majority of retrotransposons have lost this capacity through acquisition of mutations or through endogenous silencing mechanisms. Without this imminent threat of transposition, retrotransposons have the potential to act as a major source of genomic innovation. Indeed, large numbers of retrotransposons have been found to be active in specific contexts: as gene regulatory elements and promoters for protein-coding genes or long noncoding RNAs, among others. In this review, we summarise recent findings about retrotransposons, with implications in gene expression regulation, the expansion of gene isoform diversity and the generation of long noncoding RNAs. We highlight key examples that demonstrate their role in cellular identity and their versatility as markers of cell states, and we discuss how their dysregulation may contribute to the formation of and possibly therapeutic response in human cancers.

  4. Autonomic neuropathy

    DEFF Research Database (Denmark)

    Hilsted, J

    1983-01-01

    The diagnosis of autonomic neuropathy is often difficult to establish, since clinical symptoms generally appear late in the course of the disease, and may be non-specific. A number of recently developed quantifiable and reproducible autonomic nerve function tests are reviewed, with emphasis on th...

  5. Autonomic neuropathy

    DEFF Research Database (Denmark)

    Hilsted, J

    1980-01-01

    In order to elucidate the physiological significance of autonomic neuropathy in juvenile diabetics, cardiovascular, hormonal and metabolic functions have been investigated in three groups of juvenile diabetics: One group had no signs of neuropathy, one group had presumably slight autonomic...... neuropathy (reduced beat-to-beat variation in heart rate during hyperventilation) and one group had clinically severe autonomic neuropathy, defined by presence of orthostatic hypotension. In all three experimental situations we found sympathetic dysfunction causing cardiovascular and/or hormonal...... maladjustments in patients with autonomic neuropathy. Regarding metabolic functions we found normal responses to graded exercise and insulin-induced hypoglycemia in patients with autonomic neuropathy in spite of blunted catecholamine responses, suggesting increased sensitivity of glycogen stores and adipose...

  6. LINEing germ and embryonic stem cells' silencing of retrotransposons.

    Science.gov (United States)

    Ishiuchi, Takashi; Torres-Padilla, Maria-Elena

    2014-07-01

    Almost half of our genome is occupied by transposable elements. Although most of them are inactive, one type of non-long terminal repeat (LTR) retrotransposon, long interspersed nuclear element 1 (LINE1), is capable of retrotransposition. Two studies in this issue, Pezic and colleagues (pp. 1410-1428) and Castro-Diaz and colleagues (pp. 1397-1409), provide novel insight into the regulation of LINE1s in human embryonic stem cells and mouse germ cells and shed new light on the conservation of complex mechanisms to ensure silencing of transposable elements in mammals.

  7. A tumor-promoting mechanism mediated by retrotransposon-encoded reverse transcriptase is active in human transformed cell lines

    Science.gov (United States)

    Sciamanna, Ilaria; Gualtieri, Alberto; Cossetti, Cristina; Osimo, Emanuele Felice; Ferracin, Manuela; Macchia, Gianfranco; Aricò, Eleonora; Prosseda, Gianni; Vitullo, Patrizia; Misteli, Tom; Spadafora, Corrado

    2013-01-01

    LINE-1 elements make up the most abundant retrotransposon family in the human genome. Full-length LINE-1 elements encode a reverse transcriptase (RT) activity required for their own retrotranpsosition as well as that of non-autonomous Alu elements. LINE-1 are poorly expressed in normal cells and abundantly in cancer cells. Decreasing RT activity in cancer cells, by either LINE-1-specific RNA interference, or by RT inhibitory drugs, was previously found to reduce proliferation and promote differentiation and to antagonize tumor growth in animal models. Here we have investigated how RT exerts these global regulatory functions. We report that the RT inhibitor efavirenz (EFV) selectively downregulates proliferation of transformed cell lines, while exerting only mild effects on non-transformed cells; this differential sensitivity matches a differential RT abundance, which is high in the former and undetectable in the latter. Using CsCl density gradients, we selectively identify Alu and LINE-1 containing DNA:RNA hybrid molecules in cancer but not in normal cells. Remarkably, hybrid molecules fail to form in tumor cells treated with EFV under the same conditions that repress proliferation and induce the reprogramming of expression profiles of coding genes, microRNAs (miRNAs) and ultraconserved regions (UCRs). The RT-sensitive miRNAs and UCRs are significantly associated with Alu sequences. The results suggest that LINE-1-encoded RT governs the balance between single-stranded and double-stranded RNA production. In cancer cells the abundant RT reverse-transcribes retroelement-derived mRNAs forming RNA:DNA hybrids. We propose that this impairs the formation of double-stranded RNAs and the ensuing production of small regulatory RNAs, with a direct impact on gene expression. RT inhibition restores the ‘normal’ small RNA profile and the regulatory networks that depend on them. Thus, the retrotransposon-encoded RT drives a previously unrecognized mechanism crucial to the

  8. A small family of sushi-class retrotransposon-derived genes in mammals and their relation to genomic imprinting.

    Science.gov (United States)

    Youngson, Neil A; Kocialkowski, Sylvia; Peel, Nina; Ferguson-Smith, Anne C

    2005-10-01

    Ty3/gypsy retrotransposons are rare in mammalian genomes despite their abundance in invertebrate and other vertebrate classes. Here we identify a family of nine conserved mammalian genes with homology to Ty3/gypsy retrotransposons but which have lost their ability to autonomously retrotranspose. Of these, five map to the X chromosome while the remaining four are autosomal. Comparative phylogenetic analyses show them to have strongest homology to the sushi-ichi element from Fugu rubripes. Two of the autosomal gene members, Peg10 and Rtl1, are known to be imprinted, being expressed from the paternally inherited chromosome homologue. This suggests, consistent with the host-parasite response theory of the evolution of the imprinting mechanism, that parental-origin specific epigenetic control may be mediated by genomic "parasitic" elements such as these. Alternatively, these elements may preferentially integrate into regions that are differentially modified on the two homologous chromosomes such as imprinted domains and the X chromosome and acquire monoallelic expression. We assess the imprinting status of the remaining autosomal members of this family and show them to be biallelically expressed in embryo and placenta. Furthermore, the methylation status of Rtl1 was assayed throughout development and was found to resemble that of actively, silenced repetitive elements rather than imprinted sequences. This indicates that the ability to undergo genomic imprinting is not an inherent property of all members of this family of retroelements. Nonetheless, the conservation but functional divergence between the different members suggests that they have undergone positive selection and acquired distinct endogenous functions within their mammalian hosts.

  9. Inhibition of LINE-1 retrotransposon-encoded reverse transcriptase modulates the expression of cell differentiation genes in breast cancer cells.

    Science.gov (United States)

    Patnala, Radhika; Lee, Sung-Hun; Dahlstrom, Jane E; Ohms, Stephen; Chen, Long; Dheen, S Thameem; Rangasamy, Danny

    2014-01-01

    Long Interspersed Elements (L1 elements) are biologically active retrotransposons that are capable of autonomous replication using their own reverse transcriptase (RT) enzyme. Expression of the normally repressed RT has been implicated in cancer cell growth. However, at present, little is known about the expression of L1-encoded RT activity or the molecular changes that are associated with RT activity in the development of breast cancer. Here, we report that RT activity is widespread in breast cancer cells. The expression of RT protein decreased markedly in breast cancer cells after treatment with the antiretroviral drug, efavirenz. While the majority of cells showed a significant reduction in proliferation, inhibition of RT was also accompanied by cell-specific differences in morphology. MCF7 cells displayed elongated microtubule extensions that adhered tightly to their substrate, while a large fraction of the T47D cells that we studied formed long filopodia projections. These morphological changes were reversible upon cessation of RT inhibition, confirming their dependence on RT activity. We also carried out gene expression profiling with microarrays and determined the genes that were differentially expressed during the process of cellular differentiation. Genes involved in proliferation, cell migration, and invasive activity were repressed in RT-inhibited cells. Concomitantly, genes involved in cell projection, formation of vacuolar membranes, and cell-to-cell junctions were significantly upregulated in RT-inhibited cells. qRT-PCR examination of the mRNA expression of these genes in additional cell lines yielded close correlation between their differential expression and the degree of cellular differentiation. Our study demonstrates that the inhibition of L1-encoded RT can reduce the rate of proliferation and promote differentiation of breast cancer cells. Together, these results provide a direct functional link between the expression of L1 retrotransposons and

  10. A tumor-promoting mechanism mediated by retrotransposon-encoded reverse transcriptase is active in human transformed cell lines.

    Science.gov (United States)

    Sciamanna, Ilaria; Gualtieri, Alberto; Cossetti, Cristina; Osimo, Emanuele Felice; Ferracin, Manuela; Macchia, Gianfranco; Aricò, Eleonora; Prosseda, Gianni; Vitullo, Patrizia; Misteli, Tom; Spadafora, Corrado

    2013-12-01

    LINE-1 elements make up the most abundant retrotransposon family in the human genome. Full-length LINE-1 elements encode a reverse transcriptase (RT) activity required for their own retrotranpsosition as well as that of non-autonomous Alu elements. LINE-1 are poorly expressed in normal cells and abundantly in cancer cells. Decreasing RT activity in cancer cells, by either LINE-1-specific RNA interference, or by RT inhibitory drugs, was previously found to reduce proliferation and promote differentiation and to antagonize tumor growth in animal models. Here we have investigated how RT exerts these global regulatory functions. We report that the RT inhibitor efavirenz (EFV) selectively downregulates proliferation of transformed cell lines, while exerting only mild effects on non-transformed cells; this differential sensitivity matches a differential RT abundance, which is high in the former and undetectable in the latter. Using CsCl density gradients, we selectively identify Alu and LINE-1 containing DNA:RNA hybrid molecules in cancer but not in normal cells. Remarkably, hybrid molecules fail to form in tumor cells treated with EFV under the same conditions that repress proliferation and induce the reprogramming of expression profiles of coding genes, microRNAs (miRNAs) and ultraconserved regions (UCRs). The RT-sensitive miRNAs and UCRs are significantly associated with Alu sequences. The results suggest that LINE-1-encoded RT governs the balance between single-stranded and double-stranded RNA production. In cancer cells the abundant RT reverse-transcribes retroelement-derived mRNAs forming RNA:DNA hybrids. We propose that this impairs the formation of double-stranded RNAs and the ensuing production of small regulatory RNAs, with a direct impact on gene expression. RT inhibition restores the 'normal' small RNA profile and the regulatory networks that depend on them. Thus, the retrotransposon-encoded RT drives a previously unrecognized mechanism crucial to the

  11. 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

    2016-01-01

    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. PMID:27342737

  12. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders.

    Science.gov (United States)

    Sun, Cheng; Shepard, Donald B; Chong, Rebecca A; López Arriaza, José; Hall, Kathryn; Castoe, Todd A; Feschotte, Cédric; Pollock, David D; Mueller, Rachel Lockridge

    2012-01-01

    Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ~14 to ~120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders.

  13. SREBP controls oxygen-dependent mobilization of retrotransposons in fission yeast.

    Directory of Open Access Journals (Sweden)

    Alfica Sehgal

    2007-08-01

    Full Text Available Retrotransposons are mobile genetic elements that proliferate through an RNA intermediate. Transposons do not encode transcription factors and thus rely on host factors for mRNA expression and survival. Despite information regarding conditions under which elements are upregulated, much remains to be learned about the regulatory mechanisms or factors controlling retrotransposon expression. Here, we report that low oxygen activates the fission yeast Tf2 family of retrotransposons. Sre1, the yeast ortholog of the mammalian membrane-bound transcription factor sterol regulatory element binding protein (SREBP, directly induces the expression and mobilization of Tf2 retrotransposons under low oxygen. Sre1 binds to DNA sequences in the Tf2 long terminal repeat that functions as an oxygen-dependent promoter. We find that Tf2 solo long terminal repeats throughout the genome direct oxygen-dependent expression of adjacent coding and noncoding sequences, providing a potential mechanism for the generation of oxygen-dependent gene expression.

  14. SINE retrotransposons cause epigenetic reprogramming of adjacent gene promoters.

    Science.gov (United States)

    Estécio, Marcos R H; Gallegos, Juan; Dekmezian, Mhair; Lu, Yue; Liang, Shoudan; Issa, Jean-Pierre J

    2012-10-01

    Almost half of the human genome and as much as 40% of the mouse genome is composed of repetitive DNA sequences. The majority of these repeats are retrotransposons of the SINE and LINE families, and such repeats are generally repressed by epigenetic mechanisms. It has been proposed that these elements can act as methylation centers from which DNA methylation spreads into gene promoters in cancer. Contradictory to a methylation center function, we have found that retrotransposons are enriched near promoter CpG islands that stay methylation-free in cancer. Clearly, it is important to determine which influence, if any, these repetitive elements have on nearby gene promoters. Using an in vitro system, we confirm here that SINE B1 elements can influence the activity of downstream gene promoters, with acquisition of DNA methylation and loss of activating histone marks, thus resulting in a repressed state. SINE sequences themselves did not immediately acquire DNA methylation but were marked by H3K9me2 and H3K27me3. Moreover, our bisulfite sequencing data did not support that gain of DNA methylation in gene promoters occurred by methylation spreading from SINE B1 repeats. Genome-wide analysis of SINE repeats distribution showed that their enrichment is directly correlated with the presence of USF1, USF2, and CTCF binding, proteins with insulator function. In summary, our work supports the concept that SINE repeats interfere negatively with gene expression and that their presence near gene promoters is counter-selected, except when the promoter is protected by an insulator element.

  15. Identification and characterization of jute LTR retrotransposons:: Their abundance, heterogeneity and transcriptional activity.

    Science.gov (United States)

    Ahmed, Salim; Shafiuddin, Md; Azam, Muhammad Shafiul; Islam, Md Shahidul; Ghosh, Ajit; Khan, Haseena

    2011-05-01

    Long Terminal Repeat (LTR) retrotransposons constitute a significant part of eukaryotic genomes and play an important role in genome evolution especially in plants. Jute is an important fiber crop with a large genome of 1,250 Mbps. This genome is still mostly unexplored. In this study we aimed at identifying and characterizing the LTR retrotransposons of jute with a view to understanding the jute genome better. In this study, the Reverse Transcriptase domain of Ty1-copia and Ty3-gypsy LTR retrotransposons of jute were amplified by degenerate primers and their expressions were examined by reverse transcription PCR. Copy numbers of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy elements were determined by dot blot analysis. Sequence analysis revealed higher heterogeneity among Ty1-copia retrotransposons than Ty3-gypsy and clustered each of them in three groups. Copy number of RT genes in Ty1-copia was found to be higher than that of Ty3-gypsy elements from dot blot hybridization. Cumulatively Ty1-copia and Ty3-gypsy may constitute around 19% of the jute genome where two groups of Ty1-copia were found to be transcriptionally active. Since the LTR retrotransposons constitute a large portion of jute genome, these findings imply the importance of these elements in the evolution of jute genome.

  16. Identification of retrotransposon families and analysis of their transcriptional activation in wheat

    Institute of Scientific and Technical Information of China (English)

    TANG Yimiao; MA Youzhi; LI Liancheng; XIN Zhiyong

    2005-01-01

    Variations in the reverse transcriptase (RT) domain were analyzed to clarify retrotransposon family structure and their evolution in wheat genome. RT-PCR was conducted by using primers based on the conserved RT peptide motifs of plant retrotransposons to amplify the RT domain of retrotransposons in the seedlings of wheat line Pm97034 treated with powdery mildew fungus. High level of heterogeneity was detected in 51 (RT1-51) clones randomly selected and the identity of nucleotide sequence among them ranged from 75.4% to 97.9%. These sequences, in combination with previously identified seven representatives from wheat retrotransposon families (families 1―7), were used to construct a composite phylogenetic tree. Three new families, designated family 8 to family 10, were identified. Famliy 8 formed before divergence of the Pooideae subfamily and was regarged as an ancient retrotransposon family. Some members of family 4 and family 7 had transcriptional activativity, and were present with multiple copies in wheat and its related species.

  17. The Microprocessor controls the activity of mammalian retrotransposons

    DEFF Research Database (Denmark)

    Heras, Sara R.; Macias, Sara; Plass, Mireya

    2013-01-01

    More than half of the human genome is made of transposable elements whose ongoing mobilization is a driving force in genetic diversity; however, little is known about how the host regulates their activity. Here, we show that the Microprocessor (Drosha-DGCR8), which is required for microRNA biogen......More than half of the human genome is made of transposable elements whose ongoing mobilization is a driving force in genetic diversity; however, little is known about how the host regulates their activity. Here, we show that the Microprocessor (Drosha-DGCR8), which is required for micro......RNA biogenesis, also recognizes and binds RNAs derived from human long interspersed element 1 (LINE-1), Alu and SVA retrotransposons. Expression analyses demonstrate that cells lacking a functional Microprocessor accumulate LINE-1 mRNA and encoded proteins. Furthermore, we show that structured regions...... of the LINE-1 mRNA can be cleaved in vitro by Drosha. Additionally, we used a cell culture-based assay to show that the Microprocessor negatively regulates LINE-1 and Alu retrotransposition in vivo. Altogether, these data reveal a new role for the Microprocessor as a post-transcriptional repressor...

  18. [Retrotransposons: selfish DNA or active epigenetic players in somatic cells?].

    Science.gov (United States)

    Guidez, Fabien

    2014-01-01

    Transposable elements (TE) represent around 40% of the human genome. They are endogenous mobile DNA sequences able to jump and duplicate in the host genome. TE have long been considered as "junk" DNA but are now believed to be important regulators of gene expression by participating to the establishment of the DNA methylation profile. Recent advances in genome sequencing reveals a higher transposition frequency and TE driven gene expression in somatic cells than previously thought. As TE propagation is deleterious and may be involved in oncogenic mechanisms, host cells have developed silencing mechanisms mainly described in germinal and embryonic cells. However, somatic cells are also proned to TE transposition and use specific mechanisms involving tumor suppressor proteins including p53, Rb and PLZF. These transcription factors specifically target genomic retrotransposon sequences, histone deacetylase and DNA methylase activities, inducing epigenetic modifications related to gene silencing. Thus, these transcription factors negatively regulate TE expression by the formation of DNA methylation profil in somatic cells possibly associated with oncogenic mechanisms.

  19. Genome-wide Characterization of Long Terminal Repeat-retrotransposons in Apple Reveals the Differences in Heterogeneity and Copy Number between Ty1-copia and Ty3-gypsy Retrotransposons

    Institute of Scientific and Technical Information of China (English)

    Hai-Yue Sun; Hong-Yan Dai; Gui-Ling Zhao; Yue Ma; Chun-Qing Ou; He Li; Lin-Guang Li; Zhi-Hong Zhang

    2008-01-01

    The conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of long terminal repeat (LTR) retrotransposons were isolated from the Malus domestica genome using degenerate oligonucleotide primers.Sequence analysis showed that 45% of Ty1-copia and 63% of Ty3-gypsy RT sequences contained premature stop codons and/or indels disrupting the reading frame.High heterogeneity among RT sequences of both Tyl-copia and Ty3-gypsy group retrotransposons was observed,but Ty3-gypsy group retrotransposons in the apple genome are less heterogeneous than Ty1-copia elements.Retrotransposon copy number was estimated by dot blot hybridizations for Ty1-copia (~500O) and Ty3-gypsy ( ~26000).All elements of the two types of LTR retrotransposons comprise approximately 38% of the M.domestica genome,with the Ty3-gypsy group contribution being higher (33.5%) than the Ty1-copia one (4.6%).Transcription was not detected by reverse transcription-polymerase chain reaction for either Tyl.copia or Ty3-gypsy retrotransposons in the leaves of plants in vitro or in leaf explants cultured on medium supplemented with high concentration benzylaminopurine.This research reveals the differences in heterogeneity and copy number between Ty1-copia and Ty3-gypsy retrotransposons in the apple genome.Ty1-copia retrotransposon has higher heterogeneity than Ty3-gypsy retrotransposon,but the latter has a higher copy number,which implies that Ty3-gypsy retrotransposons may play a more important role in the apple genome evolution.

  20. Autonomous Search

    CERN Document Server

    Hamadi, Youssef; Saubion, Frédéric

    2012-01-01

    Decades of innovations in combinatorial problem solving have produced better and more complex algorithms. These new methods are better since they can solve larger problems and address new application domains. They are also more complex which means that they are hard to reproduce and often harder to fine-tune to the peculiarities of a given problem. This last point has created a paradox where efficient tools are out of reach of practitioners. Autonomous search (AS) represents a new research field defined to precisely address the above challenge. Its major strength and originality consist in the

  1. Molecular evolution of magellan, a maize Ty3/gypsy-like retrotransposon.

    Science.gov (United States)

    Purugganan, M D; Wessler, S R

    1994-11-22

    The magellan transposable element is responsible for a spontaneous 5.7-kb insertion in the maize wx-M allele. This element has the sequence and structural characteristics of a Ty3/gypsy-like retrotransposon. The magellan element is present in all Zea species and Tripsacum andersonii; it is absent, however, in the genomes of all other Tripsacum species analyzed. The genetic distances between magellan elements suggest that this retrotransposon is evolving faster than other Zea nuclear loci. The phylogeny of magellan within Zea and T. andersonii also reveals a pattern of interspecies transfers, resulting in the movement of magellan subfamilies between different species genomes. Interspecific hybridization may be a major mechanism by which this retrotransposon invades and establishes itself in new taxa.

  2. Identification and Characterization of Reverse Transcriptase Domain of Transcriptionally Active Retrotransposons in Wheat Genomes

    Institute of Scientific and Technical Information of China (English)

    Yi-Miao TANG; You-Zhi MA; Lian-Cheng LI; Xing-Guo YE

    2005-01-01

    To clarify activation characterization of wheat (Triticum aestivum L.) retrotransposons, transcriptionally active Ty1-copia retrotransposons were found in wheat by using RT-PCR to amplify the RT domain. Sequence analysis of random RT-PCR clones reveals that Ty1-copia retrotransposons are highly heterogeneous and can be divided into at least four groups, which are tentatively named TaRT-1 to TaRT-4.Dot blot hybridization indicates that TaRT- 1 exists in the wheat genome as multiple copies (at 30 000 copies/a hexaploid genome (ABD)). Northern blot hybridization showed that TaRT-1 is only expressed at a low level under normal conditions in seedlings, but at a high level when induced by powdery mildew fungus, jasmonic acid (JA) and salicylic acid (SA). These results suggest that the TaRT-1 expression is highly sensitive to biotic and abiotic stresses.

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

    Directory of Open Access Journals (Sweden)

    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

  4. Characterisation and physical localisation of Ty1-copia-like retrotransposons in four Alstroemeria species.

    Science.gov (United States)

    Kuipers, A G; Heslop-Harrison, J S; Jacobsen, E

    1998-06-01

    The genus Alstroemeria contains species with large genomes (2C = 36.5-78.9 pg (17,600-38,000 Mb) in those species with 2n = 2x = 16). We investigated the diversity and genomic and chromosomal organisation of Ty1-copia-like retrotransposons in four Alstroemeria species. Analysis of 33 PCR-amplified sequences corresponding to a conserved domain of the Ty1-copia reverse transcriptase (rt) gene showed high heterogeneity among predicted amino acid sequences; no two sequences were identical, but most fell into one of five subgroups. Levels of inter- and intra-specific heterogeneity of sequences were similar. HaeIII-digested genomic DNA of various Alstroemeria species contained distinct bands upon hybridisation with individual rt gene fragments. Hybridisation with the heterogeneous PCR pool of rt fragments (retrotransposon pool) revealed additional bands; some minor bands were characteristic of either Brazilian or Chilean species. In situ hybridisation of the retrotransposon pool from three species to metaphase chromosomes from the same species showed a dispersed distribution of the retrotransposon pool with exclusion from rDNA and other chromosomal sites. Alstroemeria pelegrina, which is without major heterochromatic sites, showed some clustering and small negative bands. The retrotransposon pool was excluded from major DAPI-staining bands in Alstroemeria aurea, but in contrast, the sites of the major tandemly repeated sequences in Alstroemeria inodora showed a hybridisation signal similar to that in the rest of the chromosomes. The data are discussed in the context of the contribution of Ty1-copia-like retrotransposons to plant genome size, their evolution, and their value for phylogenetic and biodiversity studies.

  5. Diabetic autonomic neuropathy.

    Science.gov (United States)

    Freeman, Roy

    2014-01-01

    Diabetes mellitus is the commonest cause of an autonomic neuropathy in the developed world. Diabetic autonomic neuropathy causes a constellation of symptoms and signs affecting cardiovascular, urogenital, gastrointestinal, pupillomotor, thermoregulatory, and sudomotor systems. Several discrete syndromes associated with diabetes cause autonomic dysfunction. The most prevalent of these are: generalized diabetic autonomic neuropathy, autonomic neuropathy associated with the prediabetic state, treatment-induced painful and autonomic neuropathy, and transient hypoglycemia-associated autonomic neuropathy. These autonomic manifestations of diabetes are responsible for the most troublesome and disabling features of diabetic peripheral neuropathy and result in a significant proportion of the mortality and morbidity associated with the disease.

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

    DEFF Research Database (Denmark)

    Persson, Jenna; Steglich, Babett; Smialowska, Agata;

    2016-01-01

    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....... 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...

  7. 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.

  8. Isolation and Characterization of Copia-like Retrotransposons from 12 Sweet Orange (Citrus sinensis Osbeck) Cultivars

    Institute of Scientific and Technical Information of China (English)

    Neng-Guo TAO; Juan XU; Yun-Jiang CHENG; Liu HONG; Wen-Wu GUO; Hua-Lin YI; Xiu-Xin DENG

    2005-01-01

    As the largest transposable element in the plant genome, retrotransposons are thought to be involved in citrus genetic instability and genome evolution, especially in sweet orange, which is prone to bud mutation. In the present study, the presence of copia-like retrotransposons, their heterogeneity, genomic distribution, and transcriptional activities in Citrus were investigated in 12 sweet orange (Citrus sinensis Osbeck) cultivars using a PCR assay designed to detect copia-like reverse transcriptase (RT)sequences. Twelve amplification products from each cultivar were cloned and sequenced. The cloned sequences showed great heterogeneity, except "Dream" navel and "Hamlin", both of which shared the same sequence. Frame shifting, termination, deletion, and substitution accounted for the heterogeneity of RT sequences. Southern blot hybridization using the RT1 clone from the "Cara Cara" navel as a probe showed that multiple copies were integrated throughout the sweet orange genomes, which made the retrotransposon possible an effective molecular marker to detect citrus evolution events and to reveal its relationship with bud mutation. No transcriptional activities of the retrotransposon were detected by RT-PCR and Northern analysis in the fruits and leaves of either "Cara Cara" or "Seike" navels.

  9. 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.

  10. Mechanism of the piRNA-mediated silencing of Drosophila telomeric retrotransposons.

    Science.gov (United States)

    Shpiz, Sergey; Olovnikov, Ivan; Sergeeva, Anna; Lavrov, Sergey; Abramov, Yuri; Savitsky, Mikhail; Kalmykova, Alla

    2011-11-01

    In the Drosophila germline, retrotransposons are silenced by the PIWI-interacting RNA (piRNA) pathway. Telomeric retroelements HeT-A, TART and TAHRE, which are involved in telomere maintenance in Drosophila, are also the targets of piRNA-mediated silencing. We have demonstrated that expression of reporter genes driven by the HeT-A promoter is under the control of the piRNA silencing pathway independent of the transgene location. In order to test directly whether piRNAs affect the transcriptional state of retrotransposons we performed a nuclear run-on (NRO) assay and revealed increased density of the active RNA polymerase complexes at the sequences of endogenous HeT-A and TART telomeric retroelements as well as HeT-A-containing constructs in the ovaries of spn-E mutants and in flies with piwi knockdown. This strongly correlates with enrichment of two histone H3 modifications (dimethylation of lysine 79 and dimethylation of lysine 4), which mark transcriptionally active chromatin, on the same sequences in the piRNA pathway mutants. spn-E mutation and piwi knockdown results in transcriptional activation of some other non-telomeric retrotransposons in the ovaries, such as I-element and HMS Beagle. Therefore piRNA-mediated transcriptional mode of silencing is involved in the control of retrotransposon expression in the Drosophila germline.

  11. HACRE1, a recently inserted copia-like retrotransposon of sunflower (Helianthus annuus L.).

    Science.gov (United States)

    Buti, M; Giordani, T; Vukich, M; Gentzbittel, L; Pistelli, L; Cattonaro, F; Morgante, M; Cavallini, A; Natali, L

    2009-11-01

    In this paper we report on the isolation and characterization, for the first time, of a complete 6511 bp retrotransposon of sunflower. Considering its protein domain order and sequence similarity to other copia elements of dicotyledons, this retrotransposon was assigned to the copia retrotransposon superfamily and named HACRE1 (Helianthus annuus copia-like retroelement 1). HACRE1 carries 5' and 3' long terminal repeats (LTRs) flanking an internal region of 4661 bp. The LTRs are identical in their sequence except for two deletions of 7 and 5 nucleotides in the 5' LTR. Based on the sequence identity of the LTRs, HACRE1 was estimated to have inserted within the last approximately 84 000 years. The isolated sequence contains a complete open reading frame with only one complete reading frame. The absence of nonsense mutations agrees with the very high sequence identity between LTRs, confirming that HACRE1 insertion is recent. The haploid genome of sunflower (inbred line HCM) contains about 160 copies of HACRE1. This retrotransposon is expressed in leaflets from 7-day-old plantlets under different light conditions, probably in relation to the occurrence of many putative light-related regulatory cis-elements in the LTRs. However, sequenced cDNAs show less variability than HACRE1 genomic sequences, indicating that only a subset of this family is expressed under these conditions.

  12. 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.

  13. Naturally occurring endo-siRNA silences LINE-1 retrotransposons in human cells through DNA methylation.

    Science.gov (United States)

    Chen, Long; Dahlstrom, Jane E; Lee, Sung-Hun; Rangasamy, Danny

    2012-07-01

    Long interspersed nuclear element 1 (LINE-1) retrotransposons are mutagens that are capable of generating deleterious mutations by inserting themselves into genes and affecting gene function in the human genome. In normal cells, the activity of LINE-1 retrotransposon is mostly repressed, maintaining a stable genome structure. In contrast, cancer cells are characterized by aberrant expression of LINE-1 retrotransposons, which, in principle, have the potential to contribute to genomic instability. The mechanistic pathways that regulate LINE-1 expression remain unclear. Using deep-sequencing small RNA analysis, we identified a subset of differentially expressed endo-siRNAs that directly regulate LINE-1 expression. Detailed analyses suggest that these endo-siRNAs are significantly depleted in human breast cancer cells compared with normal breast cells. The overexpression of these endo-siRNAs in cancer cells markedly silences endogenous LINE-1 expression through increased DNA methylation of the LINE-1 5'-UTR promoter. The finding that endo-siRNAs can silence LINE-1 activity through DNA methylation suggests that a functional link exists between the expression of endo-siRNAs and LINE-1 retrotransposons in human cells.

  14. 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

  15. Kinetic pathway of pyrophosphorolysis by a retrotransposon reverse transcriptase.

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    Manjula Pandey

    Full Text Available DNA and RNA polymerases use a common phosphoryl transfer mechanism for base addition that requires two or three acidic amino acid residues at their active sites. We previously showed, for the reverse transcriptase (RT encoded by the yeast retrotransposon Ty1, that one of the three conserved active site aspartates (D(211 can be substituted by asparagine and still retain in vitro polymerase activity, although in vivo transposition is lost. Transposition is partially restored by second site suppressor mutations in the RNAse H domain. The novel properties of this amino acid substitution led us to express the WT and D(211N mutant enzymes, and study their pre-steady state kinetic parameters. We found that the k(pol was reduced by a factor of 223 in the mutant, although the K(d for nucleotide binding was unaltered. Further, the mutant enzyme had a marked preference for Mn(2+ over Mg(2+. To better understand the functions of this residue within the Ty1 RT active site, we have now examined the in vitro properties of WT and D(211N mutant Ty1 RTs in carrying out pyrophosphorolysis, the reverse reaction to polymerization, where pyrophosphate is the substrate and dNTPs are the product. We find that pyrophosphorolysis is efficient only when the base-paired primer template region is >14 bases, and that activity increases when the primer end is blunt-ended or recessed by only a few bases. Using pre-steady state kinetic analysis, we find that the rate of pyrophosphorolysis (k(pyro in the D(211N mutant is nearly 320 fold lower than the WT enzyme, and that the mutant enzyme has an approximately 170 fold lower apparent K(d for pyrophosphate. These findings indicate that subtle substrate differences can strongly affect the enzyme's ability to properly position the primer-end to carry out pyrophosphorolysis. Further the kinetic data suggests that the D(211 residue has a role in pyrophosphate binding and release, which could affect polymerase translocation, and help

  16. 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

    2017-03-03

    The methylation of cytosines shapes the epigenetic landscape of plant genomes, coordinates transgenerational epigenetic inheritance, represses 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 the 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 classes 1 (retrotransposons) and 2 (DNA transposons), respectively. Along genes and TEs, the 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 toward 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 to leaves. This article is protected by copyright. All rights reserved.

  17. 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.

  18. Cognitive Function Related to the Sirh11/Zcchc16 Gene Acquired from an LTR Retrotransposon in Eutherians

    OpenAIRE

    Masahito Irie; Masanobu Yoshikawa; Ryuichi Ono; Hirotaka Iwafune; Tamio Furuse; Ikuko Yamada; Shigeharu Wakana; Yui Yamashita; Takaya Abe; Fumitoshi Ishino; Tomoko Kaneko-Ishino

    2015-01-01

    Author Summary Retrotransposon-derived DNA sequences occupy approximately 40% of the mammalian genome, compared with only 1.5% of protein coding genes. They have been commonly considered “junk DNA” and even potentially harmful for host organisms. However, a series of knockout (KO) mouse analyses demonstrated that at least some of the LTR retrotransposon- and retrovirus-derived sequences play essential roles in the current mammalian developmental system as endogenous genes, such as Peg10, Peg1...

  19. Autoimmune autonomic disorders.

    Science.gov (United States)

    Mckeon, Andrew; Benarroch, Eduardo E

    2016-01-01

    Autoimmune autonomic disorders occur because of an immune response directed against sympathetic, parasympathetic, and enteric ganglia, autonomic nerves, or central autonomic pathways. In general, peripheral autoimmune disorders manifest with either generalized or restricted autonomic failure, whereas central autoimmune disorders manifest primarily with autonomic hyperactivity. Some autonomic disorders are generalized, and others are limited in their anatomic extent, e.g., isolated gastrointestinal dysmotility. Historically, these disorders were poorly recognized, and thought to be neurodegenerative. Over the last 20 years a number of autoantibody biomarkers have been discovered that have enabled the identification of certain patients as having an autoimmune basis for either autonomic failure or hyperactivity. Peripheral autoimmune autonomic disorders include autoimmune autonomic ganglionopathy (AAG), paraneoplastic autonomic neuropathy, and acute autonomic and sensory neuropathy. AAG manifests with acute or subacute onset of generalized or selective autonomic failure. Antibody targeting the α3 subunit of the ganglionic-type nicotinic acetylcholine receptor (α3gAChR) is detected in approximately 50% of cases of AAG. Some other disorders are characterized immunologically by paraneoplastic antibodies with a high positive predictive value for cancer, such as antineuronal nuclear antibody, type 1 (ANNA-1: anti-Hu); others still are seronegative. Recognition of an autoimmune basis for autonomic disorders is important, as their manifestations are disabling, may reflect an underlying neoplasm, and have the potential to improve with a combination of symptomatic and immune therapies.

  20. 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 ...

  1. [Trigeminal autonomic cephalgias].

    Science.gov (United States)

    Maximova, M Yu; Piradov, M A; Suanova, E T; Sineva, N A

    2015-01-01

    Review of literature on the trigeminal autonomic cephalgias are presented. Trigeminal autonomic cephalgias are primary headaches with phenotype consisting of trigeminal pain with autonomic sign including lacrimation, rhinorrhea and miosis. Discussed are issues of classification, pathogenesis, clinical picture, diagnosis, differential diagnosis and treatment of this headache. Special attention is paid to cluster headache, paroxysmal hemicrania, SUNCT syndrome, hemicrania continua.

  2. New Insights into Nested Long Terminal Repeat Retrotransposons in Brassica Species

    Institute of Scientific and Technical Information of China (English)

    Lijuan Wei; Meili Xiao; Zeshan An; Bi Ma; Annaliese S.Mason; Wei Qian; Jiana Li

    2013-01-01

    Long terminal repeat (LTR) retrotransposons,one of the foremost types of transposons,continually change or modify gene function and reorganize the genome through bursts of dramatic proliferation.Many LTR-TEs preferentially insert within other LTR-TEs,but the cause and evolutionary significance of these nested LTR-TEs are not well understood.In this study,a total of 1.52 Gb of Brassica sequence containing 2020 bacterial artificial chromosomes (BACs) was scanned,and six bacterial artificial chromosome (BAC) clones with extremely nested LTR-TEs (LTR-TEs density:7.24/kb)were selected for further analysis.The majority of the LTR-TEs in four of the six BACs were found to be derived from the rapid proliferation of retrotransposons originating within the BAC regions,with only a few LTR-TEs originating from the proliferation and insertion of retrotransposons from outside the BAC regions approximately 5-23 Mya.LTR-TEs also preferably inserted into TA-rich repeat regions.Gene prediction by Genescan identified 207 genes in the 0.84 Mb of total BAC sequences.Only a few genes (3/207) could be matched to the Brassica expressed sequence tag (EST) database,indicating that most genes were inactive after retrotransposon insertion.Five of the six BACs were putatively centromeric.Hence,nested LTR-TEs in centromere regions are rapidly duplicated,repeatedly inserted,and act to suppress activity of genes and to reshuffle the structure of the centromeric sequences.Our results suggest that LTR-TEs burst and proliferate on a local scale to create nested LTR-TE regions,and that these nested LTR-TEs play a role in the formation of centromeres.

  3. Comparison of a retrotransposon-based marker with microsatellite markers for discriminating accessions of Vitis vinifera.

    Science.gov (United States)

    Sant'Ana, G C; Ferreira, J L; Rocha, H S; Borém, A; Pasqual, M; Cançado, G M A

    2012-05-21

    Identification and knowledge concerning genetic diversity are fundamental for efficient management and use of grapevine germplasm. Recently, new types of molecular markers have been developed, such as retrotransposon-based markers. Because of their multilocus pattern, retrotransposon-based markers might be able to differentiate grapevine accessions with just one pair of primers. In order to evaluate the efficiency of this type of marker, we compared retrotransposon marker Tvv1 with seven microsatellite markers frequently used for genotyping of the genus Vitis (VVMD7, VVMD25, VVMD5, VVMD27, VVMD31, VVS2, and VZAG62). The reference population that we used consisted of 26 accessions of Vitis, including seven European varieties of Vitis vinifera, four North American varieties and hybrids of Vitis labrusca, and 15 rootstock hybrids obtained from crosses of several Vitis species. Individually, the Tvv1 and the group of seven SSR markers were capable of distinguishing all accessions except 'White Niagara' compared to 'Red Niagara'. Using the Structure software, the retrotransposon marker Tvv1 generated two clusters: one with V. vinifera plus North American varieties and the other comprising rootstocks. The seven SSR markers generated five clusters: V. vinifera, the North American varieties, and three groups of rootstock hybrids. The percentages of variation explained by the first two components in the principal coordinate analysis were 65.21 (Tvv1) and 50.42 (SSR markers) while the Mantel correlation between the distance matrixes generated by the two types of markers was 42.5%. We conclude that the Tvv1 marker is useful for DNA fingerprinting, but it lacks efficiency for discrimination of structured groups.

  4. 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.

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

    OpenAIRE

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

    2011-01-01

    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 genom...

  6. 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.

  7. Links between human LINE-1 retrotransposons and hepatitis virus-related hepatocellular carcinoma

    Science.gov (United States)

    Honda, Tomoyuki

    2016-05-01

    Hepatocellular carcinoma (HCC) accounts for approximately 80% of liver cancers, the third most frequent cause of cancer mortality. The most prevalent risk factors for HCC are infections by hepatitis B or hepatitis C virus. Findings suggest that hepatitis virus-related HCC might be a cancer in which LINE-1 retrotransposons, often termed L1, activity plays a potential role. Firstly, hepatitis viruses can suppress host defense factors that also control L1 mobilization. Secondly, many recent studies also have indicated that hypomethylation of L1 affects the prognosis of HCC patients. Thirdly, endogenous L1 retrotransposition was demonstrated to activate oncogenic pathways in HCC. Fourthly, several L1 chimeric transcripts with host or viral genes are found in hepatitis virus-related HCC. Such lines of evidence suggest a linkage between L1 retrotransposons and hepatitis virus-related HCC. Here, I briefly summarize current understandings of the association between hepatitis virus-related HCC and L1. Then, I discuss potential mechanisms of how hepatitis viruses drive the development of HCC via L1 retrotransposons. An increased understanding of the contribution of L1 to hepatitis virus-related HCC may provide unique insights related to the development of novel therapeutics for this disease.

  8. 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.

  9. Low levels of LTR retrotransposon deletion by ectopic recombination in the gigantic genomes of salamanders.

    Science.gov (United States)

    Frahry, Matthew Blake; Sun, Cheng; Chong, Rebecca A; Mueller, Rachel Lockridge

    2015-02-01

    Across the tree of life, species vary dramatically in nuclear genome size. Mutations that add or remove sequences from genomes-insertions or deletions, or indels-are the ultimate source of this variation. Differences in the tempo and mode of insertion and deletion across taxa have been proposed to contribute to evolutionary diversity in genome size. Among vertebrates, most of the largest genomes are found within the salamanders, an amphibian clade with genome sizes ranging from ~14 to ~120 Gb. Salamander genomes have been shown to experience slower rates of DNA loss through small (i.e., salamander genomes resulting from larger deletions. Here, we focus on one type of large deletion-ectopic-recombination-mediated removal of LTR retrotransposon sequences. In ectopic recombination, double-strand breaks are repaired using a "wrong" (i.e., ectopic, or non-allelic) template sequence-typically another locus of similar sequence. When breaks occur within the LTR portions of LTR retrotransposons, ectopic-recombination-mediated repair can produce deletions that remove the internal transposon sequence and the equivalent of one of the two LTR sequences. These deletions leave a signature in the genome-a solo LTR sequence. We compared levels of solo LTRs in the genomes of four salamander species with levels present in five vertebrates with smaller genomes. Our results demonstrate that salamanders have low levels of solo LTRs, suggesting that ectopic-recombination-mediated deletion of LTR retrotransposons occurs more slowly than in other vertebrates with smaller genomes.

  10. 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.

  11. The autonomic laboratory

    Science.gov (United States)

    Low, P. A.; Opfer-Gehrking, T. L.

    1999-01-01

    The autonomic nervous system can now be studied quantitatively, noninvasively, and reproducibly in a clinical autonomic laboratory. The approach at the Mayo Clinic is to study the postganglionic sympathetic nerve fibers of peripheral nerve (using the quantitative sudomotor axon reflex test [QSART]), the parasympathetic nerves to the heart (cardiovagal tests), and the regulation of blood pressure by the baroreflexes (adrenergic tests). Patient preparation is extremely important, since the state of the patient influences the results of autonomic function tests. The autonomic technologist in this evolving field needs to have a solid core of knowledge of autonomic physiology and autonomic function tests, followed by training in the performance of these tests in a standardized fashion. The range and utilization of tests of autonomic function will likely continue to evolve.

  12. Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae.

    Science.gov (United States)

    Grandbastien, M-A; Audeon, C; Bonnivard, E; Casacuberta, J M; Chalhoub, B; Costa, A-P P; Le, Q H; Melayah, D; Petit, M; Poncet, C; Tam, S M; Van Sluys, M-A; Mhiri, C

    2005-01-01

    Tnt1 elements are a superfamily of LTR-retrotransposons distributed in the Solanaceae plant family and represent good model systems for studying regulatory and evolutionary controls established between hosts and transposable elements. Tnt1 retrotransposons tightly control their activation, by restricting expression to specific conditions. The Tnt1A element, originally discovered in tobacco, is expressed in response to stress, and its activation by microbial factors is followed by amplification, demonstrating that factors of pathogen origin can generate genetic diversity in plants. The Tnt1A promoter has the potential to be activated by various biotic and abiotic stimuli but a number of these are specifically repressed in tobacco and are revealed only when the LTR promoter is placed in a heterologous context. We propose that a tobacco- and stimulus-specific repression has been established in order to minimize activation in conditions that might generate germinal transposition. In addition to tight transcriptional controls, Tnt1A retrotransposons self-regulate their activity through gradual generation of defective copies that have reduced transcriptional activity. Tnt1 retrotransposons found in various Solanaceae species are characterized by a high level of variability in the LTR sequences involved in transcription, and have evolved by gaining new expression patterns, mostly associated with responses to diverse stress conditions. Tnt1A insertions associated with genic regions are initially favored but seem subsequently counter-selected, while insertions in repetitive DNA are maintained. On the other hand, amplification and loss of insertions may result from more brutal occurrences, as suggested by the large restructuring of Tnt1 populations observed in tobacco compared to each of its parental species. The distribution of Tnt1 elements thus appears as a dynamic flux, with amplification counterbalanced by loss of insertions. Tnt1 insertion polymorphisms are too high to

  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. Age-associated de-repression of retrotransposons in the Drosophila fat body, its potential cause and consequence.

    Science.gov (United States)

    Chen, Haiyang; Zheng, Xiaobin; Xiao, Danqing; Zheng, Yixian

    2016-06-01

    Eukaryotic genomes contain transposable elements (TE) that can move into new locations upon activation. Since uncontrolled transposition of TEs, including the retrotransposons and DNA transposons, can lead to DNA breaks and genomic instability, multiple mechanisms, including heterochromatin-mediated repression, have evolved to repress TE activation. Studies in model organisms have shown that TEs become activated upon aging as a result of age-associated deregulation of heterochromatin. Considering that different organisms or cell types may undergo distinct heterochromatin changes upon aging, it is important to identify pathways that lead to TE activation in specific tissues and cell types. Through deep sequencing of isolated RNAs, we report an increased expression of many retrotransposons in the old Drosophila fat body, an organ equivalent to the mammalian liver and adipose tissue. This de-repression correlates with an increased number of DNA damage foci and decreased level of Drosophila lamin-B in the old fat body cells. Depletion of the Drosophila lamin-B in the young or larval fat body results in a reduction of heterochromatin and a corresponding increase in retrotransposon expression and DNA damage. Further manipulations of lamin-B and retrotransposon expression suggest a role of the nuclear lamina in maintaining the genome integrity of the Drosophila fat body by repressing retrotransposons.

  15. Genetic variability in sunflower (Helianthus annuus L.) and in the Helianthus genus as assessed by retrotransposon-based molecular markers.

    Science.gov (United States)

    Vukich, M; Schulman, A H; Giordani, T; Natali, L; Kalendar, R; Cavallini, A

    2009-10-01

    The inter-retrotransposon amplified polymorphism (IRAP) protocol was applied for the first time within the genus Helianthus to assess intraspecific variability based on retrotransposon sequences among 36 wild accessions and 26 cultivars of Helianthus annuus L., and interspecific variability among 39 species of Helianthus. Two groups of LTRs, one belonging to a Copia-like retroelement and the other to a putative retrotransposon of unknown nature (SURE) have been isolated, sequenced and primers were designed to obtain IRAP fingerprints. The number of polymorphic bands in H. annuus wild accessions is as high as in Helianthus species. If we assume that a polymorphic band can be related to a retrotransposon insertion, this result suggests that retrotransposon activity continued after Helianthus speciation. Calculation of similarity indices from binary matrices (Shannon's and Jaccard's indices) show that variability is reduced among domesticated H. annuus. On the contrary, similarity indices among Helianthus species were as large as those observed among wild H. annuus accessions, probably related to their scattered geographic distribution. Principal component analysis of IRAP fingerprints allows the distinction between perennial and annual Helianthus species especially when the SURE element is concerned.

  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 di

  17. 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.

  18. Semi-Autonomous Systems Laboratory

    Data.gov (United States)

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

  19. 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...

  20. Roles for small noncoding RNAs in silencing of retrotransposons in the mammalian brain.

    Science.gov (United States)

    Nandi, Sayan; Chandramohan, Dhruva; Fioriti, Luana; Melnick, Ari M; Hébert, Jean M; Mason, Christopher E; Rajasethupathy, Priyamvada; Kandel, Eric R

    2016-10-24

    Piwi-interacting RNAs (piRNAs), long thought to be restricted to germline, have recently been discovered in neurons of Aplysia, with a role in the epigenetic regulation of gene expression underlying long-term memory. We here ask whether piwi/piRNAs are also expressed and have functional roles in the mammalian brain. Large-scale RNA sequencing and subsequent analysis of protein expression revealed the presence in brain of several piRNA biogenesis factors including a mouse piwi (Mili), as well as small RNAs, albeit at low levels, resembling conserved piRNAs in mouse testes [primarily LINE1 (long interspersed nuclear element1) retrotransposon-derived]. Despite the seeming low expression of these putative piRNAs, single-base pair CpG methylation analyses across the genome of Mili/piRNA-deficient (Mili(-/-)) mice demonstrate that brain genomic DNA is preferentially hypomethylated within intergenic areas and LINE1 promoter areas of the genome. Furthermore, Mili mutant mice exhibit behavioral deficits such as hyperactivity and reduced anxiety. These results suggest that putative piRNAs exist in mammalian brain, and similar to the role of piRNAs in testes, they may be involved in the silencing of retrotransposons, which in brain have critical roles in contributing to genomic heterogeneity underlying adaptation, stress response, and brain pathology. We also describe the presence of another class of small RNAs in the brain, with features of endogenous siRNAs, which may have taken over the role of invertebrate piRNAs in their capacity to target both transposons, as well as protein-coding genes. Thus, RNA interference through gene and retrotransposon silencing previously encountered in Aplysia may also have potential roles in the mammalian brain.

  1. Potential impact of stress activated retrotransposons on genome evolution in a marine diatom

    Directory of Open Access Journals (Sweden)

    Vardi Assaf

    2009-12-01

    Full Text Available Abstract Background Transposable elements (TEs are mobile DNA sequences present in the genomes of most organisms. They have been extensively studied in animals, fungi, and plants, and have been shown to have important functions in genome dynamics and species evolution. Recent genomic data can now enlarge the identification and study of TEs to other branches of the eukaryotic tree of life. Diatoms, which belong to the heterokont group, are unicellular eukaryotic algae responsible for around 40% of marine primary productivity. The genomes of a centric diatom, Thalassiosira pseudonana, and a pennate diatom, Phaeodactylum tricornutum, that likely diverged around 90 Mya, have recently become available. Results In the present work, we establish that LTR retrotransposons (LTR-RTs are the most abundant TEs inhabiting these genomes, with a much higher presence in the P. tricornutum genome. We show that the LTR-RTs found in diatoms form two new phylogenetic lineages that appear to be diatom specific and are also found in environmental samples taken from different oceans. Comparative expression analysis in P. tricornutum cells cultured under 16 different conditions demonstrate high levels of transcriptional activity of LTR retrotransposons in response to nitrate limitation and upon exposure to diatom-derived reactive aldehydes, which are known to induce stress responses and cell death. Regulatory aspects of P. tricornutum retrotransposon transcription also include the occurrence of nitrate limitation sensitive cis-regulatory components within LTR elements and cytosine methylation dynamics. Differential insertion patterns in different P. tricornutum accessions isolated from around the world infer the role of LTR-RTs in generating intraspecific genetic variability. Conclusion Based on these findings we propose that LTR-RTs may have been important for promoting genome rearrangements in diatoms.

  2. Testing for autonomic neuropathy

    DEFF Research Database (Denmark)

    Hilsted, J

    1984-01-01

    Autonomic neuropathy is a common complication in long-term diabetes, about 30% of the patients showing measurable signs of autonomic dysfunction after 10 years duration of disease. The diagnosis is often difficult to establish because clinical symptoms generally occur late in the course...

  3. 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

    The importance of microRNAs and long noncoding RNAs in the regulation of pluripotency has been documented; however, the noncoding components of stem cell gene networks remain largely unknown. Here we investigate the role of noncoding RNAs in the pluripotent state, with particular emphasis...... 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...

  4. Impact of Low-Energy Ion Beam Implantation on the Expression of Tyl-copia-like Retrotransposons in Wheat (Triticum aestivum)

    Institute of Scientific and Technical Information of China (English)

    YA Huiyuan; JIAO Zhen; GU Yunhong; WANG Weidong; QIN Guangyong; HUO Yuping

    2007-01-01

    Retrotransposon-like elements are major constituents of most eukaryotic genomes. For example, they account for roughly 90% of the wheat (Triticum aestivum) genome. Previous study on a wheat strain treated by low-energy N+ ions indicated the variations in AFLP (Amplified Fragment Length Polymorphism ) markers. One such variation was caused by the re-activation of Tyl-copia-like retrotransposons, implying that the mutagenic effects of low-energy ions might work through elevated activation of retrotransposons. In this paper an expression profile of Tyl-copia-like retrotransposons in wheat treated by low-energy N+ ions is reported. The reverse transcriptase (RT) domains of these retrotransposons were amplified by reverse-transcriptional polymerase chain reaction (RT-PCR) and sequentially cloned. 42 and 65 clones were obtained from the treated (CL) and control materials (CK), respectively. Sequence analysis of each clone was performed by software. Phylogeny and classification were calculated responding to the sequences of the RT domains. All the results show that there is much difference in the RT domain between the control sample and the treated sample. Especially, the RT domains from the treated group encode significantly more functional ORF (open reading frames) than those from the control sample. This observation suggests that the treated sample has higher activation of retrotransposons, possibly as a consequence of low-energy ion beam irradiation. It also suggests that retrotransposons in the two groups impact the host gene expression in two different ways and carry out different functions in wheat cells.

  5. piRNA-mediated nuclear accumulation of retrotransposon transcripts in the Drosophila female germline.

    Science.gov (United States)

    Chambeyron, Séverine; Popkova, Anna; Payen-Groschêne, Geneviève; Brun, Christine; Laouini, Dorsaf; Pelisson, Alain; Bucheton, Alain

    2008-09-30

    Germline silencing of transposable elements is essential for the maintenance of genome integrity. Recent results indicate that this repression is largely achieved through a RNA silencing pathway that involves Piwi-interacting RNAs (piRNAs). However the repressive mechanisms are not well understood. To address this question, we used the possibility to disrupt the repression of the Drosophila I element retrotransposon by hybrid dysgenesis. We show here that the repression of the functional I elements that are located in euchromatin requires proteins of the piRNA pathway, and that the amount of ovarian I element piRNAs correlates with the strength of the repression in the female germline. Antisense RNAs, which are likely used to produce antisense piRNAs, are transcribed by heterochromatic defective I elements, but efficient production of these antisense small RNAs requires the presence in the genome of euchromatic functional I elements. Finally, we demonstrate that the piRNA-induced silencing of the functional I elements is at least partially posttranscriptional. In a repressive background, these elements are still transcribed, but some of their sense transcripts are kept in nurse cell nuclear foci together with those of the Doc retrotransposon. In the absence of I element piRNAs, either in dysgenic females or in mutants of the piRNA silencing pathway, sense I element transcripts are transported toward the oocyte where retrotransposition occurs. Our results indicate that piRNAs are involved in a posttranscriptional gene-silencing mechanism resulting in RNA nuclear accumulation.

  6. [Chromosomal organization of centromeric Ty3/gypsy retrotransposons in Allium cepa L. and Allium fistulosum L].

    Science.gov (United States)

    Kiseleva, A V; Kirov, I V; Khrustaleva, L I

    2014-06-01

    This is the first report on the presence of Ty3/gypsy-like retrotransposons in the centromeric region of Allium cepa and Allium fistulosum. The paper identifies the putative Ty3/gypsy centromeric retrotransposons (CR) among the DNA sequences of A. cepa present in the NCBI database and evaluates their copy number in the genomes of Allium cepa and Allium fistulosum. The putative copy number of Ty3/gypsy CR constituted about 26000 for A. cepa and about 7000 for A. fistulosum. The chromosomal organization of Ty3/gypsy CR was analyzed with the help of fluorescent in situ hybridization (FISH). The 300-bp PCR products synthesized with genomic DNA of Allium cepa and Allium fistulosum and primers designed for the sequence ET645811 of A. cepa (Genome Survey Sequence database), displaying similarity to the reverse transcriptase of the CR Ty3/gypsy family, served as FISH hybridization probes. On the chromosomes of A. cepa, hybridization signals were mainly localized in the centromeric region. On the chromosomes of A. fistulosum the signals were less expressed in the centromeric regions, though they were abundant in other chromosomal regions. The pathways of evolution in these closely related species are discussed.

  7. Alu retrotransposons promote differentiation of human carcinoma cells through the aryl hydrocarbon receptor

    Science.gov (United States)

    Morales-Hernández, Antonio; González-Rico, Francisco J.; Román, Angel C.; Rico-Leo, Eva; Alvarez-Barrientos, Alberto; Sánchez, Laura; Macia, Ángela; Heras, Sara R.; García-Pérez, José L.; Merino, Jaime M.; Fernández-Salguero, Pedro M.

    2016-01-01

    Cell differentiation is a central process in development and in cancer growth and dissemination. OCT4 (POU5F1) and NANOG are essential for cell stemness and pluripotency; yet, the mechanisms that regulate their expression remain largely unknown. Repetitive elements account for almost half of the Human Genome; still, their role in gene regulation is poorly understood. Here, we show that the dioxin receptor (AHR) leads to differentiation of human carcinoma cells through the transcriptional upregulation of Alu retrotransposons, whose RNA transcripts can repress pluripotency genes. Despite the genome-wide presence of Alu elements, we provide evidences that those located at the NANOG and OCT4 promoters bind AHR, are transcribed by RNA polymerase-III and repress NANOG and OCT4 in differentiated cells. OCT4 and NANOG repression likely involves processing of Alu-derived transcripts through the miRNA machinery involving the Microprocessor and RISC. Consistently, stable AHR knockdown led to basal undifferentiation, impaired Alus transcription and blockade of OCT4 and NANOG repression. We suggest that transcripts produced from AHR-regulated Alu retrotransposons may control the expression of stemness genes OCT4 and NANOG during differentiation of carcinoma cells. The control of discrete Alu elements by specific transcription factors may have a dynamic role in genome regulation under physiological and diseased conditions. PMID:26883630

  8. Ty3 Retrotransposon Hijacks Mating Yeast RNA Processing Bodies to Infect New Genomes.

    Directory of Open Access Journals (Sweden)

    Virginia Bilanchone

    Full Text Available Retrotransposition of the budding yeast long terminal repeat retrotransposon Ty3 is activated during mating. In this study, proteins that associate with Ty3 Gag3 capsid protein during virus-like particle (VLP assembly were identified by mass spectrometry and screened for roles in mating-stimulated retrotransposition. Components of RNA processing bodies including DEAD box helicases Dhh1/DDX6 and Ded1/DDX3, Sm-like protein Lsm1, decapping protein Dcp2, and 5' to 3' exonuclease Xrn1 were among the proteins identified. These proteins associated with Ty3 proteins and RNA, and were required for formation of Ty3 VLP retrosome assembly factories and for retrotransposition. Specifically, Dhh1/DDX6 was required for normal levels of Ty3 genomic RNA, and Lsm1 and Xrn1 were required for association of Ty3 protein and RNA into retrosomes. This role for components of RNA processing bodies in promoting VLP assembly and retrotransposition during mating in a yeast that lacks RNA interference, contrasts with roles proposed for orthologous components in animal germ cell ribonucleoprotein granules in turnover and epigenetic suppression of retrotransposon RNAs.

  9. GASZ Is Essential for Male Meiosis and Suppression of Retrotransposon Expression in the Male Germline

    Science.gov (United States)

    Greenbaum, Michael P.; Roy, Angshumoy; Burns, Kathleen H.; Zhu, Huifeng; Han, Derek Y.; Harris, R. Alan; Coarfa, Cristian; Gunaratne, Preethi H.; Yan, Wei; Matzuk, Martin M.

    2009-01-01

    Nuage are amorphous ultrastructural granules in the cytoplasm of male germ cells as divergent as Drosophila, Xenopus, and Homo sapiens. Most nuage are cytoplasmic ribonucleoprotein structures implicated in diverse RNA metabolism including the regulation of PIWI-interacting RNA (piRNA) synthesis by the PIWI family (i.e., MILI, MIWI2, and MIWI). MILI is prominent in embryonic and early post-natal germ cells in nuage also called germinal granules that are often associated with mitochondria and called intermitochondrial cement. We find that GASZ (Germ cell protein with Ankyrin repeats, Sterile alpha motif, and leucine Zipper) co-localizes with MILI in intermitochondrial cement. Knockout of Gasz in mice results in a dramatic downregulation of MILI, and phenocopies the zygotene–pachytene spermatocyte block and male sterility defect observed in MILI null mice. In Gasz null testes, we observe increased hypomethylation and expression of retrotransposons similar to MILI null testes. We also find global shifts in the small RNAome, including down-regulation of repeat-associated, known, and novel piRNAs. These studies provide the first evidence for an essential structural role for GASZ in male fertility and epigenetic and post-transcriptional silencing of retrotransposons by stabilizing MILI in nuage. PMID:19730684

  10. GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline.

    Directory of Open Access Journals (Sweden)

    Lang Ma

    2009-09-01

    Full Text Available Nuage are amorphous ultrastructural granules in the cytoplasm of male germ cells as divergent as Drosophila, Xenopus, and Homo sapiens. Most nuage are cytoplasmic ribonucleoprotein structures implicated in diverse RNA metabolism including the regulation of PIWI-interacting RNA (piRNA synthesis by the PIWI family (i.e., MILI, MIWI2, and MIWI. MILI is prominent in embryonic and early post-natal germ cells in nuage also called germinal granules that are often associated with mitochondria and called intermitochondrial cement. We find that GASZ (Germ cell protein with Ankyrin repeats, Sterile alpha motif, and leucine Zipper co-localizes with MILI in intermitochondrial cement. Knockout of Gasz in mice results in a dramatic downregulation of MILI, and phenocopies the zygotene-pachytene spermatocyte block and male sterility defect observed in MILI null mice. In Gasz null testes, we observe increased hypomethylation and expression of retrotransposons similar to MILI null testes. We also find global shifts in the small RNAome, including down-regulation of repeat-associated, known, and novel piRNAs. These studies provide the first evidence for an essential structural role for GASZ in male fertility and epigenetic and post-transcriptional silencing of retrotransposons by stabilizing MILI in nuage.

  11. GENETIC DIVERSITY OF TRITICALE CULTIVARS BASED ON MICROSATELLITE AND RETROTRANSPOSON-BASED MARKERS

    Directory of Open Access Journals (Sweden)

    Želmíra Balážová

    2014-02-01

    Full Text Available The aim of our work was to detect genetic variability in the set of 59 winter and spring triticale (x Triticosecale Witt. varieties using combination of 4 wheat SSR and 4 retrotransposon-based markers. The number of alleles for SSR markers ranged from 8 to 10 with an average number of 8,75 alleles per locus. For IRAP markers the number of alleles ranged from 9 to 10 with an average number of 9,25 alleles per locus Totally, 72 alleles were detected, 37 alleles for IRAP markers and 35 alleles for SSR markers. For the assessment of genetic diversity the dendrogram, based on the hierarchical cluster analysis using UPGMA algorithm was prepared. Fifty nine triticale cultivars were grouped into two major groups. The first group contained all winter triticale varieties and in the second cluster were included all spring triticale varieties. The closest relationship was found out between two Polish winter triticale cultivars, Alekto and Pizarro. Results showed the utility of combination of microsatellite and retrotransposon-based markers for estimation of genetic diversity of triticale genotypes leading to genotype identification.

  12. 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.

  13. Corky, a gypsy-like retrotransposon is differentially transcribed in Quercus suber tissues

    Directory of Open Access Journals (Sweden)

    Rocheta Margarida

    2012-08-01

    Full Text Available Abstract Background Transposable elements (TEs make up a large part of eukaryotic genomes. Due to their repetitive nature and to the fact that they harbour regulatory signals, TEs can be responsible for chromosomal rearrangements, movement of gene sequences and evolution of gene regulation and function. Retrotransposon ubiquity raises the question about their function in genomes and most are transcriptionally inactive due to rearrangements that compromise their activity. However, the activity of TEs is currently considered to have been one of the major processes in genome evolution. Findings We report on the characterization of a transcriptionally active gypsy-like retrotransposon (named Corky from Quercus suber, in a comparative and quantitative study of expression levels in different tissues and distinct developmental stages through RT-qPCR. We observed Corky’s differential transcription levels in all the tissues analysed. Conclusions These results document that Corky’s transcription levels are not constant. Nevertheless, they depend upon the developmental stage, the tissue analysed and the potential occurring events during an individuals’ life span. This modulation brought upon by different developmental and environmental influences suggests an involvement of Corky in stress response and during development.

  14. 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.

  15. Isolation of Ty1-copia retrotransposon in myrtle genome and development of S-SAP molecular marker.

    Science.gov (United States)

    Woodrow, Pasqualina; Pontecorvo, Giovanni; Ciarmiello, Loredana F

    2012-04-01

    Long terminal repeat (LTR)-retrotransposons are mobile genetic elements that are ubiquitous in plants and constitute a major portion of their nuclear genomes. LTR- retrotransposons possess unique properties that make them appropriate for investigating relationships between populations, varieties and closely related species. Myrtus communis L. is an evergreen shrub growing spontaneously throughout the Mediterranean area. Accessions show significant variations for agriculturally important traits, so the development of specific molecular markers for conservation and characterization of myrtle germplasm is desirable to conserve biodiversity. In this study, we isolated the first retrotransposon Ty1-copia-like element (Tmc1) in Myrtus communis L. genome and used this as a molecular marker. We successfully employed the S-SAP marker system to specifically characterize four myrtle accessions belonging to different areas in the province of Caserta (Italy). The high level of polymorphism detected in isolated LTRs, make Tmc1 a good molecular marker for this species. Our findings confirm that retrotransposon-based molecular markers are particularly valuable tools for plant molecular characterization studies.

  16. Activation of the promoter of the Tnt1 retrotransposon in tomato after inoculation with the fungal pathogen Cladosporium fulvum

    NARCIS (Netherlands)

    Mhiri, C.; Wit, de P.J.G.M.; Grandbastien, M.A.

    1999-01-01

    The copia-like Tnt1 element of tobacco is one of the few active plant retrotransposons and is transcriptionally activated, in tobacco and in heterologous species, by biotic and abiotic stress factors. In order to establish more precisely the link between Tnt1 activation and plant defense responses,

  17. Exploiting the power of LINE-1 retrotransposon mutagenesis for identification of genes involved in embryonic stem cell differentiation.

    Science.gov (United States)

    Lenka, Nibedita; Krishnan, Shruthi; Board, Philip; Rangasamy, Danny

    2014-06-01

    Identifying the genes or epigenetic factors that control the self-renewal and differentiation of stem cells is critical to understanding the molecular basis of cell commitment. Although a number of insertional mutagenesis vectors have been developed for identifying gene functions in animal models, the L1 retrotransposition system offers additional advantages as a tool to disrupt genes in embryonic stem cells in order to identify their functions and the phenotypes associated with them. Recent advances in producing synthetic versions of L1 retrotransposon vector system and the optimization of techniques to accurately identify retrotransposon integration sites have increased their utility for gene discovery applications. We have developed a novel episomal, nonviral L1 retrotransposon vector using scaffold/matrix attachment regions that provides stable, sustained levels of retrotransposition in cell cultures without being affected by epigenetic silencing or from some of the common problems of vector integration. This modified vector contains a GFP marker whose expression occurs only after successful gene disruption events and thus the cells with disrupted genes can be easily picked for functional analysis. Here we present a method to disrupt gene function in embryonic stem cells that aid in the identification of genes involved in stem cell differentiation processes. The methods presented here can be easily adapted to the study of other types of cancer stem cells or induced pluripotent stem cells using the L1 retrotransposon as an insertional mutagen.

  18. Inherited autonomic neuropathies.

    Science.gov (United States)

    Axelrod, Felicia B; Hilz, Max J

    2003-12-01

    Inherited autonomic neuropathies are a rare group of disorders associated with sensory dysfunction. As a group they are termed the "hereditary sensory and autonomic neuropathies" (HSAN). Classification of the various autonomic and sensory disorders is ongoing. In addition to the numerical classification of four distinct forms proposed by Dyck and Ohta (1975), additional entities have been described. The best known and most intensively studied of the HSANs are familial dysautonomia (Riley-Day syndrome or HSAN type III) and congenital insensitivity to pain with anhidrosis (HSAN type IV). Diagnosis of the HSANs depends primarily on clinical examinations and specific sensory and autonomic assessments. Pathologic examinations are helpful in confirming the diagnosis and in differentiating between the different disorders. In recent years identification of specific genetic mutations for some disorders has aided diagnosis. Replacement or definitive therapies are not available for any of the disorders so that treatment remains supportive and directed toward specific symptoms.

  19. 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....

  20. Autonomic cardiac innervation

    OpenAIRE

    Hasan, Wohaib

    2013-01-01

    Autonomic cardiac neurons have a common origin in the neural crest but undergo distinct developmental differentiation as they mature toward their adult phenotype. Progenitor cells respond to repulsive cues during migration, followed by differentiation cues from paracrine sources that promote neurochemistry and differentiation. When autonomic axons start to innervate cardiac tissue, neurotrophic factors from vascular tissue are essential for maintenance of neurons before they reach their targe...

  1. Evidence for the adaptive significance of an LTR retrotransposon sequence in a Drosophila heterochromatic gene

    Directory of Open Access Journals (Sweden)

    Rodriguez Jose M

    2002-03-01

    Full Text Available Abstract Background The potential adaptive significance of transposable elements (TEs to the host genomes in which they reside is a topic that has been hotly debated by molecular evolutionists for more than two decades. Recent genomic analyses have demonstrated that TE fragments are associated with functional genes in plants and animals. These findings suggest that TEs may contribute significantly to gene evolution. Results We have analyzed two transposable elements associated with genes in the sequenced Drosophila melanogaster y; cn bw sp strain. A fragment of the Antonia long terminal repeat (LTR retrotransposon is present in the intron of Chitinase 3 (Cht3, a gene located within the constitutive heterochromatin of chromosome 2L. Within the euchromatin of chromosome 2R a full-length Burdock LTR retrotransposon is located immediately 3' to cathD, a gene encoding cathepsin D. We tested for the presence of these two TE/gene associations in strains representing 12 geographically diverse populations of D. melanogaster. While the cathD insertion variant was detected only in the sequenced y; cn bw sp strain, the insertion variant present in the heterochromatic Cht3 gene was found to be fixed throughout twelve D. melanogaster populations and in a D. mauritiana strain suggesting that it maybe of adaptive significance. To further test this hypothesis, we sequenced a 685bp region spanning the LTR fragment in the intron of Cht3 in strains representative of the two sibling species D. melanogaster and D. mauritiana (~2.7 million years divergent. The level of sequence divergence between the two species within this region was significantly lower than expected from the neutral substitution rate and lower than the divergence observed between a randomly selected intron of the Drosophila Alcohol dehydrogenase gene (Adh. Conclusions Our results suggest that a 359 bp fragment of an Antonia retrotransposon (complete LTR is 659 bp located within the intron of the

  2. Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus

    OpenAIRE

    Petit, J.; Bourgeois, E; Stenger, W.; Bes, M.; Droc, G.; Meynard, D.; Courtois, B.; Ghesquière, Alain; Sabot, François; Panaud, O.; Guiderdoni, E.

    2009-01-01

    Retrotransposons are mobile genetic elements, ubiquitous in Eukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. We investigate here the diversity of the Ty1-copia retrotransposon Tos17 in the cultivated rice of Asian origin (Oryza sativa L.) and related AA genome species of the Oryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the eleme...

  3. Genome-wide LORE1 retrotransposon mutagenesis and high-throughput insertion detection in Lotus japonicus

    DEFF Research Database (Denmark)

    Urbanski, Dorian Fabian; Malolepszy, Anna; Stougaard, Jens;

    2012-01-01

    and insertion site identification. So far, only floral dip T-DNA transformation of Arabidopsis has produced independent germinal insertions, thereby allowing generation of mutant populations from seeds of single plants. In addition, advances in insertion detection have been hampered by a lack of protocols...... including software for automated data analysis, which take full advantage of high next-generation sequencing throughput. Here we address these challenges by developing the FSTpoolit protocol and software package and we demonstrate its efficacy by detecting 8,935 LORE1 insertions in 3,744 Lotus japonicus...... plants. The identified insertions showed that the endogenous LORE1 retrotransposon is well suited for insertion mutagenesis due to its homogenous gene targeting and exonic insertion preference. Since LORE1 transposition occurs in the germline, harvesting seeds from a single founder line and cultivating...

  4. Burdock, a novel retrotransposon in Drosophila melanogaster, integrates into the coding region of the cut locus.

    Science.gov (United States)

    Ponomarenko, N A; Bannikov, V M; Anashchenko, V A; Tchurikov, N A

    1997-08-11

    The burdock element is known to be the 2.6-kb insertion into the same region of the cut locus in 12 independently obtained ct-lethal mutants. Here we have determined the complete sequences of this insertion and of the hot spot region. It was found that the burdock is a short retrotransposon with long terminal repeats and a single open reading frame (ORF). The polypeptide encoded by the burdock ORF contains two adjacent regions homologous to the gag and pol polyproteins of the gypsy mobile element. The burdock insertion interrupts the short ORF of the cut locus. The target site sequence of the burdock insertions is similar to the Drosophila topoisomerase II cleavage site.

  5. Polymorphic L1 retrotransposons are frequently in strong linkage disequilibrium with neighboring SNPs.

    Science.gov (United States)

    Higashino, Saneyuki; Ohno, Tomoyuki; Ishiguro, Koichi; Aizawa, Yasunori

    2014-05-10

    L1 retrotransposons have been the major driver of structural variation of the human genome. L1 insertion polymorphism (LIP)-mediated genomic variation can alter the transcriptome and contribute to the divergence of human phenotypes. To assess this possibility, a genome-wide association study (GWAS) including LIPs is required. Toward this ultimate goal, the present study examined linkage disequilibrium between six LIPs and their neighboring single nucleotide polymorphisms (SNPs). Genomic PCR and sequencing of L1-plus and -minus alleles from different donors revealed that all six LIPs were in strong linkage disequilibrium with at least one SNP. In addition, comparison of syntenic regions containing the identified SNP nucleotides was performed among modern humans (L1-plus and -minus alleles), archaic humans and non-human primates, revealing two different evolutionary schemes that might have resulted in the observed strong SNP-LIP linkage disequilibria. This study provides an experimental framework and guidance for a future SNP-LIP integrative GWAS.

  6. 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.

  7. 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.

  8. Characterization and cloning of p11, a transrepressor of Drosophila melanogaster retrotransposon 1731.

    Science.gov (United States)

    Lacoste, J; Codani-Simonart, S; Best-Belpomme, M; Peronnet, F

    1995-01-01

    The NssBF element has been characterized as a 26 nt sequence in the long terminal repeat of Drosophila melanogaster retrotransposon 1731. This sequence has been shown to be implicated in transcriptional repression of the 1731 promoter. We here report the cloning of a cDNA encoding a nuclear DNA binding protein named p11 that binds specifically to the NssBF element. P11 is a 98 amino acid polypeptide. It exhibits similarities with the mouse p9 single-stranded DNA binding protein, raising the possibility of a very general family of protein factors. Co-transfection experiments in human U937 cells showed repression of the 1731 promoter by overexpression of p11. Images PMID:8559667

  9. The Flow of the Gibbon LAVA Element Is Facilitated by the LINE-1 Retrotransposition Machinery.

    Science.gov (United States)

    Meyer, Thomas J; Held, Ulrike; Nevonen, Kimberly A; Klawitter, Sabine; Pirzer, Thomas; Carbone, Lucia; Schumann, Gerald G

    2016-10-30

    LINE-Alu-VNTR-Alu-like (LAVA) elements comprise a family of non-autonomous, composite, non-LTR retrotransposons specific to gibbons and may have played a role in the evolution of this lineage. A full-length LAVA element consists of portions of repeats found in most primate genomes: CT-rich, Alu-like, and VNTR regions from the SVA retrotransposon, and portions of the AluSz and L1ME5 elements. To evaluate whether the gibbon genome currently harbors functional LAVA elements capable of mobilization by the endogenous LINE-1 (L1) protein machinery and which LAVA components are important for retrotransposition, we established a trans-mobilization assay in HeLa cells. Specifically, we tested if a full-length member of the older LAVA subfamily C that was isolated from the gibbon genome and named LAVAC, or its components, can be mobilized in the presence of the human L1 protein machinery. We show that L1 proteins mobilize the LAVAC element at frequencies exceeding processed pseudogene formation and human SVAE retrotransposition by > 100-fold and ≥3-fold, respectively. We find that only the SVA-derived portions confer activity, and truncation of the 3' L1ME5 portion increases retrotransposition rates by at least 100%. Tagged de novo insertions integrated into intronic regions in cell culture, recapitulating findings in the gibbon genome. Finally, we present alternative models for the rise of the LAVA retrotransposon in the gibbon lineage.

  10. Autonomous Evolutionary Information Systems

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Traditional information systems are passive, i.e., data orknowledge is created , retrieved, modified, updated, and deleted only in response to operations issued by users or application programs, and the systems only can execute queries or t ransactions explicitly submitted by users or application programs but have no ab ility to do something actively by themselves. Unlike a traditional information system serving just as a storehouse of data or knowledge and working passively a ccording to queries or transactions explicitly issued by users and application p rograms, an autonomous evolutionary information system serves as an autonomous a nd evolutionary partner of its users that discovers new knowledge from its datab ase or knowledge-base autonomously, cooperates with its users in solving proble m s actively by providing the users with advices, and has a certain mechanism to i mprove its own state of “knowing” and ability of “working”. This paper semi nall y defines what is an autonomous evolutionary information system, explain why aut onomous evolutionary information systems are needed, and presents some new issue s, fundamental considerations, and research directions in design and development of autonomous evolutionary information systems.

  11. Autonomic disturbances in narcolepsy.

    Science.gov (United States)

    Plazzi, Giuseppe; Moghadam, Keivan Kaveh; Maggi, Leonardo Serra; Donadio, Vincenzo; Vetrugno, Roberto; Liguori, Rocco; Zoccoli, Giovanna; Poli, Francesca; Pizza, Fabio; Pagotto, Uberto; Ferri, Raffaele

    2011-06-01

    Narcolepsy is a clinical condition characterized mainly by excessive sleepiness and cataplexy. Hypnagogic hallucinations and sleep paralysis complete the narcoleptic tetrad; disrupted night sleep, automatic behaviors and weight gain are also usual complaints. Different studies focus on autonomic changes or dysfunctions among narcoleptic patients, such as pupillary abnormalities, fainting spells, erectile dysfunction, night sweats, gastric problems, low body temperature, systemic hypotension, dry mouth, heart palpitations, headache and extremities dysthermia. Even if many studies lack sufficient standardization or their results have not been replicated, a non-secondary involvement of the autonomic nervous system in narcolepsy is strongly suggested, mainly by metabolic and cardiovascular findings. Furthermore, the recent discovery of a high risk for overweight and for metabolic syndrome in narcoleptic patients represents an important warning for clinicians in order to monitor and follow them up for their autonomic functions. We review here studies on autonomic functions and clinical disturbances in narcoleptic patients, trying to shed light on the possible contribute of alterations of the hypocretin system in autonomic pathophysiology.

  12. 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.

  13. Isolation of Ty1-copia-like Retrotransposon Sequences from the Apple Genome by Chromosome Walking Based on Modified SiteFinding-polymerase Chain Reaction

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Long terminal repeat (LTR) retrotransposons are powerful tools for studying genetic biodiversity,genome evolution, gene mutation, gene cloning and gene expression. The scarcity of retrotransposon sequence information restricts the development of these studies in higher plants. In the present study, 31 reverse transcriptase (RT) genes of Tyl-copia-like retrotransposons were identified from the apple genome by amplifying the RT coding region using degenerate primers. Nineteen RT genes showed extreme heterogeneity in terms of fragment size, base pair composition and open reading frame integrality. Originating from one 266 bp cloned RT gene, a 1966 bp Ty1-copia-like retrotransposon (named Tcrm1), including RT-ribonuclease H-LTR domain sequences, was achieved by chromosome walking based on modified SiteFinding-polymerase chain reaction. The comparison between Tcrm1 and other LTR retrotransposons in gene structure and sequence homology shows that Tcrm1 is the first Ty1-copia-like retrotransposon including an LTR domain in the apple genome. Dot blot analysis revealed that Tcrm1 copy number in the apple was approximately 1×103 copies per haploid genome.

  14. Simple Autonomous Chaotic Circuits

    Science.gov (United States)

    Piper, Jessica; Sprott, J.

    2010-03-01

    Over the last several decades, numerous electronic circuits exhibiting chaos have been proposed. Non-autonomous circuits with as few as two components have been developed. However, the operation of such circuits relies on the non-ideal behavior of the devices used, and therefore the circuit equations can be quite complex. In this paper, we present two simple autonomous chaotic circuits using only opamps and linear passive components. The circuits each use one opamp as a comparator, to provide a signum nonlinearity. The chaotic behavior is robust, and independent of nonlinearities in the passive components. Moreover, the circuit equations are among the algebraically simplest chaotic systems yet constructed.

  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. Terminal-Repeat Retrotransposons with GAG Domain in Plant Genomes: A New Testimony on the Complex World of Transposable Elements

    Science.gov (United States)

    Chaparro, Cristian; Gayraud, Thomas; de Souza, Rogerio Fernandes; Domingues, Douglas Silva; Akaffou, Sélastique; Laforga Vanzela, Andre Luis; de Kochko, Alexandre; Rigoreau, Michel; Crouzillat, Dominique; Hamon, Serge; Hamon, Perla; Guyot, Romain

    2015-01-01

    A novel structure of nonautonomous long terminal repeat (LTR) retrotransposons called terminal repeat with GAG domain (TR-GAG) has been described in plants, both in monocotyledonous, dicotyledonous and basal angiosperm genomes. TR-GAGs are relatively short elements in length (<4 kb) showing the typical features of LTR-retrotransposons. However, they carry only one open reading frame coding for the GAG precursor protein involved for instance in transposition, the assembly, and the packaging of the element into the virus-like particle. GAG precursors show similarities with both Copia and Gypsy GAG proteins, suggesting evolutionary relationships of TR-GAG elements with both families. Despite the lack of the enzymatic machinery required for their mobility, strong evidences suggest that TR-GAGs are still active. TR-GAGs represent ubiquitous nonautonomous structures that could be involved in the molecular diversities of plant genomes. PMID:25573958

  17. Autonomous Hexapod Spider Robot

    DEFF Research Database (Denmark)

    Pandey, Nisha; Pandey, Bishwajeet; Hussain, Dil muhammed Akbar

    2017-01-01

    of a hexapod robot. It is controlled through Arduino-unoR3 based SSC servo control module. Servos of torque 2.5kg-cm are used in robot to show different working movements including back and forth movement and sitting posture. Another trending technology i.e. Bluetooth is used to control autonomous feature...

  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. Autonomous component carrier selection

    DEFF Research Database (Denmark)

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

    2009-01-01

    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...

  20. 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

  1. MOV10L1 is necessary for protection of spermatocytes against retrotransposons by Piwi-interacting RNAs

    Science.gov (United States)

    Frost, Robert J. A.; Hamra, F. Kent; Richardson, James A.; Qi, Xiaoxia; Bassel-Duby, Rhonda; Olson, Eric N.

    2010-01-01

    Piwi-interacting RNAs (piRNAs) comprise a broad class of small noncoding RNAs that function as an endogenous defense system against transposable elements. Here we show that the putative DExD-box helicase MOV10-like-1 (MOV10L1) is essential for silencing retrotransposons in the mouse male germline. Mov10l1 is specifically expressed in germ cells with increasing expression from gonocytes/type A spermatogonia to pachytene spermatocytes. Primary spermatocytes of Mov10l1−/− mice show activation of LTR and LINE-1 retrotransposons, followed by cell death, causing male infertility and a complete block of spermatogenesis at early prophase of meiosis I. Despite the early expression of Mov10l1, germline stem cell maintenance appears unaffected in Mov10l1−/− mice. MOV10L1 interacts with the Piwi proteins MILI and MIWI. MOV10L1 also interacts with heat shock 70-kDa protein 2 (HSPA2), a testis-enriched chaperone expressed in pachytene spermatocytes and also essential for male fertility. These studies reveal a crucial role of MOV10L1 in male fertility and piRNA-directed retrotransposon silencing in male germ cells and suggest that MOV10L1 functions as a key component of a safeguard mechanism for the genetic information in male germ cells of mammals. PMID:20547853

  2. Genomic Rearrangement in Endogenous Long Terminal Repeat Retrotransposons of Rice Lines Introgressed by Wild Rice (Zizania latifolia Griseb.)

    Institute of Scientific and Technical Information of China (English)

    Ye SHEN; Xiu-Yun LIN; Xiao-Hui SHAN; Chun-Jing LIN; Fang-Pu HAN; Jin-Song PANG; Bao LIU

    2005-01-01

    Stochastic introgression of alien DNA may impose a genomic stress to the recipient genome.Herein, we report that apparent de novo genomic rearrangements in 10 of 13 selected endogenous, low-copy, and potentially active long terminal repeat (LTR) retrotransposons occurred in one or more of threerice lines studied that were introgressed by wild rice (Zizania latifolia Griseb.). For nine retrotransposons inwhich both the reverse-transcriptase (RT) region and the LTR region were available, largely concordantrearrangements occurred at both regions in five elements and at the RT region only in the remaining fourelements. A marked proportion of the genomic changes was shared by two or all three introgression linesthat were derived from a single F1 plant. This indicates that most of the genomic changes occurred at earlydevelopmental stages of the F1 somatic cells, which then gave rise to germline cells, and, hence, ensuredinheritance of the changes to later generations. Possible causes and potential implications of the introgres-sion-induced genomic rearrangements in LTR retrotransposons are discussed in the context of plant ge-nome evolution and breeding.

  3. Mobile Autonomous Humanoid Assistant

    Science.gov (United States)

    Diftler, M. A.; Ambrose, R. O.; Tyree, K. S.; Goza, S. M.; Huber, E. L.

    2004-01-01

    A mobile autonomous humanoid robot is assisting human co-workers at the Johnson Space Center with tool handling tasks. This robot combines the upper body of the National Aeronautics and Space Administration (NASA)/Defense Advanced Research Projects Agency (DARPA) Robonaut system with a Segway(TradeMark) Robotic Mobility Platform yielding a dexterous, maneuverable humanoid perfect for aiding human co-workers in a range of environments. This system uses stereo vision to locate human team mates and tools and a navigation system that uses laser range and vision data to follow humans while avoiding obstacles. Tactile sensors provide information to grasping algorithms for efficient tool exchanges. The autonomous architecture utilizes these pre-programmed skills to form human assistant behaviors. The initial behavior demonstrates a robust capability to assist a human by acquiring a tool from a remotely located individual and then following the human in a cluttered environment with the tool for future use.

  4. Autonomous Undersea Observations

    Science.gov (United States)

    2016-06-13

    less expensive sensor systems for a variety of applications, including measurement of physical characteristics of the ocean, threat detection, and...multiple autonomous environmental sensors within an acoustic modem-based infrastructure capable of communicating to and from the sensors and to and...networks, and telesonar with high speed platforms. This effort is concentrating on the development and demonstration of the two modem- based sensors . We

  5. Autonomous robotic sweeper

    OpenAIRE

    Kržišnik, Domen

    2015-01-01

    There is already a wide range of personal/domestic robots on the market capable of performing various tasks. We haven't however been able to find any commercially available robots designed for effectively performing the task of backyard sweeping. This thesis presents the process and end result of planning, assembly and programming of an autonomous robot, capable of performing the above mentioned task. We first analyze robots with similar functions, including robotic vacuum cleaners and lawn m...

  6. 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.

  7. Trigeminal autonomic cephalalgias.

    Science.gov (United States)

    Eller, M; Goadsby, P J

    2016-01-01

    The trigeminal autonomic cephalalgias (TACs) are a group of primary headache disorders characterised by lateralized symptoms: prominent headache and ipsilateral cranial autonomic features, such as conjunctival injection, lacrimation and rhinorrhea. The TACs are: cluster headache (CH), paroxysmal hemicrania (PH), short-lasting unilateral neuralgiform headache attacks with conjunctival injection and tearing (SUNCT)/short-lasting neuralgiform headache attacks with cranial autonomic features (SUNA) and hemicrania continua (HC). Their diagnostic criteria are outlined in the International Classification of Headache Disorders, third edition-beta (ICHD-IIIb). These conditions are distinguished by their attack duration and frequency, as well as response to treatment. HC is continuous and by definition responsive to indomethacin. The main differential when considering this headache is chronic migraine. Other TACs are remarkable for their short duration and must be distinguished from other short-lasting painful conditions, such as trigeminal neuralgia and primary stabbing headache. Cluster headache is characterised by exquisitely painful attacks that occur in discrete episodes lasting 15-180 min a few times a day. In comparison, PH occurs more frequently and is of shorter duration, and like HC is responsive to indomethacin. SUNCT/SUNA is the shortest duration and highest frequency TAC; attacks can occur over a hundred times every day.

  8. Inducible Transposition of a Heat-Activated Retrotransposon in Tissue Culture.

    Science.gov (United States)

    Masuta, Yukari; Nozawa, Kosuke; Takagi, Hiroki; Yaegashi, Hiroki; Tanaka, Keisuke; Ito, Tasuku; Saito, Hideyuki; Kobayashi, Hisato; Matsunaga, Wataru; Masuda, Seiji; Kato, Atsushi; Ito, Hidetaka

    2016-12-23

    A transposition of a heat-activated retrotransposon named ONSEN required compromise of a small RNA-mediated epigenetic regulation that includes RNA-directed DNA methylation (RdDM) machinery after heat treatment. In the current study, we analyzed the transcriptional and transpositional activation of ONSEN to better understand the underlying molecular mechanism involved in the maintenance and/or induction of transposon activation in plant tissue culture. We found the transposition of heat-primed ONSEN during tissue culture independently of RdDM mutation. The heat activation of ONSEN transcripts was not significantly up-regulated in tissue culture compared with that in heat-stressed seedlings, indicating that the transposition of ONSEN was regulated independently of the transcript level. RdDM-related genes were up-regulated by heat stress in both tissue culture and seedlings. The level of DNA methylation of ONSEN did not show any change in tissue culture, and the amount of ONSEN-derived small RNAs was not affected by heat stress. The results indicated that the transposition of ONSEN was regulated by an alternative mechanism in addition to the RdDM-mediated epigenetic regulation in tissue culture. We applied the tissue culture-induced transposition of ONSEN to Japanese radish, an important breeding species of the family Brassicaceae. Several new insertions were detected in a regenerated plant derived from heat-stressed tissues and its self-fertilized progeny, revealing the possibility of molecular breeding without genetic modification.

  9. Genome-wide LORE1 retrotransposon mutagenesis and high-throughput insertion detection in Lotus japonicus.

    Science.gov (United States)

    Urbański, Dorian Fabian; Małolepszy, Anna; Stougaard, Jens; Andersen, Stig Uggerhøj

    2012-02-01

    Use of insertion mutants facilitates functional analysis of genes, but it has been difficult to identify a suitable mutagen and to establish large populations for reverse genetics in most plant species. The main challenge is developing efficient high-throughput procedures for both mutagenesis and identification of insertion sites. To date, only floral-dip T-DNA transformation of Arabidopsis has produced independent germinal insertions, thereby allowing generation of mutant populations from seeds of single plants. In addition, advances in insertion detection have been hampered by a lack of protocols, including software for automated data analysis, that take full advantage of high-throughput next-generation sequencing. We have addressed these challenges by developing the FSTpoolit protocol and software package, and here we demonstrate its efficacy by detecting 8935 LORE1 insertions in 3744 Lotus japonicus plants. The identified insertions show that the endogenous LORE1 retrotransposon is well suited for insertion mutagenesis due to homogenous gene targeting and exonic insertion preference. As LORE1 transposition occurs in the germline, harvesting seeds from a single founder line and cultivating progeny generates a complete mutant population. This ease of LORE1 mutagenesis, combined with the efficient FSTpoolit protocol, which exploits 2D pooling, Illumina sequencing and automated data analysis, allows highly cost-efficient development of a comprehensive reverse genetic resource.

  10. Serial number tagging reveals a prominent sequence preference of retrotransposon integration.

    Science.gov (United States)

    Chatterjee, Atreyi Ghatak; Esnault, Caroline; Guo, Yabin; Hung, Stevephen; McQueen, Philip G; Levin, Henry L

    2014-07-01

    Transposable elements (TE) have both negative and positive impact on the biology of their host. As a result, a balance is struck between the host and the TE that relies on directing integration to specific genome territories. The extraordinary capacity of DNA sequencing can create ultra dense maps of integration that are being used to study the mechanisms that position integration. Unfortunately, the great increase in the numbers of insertion sites detected comes with the cost of not knowing which positions are rare targets and which sustain high numbers of insertions. To address this problem we developed the serial number system, a TE tagging method that measures the frequency of integration at single nucleotide positions. We sequenced 1 million insertions of retrotransposon Tf1 in the genome of Schizosaccharomyces pombe and obtained the first profile of integration with frequencies for each individual position. Integration levels at individual nucleotides varied over two orders of magnitude and revealed that sequence recognition plays a key role in positioning integration. The serial number system is a general method that can be applied to determine precise integration maps for retroviruses and gene therapy vectors.

  11. 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.

  12. Promoter competition as a mechanism of transcriptional interference mediated by retrotransposons.

    Science.gov (United States)

    Conte, Caroline; Dastugue, Bernard; Vaury, Chantal

    2002-07-15

    Enhancers can function over great distances and interact with almost any kind of promoter, but insulators or promoter competition generally limit their effect to a single gene. We provide in vivo evidence that retroelements may establish promoter competition with their neighboring genes and restrict the range of action of an enhancer. We report that the retroelement Idefix from Drosophila melanogaster inhibits white gene expression in testes by a promoter competition mechanism that does not occur in the eyes. The sequence specificity of the two TATA-less promoters of white and Idefix is a prime determinant in the competition that takes place in tissues where both are transcriptionally active. This study brings to light a novel mechanism whereby transcriptional interference by an active retrotransposon may perturb expression of neighboring genes. This capacity to interfere with the transcriptional regulation of their host, together with the facts that retroelements preferentially move within the germline and do not excise to replicate, suggest that these elements are cis-regulatory sequences able to imprint specific and heritable controls essential for eukaryotic gene regulation.

  13. Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration.

    Science.gov (United States)

    Zhu, Wei; Kuo, Dwight; Nathanson, Jason; Satoh, Akira; Pao, Gerald M; Yeo, Gene W; Bryant, Susan V; Voss, S Randal; Gardiner, David M; Hunter, Tony

    2012-09-01

    Salamanders possess an extraordinary capacity for tissue and organ regeneration when compared to mammals. In our effort to characterize the unique transcriptional fingerprint emerging during the early phase of salamander limb regeneration, we identified transcriptional activation of some germline-specific genes within the Mexican axolotl (Ambystoma mexicanum) that is indicative of cellular reprogramming of differentiated cells into a germline-like state. In this work, we focus on one of these genes, the long interspersed nucleotide element-1 (LINE-1) retrotransposon, which is usually active in germ cells and silent in most of the somatic tissues in other organisms. LINE-1 was found to be dramatically upregulated during regeneration. In addition, higher genomic LINE-1 content was also detected in the limb regenerate when compared to that before amputation indicating that LINE-1 retrotransposition is indeed active during regeneration. Active LINE-1 retrotransposition has been suggested to have a potentially deleterious impact on genomic integrity. Silencing of activated LINE-1 by small RNAs has been reported to be part of the machinery aiming to maintain genomic integrity. Indeed, we were able to identify putative LINE-1-related piRNAs in the limb blastema. Transposable element-related piRNAs have been identified frequently in the germline in other organisms. Thus, we present here a scenario in which a unique germline-like state is established during axolotl limb regeneration, and the re-activation of LINE-1 may serve as a marker for cellular dedifferentiation in the early-stage of limb regeneration.

  14. TDRD5 is required for retrotransposon silencing, chromatoid body assembly, and spermiogenesis in mice.

    Science.gov (United States)

    Yabuta, Yukihiro; Ohta, Hiroshi; Abe, Takaya; Kurimoto, Kazuki; Chuma, Shinichiro; Saitou, Mitinori

    2011-03-01

    The Tudor domain-containing proteins (TDRDs) are an evolutionarily conserved family of proteins involved in germ cell development. We show here that in mice, TDRD5 is a novel component of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Tdrd5-deficient males are sterile because of spermiogenic arrest at the round spermatid stage, with occasional failure in meiotic prophase. Without TDRD5, IMCs and CBs are disorganized, with mislocalization of their key components, including TDRD1/6/7/9 and MIWI/MILI/MIWI2. In addition, Tdrd5-deficient germ cells fail to repress LINE-1 retrotransposons with DNA-demethylated promoters. Cyclic adenosine monophosphate response element modulator (CREM) and TRF2, key transcription factors for spermiogenesis, are expressed in Tdrd5-deficient round spermatids, but their targets, including Prm1/Prm2/Tnp1, are severely down-regulated, which indicates the importance of IMC/CB-mediated regulation for postmeiotic gene expression. Strikingly, Tdrd5-deficient round spermatids injected into oocytes contribute to fertile offspring, demonstrating that acquisition of a functional haploid genome may be uncoupled from TDRD5 function.

  15. Autonomic disorders in multiple sclerosis.

    Science.gov (United States)

    Lensch, E; Jost, W H

    2011-01-01

    Multiple sclerosis is an inflammatory disease leading to disseminated lesions of the central nervous system resulting in both somatomotor and autonomic disturbances. These involve the central centers of the autonomic nervous system, as well as the automatic control and pathway systems. All autonomic functions may be disordered individually or in combined form. There is no other disease with a clinical picture so multifaceted. Besides cardiovascular dysfunctions disorders of bladder and rectum have become apparent. Somatomotor and autonomic disturbances occur with similar frequency; however the focused exam often heavily favors somatomotor symptoms. Autonomic disturbances should primarily be taken into account on history taking and clinical examination. Individual diagnosis and treatment is a secondary feature. Impairments of the autonomic nervous systems in multiple sclerosis are frequently overlooked.

  16. Autonomic Disorders in Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    E. Lensch

    2011-01-01

    Full Text Available Multiple sclerosis is an inflammatory disease leading to disseminated lesions of the central nervous system resulting in both somatomotor and autonomic disturbances. These involve the central centers of the autonomic nervous system, as well as the automatic control and pathway systems. All autonomic functions may be disordered individually or in combined form. There is no other disease with a clinical picture so multifaceted. Besides cardiovascular dysfunctions disorders of bladder and rectum have become apparent. Somatomotor and autonomic disturbances occur with similar frequency; however the focused exam often heavily favors somatomotor symptoms. Autonomic disturbances should primarily be taken into account on history taking and clinical examination. Individual diagnosis and treatment is a secondary feature. Impairments of the autonomic nervous systems in multiple sclerosis are frequently overlooked.

  17. Catecholamines and diabetic autonomic neuropathy

    DEFF Research Database (Denmark)

    Hilsted, J

    1995-01-01

    In diabetic patients with autonomic neuropathy plasma noradrenaline concentration, used as an index of sympathetic nervous activity, is low. This decrease is, however, only found in patients with a long duration of diabetes with clinically severe autonomic neuropathy. This apparent insensitivity...... 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...

  18. Jam avoidance with autonomous systems

    CERN Document Server

    Tordeux, Antoine

    2016-01-01

    Many car-following models are developed for jam avoidance in highways. Two mechanisms are used to improve the stability: feedback control with autonomous models and increasing of the interaction within cooperative ones. In this paper, we compare the linear autonomous and collective optimal velocity (OV) models. We observe that the stability is significantly increased by adding predecessors in interaction with collective models. Yet autonomous and collective approaches are close when the speed difference term is taking into account. Within the linear OV models tested, the autonomous models including speed difference are sufficient to maximise the stability.

  19. 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...

  20. Autonomous mobile robot teams

    Science.gov (United States)

    Agah, Arvin; Bekey, George A.

    1994-01-01

    This paper describes autonomous mobile robot teams performing tasks in unstructured environments. The behavior and the intelligence of the group is distributed, and the system does not include a central command base or leader. The novel concept of the Tropism-Based Cognitive Architecture is introduced, which is used by the robots in order to produce behavior transforming their sensory information to proper action. The results of a number of simulation experiments are presented. These experiments include worlds where the robot teams must locate, decompose, and gather objects, and defend themselves against hostile predators, while navigating around stationary and mobile obstacles.

  1. 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.

  2. Terminal-repeat retrotransposons with GAG domain in plant genomes: a new testimony on the complex world of transposable elements.

    Science.gov (United States)

    Chaparro, Cristian; Gayraud, Thomas; de Souza, Rogerio Fernandes; Domingues, Douglas Silva; Akaffou, Sélastique; Laforga Vanzela, Andre Luis; Kochko, Alexandre de; Rigoreau, Michel; Crouzillat, Dominique; Hamon, Serge; Hamon, Perla; Guyot, Romain

    2015-01-07

    A novel structure of nonautonomous long terminal repeat (LTR) retrotransposons called terminal repeat with GAG domain (TR-GAG) has been described in plants, both in monocotyledonous, dicotyledonous and basal angiosperm genomes. TR-GAGs are relatively short elements in length (element into the virus-like particle. GAG precursors show similarities with both Copia and Gypsy GAG proteins, suggesting evolutionary relationships of TR-GAG elements with both families. Despite the lack of the enzymatic machinery required for their mobility, strong evidences suggest that TR-GAGs are still active. TR-GAGs represent ubiquitous nonautonomous structures that could be involved in the molecular diversities of plant genomes.

  3. The impact of Ty3-gypsy group LTR retrotransposons Fatima on B-genome specificity of polyploid wheats

    Directory of Open Access Journals (Sweden)

    Huneau Cecile

    2011-06-01

    Full Text Available Abstract Background Transposable elements (TEs are a rapidly evolving fraction of the eukaryotic genomes and the main contributors to genome plasticity and divergence. Recently, occupation of the A- and D-genomes of allopolyploid wheat by specific TE families was demonstrated. Here, we investigated the impact of the well-represented family of gypsy LTR-retrotransposons, Fatima, on B-genome divergence of allopolyploid wheat using the fluorescent in situ hybridisation (FISH method and phylogenetic analysis. Results FISH analysis of a BAC clone (BAC_2383A24 initially screened with Spelt1 repeats demonstrated its predominant localisation to chromosomes of the B-genome and its putative diploid progenitor Aegilops speltoides in hexaploid (genomic formula, BBAADD and tetraploid (genomic formula, BBAA wheats as well as their diploid progenitors. Analysis of the complete BAC_2383A24 nucleotide sequence (113 605 bp demonstrated that it contains 55.6% TEs, 0.9% subtelomeric tandem repeats (Spelt1, and five genes. LTR retrotransposons are predominant, representing 50.7% of the total nucleotide sequence. Three elements of the gypsy LTR retrotransposon family Fatima make up 47.2% of all the LTR retrotransposons in this BAC. In situ hybridisation of the Fatima_2383A24-3 subclone suggests that individual representatives of the Fatima family contribute to the majority of the B-genome specific FISH pattern for BAC_2383A24. Phylogenetic analysis of various Fatima elements available from databases in combination with the data on their insertion dates demonstrated that the Fatima elements fall into several groups. One of these groups, containing Fatima_2383A24-3, is more specific to the B-genome and proliferated around 0.5-2.5 MYA, prior to allopolyploid wheat formation. Conclusion The B-genome specificity of the gypsy-like Fatima, as determined by FISH, is explained to a great degree by the appearance of a genome-specific element within this family for Ae

  4. Learning for Autonomous Navigation

    Science.gov (United States)

    Angelova, Anelia; Howard, Andrew; Matthies, Larry; Tang, Benyang; Turmon, Michael; Mjolsness, Eric

    2005-01-01

    Robotic ground vehicles for outdoor applications have achieved some remarkable successes, notably in autonomous highway following (Dickmanns, 1987), planetary exploration (1), and off-road navigation on Earth (1). Nevertheless, major challenges remain to enable reliable, high-speed, autonomous navigation in a wide variety of complex, off-road terrain. 3-D perception of terrain geometry with imaging range sensors is the mainstay of off-road driving systems. However, the stopping distance at high speed exceeds the effective lookahead distance of existing range sensors. Prospects for extending the range of 3-D sensors is strongly limited by sensor physics, eye safety of lasers, and related issues. Range sensor limitations also allow vehicles to enter large cul-de-sacs even at low speed, leading to long detours. Moreover, sensing only terrain geometry fails to reveal mechanical properties of terrain that are critical to assessing its traversability, such as potential for slippage, sinkage, and the degree of compliance of potential obstacles. Rovers in the Mars Exploration Rover (MER) mission have got stuck in sand dunes and experienced significant downhill slippage in the vicinity of large rock hazards. Earth-based off-road robots today have very limited ability to discriminate traversable vegetation from non-traversable vegetation or rough ground. It is impossible today to preprogram a system with knowledge of these properties for all types of terrain and weather conditions that might be encountered.

  5. 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.

  6. 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.

  7. A bioinformatics search pipeline, RNA2DSearch, identifies RNA localization elements in Drosophila retrotransposons.

    Science.gov (United States)

    Hamilton, Russell S; Hartswood, Eve; Vendra, Georgia; Jones, Cheryl; Van De Bor, Veronique; Finnegan, David; Davis, Ilan

    2009-02-01

    mRNA localization is a widespread mode of delivering proteins to their site of function. The embryonic axes in Drosophila are determined in the oocyte, through Dynein-dependent transport of gurken/TGF-alpha mRNA, containing a small localization signal that assigns its destination. A signal with a similar secondary structure, but lacking significant sequence similarity, is present in the I factor retrotransposon mRNA, also transported by Dynein. It is currently unclear whether other mRNAs exist that are localized to the same site using similar signals. Moreover, searches for other genes containing similar elements have not been possible due to a lack of suitable bioinformatics methods for searches of secondary structure elements and the difficulty of experimentally testing all the possible candidates. We have developed a bioinformatics approach for searching across the genome for small RNA elements that are similar to the secondary structures of particular localization signals. We have uncovered 48 candidates, of which we were able to test 22 for their localization potential using injection assays for Dynein mediated RNA localization. We found that G2 and Jockey transposons each contain a gurken/I factor-like RNA stem-loop required for Dynein-dependent localization to the anterior and dorso-anterior corner of the oocyte. We conclude that I factor, G2, and Jockey are members of a "family" of transposable elements sharing a gurken-like mRNA localization signal and Dynein-dependent mechanism of transport. The bioinformatics pipeline we have developed will have broader utility in fields where small RNA signals play important roles.

  8. Stepwise evolution of two giant composite LTR-retrotransposon-like elements DA and Xiao

    Directory of Open Access Journals (Sweden)

    Li Xuanyang

    2009-06-01

    Full Text Available Abstract Background We recently discovered two composite long terminal repeat (LTR-retrotransposon-like elements which we named DA (~300 kb and Xiao (~30 kb, meaning big and small in Chinese respectively. Xiao and DA (three types of DA identified were found to have been derived from several donor sites and have spread to 30 loci in the human genome, totaling to 5 Mb. Our bioinformatics analyses with the released human, chimp, rhesus macaque, orangutan, and marmoset genomic sequences indicate that DA and Xiao emerged ~25 million years (Myr ago. Results To better understand the evolution of these two complex elements, we investigated various internal junctions of DA and Xiao as well as orthologous genomic sites of the 30 DA/Xiao loci in non-human primates including great apes, lesser apes, Old World monkeys, New World monkeys, and a prosimian. We found that Xiao and type I DA first emerged in the genome between 25 and 18 Myr ago, whereas type II and Type III DAs emerged between 14 and 7 Myr ago. Xiao and DA were most active in great apes, with their amplification peaking during 25-14 and 14-7 Myr ago, respectively. Neither DA nor Xiao seem to have been active in the human and chimp genomes during last 6 Myr. Conclusion The study has led to a more accurate age determination of the DA and Xiao elements than our previous bioinformatics analyses, and indicates that the amplification activity of the elements coincided with that of group I HERV-Es during evolution. It has also illustrated an evolutionary path with stepwise structural changes for the elements during past 25 Myr, and in doing so has shed more light on these two intriguing and complex elements that have reshaped our genome.

  9. Evolutionary dynamics of the Ty3/gypsy LTR retrotransposons in the genome of Anopheles gambiae.

    Directory of Open Access Journals (Sweden)

    Jose Manuel C Tubio

    Full Text Available Ty3/gypsy elements represent one of the most abundant and diverse LTR-retrotransposon (LTRr groups in the Anopheles gambiae genome, but their evolutionary dynamics have not been explored in detail. Here, we conduct an in silico analysis of the distribution and abundance of the full complement of 1045 copies in the updated AgamP3 assembly. Chromosomal distribution of Ty3/gypsy elements is inversely related to arm length, with densities being greatest on the X, and greater on the short versus long arms of both autosomes. Taking into account the different heterochromatic and euchromatic compartments of the genome, our data suggest that the relative abundance of Ty3/gypsy LTRrs along each chromosome arm is determined mainly by the different proportions of heterochromatin, particularly pericentric heterochromatin, relative to total arm length. Additionally, the breakpoint regions of chromosomal inversion 2La appears to be a haven for LTRrs. These elements are underrepresented more than 7-fold in euchromatin, where 33% of the Ty3/gypsy copies are associated with genes. The euchromatin on chromosome 3R shows a faster turnover rate of Ty3/gypsy elements, characterized by a deficit of proviral sequences and the lowest average sequence divergence of any autosomal region analyzed in this study. This probably reflects a principal role of purifying selection against insertion for the preservation of longer conserved syntenyc blocks with adaptive importance located in 3R. Although some Ty3/gypsy LTRrs show evidence of recent activity, an important fraction are inactive remnants of relatively ancient insertions apparently subject to genetic drift. Consistent with these computational predictions, an analysis of the occupancy rate of putatively older insertions in natural populations suggested that the degenerate copies have been fixed across the species range in this mosquito, and also are shared with the sibling species Anopheles arabiensis.

  10. Proportionality and Autonomous Weapons Systems

    NARCIS (Netherlands)

    van den Boogaard, J.

    2015-01-01

    Given the swift technologic development, it may be expected that the availability of the first truly autonomous weapons systems is fast approaching. Once they are deployed, these weapons will use artificial intelligence to select and attack targets without further human intervention. Autonomous weap

  11. 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…

  12. 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...

  13. Autonomous Gaussian Decomposition

    CERN Document Server

    Lindner, Robert R; Murray, Claire E; Stanimirović, Snežana; Babler, Brian L; Heiles, Carl; Hennebelle, Patrick; Goss, W M; Dickey, John

    2014-01-01

    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 21cm absorption spectra from the 21cm SPectral line Observations of Neutral Gas with the EVLA (21-SPONGE) survey. We use AGD with Monte Carlo methods to derive the HI 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 up...

  14. Cognitive Function Related to the Sirh11/Zcchc16 Gene Acquired from an LTR Retrotransposon in Eutherians.

    Directory of Open Access Journals (Sweden)

    Masahito Irie

    2015-09-01

    Full Text Available Gene targeting of mouse Sushi-ichi-related retrotransposon homologue 11/Zinc finger CCHC domain-containing 16 (Sirh11/Zcchc16 causes abnormal behaviors related to cognition, including attention, impulsivity and working memory. Sirh11/Zcchc16 encodes a CCHC type of zinc-finger protein that exhibits high homology to an LTR retrotransposon Gag protein. Upon microdialysis analysis of the prefrontal cortex region, the recovery rate of noradrenaline (NA was reduced compared with dopamine (DA after perfusion of high potassium-containing artificial cerebrospinal fluid in knockout (KO mice. These data indicate that Sirh11/Zcchc16 is involved in cognitive function in the brain, possibly via the noradrenergic system, in the contemporary mouse developmental systems. Interestingly, it is highly conserved in three out of the four major groups of the eutherians, euarchontoglires, laurasiatheria and afrotheria, but is heavily mutated in xenarthran species such as the sloth and armadillo, suggesting that it has contributed to brain evolution in the three major eutherian lineages, including humans and mice. Sirh11/Zcchc16 is the first SIRH gene to be involved in brain function, instead of just the placenta, as seen in the case of Peg10, Peg11/Rtl1 and Sirh7/Ldoc1.

  15. Variation in Copy Number of Ty3/Gypsy Centromeric Retrotransposons in the Genomes of Thinopyrum intermedium and Its Diploid Progenitors.

    Directory of Open Access Journals (Sweden)

    Mikhail G Divashuk

    Full Text Available Speciation and allopolyploidization in cereals may be accompanied by dramatic changes in abundance of centromeric repeated transposable elements. Here we demonstrate that the reverse transcriptase part of Ty3/gypsy centromeric retrotransposon (RT-CR is highly conservative in the segmental hexaploid Thinopyrum intermedium (JrJvsSt and its possible diploid progenitors Th. bessarabicum (Jb, Pseudoroegneria spicata (St and Dasypyrum villosum (V but the abundance of the repeats varied to a large extent. Fluorescence in situ hybridization (FISH showed hybridization signals in centromeric region of all chromosomes in the studied species, although the intensity of the signals drastically differed. In Th. intermedium, the strongest signal of RT-CR probe was detected on the chromosomes of Jv, intermediate on Jr and faint on Js and St subgenome suggesting different abundance of RT-CR on the individual chromosomes rather than the sequence specificity of RT-CRs of the subgenomes. RT-CR quantification using real-time PCR revealed that its content per genome in Th. bessarabicum is ~ 2 times and P. spicata is ~ 1,5 times higher than in genome of D. villosum. The possible burst of Ty3/gypsy centromeric retrotransposon in Th. intermedium during allopolyploidization and its role in proper mitotic and meiotic chromosome behavior in a nascent allopolyploid is discussed.

  16. Mobile Intelligent Autonomous Systems

    Directory of Open Access Journals (Sweden)

    Jitendra R. Raol

    2010-01-01

    Full Text Available Mobile intelligent autonomous systems (MIAS is a fast emerging research area. Although it can be regarded as a general R&D area, it is mainly directed towards robotics. Several important subtopics within MIAS research are:(i perception and reasoning, (ii mobility and navigation,(iii haptics and teleoperation, (iv image fusion/computervision, (v modelling of manipulators, (vi hardware/software architectures for planning and behaviour learning leadingto robotic architecture, (vii vehicle-robot path and motionplanning/control, (viii human-machine interfaces for interaction between humans and robots, and (ix application of artificial neural networks (ANNs, fuzzy logic/systems (FLS,probabilistic/approximate reasoning (PAR, Bayesian networks(BN and genetic algorithms (GA to the above-mentioned problems. Also, multi-sensor data fusion (MSDF playsvery crucial role at many levels of the data fusion process:(i kinematic fusion (position/bearing tracking, (ii imagefusion (for scene recognition, (iii information fusion (forbuilding world models, and (iv decision fusion (for tracking,control actions. The MIAS as a technology is useful for automation of complex tasks, surveillance in a hazardousand hostile environment, human-assistance in very difficultmanual works, medical robotics, hospital systems, autodiagnosticsystems, and many other related civil and military systems. Also, other important research areas for MIAScomprise sensor/actuator modelling, failure management/reconfiguration, scene understanding, knowledge representation, learning and decision-making. Examples ofdynamic systems considered within the MIAS would be:autonomous systems (unmanned ground vehicles, unmannedaerial vehicles, micro/mini air vehicles, and autonomousunder water vehicles, mobile/fixed robotic systems, dexterousmanipulator robots, mining robots, surveillance systems,and networked/multi-robot systems, to name a few.Defence Science Journal, 2010, 60(1, pp.3-4,

  17. 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

  18. Autonomous software: Myth or magic?

    CERN Document Server

    Allan, Alasdair; Saunders, Eric S

    2008-01-01

    We discuss work by the eSTAR project which demonstrates a fully closed loop autonomous system for the follow up of possible micro-lensing anomalies. Not only are the initial micro-lensing detections followed up in real time, but ongoing events are prioritised and continually monitored, with the returned data being analysed automatically. If the ``smart software'' running the observing campaign detects a planet-like anomaly, further follow-up will be scheduled autonomously and other telescopes and telescope networks alerted to the possible planetary detection. We further discuss the implications of this, and how such projects can be used to build more general autonomous observing and control systems.

  19. High-throughput retrotransposon-based fluorescent markers: improved information content and allele discrimination

    Directory of Open Access Journals (Sweden)

    Baker David

    2009-07-01

    Full Text Available Abstract Background Dense genetic maps, together with the efficiency and accuracy of their construction, are integral to genetic studies and marker assisted selection for plant breeding. High-throughput multiplex markers that are robust and reproducible can contribute to both efficiency and accuracy. Multiplex markers are often dominant and so have low information content, this coupled with the pressure to find alternatives to radio-labelling, has led us to adapt the SSAP (sequence specific amplified polymorphism marker method from a 33P labelling procedure to fluorescently tagged markers analysed from an automated ABI 3730 xl platform. This method is illustrated for multiplexed SSAP markers based on retrotransposon insertions of pea and is applicable for the rapid and efficient generation of markers from genomes where repetitive element sequence information is available for primer design. We cross-reference SSAP markers previously generated using the 33P manual PAGE system to fluorescent peaks, and use these high-throughput fluorescent SSAP markers for further genetic studies in Pisum. Results The optimal conditions for the fluorescent-labelling method used a triplex set of primers in the PCR. These included a fluorescently labelled specific primer together with its unlabelled counterpart, plus an adapter-based primer with two bases of selection on the 3' end. The introduction of the unlabelled specific primer helped to optimise the fluorescent signal across the range of fragment sizes expected, and eliminated the need for extensive dilutions of PCR amplicons. The software (GeneMarker Version 1.6 used for the high-throughput data analysis provided an assessment of amplicon size in nucleotides, peak areas and fluorescence intensity in a table format, so providing additional information content for each marker. The method has been tested in a small-scale study with 12 pea accessions resulting in 467 polymorphic fluorescent SSAP markers of which

  20. C. elegans germ cells show temperature and age-dependent expression of Cer1, a Gypsy/Ty3-related retrotransposon.

    Directory of Open Access Journals (Sweden)

    Shannon Dennis

    Full Text Available Virus-like particles (VLPs have not been observed in Caenorhabditis germ cells, although nematode genomes contain low numbers of retrotransposon and retroviral sequences. We used electron microscopy to search for VLPs in various wild strains of Caenorhabditis, and observed very rare candidate VLPs in some strains, including the standard laboratory strain of C. elegans, N2. We identified the N2 VLPs as capsids produced by Cer1, a retrotransposon in the Gypsy/Ty3 family of retroviruses/retrotransposons. Cer1 expression is age and temperature dependent, with abundant expression at 15°C and no detectable expression at 25°C, explaining how VLPs escaped detection in previous studies. Similar age and temperature-dependent expression of Cer1 retrotransposons was observed for several other wild strains, indicating that these properties are common, if not integral, features of this retroelement. Retrotransposons, in contrast to DNA transposons, have a cytoplasmic stage in replication, and those that infect non-dividing cells must pass their genomic material through nuclear pores. In most C. elegans germ cells, nuclear pores are largely covered by germline-specific organelles called P granules. Our results suggest that Cer1 capsids target meiotic germ cells exiting pachytene, when free nuclear pores are added to the nuclear envelope and existing P granules begin to be removed. In pachytene germ cells, Cer1 capsids concentrate away from nuclei on a subset of microtubules that are exceptionally resistant to microtubule inhibitors; the capsids can aggregate these stable microtubules in older adults, which exhibit a temperature-dependent decrease in egg viability. When germ cells exit pachytene, the stable microtubules disappear and capsids redistribute close to nuclei that have P granule-free nuclear pores. This redistribution is microtubule dependent, suggesting that capsids that are released from stable microtubules transfer onto new, dynamic microtubules

  1. SIRTF autonomous star tracker

    Science.gov (United States)

    van Bezooijen, Roelof W. H.

    2003-03-01

    Two redundant AST-301 autonomous star trackers (AST) serve as the primary attitude sensors for JPL's space infrared telescope facility (SIRTF). These units, which employ a 1553B interface to output their attitude quaternions and uncertainty at a 2 Hz rate, provide a 1 σaccuracy of better than 0.18, 0.18, and 5.1 arcsec about their X, Y, and Z axes, respectively. This is a factor 5.5 better than the accuracy of the flight-proven AST-201 from which the trackers were derived. To obtain this improvement, the field of view (FOV) was reduced to 5 by 5 degrees, the accurate Tycho-1 and ACT catalogs were used for selecting the 71,830 guide stars, star image centroiding was improved to better than 1/50th of a pixel, and optimal attitude estimation was implemented. In addition, the apparent direction to each guide star in the FOV is compensated for proper motion, parallax, velocity aberration, and optical distortion. The AST-301 employs autonomous time-delayed integration (TDI) to achieve image motion compensation (IMC) about its X axis that prevents accuracy degradation, even at rates of 2.1 deg/s, making it actually suitable for use on spinning spacecraft. About the Y axis, a software function called "image motion accommodation" (IMA) processes smeared images to maximize the signal to noise ratio of the resulting synthetic images, which enables robust and accurate tracking at rates tested up to 0.42 deg/s. The AST-301 is capable of acquiring its attitude anywhere in the sky in less than 3 seconds with a 99.98% probability of success, without requiring any a priori attitude knowledge. Following a description of the 7.1 kg AST-301, its operation and IMA, the methodology for translating the night sky test data into performance numbers is presented, while, in addition, the results of tests used to measure alignment stability over temperature are included.

  2. Framework for Autonomous Optimization Project

    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...

  3. 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.

  4. Autonomic Function in Neurodegenerative Diseases

    DEFF Research Database (Denmark)

    Sørensen, Gertrud Laura; Jennum, Poul Jørgen

    2013-01-01

    , which includes the cardiac centre and controls autonomic functions, and therefore autonomic dysfunction may be experienced early in the disease course. Sleep disturbances are also common non-motor complications of PD, and therefore PD patients undergo polysomnography at the Danish Center for Sleep......Neurodegenerative diseases are highly debilitating and often lead to severe morbidity and even death. Parkinson’s disease (PD) is the second most common neurodegenerative disease after Alzheimer’s disease. According to the Braak staging study, the progressionof PD starts in the medulla oblongata...... Medicine to assess the sleep disturbances. The aim of this PhD dissertation was to: 1) Develop a method to investigate autonomic changes during sleep in neurodegenerative diseases, and apply this method on PD, iRBD and narcolepsy patients to evaluate the autonomic function in these diseases. 2) Validate...

  5. 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.

  6. [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.

  7. 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.

  8. 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

  9. The take and give between retrotransposable elements and their hosts.

    Science.gov (United States)

    Beauregard, Arthur; Curcio, M Joan; Belfort, Marlene

    2008-01-01

    Retrotransposons mobilize via RNA intermediates and usually carry with them the agent of their mobility, reverse transcriptase. Retrotransposons are streamlined, and therefore rely on host factors to proliferate. However, retrotransposons are exposed to cellular forces that block their paths. For this review, we have selected for our focus elements from among target-primed (TP) retrotransposons, also called non-LTR retrotransposons, and extrachromosomally-primed (EP) retrotransposons, also called LTR retrotransposons. The TP retrotransposons considered here are group II introns, LINEs and SINEs, whereas the EP elements considered are the Ty and Tf retrotransposons, with a brief comparison to retroviruses. Recurring themes for these elements, in hosts ranging from bacteria to humans, are tie-ins of the retrotransposons to RNA metabolism, DNA replication and repair, and cellular stress. Likewise, there are parallels among host-cell defenses to combat rampant retrotransposon spread. The interactions between the retrotransposon and the host, and their coevolution to balance the tension between retrotransposon proliferation and host survival, form the basis of this review.

  10. SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age

    Science.gov (United States)

    Van Meter, Michael; Kashyap, Mehr; Rezazadeh, Sarallah; Geneva, Anthony J.; Morello, Timothy D.; Seluanov, Andrei; Gorbunova, Vera

    2014-01-01

    L1 retrotransposons are an abundant class of transposable elements which pose a threat to genome stability and may play a role in age-related pathologies such as cancer. Recent evidence indicates that L1s become more active in somatic tissues during the course of aging; the mechanisms underlying this phenomenon remain unknown, however. Here we report that the longevity regulating protein, SIRT6, is a powerful repressor of L1 activity. Specifically, SIRT6 binds to the 5′UTR of L1 loci, where it mono-ADP ribosylates the nuclear corepressor protein, KAP1, and facilitates KAP1 interaction with the heterochromatin factor, HP1α, thereby contributing to the packaging of L1 elements into transcriptionally repressive heterochromatin. During the course of aging, and also in response to DNA damage, however, we find that SIRT6 is depleted from L1 loci, allowing for the activation of these previously silenced retroelements. PMID:25247314

  11. Retrotransposon Ty1 RNA contains a 5'-terminal long-range pseudoknot required for efficient reverse transcription.

    Science.gov (United States)

    Huang, Qing; Purzycka, Katarzyna J; Lusvarghi, Sabrina; Li, Donghui; Legrice, Stuart F J; Boeke, Jef D

    2013-03-01

    Ty1 retrotransposon RNA has the potential to fold into a variety of distinct structures, mutation of which affects retrotransposition frequencies. We show here that one potential functional structure is located at the 5' end of the genome and can assume a pseudoknot conformation. Chemoenzymatic probing of wild-type and mutant mini-Ty1 RNAs supports the existence of such a structure, while molecular genetic analyses show that mutations disrupting pseudoknot formation interfere with retrotransposition, indicating that it provides a critical biological function. These defects are enhanced at higher temperatures. When these mutants are combined with compensatory changes, retrotransposition is restored, consistent with pseudoknot architecture. Analyses of mutants suggest a defect in Ty1 reverse transcription. Collectively, our data allow modeling of a three-dimensional structure for this novel critical cis-acting signal of the Ty1 genome.

  12. 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.

  13. 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.

  14. Integrated Motion Planning and Autonomous Control Technology for Autonomous ISR Project

    Data.gov (United States)

    National Aeronautics and Space Administration — SSCI and MIT propose to design, implement and test a comprehensive Integrated Mission Planning & Autonomous Control Technology (IMPACT) for Autonomous ISR...

  15. Response of rice gypsy retrotransposons to different stress conditions%水稻gypsy类逆转座子对不同胁迫条件的响应

    Institute of Scientific and Technical Information of China (English)

    徐玲; 杨静; 刘林; 李成云

    2012-01-01

    LTR retrotransposons are the largest and most widely distributed transposable elements in rice, of which Ty3-gypsy class are more numerous. Using degenerate primers based on conserved region of reverse transcriptase gene in Ty3-gypsy retrotransposons, transcript fragments were amplified by RT-PCR and sequenced respectively from cDNAs of rice variety Acuche treated by 5 different stresses (M oryza, SA, 2,4-D, high-salt and tissue culture) to analyze the characteristics of Ty3-gypsy retrotransposons activated by different stresses. The results showed that all the 5 different stresses could activate Tyl-gypsy retrotransposon; amino acid sequences of reverse transcriptase of retrotransposons responding to different stresses were highly conserved and distributed crossly, only few of them showed specificity of stress response, suggesting that many Ty3-gy/wy retrotransposons could respond to different stresses.%LTR类逆转座子是水稻基因组中数量最多、分布最广的转座元件,其中Ty3-ypsy类所占比例较大.根据Ty3-gypsy类逆转座子逆转录酶的保守区域,采用简并引物,通过RT-PCR,对5种胁迫处理(稻瘟菌、水杨酸、2,4-D、高盐及组织培养)后的云南地方水稻品种月亮谷的cDNA进行扩增,并测序获得了一批转录片段,分析不同胁迫条件诱导激活的Ty3-ypsy类逆转座子的特点.结果表明:5种胁迫处理都能诱导月亮谷中Ty3-gypsy类逆转座子的表达;对不同胁迫响应的逆转座子序列大部分同源性较高,且呈交叉分布,仅有少部分具有胁迫响应的特异性,说明很多Ty3-gypsy类逆转座子能对不同胁迫进行响应.

  16. 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.

  17. Autonomous mobile robots: Vehicles with cognitive control

    Energy Technology Data Exchange (ETDEWEB)

    Meystel, A.

    1987-01-01

    This book explores a new rapidly developing area of robotics. It describes the state-of-the-art intelligence control, applied machine intelligence, and research and initial stages of manufacturing of autonomous mobile robots. A complete account of the theoretical and experimental results obtained during the last two decades together with some generalizations on Autonomous Mobile Systems are included in this book. Contents: Introduction; Requirements and Specifications; State-of-the-art in Autonomous Mobile Robots Area; Structure of Intelligent Mobile Autonomous System; Planner, Navigator; Pilot; Cartographer; Actuation Control; Computer Simulation of Autonomous Operation; Testing the Autonomous Mobile Robot; Conclusions; Bibliography.

  18. Autonomous underwater riser inspection tool

    Energy Technology Data Exchange (ETDEWEB)

    Camerini, Claudio; Marnet, Robson [Petrobras SA, (Brazil); Freitas, Miguel; Von der Weid, Jean Pierre [CPTI/PUC-Rio, Rio de Janeiro, (Brazil); Artigas Lander, Ricardo [EngeMOVI, Curitiba, (Brazil)

    2010-07-01

    The detection of damage on the riser is a serious concern for pipeline companies. Visual examinations by remotely operated vehicle (ROV) are presently carried out to detect the defects but this process has limitations and is expensive. This paper presents the development of a new tool to ensure autonomous underwater riser inspection (AURI) that uses the riser itself for guidance. The AURI, which is autonomous in terms of control and power supply, is equipped with several cameras that perform a complete visual inspection of the riser with 100 % coverage of the external surface of the riser. The paper presents the detailed characteristics of the first AURI prototype, describes its launching procedure and provides the preliminary test results from pool testing. The results showed that the AURI is a viable system for autonomous riser inspection. Offshore tests on riser pipelines are scheduled to be performed shortly.

  19. Hereditary sensory and autonomic neuropathies.

    Science.gov (United States)

    Auer-Grumbach, Michaela

    2013-01-01

    Hereditary sensory and autonomic neuropathies (HSN/HSAN) are clinically and genetically heterogeneous disorders of the peripheral nervous system that predominantly affect the sensory and autonomic neurons. Hallmark features comprise not only prominent sensory signs and symptoms and ulcerative mutilations but also variable autonomic and motor disturbances. Autosomal dominant and autosomal recessive inheritance has been reported. Molecular genetics studies have identified disease-causing mutations in 11 genes. Some of the affected proteins have nerve-specific roles but underlying mechanisms have also been shown to involve sphingolipid metabolism, vesicular transport, structural integrity, and transcription regulation. Genetic and functional studies have substantially improved the understanding of the pathogenesis of the HSN/HSAN and will help to find preventive and causative therapies in the future.

  20. Gas House Autonomous System Monitoring

    Science.gov (United States)

    Miller, Luke; Edsall, Ashley

    2015-01-01

    Gas House Autonomous System Monitoring (GHASM) will employ Integrated System Health Monitoring (ISHM) of cryogenic fluids in the High Pressure Gas Facility at Stennis Space Center. The preliminary focus of development incorporates the passive monitoring and eventual commanding of the Nitrogen System. ISHM offers generic system awareness, adept at using concepts rather than specific error cases. As an enabler for autonomy, ISHM provides capabilities inclusive of anomaly detection, diagnosis, and abnormality prediction. Advancing ISHM and Autonomous Operation functional capabilities enhances quality of data, optimizes safety, improves cost effectiveness, and has direct benefits to a wide spectrum of aerospace applications.

  1. 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...

  2. Discerning non-autonomous dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Clemson, Philip T.; Stefanovska, Aneta, E-mail: aneta@lancaster.ac.uk

    2014-09-30

    Structure and function go hand in hand. However, while a complex structure can be relatively safely broken down into the minutest parts, and technology is now delving into nanoscales, the function of complex systems requires a completely different approach. Here the complexity clearly arises from nonlinear interactions, which prevents us from obtaining a realistic description of a system by dissecting it into its structural component parts. At best, the result of such investigations does not substantially add to our understanding or at worst it can even be misleading. Not surprisingly, the dynamics of complex systems, facilitated by increasing computational efficiency, is now readily tackled in the case of measured time series. Moreover, time series can now be collected in practically every branch of science and in any structural scale—from protein dynamics in a living cell to data collected in astrophysics or even via social networks. In searching for deterministic patterns in such data we are limited by the fact that no complex system in the real world is autonomous. Hence, as an alternative to the stochastic approach that is predominantly applied to data from inherently non-autonomous complex systems, theory and methods specifically tailored to non-autonomous systems are needed. Indeed, in the last decade we have faced a huge advance in mathematical methods, including the introduction of pullback attractors, as well as time series methods that cope with the most important characteristic of non-autonomous systems—their time-dependent behaviour. Here we review current methods for the analysis of non-autonomous dynamics including those for extracting properties of interactions and the direction of couplings. We illustrate each method by applying it to three sets of systems typical for chaotic, stochastic and non-autonomous behaviour. For the chaotic class we select the Lorenz system, for the stochastic the noise-forced Duffing system and for the non-autonomous

  3. 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.

  4. Discerning non-autonomous dynamics

    Science.gov (United States)

    Clemson, Philip T.; Stefanovska, Aneta

    2014-09-01

    Structure and function go hand in hand. However, while a complex structure can be relatively safely broken down into the minutest parts, and technology is now delving into nanoscales, the function of complex systems requires a completely different approach. Here the complexity clearly arises from nonlinear interactions, which prevents us from obtaining a realistic description of a system by dissecting it into its structural component parts. At best, the result of such investigations does not substantially add to our understanding or at worst it can even be misleading. Not surprisingly, the dynamics of complex systems, facilitated by increasing computational efficiency, is now readily tackled in the case of measured time series. Moreover, time series can now be collected in practically every branch of science and in any structural scale-from protein dynamics in a living cell to data collected in astrophysics or even via social networks. In searching for deterministic patterns in such data we are limited by the fact that no complex system in the real world is autonomous. Hence, as an alternative to the stochastic approach that is predominantly applied to data from inherently non-autonomous complex systems, theory and methods specifically tailored to non-autonomous systems are needed. Indeed, in the last decade we have faced a huge advance in mathematical methods, including the introduction of pullback attractors, as well as time series methods that cope with the most important characteristic of non-autonomous systems-their time-dependent behaviour. Here we review current methods for the analysis of non-autonomous dynamics including those for extracting properties of interactions and the direction of couplings. We illustrate each method by applying it to three sets of systems typical for chaotic, stochastic and non-autonomous behaviour. For the chaotic class we select the Lorenz system, for the stochastic the noise-forced Duffing system and for the non-autonomous the

  5. piRNA-associated proteins and retrotransposons are differentially expressed in murine testis and ovary of aryl hydrocarbon receptor deficient mice

    Science.gov (United States)

    Rico-Leo, Eva M.; Moreno-Marín, Nuria; González-Rico, Francisco J.; Barrasa, Eva; Ortega-Ferrusola, Cristina; Martín-Muñoz, Patricia; Sánchez-Guardado, Luis O.; Llano, Elena; Alvarez-Barrientos, Alberto; Infante-Campos, Ascensión; Catalina-Fernández, Inmaculada; Hidalgo-Sánchez, Matías; de Rooij, Dirk G.; Pendás, Alberto M.; Peña, Fernando J.; Merino, Jaime M.

    2016-01-01

    Previous studies suggested that the aryl hydrocarbon receptor (AhR) contributes to mice reproduction and fertility. However, the mechanisms involved remain mostly unknown. Retrotransposon silencing by Piwi-interacting RNAs (piRNAs) is essential for germ cell maturation and, remarkably, AhR has been identified as a regulator of murine B1-SINE retrotransposons. Here, using littermate AhR+/+ and AhR−/− mice, we report that AhR regulates the general course of spermatogenesis and oogenesis by a mechanism likely to be associated with piRNA-associated proteins, piRNAs and retrotransposons. piRNA-associated proteins MVH and Miwi are upregulated in leptotene to pachytene spermatocytes with a more precocious timing in AhR−/− than in AhR+/+ testes. piRNAs and transcripts from B1-SINE, LINE-1 and IAP retrotransposons increased at these meiotic stages in AhR-null testes. Moreover, B1-SINE transcripts colocalize with MVH and Miwi in leptonema and pachynema spermatocytes. Unexpectedly, AhR−/− males have increased sperm counts, higher sperm functionality and enhanced fertility than AhR+/+ mice. In contrast, piRNA-associated proteins and B1-SINE and IAP-derived transcripts are reduced in adult AhR−/− ovaries. Accordingly, AhR-null female mice have lower numbers of follicles when compared with AhR+/+ mice. Thus, AhR deficiency differentially affects testis and ovary development possibly by a process involving piRNA-associated proteins, piRNAs and transposable elements. PMID:28003471

  6. In Drosophila melanogaster the COM locus directs the somatic silencing of two retrotransposons through both Piwi-dependent and -independent pathways.

    Directory of Open Access Journals (Sweden)

    Sophie Desset

    Full Text Available BACKGROUND: In the Drosophila germ line, repeat-associated small interfering RNAs (rasiRNAs ensure genomic stability by silencing endogenous transposable elements. This RNA silencing involves small RNAs of 26-30 nucleotides that are mainly produced from the antisense strand and function through the Piwi protein. Piwi belongs to the subclass of the Argonaute family of RNA interference effector proteins, which are expressed in the germline and in surrounding somatic tissues of the reproductive apparatus. In addition to this germ-line expression, Piwi has also been implicated in diverse functions in somatic cells. PRINCIPAL FINDINGS: Here, we show that two LTR retrotransposons from Drosophila melanogaster, ZAM and Idefix, are silenced by an RNA silencing pathway that has characteristics of the rasiRNA pathway and that specifically recognizes and destroys the sense-strand RNAs of the retrotransposons. This silencing depends on Piwi in the follicle cells surrounding the oocyte. Interestingly, this silencing is active in all the somatic tissues examined from embryos to adult flies. In these somatic cells, while the silencing still involves the strict recognition of sense-strand transcripts, it displays the marked difference of being independent of the Piwi protein. Finally, we present evidence that in all the tissues examined, the repression is controlled by the heterochromatic COM locus. CONCLUSION: Our data shed further light on the silencing mechanism that acts to target Drosophila LTR retrotransposons in somatic cells throughout fly development. They demonstrate that different RNA silencing pathways are involved in ovarian versus other somatic tissues, since Piwi is necessary for silencing in the former tissues but is dispensable in the latter. They further demonstrate that these pathways are controlled by the heterochromatic COM locus which ensures the overall protection of Drosophila against the detrimental effects of random retrotransposon

  7. 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...

  8. 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...

  9. 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.

  10. Objects as Temporary Autonomous Zones

    Directory of Open Access Journals (Sweden)

    Tim Morton

    2011-09-01

    Full Text Available From Hakim Bey's instructions on creating temporary autonomous zones we see an oscillation "between performance art and politics, circus clowning and revolution." In this essay Tim Morton discusses anarchist politics as, "the creation of fresh objects in a reality without a top or a bottom object, or for that matter a middle object."

  11. Objects as Temporary Autonomous Zones

    OpenAIRE

    Tim Morton

    2011-01-01

    From Hakim Bey's instructions on creating temporary autonomous zones we see an oscillation "between performance art and politics, circus clowning and revolution." In this essay Tim Morton discusses anarchist politics as, "the creation of fresh objects in a reality without a top or a bottom object, or for that matter a middle object."

  12. 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 fu...

  13. Autonomous vertical profiler data management

    Digital Repository Service at National Institute of Oceanography (India)

    Afzulpurkar, S.; Navelkar, G.S.; Desa, E.S.; Madhan, R.; Dabholkar, N; Prabhudesai, S.P.; Mascarenhas, A.A

    The Autonomous Vertical Profiler (AVP), developed at NIO [1] [2], collects position and water column data over a period of 3 days and transmits through a satellite modem which is collated and stored on a PC. Data includes GPS positions, water column...

  14. Designing Assessment for Autonomous Learning

    Science.gov (United States)

    Hay, Marie; Mathers, Lucy

    2012-01-01

    This paper aims to disseminate and evaluate an autonomous learning framework developed through collaborative research with first- and second-year undergraduate students at De Montfort University. Central to the framework is the involvement of students in the assessment of their peers and themselves using dialogue about the assessment and feedback…

  15. 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 .

  16. Autonomic dysreflexia: a medical emergency

    Science.gov (United States)

    Bycroft, J; Shergill, I; Choong, E; Arya, N; Shah, P

    2005-01-01

    Autonomic dysreflexia is an important clinical diagnosis that requires prompt treatment to avoid devastating complications. The condition may present itself to all members of medical and surgical specialties, who may not be accustomed to treating it. It is the clinician's responsibility to have a basic understanding of the pathophysiology of the condition and the simple steps required to treat it. PMID:15811886

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

    Directory of Open Access Journals (Sweden)

    Das Arpita

    2005-05-01

    Full Text Available Abstract Background 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. Results 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. Conclusion A combination of empirical sequencing and retrieval of unannotated Genome Survey Sequence database entries was successfully used to construct a full-length representative of

  18. 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

  19. Experiences in Benchmarking of Autonomic Systems

    Science.gov (United States)

    Etchevers, Xavier; Coupaye, Thierry; Vachet, Guy

    Autonomic computing promises improvements of systems quality of service in terms of availability, reliability, performance, security, etc. However, little research and experimental results have so far demonstrated this assertion, nor provided proof of the return on investment stemming from the efforts that introducing autonomic features requires. Existing works in the area of benchmarking of autonomic systems can be characterized by their qualitative and fragmented approaches. Still a crucial need is to provide generic (i.e. independent from business, technology, architecture and implementation choices) autonomic computing benchmarking tools for evaluating and/or comparing autonomic systems from a technical and, ultimately, an economical point of view. This article introduces a methodology and a process for defining and evaluating factors, criteria and metrics in order to qualitatively and quantitatively assess autonomic features in computing systems. It also discusses associated experimental results on three different autonomic systems.

  20. 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.

  1. Cardiac autonomic nerve distribution and arrhythmia

    Institute of Scientific and Technical Information of China (English)

    Quan Liu; Dongmei Chen; Yonggang Wang; Xin Zhao; Yang Zheng

    2012-01-01

    OBJECTIVE: To analyze the distribution characteristics of cardiac autonomic nerves and to explore the correlation between cardiac autonomic nerve distribution and arrhythmia.DATA RETRIEVAL: A computer-based retrieval was performed for papers examining the distribution of cardiac autonomic nerves, using "heart, autonomic nerve, sympathetic nerve, vagus nerve, nerve distribution, rhythm and atrial fibrillation" as the key words.SELECTION CRITERIA: A total of 165 studies examining the distribution of cardiac autonomic nerve were screened, and 46 of them were eventually included.MAIN OUTCOME MEASURES: The distribution and characteristics of cardiac autonomic nerves were observed, and immunohistochemical staining was applied to determine the levels of tyrosine hydroxylase and acetylcholine transferase (main markers of cardiac autonomic nerve distribution). In addition, the correlation between cardiac autonomic nerve distribution and cardiac arrhythmia was investigated.RESULTS: Cardiac autonomic nerves were reported to exhibit a disordered distribution in different sites, mainly at the surface of the cardiac atrium and pulmonary vein, forming a ganglia plexus. The distribution of the pulmonary vein autonomic nerve was prominent at the proximal end rather than the distal end, at the upper left rather than the lower right, at the epicardial membrane rather than the endocardial membrane, at the left atrium rather than the right atrium, and at the posterior wall rather than the anterior wall. The main markers used for cardiac autonomic nerves were tyrosine hydroxylase and acetylcholine transferase. Protein gene product 9.5 was used to label the immunoreactive nerve distribution, and the distribution density of autonomic nerves was determined using a computer-aided morphometric analysis system.CONCLUSION: The uneven distribution of the cardiac autonomic nerves is the leading cause of the occurrence of arrhythmia, and the cardiac autonomic nerves play an important role in the

  2. Chaotic neurodynamics for autonomous agents.

    Science.gov (United States)

    Harter, Derek; Kozma, Robert

    2005-05-01

    Mesoscopic level neurodynamics study the collective dynamical behavior of neural populations. Such models are becoming increasingly important in understanding large-scale brain processes. Brains exhibit aperiodic oscillations with a much more rich dynamical behavior than fixed-point and limit-cycle approximation allow. Here we present a discretized model inspired by Freeman's K-set mesoscopic level population model. We show that this version is capable of replicating the important principles of aperiodic/chaotic neurodynamics while being fast enough for use in real-time autonomous agent applications. This simplification of the K model provides many advantages not only in terms of efficiency but in simplicity and its ability to be analyzed in terms of its dynamical properties. We study the discrete version using a multilayer, highly recurrent model of the neural architecture of perceptual brain areas. We use this architecture to develop example action selection mechanisms in an autonomous agent.

  3. Cardiovascular autonomic neuropathy in diabetes

    DEFF Research Database (Denmark)

    Spallone, Vincenza; Ziegler, Dan; Freeman, Roy

    2011-01-01

    in type 2 diabetes. CAN is a risk marker of mortality and cardiovascular morbidity, and possibly a progression promoter of diabetic nephropathy. Criteria for CAN diagnosis and staging are: 1. one abnormal cardio-vagal test identifies possible or early CAN; 2. at least two abnormal cardio-vagal tests....... diagnosis of CAN clinical forms, 2. detection and tailored treatment of CAN clinical correlates (e.g. tachycardia, OH, nondipping, QT interval prolongation), 3. risk stratification for diabetic complications and cardiovascular morbidity and mortality, and 4. modulation of targets of diabetes therapy......Cardiovascular Autonomic Neuropathy (CAN) Subcommittee of Toronto Consensus Panel on Diabetic Neuropathy worked to update CAN guidelines, with regard to epidemiology, clinical impact, diagnosis, usefulness of CAN testing, and management. CAN is the impairment of cardiovascular autonomic control...

  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...... investigates the missing links and gaps between the research and developments efforts and the real-world application requirements, in order to bring the AIMM technology from laboratories to manufacturing environments. The investigation is based on 12 general application requirements for robotics......; 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...

  5. 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.

  6. Precise excision of the retrotransposon gypsy from the forked and cut loci in a genetically unstable D. melanogaster strain.

    Science.gov (United States)

    Kuzin, A B; Lyubomirskaya, N V; Khudaibergenova, B M; Ilyin, Y V; Kim, A I

    1994-11-11

    The genetically unstable Mutator Strain of D. melanogaster is characterised by a high frequency of spontaneous mutations and their reversions. Three forked mutants were obtained independently and several reversions arose spontaneously with frequency of 10(-3)-10(-4). The sites of integration and excision of the gypsy retrotransposon were analysed by Southern blot analysis and sequencing of PCR fragments. In all cases gypsy had inserted at the end of the third exon of the major transcript of the forked gene, causing the duplication of TCCA target sequence. All the reversions resulted from precise excision of the gypsy. A double mutant containing ct6 and f1, caused by gypsy insertions into untranslated regions of the corresponding genes, was constructed. Two spontaneous ct6f+ revertants as well as one ct+f1 revertant were obtained from this line. Sequence analysis of gypsy integration and excision sites revealed that in all cases gypsy excision was also precise. These experiments constitute the first demonstration of precise excision of LTR-containing elements from their host genomes.

  7. Coupling of enhancer and insulator properties identified in two retrotransposons modulates their mutagenic impact on nearby genes.

    Science.gov (United States)

    Conte, Caroline; Dastugue, Bernard; Vaury, Chantal

    2002-03-01

    We recently reported a novel transposition system in which two retroelements from Drosophila melanogaster, ZAM and Idefix, are highly mobilized and preferentially insert within intergenic regions. Among the loci where new copies are detected, a hot spot for their insertion was identified at the white locus, where up to three elements occurred within a 3-kb fragment upstream of the transcriptional start site of white. We have used these insertions as molecular entry points to throw light on the mutagenic effect exerted by multiple insertions of retrotransposons within intergenic regions of a genome. Analysis of the molecular mechanisms by which ZAM and Idefix elements interfere with the regulation of the white gene has shown that ZAM bears cis-acting regulatory sequences able to enhance transcription of the white gene in the eyes of the flies. This activation may be counteracted by Idefix, which acts as an insulator able to isolate the white gene from the upstream ZAM enhancer. In addition to revealing a novel insulator sequence with its own specific features, our data clearly illustrate how retroelements can act as epigenetic factors able to interfere with the transcriptional regulation of their host.

  8. Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters.

    Science.gov (United States)

    Zanni, Vanessa; Eymery, Angéline; Coiffet, Michael; Zytnicki, Matthias; Luyten, Isabelle; Quesneville, Hadi; Vaury, Chantal; Jensen, Silke

    2013-12-03

    Most of our understanding of Drosophila heterochromatin structure and evolution has come from the annotation of heterochromatin from the isogenic y; cn bw sp strain. However, almost nothing is known about the heterochromatin's structural dynamics and evolution. Here, we focus on a 180-kb heterochromatic locus producing Piwi-interacting RNAs (piRNA cluster), the flamenco (flam) locus, known to be responsible for the control of at least three transposable elements (TEs). We report its detailed structure in three different Drosophila lines chosen according to their capacity to repress or not to repress the expression of two retrotransposons named ZAM and Idefix, and we show that they display high structural diversity. Numerous rearrangements due to homologous and nonhomologous recombination, deletions and segmental duplications, and loss and gain of TEs are diverse sources of active genomic variation at this locus. Notably, we evidence a correlation between the presence of ZAM and Idefix in this piRNA cluster and their silencing. They are absent from flam in the strain where they are derepressed. We show that, unexpectedly, more than half of the flam locus results from recent TE insertions and that most of the elements concerned are prone to horizontal transfer between species of the melanogaster subgroup. We build a model showing how such high and constant dynamics of a piRNA master locus open the way to continual emergence of new patterns of piRNA biogenesis leading to changes in the level of transposition control.

  9. Retrotransposon and gene activation in wheat in response to mycotoxigenic and non-mycotoxigenic-associated Fusarium stress

    DEFF Research Database (Denmark)

    Ansari, Khairul Islam; Walter, Stephanie; Brennan, Josephine M.;

    2007-01-01

    tolerance), bZIP expression was significantly more DON-up-regulated in lines that inherited this QTL. Basal accumulation of the bZIP transcript in spikelets treated with Tween20 (control), DON and in DON-relative to Tween20-treated spikelets was negatively correlated with DON-induced bleaching above (but...... zipper protein transcription factor (bZIP), retrotransposon-like homologs and genes of unknown function in the roots of wheat cultivars CM82036 and Remus. Fusarium head blight (FHB) studies using Fusarium graminearum and its trichothecene-minus (Tri5(-)) mutant derivative and adult plant DON tests showed...... not below) the treated spikelets (AUDPC(DON)) (r = -0.41, -0.75 and -0.72, respectively; P ZIP-specific PCR analysis of 'CyChinese spring' and its 3BS deletion derivatives indicated that bZIP is located in chromosomal region(s) other than 3BS. These results, and the fact that a homologous cold...

  10. Natural epigenetic protection against the I-factor, a Drosophila LINE retrotransposon, by remnants of ancestral invasions.

    Science.gov (United States)

    Dramard, Xavier; Heidmann, Thierry; Jensen, Silke

    2007-03-21

    Transposable elements are major components of most eukaryotic genomes. Such sequences are generally defective for transposition and have little or no coding capacity. Because transposition can be highly mutagenic, mobile elements that remain functional are tightly repressed in all living species. Drosophila pericentromeric heterochromatin naturally contains transposition-defective, non-coding derivatives of a LINE retrotransposon related to the I-factor. The I-factor is a good model to study the regulation of transposition in vivo because, under specific conditions, current functional copies of this mobile element can transpose at high frequency, specifically in female germ cells, with deleterious effects including female sterility. However, this high transpositional activity becomes spontaneously repressed upon ageing or heat treatment, by a maternally transmitted, transgenerational epigenetic mechanism of unknown nature. We have analyzed, by quantitative real time RT-PCR, the RNA profile of the transposition-defective I-related sequences, in the Drosophila ovary during ageing and upon heat treatment, and also in female somatic tissues and in males, which are not permissive for I-factor transposition. We found evidence for a role of transcripts from these ancestral remnants in the natural epigenetic protection of the Drosophila melanogaster genome against the deleterious effects of new invasions by functional I-factors. These results provide a molecular basis for a probably widespread natural protection against transposable elements by persisting vestiges of ancient invasions.

  11. Insertion of an SVA-E retrotransposon into the CASP8 gene is associated with protection against prostate cancer.

    Science.gov (United States)

    Stacey, Simon N; Kehr, Birte; Gudmundsson, Julius; Zink, Florian; Jonasdottir, Aslaug; Gudjonsson, Sigurjon A; Sigurdsson, Asgeir; Halldorsson, Bjarni V; Agnarsson, Bjarni A; Benediktsdottir, Kristrun R; Aben, Katja K H; Vermeulen, Sita H; Cremers, Ruben G; Panadero, Angeles; Helfand, Brian T; Cooper, Phillip R; Donovan, Jenny L; Hamdy, Freddie C; Jinga, Viorel; Okamoto, Ichiro; Jonasson, Jon G; Tryggvadottir, Laufey; Johannsdottir, Hrefna; Kristinsdottir, Anna M; Masson, Gisli; Magnusson, Olafur T; Iordache, Paul D; Helgason, Agnar; Helgason, Hannes; Sulem, Patrick; Gudbjartsson, Daniel F; Kong, Augustine; Jonsson, Eirikur; Barkardottir, Rosa B; Einarsson, Gudmundur V; Rafnar, Thorunn; Thorsteinsdottir, Unnur; Mates, Ioan N; Neal, David E; Catalona, William J; Mayordomo, José I; Kiemeney, Lambertus A; Thorleifsson, Gudmar; Stefansson, Kari

    2016-03-01

    Transcriptional and splicing anomalies have been observed in intron 8 of the CASP8 gene (encoding procaspase-8) in association with cutaneous basal-cell carcinoma (BCC) and linked to a germline SNP rs700635. Here, we show that the rs700635[C] allele, which is associated with increased risk of BCC and breast cancer, is protective against prostate cancer [odds ratio (OR) = 0.91, P = 1.0 × 10(-6)]. rs700635[C] is also associated with failures to correctly splice out CASP8 intron 8 in breast and prostate tumours and in corresponding normal tissues. Investigation of rs700635[C] carriers revealed that they have a human-specific short interspersed element-variable number of tandem repeat-Alu (SINE-VNTR-Alu), subfamily-E retrotransposon (SVA-E) inserted into CASP8 intron 8. The SVA-E shows evidence of prior activity, because it has transduced some CASP8 sequences during subsequent retrotransposition events. Whole-genome sequence (WGS) data were used to tag the SVA-E with a surrogate SNP rs1035142[T] (r(2) = 0.999), which showed associations with both the splicing anomalies (P = 6.5 × 10(-32)) and with protection against prostate cancer (OR = 0.91, P = 3.8 × 10(-7)).

  12. Biology-Inspired Autonomous Control

    Science.gov (United States)

    2011-08-31

    of, and perhaps will not be tolerated in, manmade critical systems. Although this paper does not directly address questions of ethics associated...political, ethical , and moral issues associated with the use of autonomous systems in warfare will be debated long after the technology hurdles to...accessible discussion on the interplay of biochemistry, genetics and embryology in animal evolution; Wagner, 2005 describes biological concepts of

  13. Autonomous spacecraft rendezvous and docking

    Science.gov (United States)

    Tietz, J. C.; Almand, B. J.

    A storyboard display is presented which summarizes work done recently in design and simulation of autonomous video rendezvous and docking systems for spacecraft. This display includes: photographs of the simulation hardware, plots of chase vehicle trajectories from simulations, pictures of the docking aid including image processing interpretations, and drawings of the control system strategy. Viewgraph-style sheets on the display bulletin board summarize the simulation objectives, benefits, special considerations, approach, and results.

  14. [Autonomic nervous system in diabetes].

    Science.gov (United States)

    Emdin, M

    2001-08-01

    Hyperglycemia and hyperinsulinemia have a primary role in determining the early functional and later anatomic changes at the level of the autonomic pathways controlling the circulation, and besides in directly influencing cardiac and vascular cellular targets and feed-back baroreceptor system sensitivity to neurohumoral modulation in patients with diabetes mellitus. The basic mechanisms of dysfunction and damage, and the clinical and prognostic value of diabetic cardiovascular dysautonomia are discussed together with the diagnostic apparatus and the possible therapeutic approaches.

  15. 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.

  16. 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.

  17. Semi autonomous mine detection system

    Science.gov (United States)

    Few, Doug; Versteeg, Roelof; 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, 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.

  18. Attainability of Carnot efficiency with autonomous engines

    Science.gov (United States)

    Shiraishi, Naoto

    2015-11-01

    The maximum efficiency of autonomous engines with a finite chemical potential difference is investigated. We show that, without a particular type of singularity, autonomous engines cannot attain the Carnot efficiency. This singularity is realized in two ways: single particle transports and the thermodynamic limit. We demonstrate that both of these ways actually lead to the Carnot efficiency in concrete setups. Our results clearly illustrate that the singularity plays a crucial role in the maximum efficiency of autonomous engines.

  19. Navigation and Control of an Autonomous Vehicle

    OpenAIRE

    Schworer, Ian Josef

    2005-01-01

    The navigation and control of an autonomous vehicle is a highly complex task. Making a vehicle intelligent and able to operate â unmannedâ requires extensive theoretical as well as practical knowledge. An autonomous vehicle must be able to make decisions and respond to situations completely on its own. Navigation and control serves as the major limitation of the overall performance, accuracy and robustness of an autonomous vehicle. This thesis will address this problem and propose a uni...

  20. Attainability of Carnot efficiency with autonomous engines.

    Science.gov (United States)

    Shiraishi, Naoto

    2015-11-01

    The maximum efficiency of autonomous engines with a finite chemical potential difference is investigated. We show that, without a particular type of singularity, autonomous engines cannot attain the Carnot efficiency. This singularity is realized in two ways: single particle transports and the thermodynamic limit. We demonstrate that both of these ways actually lead to the Carnot efficiency in concrete setups. Our results clearly illustrate that the singularity plays a crucial role in the maximum efficiency of autonomous engines.

  1. Test and Evaluation of Autonomous Ground Vehicles

    OpenAIRE

    Yang Sun; Guangming Xiong; Weilong Song; Jianwei Gong; Huiyan Chen

    2014-01-01

    A preestablished test and evaluation system will benefit the development of autonomous ground vehicles. This paper proposes a design method for a scientific and comprehensive test and evaluation system for autonomous ground vehicles competitions. It can better guide and regulate the development of China’s autonomous ground vehicles. The test and evaluation system includes the test contents, the test environment, the test methods, and the evaluation methods. Using a hierarchical design approac...

  2. 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.

  3. 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.

  4. Design of a Miniature Autonomous Surveillance Robot

    Institute of Scientific and Technical Information of China (English)

    ZHENG Chang-e; HUANG Qiang; HUANG Yuan-can

    2009-01-01

    The small size of miniature robots poses great challenges for the mechanical and deetrieal design and the implementation of autonomous capabilities.In this paper,the mechanical and electrical design for a twowheeled cylindrical miniature autonomous robot ("BMS-1",BIT MicroScout-1) is presented and some autonomous capabilities are implemented by multiple sensors and some arithmetic models.Several experimental results show that BMS-1 is useful for surveillance in confined spaces and suitable for large-scale surveillance due to some autonomous capabilities.

  5. 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.

  6. Autonomic symptoms in idiopathic REM behavior disorder

    DEFF Research Database (Denmark)

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

    2014-01-01

    , and sexual dysfunction. Our results show that compared to control subjects with a similar overall age and sex distribution, patients with iRBD experience significantly more problems with gastrointestinal, urinary, and cardiovascular functioning. The most prominent differences in severity of autonomic......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...

  7. Autonomous Dome for Robotic Telescope

    CERN Document Server

    Kumar, Akash; Ganesh, Shashikiran

    2016-01-01

    Physical Research Laboratory operates a 50cm robotic observatory at Mount Abu. This Automated Telescope for Variability Studies (ATVS) makes use of Remote Telescope System 2 (RTS2) for autonomous operations. The observatory uses a 3.5m 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.

  8. 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.

  9. Autonomous Real Time Requirements Tracing

    Science.gov (United States)

    Plattsmier, George; Stetson, Howard

    2014-01-01

    One of the more challenging aspects of software development is the ability to verify and validate the functional software requirements dictated by the Software Requirements Specification (SRS) and the Software Detail Design (SDD). Insuring the software has achieved the intended requirements is the responsibility of the Software Quality team and the Software Test team. The utilization of Timeliner-TLX(sup TM) Auto- Procedures for relocating ground operations positions to ISS automated on-board operations has begun the transition that would be required for manned deep space missions with minimal crew requirements. This transition also moves the auto-procedures from the procedure realm into the flight software arena and as such the operational requirements and testing will be more structured and rigorous. The autoprocedures would be required to meet NASA software standards as specified in the Software Safety Standard (NASASTD- 8719), the Software Engineering Requirements (NPR 7150), the Software Assurance Standard (NASA-STD-8739) and also the Human Rating Requirements (NPR-8705). The Autonomous Fluid Transfer System (AFTS) test-bed utilizes the Timeliner-TLX(sup TM) Language for development of autonomous command and control software. The Timeliner-TLX(sup TM) system has the unique feature of providing the current line of the statement in execution during real-time execution of the software. The feature of execution line number internal reporting unlocks the capability of monitoring the execution autonomously by use of a companion Timeliner-TLX(sup TM) sequence as the line number reporting is embedded inside the Timeliner-TLX(sup TM) execution engine. This negates I/O processing of this type data as the line number status of executing sequences is built-in as a function reference. This paper will outline the design and capabilities of the AFTS Autonomous Requirements Tracker, which traces and logs SRS requirements as they are being met during real-time execution of the

  10. 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.

  11. Autonomous systems for plant protection

    DEFF Research Database (Denmark)

    Griepentrog, Hans W.; Ruckelshausen, Arno; Jørgensen, Rasmus Nyholm;

    2010-01-01

    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...... 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...

  12. 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.

  13. Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

    Directory of Open Access Journals (Sweden)

    Domingues Douglas S

    2012-04-01

    Full Text Available Abstract Background Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. Results Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. FISH analysis resulted in the expected pattern of Gypsy/heterochromatin, Copia/euchromatin, but in two lineages there was localized clustering on some chromosomes. Analysis of related ESTs and RT-PCR showed transcriptional variation between tissues and families. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. Conclusions Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome.

  14. 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

  15. Analysis of the features and source gene composition of the AluYg6 subfamily of human retrotransposons

    Directory of Open Access Journals (Sweden)

    Brookfield John FY

    2007-07-01

    Full Text Available Abstract Background Alu elements are a family of SINE retrotransposons in primates. They are classified into subfamilies according to specific diagnostic mutations from the general Alu consensus. It is now believed that there may be several retrotranspositionally-competent source genes within an Alu subfamily. To investigate the evolution of young Alu elements it is critical to have access to complete subfamilies, which, following the release of the final human genome assembly, can now be obtained using in silico methods. Results 380 elements belonging to the young AluYg6 subfamily were identified in the human genome, a number significantly exceeding prior expectations. An AluYg6 element was also identified in the chimpanzee genome, indicating that the subfamily is older than previously estimated, and appears to have undergone a period of dormancy before its expansion. The relative contributions of back mutation and gene conversion to variation at the six diagnostic positions are examined, and cases of complete forward gene conversion events are reported. Two small subfamilies derived from AluYg6 have been identified, named AluYg6a2 and AluYg5b3, which contain 40 and 27 members, respectively. These small subfamilies are used to illustrate the ambiguity regarding Alu subfamily definition, and to assess the contribution of secondary source genes to the AluYg6 subfamily. Conclusion The number of elements in the AluYg6 subfamily greatly exceeds prior expectations, indicating that the current knowledge of young Alu subfamilies is incomplete, and that prior analyses that have been carried out using these data may have generated inaccurate results. A definition of primary and secondary source genes has been provided, and it has been shown that several source genes have contributed to the proliferation of the AluYg6 subfamily. Access to the sequence data for the complete AluYg6 subfamily will be invaluable in future computational analyses investigating

  16. 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 BACKGROUND: 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. METHODOLOGY/PRINCIPAL FINDINGS: 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. CONCLUSIONS/SIGNIFICANCE: 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.

  17. Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes

    Directory of Open Access Journals (Sweden)

    de la Chaux Nicole

    2009-08-01

    Full Text Available Abstract Background Roo is the most abundant retrotransposon in the fruit fly Drosophila melanogaster. Its evolutionary origins and dynamics are thus of special interest for understanding the evolutionary history of Drosophila genome organization. We here study the phylogenetic distribution and evolution of roo, and its highly diverged relative rooA in 12 completely sequenced genomes of the genus Drosophila. Results We identify a total of 164 roo copies, 57 of which were previously unidentified copies that occur in 9 of the 12 genomes. Additionally we find 66 rooA copies in four genomes and remnants of this element in two additional genomes. We further increased the number of elements by searching for individual roo/rooA sequence domains. Most of our roo and rooA elements have been recently inserted. Most elements within a genome are highly similar. A comparison of the phylogenetic tree of our roo and rooA elements shows that the split between roo and rooA took place early in Drosophila evolution. Furthermore there is one incongruency between the species tree and the phylogenetic tree of the roo element. This incongruency regards the placement of elements from D. mojavensis, which are more closely related to D. melanogaster than elements from D. willistoni. Conclusion Within genomes, the evolutionary dynamics of roo and rooA range from recent transpositional activity to slow decay and extinction. Among genomes, the balance of phylogenetic evidence, sequence divergence distribution, and the occurrence of solo-LTR elements suggests an origin of roo/rooA within the Drosophila clade. We discuss the possibility of a horizontal gene transfer of roo within this clade.

  18. Plant Watering Autonomous Mobile Robot

    Directory of Open Access Journals (Sweden)

    Hema Nagaraja

    2012-07-01

    Full Text Available Now days, due to busy routine life, people forget to water their plants. In this paper, we present a completely autonomous and a cost-effective system for watering indoor potted plants placed on an even surface. The system comprises of a mobile robot and a temperature-humidity sensing module. The system is fully adaptive to any environment and takes into account the watering needs of the plants using the temperature-humidity sensing module. The paper describes the hardware architecture of the fully automated watering system, which uses wireless communication to communicate between the mobile robot and the sensing module. This gardening robot is completely portable and is equipped with a Radio Frequency Identification (RFID module, a microcontroller, an on-board water reservoir and an attached water pump. It is capable of sensing the watering needs of the plants, locating them and finally watering them autonomously without any human intervention. Mobilization of the robot to the potted plant is achieved by using a predefined path. For identification, an RFID tag is attached to each potted plant. The paper also discusses the detailed implementation of the system supported with complete circuitry. Finally, the paper concludes with system performance including the analysis of the water carrying capacity and time requirements to water a set of plants.

  19. Multi-agent autonomous system

    Science.gov (United States)

    Fink, Wolfgang (Inventor); Dohm, James (Inventor); Tarbell, Mark A. (Inventor)

    2010-01-01

    A multi-agent autonomous system for exploration of hazardous or inaccessible locations. The multi-agent autonomous system includes simple surface-based agents or craft controlled by an airborne tracking and command system. The airborne tracking and command system includes an instrument suite used to image an operational area and any craft deployed within the operational area. The image data is used to identify the craft, targets for exploration, and obstacles in the operational area. The tracking and command system determines paths for the surface-based craft using the identified targets and obstacles and commands the craft using simple movement commands to move through the operational area to the targets while avoiding the obstacles. Each craft includes its own instrument suite to collect information about the operational area that is transmitted back to the tracking and command system. The tracking and command system may be further coupled to a satellite system to provide additional image information about the operational area and provide operational and location commands to the tracking and command system.

  20. 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.

  1. 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.

  2. Goal Reasoning for an Autonomous Squad Member

    Science.gov (United States)

    2015-05-01

    2015 Annual Conference on Advances in Cognitive Systems: Workshop on Goal Reasoning Goal Reasoning for an Autonomous Squad Member Kellen...20375 USA Abstract Autonomous agents are beginning to play larger roles within team-oriented tasks and missions in various domains. Many reasoning ...present a goal reasoning system for this agent that integrates natural language processing, explanation generation, and plan recognition components

  3. 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...

  4. 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...

  5. 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.

  6. 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.

  7. 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.

  8. 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,

  9. 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 t

  10. Technologies for highly miniaturized autonomous sensor networks

    NARCIS (Netherlands)

    Baert, K.; Gyselinckx, B.; Torfs, T.; Leonov, V.; Yazicioglu, F.; Brebels, S.; Donnay, S.; Vanfleteren, J.; Beyne, E.; Hoof, C. van

    2006-01-01

    Recent results of the autonomous sensor research program HUMAN++ will be summarized in this paper. The research program aims to achieve highly miniaturized and (nearly) autonomous sensor systems that assist our health and comfort. Although the application examples are dedicated to human monitoring/a

  11. Shh-mediated degradation of Hhip allows cell autonomous and non-cell autonomous Shh signalling.

    Science.gov (United States)

    Kwong, Lina; Bijlsma, Maarten F; Roelink, Henk

    2014-09-12

    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 the pathway. Hhip overexpression has a severe effect on neural tube development, raising the question why normal sites of Hhip expression have a seemingly unimpaired response to Shh. Here we show that although Hhip is able to leave its sites of synthesis to inhibit Shh non-cell autonomously, activation of Smoothened (Smo) drastically increases Hhip internalization and degradation cell autonomously. Although Hhip is unable to cell autonomously inhibit the consequences of Smo activation, it can inhibit the Shh response non-cell autonomously. Our data provide a mechanism by which the Shh ligand can activate the response and negate cell autonomous effects of Hhip, while Hhip can still induce non-cell autonomous inhibition.

  12. Autonomic Management for Multi-agent Systems

    CERN Document Server

    Salih, Nadir K; Viju, PG K; Mohamed, Abdelmotalib A

    2011-01-01

    Autonomic computing is a computing system that can manage itself by self-configuration, self-healing, self-optimizing and self-protection. Researchers have been emphasizing the strong role that multi agent systems can play progressively towards the design and implementation of complex autonomic systems. The important of autonomic computing is to create computing systems capable of managing themselves to a far greater extent than they do today. With the nature of autonomy, reactivity, sociality and pro-activity, software agents are promising to make autonomic computing system a reality. This paper mixed multi-agent system with autonomic feature that completely hides its complexity from users/services. Mentioned Java Application Development Framework as platform example of this environment, could applied to web services as front end to users. With multi agent support it also provides adaptability, intelligence, collaboration, goal oriented interactions, flexibility, mobility and persistence in software systems

  13. 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.

  14. Cardiovascular autonomic neuropathy in the diabetic patients.

    Directory of Open Access Journals (Sweden)

    Maria Eugenia Niño Mantilla

    2007-11-01

    Full Text Available the dysfunction of the autonomic nervous system is a serious problem in diabetic patients. The cardiovacular autonomic neuropathy is the most important autonomic dysfuntion for it´s implication in the increasesof the mortality rate in diabetis patients. tis ethiopatogenesis is the result of a multifactorial process caused by chronic hyperglycemia, ending up in damage of the autonomic fibers thet innervate the heart and blood vessels, leading to dysfuntional hearth rate control and abnormal vascular dynamics. the associated clinical manifestations include orthotatic hypotension, excecise intolerance, intraoperative cardiovascular liability and silent myocardial ischemia. Being important its recognition, quantitative test to evaluate the cardiovascular funtion, to value its evolution and the effects of the treatment ahould be done, being the most used, the hearth rate response to standing test, and teh valsalva maneuver. the handling of this entity is done improving control of glucose blood levels its the most effective way to prevent the cardiovascular autonomic neuropathy in the diabetic patients.

  15. Whole genome surveys of rice, maize and sorghum reveal multiple horizontal transfers of the LTR-retrotransposon Route66 in Poaceae

    Directory of Open Access Journals (Sweden)

    Manicacci Domenica

    2009-03-01

    Full Text Available Abstract Background Horizontal transfers (HTs refer to the transmission of genetic material between phylogenetically distant species. Although most of the cases of HTs described so far concern genes, there is increasing evidence that some involve transposable elements (TEs in Eukaryotes. The availability of the full genome sequence of two cereal species, (i.e. rice and Sorghum, as well as the partial genome sequence of maize, provides the opportunity to carry out genome-wide searches for TE-HTs in Poaceae. Results We have identified an LTR-retrotransposon, that we named Route66, with more than 95% sequence identity between rice and Sorghum. Using a combination of in silico and molecular approaches, we are able to present a substantial phylogenetic evidence that Route66 has been transferred horizontally between Panicoideae and several species of the genus Oryza. In addition, we show that it has remained active after these transfers. Conclusion This study constitutes a new case of HTs for an LTR-retrotransposon and we strongly believe that this mechanism could play a major role in the life cycle of transposable elements. We therefore propose to integrate classe I elements into the previous model of transposable element evolution through horizontal transfers.

  16. Double strand break repair by capture of retrotransposon sequences and reverse-transcribed spliced mRNA sequences in mouse zygotes.

    Science.gov (United States)

    Ono, Ryuichi; Ishii, Masayuki; Fujihara, Yoshitaka; Kitazawa, Moe; Usami, Takako; Kaneko-Ishino, Tomoko; Kanno, Jun; Ikawa, Masahito; Ishino, Fumitoshi

    2015-07-28

    The CRISPR/Cas system efficiently introduces double strand breaks (DSBs) at a genomic locus specified by a single guide RNA (sgRNA). The DSBs are subsequently repaired through non-homologous end joining (NHEJ) or homologous recombination (HR). Here, we demonstrate that DSBs introduced into mouse zygotes by the CRISPR/Cas system are repaired by the capture of DNA sequences deriving from retrotransposons, genomic DNA, mRNA and sgRNA. Among 93 mice analysed, 57 carried mutant alleles and 22 of them had long de novo insertion(s) at DSB-introduced sites; two were spliced mRNAs of Pcnt and Inadl without introns, indicating the involvement of reverse transcription (RT). Fifteen alleles included retrotransposons, mRNAs, and other sequences without evidence of RT. Two others were sgRNAs with one containing T7 promoter-derived sequence suggestive of a PCR product as its origin. In conclusion, RT-product-mediated DSB repair (RMDR) and non-RMDR repair were identified in the mouse zygote. We also confirmed that both RMDR and non-RMDR take place in CRISPR/Cas transfected NIH-3T3 cells. Finally, as two de novo MuERV-L insertions in C57BL/6 mice were shown to have characteristic features of RMDR in natural conditions, we hypothesize that RMDR contributes to the emergence of novel DNA sequences in the course of evolution.

  17. Expression of the Idefix retrotransposon in early follicle cells in the germarium of Drosophila melanogaster is determined by its LTR sequences and a specific genomic context.

    Science.gov (United States)

    Tcheressiz, S; Calco, V; Arnaud, F; Arthaud, L; Dastugue, B; Vaury, C

    2002-04-01

    Retrotransposons are transcriptionally activated in different tissues and cell types by a variety of genomic and environmental factors. Transcription of LTR retrotransposons is controlled by cis-acting regulatory sequences in the 5' LTR. Mobilization of two LTR retroelements, Idefix and ZAM, occurs in the unstable RevI line of Drosophila melanogaster, in which their copy numbers are high, while they are low in all other stocks tested. Here we show that both a full-length and a subgenomic Idefix transcript that are necessary for its mobilization are present in the Rev1 line, but not in the other lines. Studies on transgenic strains demonstrate that the 5' LTR of Idefix contains sequences that direct the tissue-specific expression of the retroelement in testes and ovaries of adult flies. In ovaries, expression occurs in the early follicle and in other somatic cells of the germarium, and is strictly associated with the unstable genetic context conferred by the RevI line. Control of tissue-specific Idefix expression by interactions between cis-acting sequences of its LTR and trans-acting genomic factors provides an opportunity to use this retroelement as a tool for the study of the early follicle cell lineage in the germarium.

  18. Differential Expression of Retrotransposon WIS 2-1A Response to Vacuum,Low-Energy N+ Implantation and 60Coγ-ray Irradiation in Wheat

    Institute of Scientific and Technical Information of China (English)

    ZHAO Huiru; GU Yunhong; YA Huiyuan; JIAO Zhen; QIN Guangyong

    2009-01-01

    Mutagenesis and retrotransposons have a close relationship,but little attention has been paid yet to the activity of rtrotransposons produced by physical mutagens. The variation of retrotransposon WIS 2-1A activity in wheat(Triticum aestivum L.)embryos at three different growth times(30 h,45 h and 60 h)was investigated after they had been treated with N+ implantation in a vacuum of 5x10-2 Pa and irradiation by 60Coγ-ray respectively.For each of the three growth times the expression of WIS 2-1A showed almost entirely a same trend of downregulation,upregulation,then downregulation,and upregulation again with the increase in dose of N+ implantation,but the expression appeared irregular with the increase in irradiation of 60Coγ-ray.In conclusion,the acutely activating effect of WIS 2-1A stimulated by vacuum and high dose N+ implantation within a shorter incubation time may provide a convenient tool to advance the research on mutagenic breeding and function genes.

  19. Digital autonomous terminal access communications

    Science.gov (United States)

    Novacki, S.

    1987-01-01

    A significant problem for the Bus Monitor Unit is to identify the source of a given transmission. This problem arises from the fact that the label which identifies the source of the transmission as it is put into the bus is intercepted by the Digital Autonomous Terminal Access Communications (DATAC) terminal and removed from the transmission. Thus, a given subsystem will see only data associated with a label and never the identifying label itself. The Bus Monitor must identify the source of the transmission so as to be able to provide some type of error identification/location in the event that some problem with the data transmission occurs. Steps taken to alleviate this problem by modifications to the DATAC terminal are discussed.

  20. Autonomous Spacecraft Navigation With Pulsars

    CERN Document Server

    Becker, Werner; Jessner, Axel

    2013-01-01

    An external reference system suitable for deep space navigation can be defined by fast spinning and strongly magnetized neutron stars, called pulsars. Their beamed periodic signals have timing stabilities comparable to atomic clocks and provide characteristic temporal signatures that can be used as natural navigation beacons, quite similar to the use of GPS satellites for navigation on Earth. By comparing pulse arrival times measured on-board a spacecraft with predicted pulse arrivals at a reference location, the spacecraft position can be determined autonomously and with high accuracy everywhere in the solar system and beyond. The unique properties of pulsars make clear already today that such a navigation system will have its application in future astronautics. In this paper we describe the basic principle of spacecraft navigation using pulsars and report on the current development status of this novel technology.

  1. Mechanical autonomous stochastic heat engines

    Science.gov (United States)

    Serra-Garcia, Marc; Foehr, Andre; Moleron, Miguel; Lydon, Joseph; Chong, Christopher; Daraio, Chiara; . Team

    Stochastic heat engines extract work from the Brownian motion of a set of particles out of equilibrium. So far, experimental demonstrations of stochastic heat engines have required extreme operating conditions or nonautonomous external control systems. In this talk, we will present a simple, purely classical, autonomous stochastic heat engine that uses the well-known tension induced nonlinearity in a string. Our engine operates between two heat baths out of equilibrium, and transfers energy from the hot bath to a work reservoir. This energy transfer occurs even if the work reservoir is at a higher temperature than the hot reservoir. The talk will cover a theoretical investigation and experimental results on a macroscopic setup subject to external noise excitations. This system presents an opportunity for the study of non equilibrium thermodynamics and is an interesting candidate for innovative energy conversion devices.

  2. 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...

  3. Autonomous Guidance, Navigation and Control

    Science.gov (United States)

    Bordano, A. J.; Mcswain, G. G.; Fernandes, S. T.

    1991-01-01

    The NASA Autonomous Guidance, Navigation and Control (GN&C) Bridging program is reviewed to demonstrate the program plan and GN&C systems for the Space Shuttle. The ascent CN&C system is described in terms of elements such as the general-purpose digital computers, sensors for the navigation subsystem, the guidance-system software, and the flight-control subsystem. Balloon-based and lidar wind soundings are used for operations assessment on the day of launch, and the guidance software is based on dedicated units for atmospheric powered flight, vacuum powered flight, and abort-specific situations. Optimization of the flight trajectories is discussed, and flight-control responses are illustrated for wavelengths of 500-6000 m. Alternate sensors are used for load relief, and adaptive GN&C systems based on alternate gain synthesis are used for systems failures.

  4. Autonomous navigation system and method

    Science.gov (United States)

    Bruemmer, David J [Idaho Falls, ID; Few, Douglas A [Idaho Falls, ID

    2009-09-08

    A robot platform includes perceptors, locomotors, and a system controller, which executes instructions for autonomously navigating a robot. The instructions repeat, on each iteration through an event timing loop, the acts of defining an event horizon based on the robot's current velocity, detecting a range to obstacles around the robot, testing for an event horizon intrusion by determining if any range to the obstacles is within the event horizon, and adjusting rotational and translational velocity of the robot accordingly. If the event horizon intrusion occurs, rotational velocity is modified by a proportion of the current rotational velocity reduced by a proportion of the range to the nearest obstacle and translational velocity is modified by a proportion of the range to the nearest obstacle. If no event horizon intrusion occurs, translational velocity is set as a ratio of a speed factor relative to a maximum speed.

  5. Autonomous navigation system and method

    Energy Technology Data Exchange (ETDEWEB)

    Bruemmer, David J [Idaho Falls, ID; Few, Douglas A [Idaho Falls, ID

    2009-09-08

    A robot platform includes perceptors, locomotors, and a system controller, which executes instructions for autonomously navigating a robot. The instructions repeat, on each iteration through an event timing loop, the acts of defining an event horizon based on the robot's current velocity, detecting a range to obstacles around the robot, testing for an event horizon intrusion by determining if any range to the obstacles is within the event horizon, and adjusting rotational and translational velocity of the robot accordingly. If the event horizon intrusion occurs, rotational velocity is modified by a proportion of the current rotational velocity reduced by a proportion of the range to the nearest obstacle and translational velocity is modified by a proportion of the range to the nearest obstacle. If no event horizon intrusion occurs, translational velocity is set as a ratio of a speed factor relative to a maximum speed.

  6. Responsibility and autonomous nursing practice.

    Science.gov (United States)

    Holden, R J

    1991-04-01

    In this paper, the consequences were there greater autonomy in nursing practice, are considered. Autonomous practice implies accountability which entails both personal and professional responsibility: a personal responsibility to endorse ethical conduct consistent with professional practice; and a professional responsibility to exercise discretionary powers to the ultimate benefit of the patient. In this context, discretionary responsibility implies: recognizing a patient's wants may not be consistent with a patient's needs; abstaining from collusion with noncompliant patients; supporting the patient's right to refuse treatment only after full psychological exploration; understanding the psychological ramifications of informed consent from a practitioner and recipient point of view; maintaining appropriate personal and professional boundaries; and fostering collegiate relationships with the medical fraternity grounded on egalitarian principles. The author provides a philosophical and psychological analysis of responsibility in an effort to achieve a deeper understanding of the relationship this has with the concepts of 'freedom' and 'accountability'.

  7. 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.

  8. 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?

  9. APDS: Autonomous Pathogen Detection System

    Energy Technology Data Exchange (ETDEWEB)

    Langlois, R G; Brown, S; Burris, L; Colston, B; Jones, L; Makarewicz, T; Mariella, R; Masquelier, D; McBride, M; Milanovich, F; Masarabadi, S; Venkateswaran, K; Marshall, G; Olson, D; Wolcott, D

    2002-02-14

    An early warning system to counter bioterrorism, the Autonomous Pathogen Detection System (APDS) continuously monitors the environment for the presence of biological pathogens (e.g., anthrax) and once detected, it sounds an alarm much like a smoke detector warns of a fire. Long before September 11, 2001, this system was being developed to protect domestic venues and events including performing arts centers, mass transit systems, major sporting and entertainment events, and other high profile situations in which the public is at risk of becoming a target of bioterrorist attacks. Customizing off-the-shelf components and developing new components, a multidisciplinary team developed APDS, a stand-alone system for rapid, continuous monitoring of multiple airborne biological threat agents in the environment. The completely automated APDS samples the air, prepares fluid samples in-line, and performs two orthogonal tests: immunoassay and nucleic acid detection. When compared to competing technologies, APDS is unprecedented in terms of flexibility and system performance.

  10. 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.

  11. 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.

  12. 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.

  13. An LTR Retrotransposon-Derived Gene Displays Lineage-Specific Structural and Putative Species-Specific Functional Variations in Eutherians

    Science.gov (United States)

    Irie, Masahito; Koga, Akihiko; Kaneko-Ishino, Tomoko; Ishino, Fumitoshi

    2016-01-01

    Amongst the 11 eutherian-specific genes acquired from a sushi-ichi retrotransposon is the CCHC type zinc-finger protein-encoding gene SIRH11/ZCCHC16. Its contribution to eutherian brain evolution is implied because of its involvement in cognitive function in mice, possibly via the noradrenergic system. Although, the possibility that Sirh11/Zcchc16 functions as a non-coding RNA still remains, dN/dS ratios in pairwise comparisons between its orthologs have provided supportive evidence that it acts as a protein. It became a pseudogene in armadillos (Cingulata) and sloths (Pilosa), the only two extant orders of xenarthra, which prompted us to examine the lineage-specific variations of SIRH11/ZCCHC16 in eutherians. We examined the predicted SIRH11/ZCCHC16 open reading frame (ORF) in 95 eutherian species based on the genomic DNA information in GenBank. A large variation in the SIRH11/ZCCHC16 ORF was detected in several lineages. These include a lack of a CCHC RNA-binding domain in its C-terminus, observed in gibbons (Hylobatidae: Primates) and megabats (Megachiroptera: Chiroptera). A lack of the N-terminal half, on the other hand, was observed in New World monkeys (Platyrrhini: Primates) and species belonging to New World and African Hystricognaths (Caviomorpha and Bathyergidae: Rodents) along with Cetacea and Ruminantia (Cetartiodactyla). Among the hominoids, interestingly, three out of four genera of gibbons have lost normal SIRH11/ZCCHC16 function by deletion or the lack of the CCHC RNA-binding domain. Our extensive dN/dS analysis suggests that such truncated SIRH11/ZCCHC16 ORFs are functionally diversified even within lineages. Combined, our results show that SIRH11/ZCCHC16 may contribute to the diversification of eutherians by lineage-specific structural changes after its domestication in the common eutherian ancestor, followed by putative species-specific functional changes that enhanced fitness and occurred as a consequence of complex natural selection events

  14. 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

  15. Multiculturalismo, interculturalismo y autonomía

    Directory of Open Access Journals (Sweden)

    Edwin Cruz Rodríguez

    2014-01-01

    Full Text Available Este artículo examina dos enfoques teóri- cos sobre la autonomía: el multiculturalis- mo liberal y el interculturalismo latinoa- mericano. El argumento principal es que el enfoque intercultural es idóneo para fun- damentar la autonomía que el multicultu- ralismo porque tiene un mayor alcance metodológico y sus horizontes normativos son más amplios. En primer lugar, se exa- minan las críticas del interculturalismo al multiculturalismo liberal de Kymlicka. Se- guidamente, se estudian sus concepciones de la autonomía.

  16. PHM Enabled Autonomous Propellant Loading Operations

    Science.gov (United States)

    Walker, Mark; Figueroa, Fernando

    2017-01-01

    The utility of Prognostics and Health Management (PHM) software capability applied to Autonomous Operations (AO) remains an active research area within aerospace applications. The ability to gain insight into which assets and subsystems are functioning properly, along with the derivation of confident predictions concerning future ability, reliability, and availability, are important enablers for making sound mission planning decisions. When coupled with software that fully supports mission planning and execution, an integrated solution can be developed that leverages state assessment and estimation for the purposes of delivering autonomous operations. The authors have been applying this integrated, model-based approach to the autonomous loading of cryogenic spacecraft propellants at Kennedy Space Center.

  17. Enhanced mission performance from autonomous instrument guidance

    DEFF Research Database (Denmark)

    Jørgensen, John Leif; Jørgensen, Peter Siegbjørn; Betto, Maurizio;

    2006-01-01

    examples of such autonomous space instrumentation. With its full autonomy, this star tracker is capable of providing, in real-time, the absolute orientation with respect to the celestial reference frame with an accuracy of a few arc seconds. This high accuracy along with the robust operations, low weight...... acquisition and pointing (PROBA). Here three applications of the mu ASC as an autonomous onboard precision guide for precision vector instrumentation are presented. These are autonomous onboard antenna guidance, telescope guidance and tracking and high accuracy and wide range laser rangers....

  18. Analysis of LINE-1 expression in human pluripotent cells.

    Science.gov (United States)

    Muñoz-Lopez, Martin; Garcia-Cañadas, Marta; Macia, Angela; Morell, Santiago; Garcia-Perez, Jose L

    2012-01-01

    Half of the human genome is composed of repeated DNA, and some types are mobile within our genome (transposons and retrotransposons). Despite their abundance, only a small fraction of them are currently active in our genome (Long Interspersed Element-1 (LINE-1), Alu, and SVA elements). LINE-1 or L1 elements are a family of active non-LTR retrotransposons, the ongoing mobilization of which still impacts our genome. As selfish DNA elements, L1 activity is more prominent in early human development, where new insertions would be transmitted to the progeny. Here, we describe the conventional methods aimed to determine the expression level of LINE-1 elements in pluripotent human cells.

  19. 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.

  20. 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...

  1. Autonomic contributions to empathy: evidence from patients with primary autonomic failure.

    Science.gov (United States)

    Chauhan, Bina; Mathias, Christopher J; Critchley, Hugo D

    2008-06-01

    Empathy for the emotions of others may require simulatory engagement of corresponding autonomic arousal states. We tested the hypothesis that disruption of autonomic control impairs the ability to empathize emotionally with others. Fifteen patients with primary autonomic failure showed attenuated scores on the Mehrabian Balanced Emotional Empathy Scale (BEES), compared to both younger and older controls. This effect was not accounted for by age, gender, mood state or functional disability. These early observations provide preliminary evidence for a direct contribution of autonomic responsivity to the 'higher-order' social cognitive process of empathy, and may inform the dynamics of supportive care.

  2. Autonomic html interface generator for web applications

    CERN Document Server

    Bassil, Youssef; 10.5121/ijwest.2012.3104

    2012-01-01

    Recent advances in computing systems have led to a new digital era in which every area of life is nearly interrelated with information technology. However, with the trend towards large-scale IT systems, a new challenge has emerged. The complexity of IT systems is becoming an obstacle that hampers the manageability, operability, and maintainability of modern computing infrastructures. Autonomic computing popped up to provide an answer to these ever-growing pitfalls. Fundamentally, autonomic systems are self-configuring, self-healing, self-optimizing, and self-protecting; hence, they can automate all complex IT processes without human intervention. This paper proposes an autonomic HTML web-interface generator based on XML Schema and Style Sheet specifications for self-configuring graphical user interfaces of web applications. The goal of this autonomic generator is to automate the process of customizing GUI web-interfaces according to the ever-changing business rules, policies, and operating environment with th...

  3. Rover: Autonomous concepts for Mars exploration

    Science.gov (United States)

    Baiget, A.; Castets, B.; Chochon, H.; Hayard, M.; Lamarre, H.; Lamothe, A.

    1993-01-01

    The development of a mobile, autonomous vehicle that will be launched towards an unknown planet is considered. The rover significant constraints are: Ariane 5 compatibility, Earth/Mars transfer capability, 1000 km autonomous moving in Mars environment, on board localization, and maximum science capability. Two different types of subsystem were considered: classical subsystems (mechanical and mechanisms, thermal, telecommunications, power, onboard data processing) and robotics subsystem, (perception/navigation, autonomous displacement generation, autonomous localization). The needs of each subsystem were studied in terms of energy and data handling capability, in order to choose an on board architecture which best use the available capability, by means of specialized parts. A compromise must always be done between every subsystem in order to obtain the real need with respect to the goal, for example: between perception/navigation and the motion capability. A compromise must also be found between mechanical assembly and calibration need, which is a real problem.

  4. 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.

  5. Cranial Autonomic Symptoms in Pediatric Migraine

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2013-09-01

    Full Text Available Investigators at the University of California, San Francisco, examined the frequency of cranial autonomic symptoms in all pediatric and adolescent patients with migraine seen in 4 different clinical settings during July 2010 to June 2012.

  6. Tracked robot controllers for climbing obstacles autonomously

    Science.gov (United States)

    Vincent, Isabelle

    2009-05-01

    Research in mobile robot navigation has demonstrated some success in navigating flat indoor environments while avoiding obstacles. However, the challenge of analyzing complex environments to climb obstacles autonomously has had very little success due to the complexity of the task. Unmanned ground vehicles currently exhibit simple autonomous behaviours compared to the human ability to move in the world. This paper presents the control algorithms designed for a tracked mobile robot to autonomously climb obstacles by varying its tracks configuration. Two control algorithms are proposed to solve the autonomous locomotion problem for climbing obstacles. First, a reactive controller evaluates the appropriate geometric configuration based on terrain and vehicle geometric considerations. Then, a reinforcement learning algorithm finds alternative solutions when the reactive controller gets stuck while climbing an obstacle. The methodology combines reactivity to learning. The controllers have been demonstrated in box and stair climbing simulations. The experiments illustrate the effectiveness of the proposed approach for crossing obstacles.

  7. 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.

  8. 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.

  9. Comparative anatomy of the autonomic nervous system.

    Science.gov (United States)

    Nilsson, Stefan

    2011-11-16

    This short review aims to point out the general anatomical features of the autonomic nervous systems of non-mammalian vertebrates. In addition it attempts to outline the similarities and also the increased complexity of the autonomic nervous patterns from fish to tetrapods. With the possible exception of the cyclostomes, perhaps the most striking feature of the vertebrate autonomic nervous system is the similarity between the vertebrate classes. An evolution of the complexity of the system can be seen, with the segmental ganglia of elasmobranchs incompletely connected longitudinally, while well developed paired sympathetic chains are present in teleosts and the tetrapods. In some groups the sympathetic chains may be reduced (dipnoans and caecilians), and have yet to be properly described in snakes. Cranial autonomic pathways are present in the oculomotor (III) and vagus (X) nerves of gnathostome fish and the tetrapods, and with the evolution of salivary and lachrymal glands in the tetrapods, also in the facial (VII) and glossopharyngeal (IX) nerves.

  10. AGATE: Autonomous Go and Touch Exploration Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The innovation (AGATE, for Autonomous Go And Touch Exploration) will enable single-sol "go and touch" instrument placement from distances of up to five meters for...

  11. Autonomic Nervous System Dysfunction in Parkinson's Disease.

    Science.gov (United States)

    Zesiewicz, Theresa A.; Baker, Matthew J.; Wahba, Mervat; Hauser, Robert A.

    2003-03-01

    Autonomic nervous system (ANS) dysfunction is common in Parkinson's disease (PD), affects 70% to 80% of patients, and causes significant morbidity and discomfort. Autonomic nervous system dysfunction symptoms in PD include sexual dysfunction, swallowing and gastrointestinal disorders, bowel and bladder abnormalities, sleep disturbances, and derangements of cardiovascular regulation, particularly, orthostatic hypotension. Autonomic nervous system dysfunction in PD may be caused by an underlying degenerative process that affects the autonomic ganglia, brainstem nuclei, and hypothalamic nuclei. Anti-parkinsonian medications can cause or worsen symptoms of ANS dysfunction. The care of a PD patient with ANS dysfunction relies on its recognition and directed treatment, including coordinated care between the neurologist and appropriate subspecialist. Pharmacotherapy may be useful to treat orthostasis, gastrointestinal, urinary, and sexual dysfunction.

  12. Visual navigation for an autonomous mobile vehicle

    OpenAIRE

    Peterson, Kevin Robert

    1992-01-01

    Approved for public release; distribution is unlimited Image understanding for a mobile robotic vehicle is an important and complex task for ensuring safe navigation and extended autonomous operations. The goal of this work is to implement a working vision-based navigation control mechanism within a known environment onboard the autonomous mobile vehicle Yamabico-II. Although installing a working hardware system was not accomplished, the image processing, model description, pattern match...

  13. Autonomic Circulatory Control during Pregnancy in Humans

    OpenAIRE

    2009-01-01

    Pregnancy is associated with dramatic alterations in maternal hemodynamics, which begin early (i.e., following conception, 4 to 5 weeks of gestation) and are accompanied by changing levels of various pressor hormones and vasoactive metabolites. It has been proposed that these changes occur through autonomic control mechanisms, but the actual role of the autonomic nervous system in pregnancy is poorly understood. New research has shed more light on the links between pregnancy and cardiovascula...

  14. Intelligent control system of autonomous objects

    Science.gov (United States)

    Engel, E. A.; Kovalev, I. V.; Engel, N. E.; Brezitskaya, V. V.; Prohorovich, G. A.

    2017-02-01

    This paper presents an intelligent control system of autonomous objects as framework. The intelligent control framework includes two different layers: a reflexive layer and a reactive layer. The proposed multiagent adaptive fuzzy neuronet combines low-level reaction with high-level reasoning in an intelligent control framework. The formed as the multiagent adaptive fuzzy neuronet the intelligent control system on the base of autonomous object’s state, creates the effective control signal under random perturbations.

  15. Blood pressure regulation in diabetic autonomic neuropathy

    DEFF Research Database (Denmark)

    Hilsted, J

    1985-01-01

    experimental situations insufficient contraction of resistance vessels has been demonstrated. The vasoconstrictor defects demonstrated are of a magnitude sufficient to account for the prevailing hypotension. Furthermore, during exercise cardiac output is low in patients with autonomic neuropathy, a finding...... 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....

  16. Autonomous gliding entry guidance with

    Directory of Open Access Journals (Sweden)

    Guo Jie

    2015-10-01

    Full Text Available This paper presents a novel three-dimensional autonomous entry guidance for relatively high lift-to-drag ratio vehicles satisfying geographic constraints and other path constraints. The guidance is composed of onboard trajectory planning and robust trajectory tracking. For trajectory planning, a longitudinal sub-planner is introduced to generate a feasible drag-versus-energy profile by using the interpolation between upper boundary and lower boundary of entry corridor to get the desired trajectory length. The associated magnitude of the bank angle can be specified by drag profile, while the sign of bank angle is determined by lateral sub-planner. Two-reverse mode is utilized to satisfy waypoint constraints and dynamic heading error corridor is utilized to satisfy no-fly zone constraints. The longitudinal and lateral sub-planners are iteratively employed until all of the path constraints are satisfied. For trajectory tracking, a novel tracking law based on the active disturbance rejection control is introduced. Finally, adaptability tests and Monte Carlo simulations of the entry guidance approach are performed. Results show that the proposed entry guidance approach can adapt to different entry missions and is able to make the vehicle reach the prescribed target point precisely in spite of geographic constraints.

  17. Development of autonomous triggering instrumentation

    Science.gov (United States)

    Watkins, Steve E.; Swift, Theresa M.; Fonda, James W.

    2008-03-01

    Triggering instrumentation for autonomous monitoring of load-induced strain is described for economical, fast bridge inspection. The development addresses one aspect for the management of transportation infrastructure - bridge monitoring and inspection. The objectives are to provide quantitative performance information from a load test, to minimize the setup time at the bridge, and to minimize the closure time to traffic. Multiple or networked measurements can be made for a prescribed loading sequence. The proposed smart system consists of in-situ strain sensors, an embedded data acquisition module, and a measurement triggering system. A companion control unit is mounted on the truck serving as the load. As the truck moves to the proper position, the desired measurement is automatically relayed back to the control unit. In this work, the testing protocol is developed and the performance parameters for the triggering and data acquisition are measured. The test system uses a dedicated wireless sensor mote and an infrared positioning system. The electronic procedure offers improvements in available information and economics.

  18. Autonomous intelligent cruise control system

    Science.gov (United States)

    Baret, Marc; Bomer, Thierry T.; Calesse, C.; Dudych, L.; L'Hoist, P.

    1995-01-01

    Autonomous intelligent cruise control (AICC) systems are not only controlling vehicles' speed but acting on the throttle and eventually on the brakes they could automatically maintain the relative speed and distance between two vehicles in the same lane. And more than just for comfort it appears that these new systems should improve the safety on highways. By applying a technique issued from the space research carried out by MATRA, a sensor based on a charge coupled device (CCD) was designed to acquire the reflected light on standard-mounted car reflectors of pulsed laser diodes emission. The CCD is working in a unique mode called flash during transfer (FDT) which allows identification of target patterns in severe optical environments. It provides high accuracy for distance and angular position of targets. The absence of moving mechanical parts ensures high reliability for this sensor. The large field of view and the high measurement rate give a global situation assessment and a short reaction time. Then, tracking and filtering algorithms have been developed in order to select the target, on which the equipped vehicle determines its safety distance and speed, taking into account its maneuvering and the behaviors of other vehicles.

  19. 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.

  20. Mechanical Autonomous Stochastic Heat Engine

    Science.gov (United States)

    Serra-Garcia, Marc; Foehr, André; Molerón, Miguel; Lydon, Joseph; Chong, Christopher; Daraio, Chiara

    2016-07-01

    Stochastic heat engines are devices that generate work from random thermal motion using a small number of highly fluctuating degrees of freedom. Proposals for such devices have existed for more than a century and include the Maxwell demon and the Feynman ratchet. Only recently have they been demonstrated experimentally, using, e.g., thermal cycles implemented in optical traps. However, recent experimental demonstrations of classical stochastic heat engines are nonautonomous, since they require an external control system that prescribes a heating and cooling cycle and consume more energy than they produce. We present a heat engine consisting of three coupled mechanical resonators (two ribbons and a cantilever) subject to a stochastic drive. The engine uses geometric nonlinearities in the resonating ribbons to autonomously convert a random excitation into a low-entropy, nonpassive oscillation of the cantilever. The engine presents the anomalous heat transport property of negative thermal conductivity, consisting in the ability to passively transfer energy from a cold reservoir to a hot reservoir.

  1. 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.

  2. 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.

  3. [Autonomic dysfunction syndrome and diabetic cardiac autonomic neuropathy in children with diabetes mellitus type I. The correction method].

    Science.gov (United States)

    Manukian, V Iu; Bolotova, N V; Aver'ianov, A P; Filina, N Iu; Raĭgorodskiĭ, Iu M

    2011-01-01

    We assessed the state of the autonomic nervous system in 90 children with diabetes mellitus type I. The autonomic dysfunction syndrome was found in 58,9% and diabetic cardiac autonomic neuropathy in 28,9% of patients. We revealed the high risk of the development of diabetic cardiac autonomic neuropathy in children with diabetes mellitus type I in the presence of the autonomic dysfunction syndrome. It has been shown that the early treatment of functional disturbances of the autonomic nervous system using transcranial magnetic stimulation is necessary to prevent the manifestation of diabetic cardiac autonomic neuropathy.

  4. A Novel Retrotransposon Inserted in the Dominant Vrn-B1 Allele Confers Spring Growth Habit in Tetraploid Wheat (Triticum turgidum L.).

    Science.gov (United States)

    Chu, C-G; Tan, C T; Yu, G-T; Zhong, S; Xu, S S; Yan, L

    2011-12-01

    Vernalization genes determine winter/spring growth habit in temperate cereals and play important roles in plant development and environmental adaptation. In wheat (Triticum L. sp.), it was previously shown that allelic variation in the vernalization gene VRN1 was due to deletions or insertions either in the promoter or in the first intron. Here, we report a novel Vrn-B1 allele that has a retrotransposon in its promoter conferring spring growth habit. The VRN-B1 gene was mapped in a doubled haploid population that segregated for winter-spring growth habit but was derived from two spring tetraploid wheat genotypes, the durum wheat (T. turgidum subsp. durum) variety 'Lebsock' and T. turgidum subsp. carthlicum accession PI 94749. Genetic analysis revealed that Lebsock carried the dominant Vrn-A1 and recessive vrn-B1 alleles, whereas PI 94749 had the recessive vrn-A1 and dominant Vrn-B1 alleles. The Vrn-A1 allele in Lebsock was the same as the Vrn-A1c allele previously reported in hexaploid wheat. No differences existed between the vrn-B1 and Vrn-B1 alleles, except that a 5463-bp insertion was detected in the 5'-UTR region of the Vrn-B1 allele. This insertion was a novel retrotransposon (designated as retrotrans_VRN), which was flanked by a 5-bp target site duplication and contained primer binding site and polypurine tract motifs, a 325-bp long terminal repeat, and an open reading frame encoding 1231 amino acids. The insertion of retrotrans_VRN resulted in expression of Vrn-B1 without vernalization. Retrotrans_VRN is prevalent among T. turgidum subsp. carthlicum accessions, less prevalent among T. turgidum subsp. dicoccum accessions, and rarely found in other tetraploid wheat subspecies.

  5. 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.

  6. Autonomous and autonomic systems with applications to NASA intelligent spacecraft operations and exploration systems

    CERN Document Server

    Truszkowski, Walt; Rouff, Christopher; Karlin, Jay; Rash, James; Hinchey, Michael; Sterritt, Roy

    2009-01-01

    This book provides an in-depth discussion of autonomous and autonomic systems, their interdependencies, differences and similarities. Current and pending issues in these evermore increasingly important subjects are highlighted and discussed. Concepts, ideas and experiences are explored in relation to real-life NASA systems in spacecraft control and in the exploration domain.

  7. 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...

  8. Test and Evaluation of Autonomous Ground Vehicles

    Directory of Open Access Journals (Sweden)

    Yang Sun

    2014-01-01

    Full Text Available A preestablished test and evaluation system will benefit the development of autonomous ground vehicles. This paper proposes a design method for a scientific and comprehensive test and evaluation system for autonomous ground vehicles competitions. It can better guide and regulate the development of China's autonomous ground vehicles. The test and evaluation system includes the test contents, the test environment, the test methods, and the evaluation methods. Using a hierarchical design approach, the test content is designed to be stage by stage, moving from simplicity to complexity and from individual modules to the entire vehicle. The hierarchical test environment is established according to the levels of test content. The test method based on multilevel platforms and sensors is put forward to ensure the accuracy of test results. A fuzzy comprehensive evaluation method combined with analytic hierarchy process (AHP is used for the comprehensive evaluation which can quantitatively evaluate the individual module and the overall technical performance of autonomous ground vehicles. The proposed test and evaluation system has been successfully applied to real autonomous ground vehicle competitions.

  9. 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.

  10. Autonomous Learning and Improving Communicative Competence

    Institute of Scientific and Technical Information of China (English)

    李宝红; 孙晓黎

    2013-01-01

    Nowadays, English as a world language becomes more and more important. Consequently, English learning becomes more and more popular. As we know, an important object for English learners is to improve their communicative competence. So autonomous learning is a good way to improve communicative competence. In this paper, two terms, autonomous learning and communicative competence, and their relationship will be introduced from the perspective of English learning. Autonomous learning is self-managed learning, which is contrary to passive learning and mechanical learning, according to intrinsic property of language learning. Communicative competence is a concept introduced by Dell Hymes and is discussed and refined by many oth⁃er linguists. According to Hymes, communicative competence is the ability not only to apply the grammatical rules of language in order to form grammatically correct sentences but also to know when and where to use these sentences and to whom. Communi⁃cative competence includes 4 aspects: Possibility, feasibility, appropriateness and performance. Improving communicative compe⁃tence is the result of autonomous learning, autonomous learning is the motivation of improving communicative competence. English, of course, is a bridge connecting China to the world, and fostering students’communicative competence through auton⁃omous learning is the vital element of improving English learning in China.

  11. Cutaneous autonomic denervation in Parkinson's disease.

    Science.gov (United States)

    Navarro-Otano, Judith; Casanova-Mollà, Jordi; Morales, Merche; Valls-Solé, Josep; Tolosa, Eduard

    2015-08-01

    Numerous studies have detailed involvement of the peripheral autonomic nervous system (PANS) in Parkinson's disease (PD). We assessed autonomic innervation of dermal annexes through quantitative fluorescence measurement from skin obtained via punch biopsies at distal leg region in PD and control subjects. We defined a ratio between the area corresponding to protein gen product (PGP) immunoreactivity and the area corresponding to blood vessel or sweat gland as a quantitative measure of autonomic innervation. Presence of alpha-synuclein (AS) deposits in dermis and hypodermis was also assessed by immunohistochemistry. Skin biopsies form six PD patients and six healthy controls were studied. Autonomic innervation scores were lower in PD than in controls in both blood vessels and sweat glands. No AS or phosphorylated AS (pAS) immunoreactivity was detected in dermis or hypodermis in any of the studied subjects. The results of this investigation suggest that autonomic innervation of dermal annexes in living patients with PD is reduced compared to controls. AS or pAS deposits were not found in dermis or hypodermis suggesting that distal leg skin study is not useful for in vivo detection of AS in PD.

  12. Cardiovascular autonomic dysfunction in Parkinson's disease.

    Science.gov (United States)

    Ziemssen, Tjalf; Reichmann, Heinz

    2010-02-15

    Symptoms of cardiovascular dysautonomia are a common occurrence in Parkinson's disease (PD). In addition to this dysautonomia as part of PD itself, dysfunction of the autonomic nervous system (ANS) can be triggered as a side-effect of drug treatment interacting with the ANS or - if prominent and early - an indication of a different disease such as multiple system atrophy (MSA). Various diagnostic tests are available to demonstrate autonomic failure. While autonomic function tests can differentiate parasympathetic from sympathetic dysfunction, cardiac imaging can define the pathophysiologically involved site of a lesion. Standard tests such as 24-h ambulatory blood pressure measurements can identify significant autonomic failure which needs treatment. The most frequent and disturbing symptom of cardiovascular autonomic dysfunction is orthostatic hypotension. Symptoms include generalized weakness, light-headiness, mental "clouding" up to syncope. Factors like heat, food, alcohol, exercise, activities which increase intrathoraric pressure (e.g. defecation, coughing) and certain drugs (e.g. vasodilators) can worsen a probably asymptomatic orthostatic hypotension. Non-medical and medical therapies can help the patient to cope with a disabling symptomatic orthostatic hypotension. Supine hypertension is often associated with orthostatic hypotension. The prognostic role of cardiovagal and baroreflex dysfunction is still not yet known.

  13. Autonomous forward inference via DNA computing

    Institute of Scientific and Technical Information of China (English)

    Fu Yan; Li Gen; Li Yin; Meng Dazhi

    2007-01-01

    Recent studies direct the researchers into building DNA computing machines with intelligence, which is measured by three main points: autonomous, programmable and able to learn and adapt. Logical inference plays an important role in programmable information processing or computing. Here we present a new method to perform autonomous molecular forward inference for expert system.A novel repetitive recognition site (RRS) technique is invented to design rule-molecules in knowledge base. The inference engine runs autonomously by digesting the rule-molecule, using a Class ⅡB restriction enzyme PpiⅠ. Concentration model has been built to show the feasibility of the inference process under ideal chemical reaction conditions. Moreover, we extend to implement a triggering communication between molecular automata, as a further application of the RRS technique in our model.

  14. Technology readiness level six and autonomous mobility

    Science.gov (United States)

    Bodt, Barry A.; Camden, Rick S.

    2004-09-01

    During FY03, the U.S. Army Research Laboratory undertook a series of experiments designed to assess the maturity of autonomous mobility technology for the Future Combat Systems Armed Robotic Vehicle concept. The experiments assessed the technology against a level 6 standard in the technology readiness level (TRL) maturation schedule identified by a 1999 Government Accounting Office report. During the course of experimentation, 646 missions were conducted over a total distance of ~560 km and time of ~100 hr. Autonomous operation represented 96% and 88% of total distance and time, respectively. To satisfy the TRL 6 "relevant environment" standard, several experimental factors were varied over the three-site test as part of a formal, statistical, experimental design. This paper reports the specific findings pertaining to relevant-environment questions that were posed for the study and lends additional support to the Lead System Integrator decision that TRL 6 has been attained for the autonomous navigation system.

  15. Autonomous Preservation Tools in Minimal Effort Ingest

    DEFF Research Database (Denmark)

    Jurik, Bolette Ammitzbøll; Blekinge, Asger Askov; Andersen, Thorbjørn Ravn

    2016-01-01

    This poster presents the concept of Autonomous Preservation Tools, as developed by the State and University Library, Denmark. The work expands the idea of Minimal Effort Ingest, where most preservation actions such as Quality Assurance and enrichment of the digital objects are performed after con...... content is ingested for preservation, rather than before. We present our Newspaper Digitisation Project as a case-study of real-world implementations of Autonomous Preservation Tools.......This poster presents the concept of Autonomous Preservation Tools, as developed by the State and University Library, Denmark. The work expands the idea of Minimal Effort Ingest, where most preservation actions such as Quality Assurance and enrichment of the digital objects are performed after...

  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. Autonomous Deep-Space Optical Navigation Project

    Science.gov (United States)

    D'Souza, Christopher

    2014-01-01

    This project will advance the Autonomous Deep-space navigation capability applied to Autonomous Rendezvous and Docking (AR&D) Guidance, Navigation and Control (GNC) system by testing it on hardware, particularly in a flight processor, with a goal of limited testing in the Integrated Power, Avionics and Software (IPAS) with the ARCM (Asteroid Retrieval Crewed Mission) DRO (Distant Retrograde Orbit) Autonomous Rendezvous and Docking (AR&D) scenario. The technology, which will be harnessed, is called 'optical flow', also known as 'visual odometry'. It is being matured in the automotive and SLAM (Simultaneous Localization and Mapping) applications but has yet to be applied to spacecraft navigation. In light of the tremendous potential of this technique, we believe that NASA needs to design a optical navigation architecture that will use this technique. It is flexible enough to be applicable to navigating around planetary bodies, such as asteroids.

  18. A Collaborative Knowledge Plane for Autonomic Networks

    Science.gov (United States)

    Mbaye, Maïssa; Krief, Francine

    Autonomic networking aims to give network components self-managing capabilities. Several autonomic architectures have been proposed. Each of these architectures includes sort of a knowledge plane which is very important to mimic an autonomic behavior. Knowledge plane has a central role for self-functions by providing suitable knowledge to equipment and needs to learn new strategies for more accuracy.However, defining knowledge plane's architecture is still a challenge for researchers. Specially, defining the way cognitive supports interact each other in knowledge plane and implementing them. Decision making process depends on these interactions between reasoning and learning parts of knowledge plane. In this paper we propose a knowledge plane's architecture based on machine learning (inductive logic programming) paradigm and situated view to deal with distributed environment. This architecture is focused on two self-functions that include all other self-functions: self-adaptation and self-organization. Study cases are given and implemented.

  19. Autonomous Robot Navigation based on Visual Landmarks

    DEFF Research Database (Denmark)

    Livatino, Salvatore

    2005-01-01

    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...... of the proposed method is based on a system with a simple setup. The novelty and potentiality, are in combining algorithms for panoramic view-synthesis, attention selection, stereo reconstruction, triangulation, optimal triplet selection, and image-based rendering. Experiments demonstrate that the system can...

  20. 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.

  1. An Autonomous Reference Frame for Relativistic GNSS

    CERN Document Server

    Kostić, Uroš; Carloni, Sante; Delva, Pacôme; Gomboc, Andreja

    2014-01-01

    Current GNSS systems rely on global reference frames which are fixed to the Earth (via the ground stations) so their precision and stability in time are limited by our knowledge of the Earth dynamics. These drawbacks could be avoided by giving to the constellation of satellites the possibility of constituting by itself a primary and autonomous positioning system, without any a priori realization of a terrestrial reference frame. Our work shows that it is possible to construct such a system, an Autonomous Basis of Coordinates, via emission coordinates. Here we present the idea of the Autonomous Basis of Coordinates and its implementation in the perturbed space-time of Earth, where the motion of satellites, light propagation, and gravitational perturbations are treated in the formalism of general relativity.

  2. 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.

  3. Autonomous operations through onboard artificial intelligence

    Science.gov (United States)

    Sherwood, R. L.; Chien, S.; Castano, R.; Rabideau, G.

    2002-01-01

    The Autonomous Sciencecraft Experiment (ASE) will fly onboard the Air Force TechSat 21 constellation of three spacecraft scheduled for launch in 2006. ASE uses onboard continuous planning, robust task and goal-based execution, model-based mode identification and reconfiguration, and onboard machine learning and pattern recognition to radically increase science return by enabling intelligent downlink selection and autonomous retargeting. Demonstration of these capabilities in a flight environment will open up tremendous new opportunities in planetary science, space physics, and earth science that would be unreachable without this technology.

  4. CMU's autonomous helicopter explores new territory.

    Science.gov (United States)

    Charles, J.

    1998-10-01

    In the summer of 1998, several members of Carnegie Mellon University's (CMUs) Autonomous Helicopter Project team joined NASA on a multidisciplinary expedition to the Canadian Arctic's Haughton Crater. NASA was willing to travel to such a remote corner of the globe because of its similarity to an even more remote locale - Mars. Researchers are studying the 23-million-year-old meteorite impact crater in the hope of learning more about Mars's environment. While there, they also tested a number of technologies that will enable future exploration of Mars, including CMU's autonomous helicopter.

  5. Evolutionary strategy for achieving autonomous navigation

    Science.gov (United States)

    Gage, Douglas W.

    1999-01-01

    An approach is presented for the evolutionary development of supervised autonomous navigation capabilities for small 'backpackable' ground robots, in the context of a DARPA- sponsored program to provide robotic support to small units of dismounted warfighters. This development approach relies on the implementation of a baseline visual serving navigation capability, including tools to support operator oversight and override, which is then enhanced with semantically referenced commands and a mission scripting structure. As current and future machine perception techniques are able to automatically designate visual serving goal points, this approach should provide a natural evolutionary pathway to higher levels of autonomous operation and reduced requirements for operator intervention.

  6. 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.

  7. Road boundary detection for autonomous vehicle navigation

    Energy Technology Data Exchange (ETDEWEB)

    Davis, L.S.; Kushner, T.R.; LeMoigne, J.J.; Waxman, A.M.

    1986-03-01

    The Computer Vision Laboratory at the University Maryland for the past year has been developing a computer vision system for autonomous ground navigation of roads and road networks for the Defense Advanced Research Projects Agency's Strategic Computing Program. The complete system runs on a VAX 11/785, but certain parts of it have been reimplemented on a VICOM image processing sysem for experimentation on an autonomous vehicle built for the Martin Marietta Corp., Aerospace Division, in Denver, Colorado. A brief overview is given of the principal software components of the system and the VICOM implementation in detail.

  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. Autonomous control of multi-fingered hand

    Institute of Scientific and Technical Information of China (English)

    JIANG Li; LIU Hong

    2006-01-01

    This paper describes a novel autonomous control strategy of multi-fingered hand based on a modular control system of dexterous manipulation. A simple proportional-integral-derivative(PID) position control with friction compensation, which requires few friction parameters, is used to realize accurate and smooth trajectory tracking in pregrasp phase. In grasp and manipulation phases, an event-driven switcher is adopted to determine the switching between unconstrained position control and constrained torque control, and an improved explicit integral force control strategy is implemented to realize simultaneously stable contact transition and accurate force tracking. Experimental results have verified the effectiveness of the proposed autonomous control strategy of multi-fingered hand.

  10. Diagnosis and behavior in autonomic trigeminal headaches

    Directory of Open Access Journals (Sweden)

    Erélido Hernández Valero

    2008-04-01

    Full Text Available Autonomic trigeminal headaches are primary headaches which include: cluster headaches, paroxistical hemicranea, and syndrome of unilateral headache in a neuralgic way, of short duration, accompanied by cojunctival injection and tearing and the continuous hemicranea. It is also accompanied by autonomic manifestations such as: palpebrate ptosis, tearing, nasal congestion, rhinorrhea, Horner syndrome (palpebrate ptosis, miosis, and enophthalmos and changes in the coloration of the periocular skin and in the cheek. In this paper we propose the most likely diagnosis and therapeutic to this nosologic entity

  11. NEURON: Enabling Autonomicity in Wireless Sensor Networks

    Science.gov (United States)

    Zafeiropoulos, Anastasios; Gouvas, Panagiotis; Liakopoulos, Athanassios; Mentzas, Gregoris; Mitrou, Nikolas

    2010-01-01

    Future Wireless Sensor Networks (WSNs) will be ubiquitous, large-scale networks interconnected with the existing IP infrastructure. Autonomic functionalities have to be designed in order to reduce the complexity of their operation and management, and support the dissemination of knowledge within a WSN. In this paper a novel protocol for energy efficient deployment, clustering and routing in WSNs is proposed that focuses on the incorporation of autonomic functionalities in the existing approaches. The design of the protocol facilitates the design of innovative applications and services that are based on overlay topologies created through cooperation among the sensor nodes. PMID:22399931

  12. NEURON: Enabling Autonomicity in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Anastasios Zafeiropoulos

    2010-05-01

    Full Text Available Future Wireless Sensor Networks (WSNs will be ubiquitous, large-scale networks interconnected with the existing IP infrastructure. Autonomic functionalities have to be designed in order to reduce the complexity of their operation and management, and support the dissemination of knowledge within a WSN. In this paper a novel protocol for energy efficient deployment, clustering and routing in WSNs is proposed that focuses on the incorporation of autonomic functionalities in the existing approaches. The design of the protocol facilitates the design of innovative applications and services that are based on overlay topologies created through cooperation among the sensor nodes.

  13. Towards Autonomous Control of HVAC Systems

    DEFF Research Database (Denmark)

    Brath, P.

    This thesis considered development of an autonomous control system for heating ventilation and air conditioning applications. By including auto-tuning, adaptation, diagnosis and supervision functions in the control system used in the HVAC industry will move the control of HVAC systems towards...... autonomous control. Together with better tuned controllers and more dedicated control it would be possible to decrease the energy consumption, save money and increase the indoor air climate. A flexible HVAC test system was designed and implemented. Standard components and sensors were used in the design...

  14. Light Sailboats: Laser driven autonomous microrobots

    CERN Document Server

    Búzás, Anrdás; Mathesz, Anna; Oroszi, László; Vizsnyiczai, Gaszton; Vicsek, Tamás; Ormos, Pál; 10.1063/1.4737646

    2012-01-01

    We introduce a system of light driven microscopic autonomous moving particles that move on a flat surface. The design is simple, yet effective: Micrometer sized objects with wedge shape are produced by photopolymerization, they are covered with a reflective surface. When the area of motion is illuminated perpendicularly from above, the light is deflected to the side by the wedge shaped objects, in the direction determined by the position and orientation of the particles. The momentum change during reflection provides the driving force for an effectively autonomous motion. The system is an efficient tool to study self propelled microscopic robots.

  15. 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...

  16. Genetics Home Reference: hereditary sensory and autonomic neuropathy type V

    Science.gov (United States)

    ... Conditions HSAN5 hereditary sensory and autonomic neuropathy type V Enable Javascript to view the expand/collapse boxes. ... All Description Hereditary sensory and autonomic neuropathy type V ( HSAN5 ) is a condition that primarily affects the ...

  17. Hard-real-time resource management for autonomous spacecraft

    Science.gov (United States)

    Gat, E.

    2000-01-01

    This paper describes tickets, a computational mechanism for hard-real-time autonomous resource management. Autonomous spacecraftcontrol can be considered abstractly as a computational process whose outputs are spacecraft commands.

  18. College English Students’ Autonomous Learning Motivation and Cultivation Model Research

    Institute of Scientific and Technical Information of China (English)

    王艳荣; 李娥

    2015-01-01

    Studying the autonomous learning motivation and excitation model can stimulate intrinsic motivation of foreign language learners,develop students self-management strategy evaluation are very necessary.The purpose of this paper is to give students the skills of listening and speaking for their autonomous learning.Then study the cultivation and motivation of college English students autonomous learning,hoping to make students to learn autonomous learning and stimulate their motivation fully.

  19. Diversity of the Ty-1 copia retrotransposon Tos17 in rice (Oryza sativa L.) and the AA genome of the Oryza genus.

    Science.gov (United States)

    Petit, Julie; Bourgeois, Emmanuelle; Stenger, Wilfried; Bès, Martine; Droc, Gaétan; Meynard, Donaldo; Courtois, Brigitte; Ghesquière, Alain; Sabot, François; Panaud, Olivier; Guiderdoni, Emmanuel

    2009-12-01

    Retrotransposons are mobile genetic elements, ubiquitous in Eukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. We investigate here the diversity of the Ty1-copia retrotransposon Tos17 in the cultivated rice of Asian origin (Oryza sativa L.) and related AA genome species of the Oryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the element in the lineages. In that aim, we used a combination of Southern hybridization with a reverse transcriptase (RT) probe and an adapter-PCR mediated amplification, which allowed the sequencing of the genomic regions flanking Tos17 insertions. This analysis was carried out in a collection of 47 A-genome Oryza species accessions and 202 accessions of a core collection of Oryza sativa L. representative of the diversity of the species. Our Southern hybridization results show that Tos17 is present in all the accessions of the A-genome Oryza species, except for the South American species O. glumaepatula and the African species O. glaberrima and O. breviligulata. In O. sativa, the number of putative copies of Tos17 per accession ranged from 1 to 11 and multivariate analysis based on presence/absence of putative copies yielded a varietal clustering which is consistent with the isozyme classification of rice. Adapter PCR amplification and sequencing of flanking regions of Tos17 insertions in A-genome species other than O. sativa, followed by anchoring on the Nipponbare genome sequence, revealed 13 insertion sites of Tos17 in the surveyed O. rufipogon and O. longistaminata accessions, including one shared by both species. In O. sativa, the same approach revealed 25 insertions in the 6 varietal groups. Four insertion sites located on chromosomes 1, 2, 10, and 11 were found orthologous in O. rufipogon and O. sativa. The chromosome 1 insertion was also shared between O. rufipogon and O

  20. Geometric formulations and variational integrators of discrete autonomous Birkhoff systems

    Institute of Scientific and Technical Information of China (English)

    Liu Shi-Xing; Liu Chang; Guo Yong-Xin

    2011-01-01

    The variational integrators of autonomous Birkhoff systems are obtained by the discrete variational principle. The geometric structure of the discrete autonomous Birkhoff system is formulated. The discretization of mathematical pendulum shows that the discrete variational method is as effective as symplectic scheme for the autonomous Birkhoff systems.

  1. Modeling and Model Identification of Autonomous Underwater Vehicles

    Science.gov (United States)

    2015-06-01

    IDENTIFICATION OF AUTONOMOUS UNDERWATER VEHICLES by Jose Alberti June 2015 Thesis Advisor: Noel du Toit Second Reader: Douglas...Master’s Thesis 4. TITLE AND SUBTITLE MODELING AND MODEL IDENTIFICATION OF AUTONOMOUS UNDERWATER VEHICLES 5. FUNDING NUMBERS 6. AUTHOR(S...unlimited 12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) As autonomous underwater vehicles (AUVs) are deployed in more complex

  2. Agent-based Multimodal Interface for Dynamically Autonomous Mobile Robots

    Science.gov (United States)

    2003-01-01

    Agent-based Multimodal Interface for Dynamically Autonomous Mobile Robots Donald Sofge, Magdalena Bugajska, William Adams, Dennis...computing paradigm for integrated distributed artificial intelligence systems on autonomous mobile robots (Figure 1). Figure 1 – CoABS Grid...Architecture for Dynamically Autonomous Mobile Robots The remainder of the paper is organized as follows. Section 2 describes our integrated AI

  3. Peripheral autonomic neuropathy: diagnostic contribution of skin biopsy.

    Science.gov (United States)

    Donadio, Vincenzo; Incensi, Alex; Giannoccaro, Maria Pia; Cortelli, Pietro; Di Stasi, Vitantonio; Pizza, Fabio; Jaber, Masen Abdel; Baruzzi, Agostino; Liguori, Rocco

    2012-11-01

    Skin biopsy has gained widespread use for the diagnosis of somatic small-fiber neuropathy, but it also provides information on sympathetic fiber morphology. We aimed to ascertain the diagnostic accuracy of skin biopsy in disclosing sympathetic nerve abnormalities in patients with autonomic neuropathy. Peripheral nerve fiber autonomic involvement was confirmed by routine autonomic laboratory test abnormalities. Punch skin biopsies were taken from the thigh and lower leg of 28 patients with various types of autonomic neuropathy for quantitative evaluation of skin autonomic innervation. Results were compared with scores obtained from 32 age-matched healthy controls and 25 patients with somatic neuropathy. The autonomic cutoff score was calculated using the receiver operating characteristic curve analysis. Skin biopsy disclosed a significant autonomic innervation decrease in autonomic neuropathy patients versus controls and somatic neuropathy patients. Autonomic innervation density was abnormal in 96% of patients in the lower leg and in 79% of patients in the thigh. The abnormal findings disclosed by routine autonomic tests ranged from 48% to 82%. These data indicate the high sensitivity and specificity of skin biopsy in detecting sympathetic abnormalities; this method should be useful for the diagnosis of autonomic neuropathy, together with currently available routine autonomic testing.

  4. 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.

  5. Applying energy autonomous robots for dike inspection

    NARCIS (Netherlands)

    Dresscher, Douwe; Vries, de Theo 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 comp

  6. [Emotion, amygdala, and autonomic nervous system].

    Science.gov (United States)

    Ueyama, Takashi

    2012-10-01

    Emotion refers to the dynamic changes of feeling accompanied by the alteration of physical and visceral activities. Autonomic nervous system (sympathetic and parasympathetic) regulates the visceral activities. Therefore, monitoring and analyzing autonomic nervous activity help understand the emotional changes. To this end, the survey of the expression of immediate early genes (IEGs), such as c-Fos in the brain and target organs, and the viral transneuronal labeling method using the pseudorabies virus (PRV) have enabled the visualization of the neurocircuitry of emotion. By comparing c-Fos expression and data from PRV or other neuroanatomical labeling techniques, the central sites that regulate emotional stress-induced autonomic activation can be deduced. Such regions have been identified in the limbic system (e. g., the extended amygdaloid complex; lateral septum; and infralimbic, insular, and ventromedial temporal cortical regions), as well as in several hypothalamic and brainstem nuclei. The amygdala is structurally diverse and comprises several subnuclei, which play a role in emotional process via projections from the cortex and a variety of subcortical structures. All amygdaloid subnuclei receive psychological information from other limbic systems, while the lateral and central subnuclei receive peripheral and sensory information. Output to the hypothalamus and peripheral sympathetic system mainly originates from the medial amygdala. As estrogen receptor α, estrogen receptor β, and androgen receptor are expressed in the medial amygdala, sex steroids may modulate the autonomic nervous activities.

  7. Spatial abstraction for autonomous robot navigation.

    Science.gov (United States)

    Epstein, Susan L; Aroor, Anoop; Evanusa, Matthew; Sklar, Elizabeth I; Parsons, Simon

    2015-09-01

    Optimal navigation for a simulated robot relies on a detailed map and explicit path planning, an approach problematic for real-world robots that are subject to noise and error. This paper reports on autonomous robots that rely on local spatial perception, learning, and commonsense rationales instead. Despite realistic actuator error, learned spatial abstractions form a model that supports effective travel.

  8. ON FIRST INTEGRALS OF POLYNOMIAL AUTONOMOUS SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    WANG Yuzhen; CHENG Daizhan; LI Chunwen

    2002-01-01

    Using Carleman linearization procedure, this paper investigates the problemof first integrals of polynomial autonomous systems and proposes a procedure to find thefirst integrals of polynomial family for the systems. A generalized eigenequation is obtainedand then the problem is reduced to the solvability of the eigenequation. The result is ageneralization of some known results.

  9. 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 performan

  10. 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...

  11. 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 it

  12. Autonomic Modification of Intestinal Smooth Muscle Contractility

    Science.gov (United States)

    Montgomery, Laura E. A.; Tansey, Etain A.; Johnson, Chris D.; Roe, Sean M.; Quinn, Joe G.

    2016-01-01

    Intestinal smooth muscle contracts rhythmically in the absence of nerve and hormonal stimulation because of the activity of pacemaker cells between and within the muscle layers. This means that the autonomic nervous system modifies rather than initiates intestinal contractions. The practical described here gives students an opportunity to observe…

  13. Autonomous behavior of hematopoietic stem cells

    NARCIS (Netherlands)

    Kamminga, LM; Akkerman, [No Value; Weersing, E; Ausema, A; Dontje, B; Van Zant, G; de Haan, G

    2000-01-01

    Objective. Mechanisms that affect the function of primitive hematopoietic stem cells with long-term proliferative potential remain largely unknown. Here we assessed whether properties of stem cells are cell-extrinsically or cell-autonomously regulated. Materials and Methods. We developed a model in

  14. 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.

  15. 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.

  16. Autonomous Learning from a Social Cognitive Perspective

    Science.gov (United States)

    Ponton, Michael K.; Rhea, Nancy E.

    2006-01-01

    The current perspective of autonomous learning defines it as the agentive exhibition of resourcefulness, initiative, and persistence in self-directed learning. As a form of human agency, it has been argued in the literature that this perspective should be consistent with Bandura's (1986) Social Cognitive Theory (SCT). The purpose of this article…

  17. 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.

  18. My Understanding on Cultivation of Autonomous Learning

    Institute of Scientific and Technical Information of China (English)

    张金玉

    2007-01-01

    Autonomous learning has been popular in western education system for some time, this article aims to analyze the connotation and the necessity of cultivating learner autonomy, and then offer some strategies about the cultivation of learner autonomy from a chinese perspective.

  19. Stochastic self-monitoring of autonomous systems

    OpenAIRE

    2012-01-01

    A probabilistic method is presented for high level task planning of autonomous, mobile systems under partial observability of states and partial knowledge of transition laws. Partial state observability is addressed by directed Markov fields which support the detection of relationships between pairs of observed variables in competition to other such pairs.

  20. Advanced manipulation for autonomous mobile robots

    Energy Technology Data Exchange (ETDEWEB)

    Babcock, S.M.; Hamel, W.R.; Killough, S.M.

    1986-01-01

    This paper describes the development, mechanical configuration, and control system architecture of a lightweight, high performance, seven-degree-of-freedom manipulator at the Center for Engineering Systems Advanced Research (CESAR). Current activities focusing on modeling and parameter identification will provide a well-characterized manipulator for analytical and experimental research in manipulator dynamics and controls, coordinated manipulation, and autonomous mobile robotics.

  1. 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 res

  2. 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

  3. Autonomic nervous system and immune system interactions.

    Science.gov (United States)

    Kenney, M J; Ganta, C K

    2014-07-01

    The present review assesses the current state of literature defining integrative autonomic-immune physiological processing, focusing on studies that have employed electrophysiological, pharmacological, molecular biological, and central nervous system experimental approaches. Central autonomic neural networks are informed of peripheral immune status via numerous communicating pathways, including neural and non-neural. Cytokines and other immune factors affect the level of activity and responsivity of discharges in sympathetic and parasympathetic nerves innervating diverse targets. Multiple levels of the neuraxis contribute to cytokine-induced changes in efferent parasympathetic and sympathetic nerve outflows, leading to modulation of peripheral immune responses. The functionality of local sympathoimmune interactions depends on the microenvironment created by diverse signaling mechanisms involving integration between sympathetic nervous system neurotransmitters and neuromodulators; specific adrenergic receptors; and the presence or absence of immune cells, cytokines, and bacteria. Functional mechanisms contributing to the cholinergic anti-inflammatory pathway likely involve novel cholinergic-adrenergic interactions at peripheral sites, including autonomic ganglion and lymphoid targets. Immune cells express adrenergic and nicotinic receptors. Neurotransmitters released by sympathetic and parasympathetic nerve endings bind to their respective receptors located on the surface of immune cells and initiate immune-modulatory responses. Both sympathetic and parasympathetic arms of the autonomic nervous system are instrumental in orchestrating neuroimmune processes, although additional studies are required to understand dynamic and complex adrenergic-cholinergic interactions. Further understanding of regulatory mechanisms linking the sympathetic nervous, parasympathetic nervous, and immune systems is critical for understanding relationships between chronic disease

  4. A Localisation and Navigation System for an Autonomous Wheel Loader

    OpenAIRE

    Lilja, Robin

    2011-01-01

    Autonomous vehicles are an emerging trend in robotics, seen in a vast range of applications and environments. Consequently, Volvo Construction Equipment endeavour to apply the concept of autonomous vehicles onto one of their main products. In the company’s Autonomous Machine project an autonomous wheel loader is being developed. As an ob jective given by the company; a demonstration proving the possibility of conducting a fully autonomous load and haul cycle should be performed. Conducting su...

  5. 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.

  6. A small RNA mediated regulation of a stress-activated retrotransposon and the tissue specific transposition during the reproductive period in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Wataru eMatsunaga

    2015-02-01

    Full Text Available Transposable elements (TEs are key elements that facilitate genome evolution of the host organism. A number of studies have assessed the functions of TEs, which change gene expression in the host genome. Activation of TEs is controlled by epigenetic modifications such as DNA methylation and histone modifications. Several recent studies have reported that TEs can also be activated by biotic or abiotic stress in some plants. We focused on a Ty1/copia retrotransposon, ONSEN, that is activated by heat stress in Arabidopsis. We found that transcriptional activation of ONSEN was regulated by an siRNA-related pathway, and the activation could also be induced by oxidative stress. Mutants deficient in small interfering RNA (siRNA biogenesis that were exposed to heat stress at the initial stages of vegetative growth showed transgenerational transposition. The transposition was also detected in the progeny, which originated from tissue that had differentiated after exposure to the heat stress. The results indicated that in some undifferentiated cells, transpositional activity could be maintained quite long after exposure to the heat stress.

  7. Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells.

    Science.gov (United States)

    Bulut-Karslioglu, Aydan; De La Rosa-Velázquez, Inti A; Ramirez, Fidel; Barenboim, Maxim; Onishi-Seebacher, Megumi; Arand, Julia; Galán, Carmen; Winter, Georg E; Engist, Bettina; Gerle, Borbala; O'Sullivan, Roderick J; Martens, Joost H A; Walter, Jörn; Manke, Thomas; Lachner, Monika; Jenuwein, Thomas

    2014-07-17

    Heterochromatin is required to restrict aberrant expression of retrotransposons, but it remains poorly defined due to the underlying repeat-rich sequences. We dissected Suv39h-dependent histone H3 lysine 9 trimethylation (H3K9me3) by genome-wide ChIP sequencing in mouse embryonic stem cells (ESCs). Refined bioinformatic analyses of repeat subfamilies indicated selective accumulation of Suv39h-dependent H3K9me3 at interspersed repetitive elements that cover ∼5% of the ESC epigenome. The majority of the ∼8,150 intact long interspersed nuclear elements (LINEs) and endogenous retroviruses (ERVs), but only a minor fraction of the >1.8 million degenerate and truncated LINEs/ERVs, are enriched for Suv39h-dependent H3K9me3. Transcriptional repression of intact LINEs and ERVs is differentially regulated by Suv39h and other chromatin modifiers in ESCs but governed by DNA methylation in committed cells. These data provide a function for Suv39h-dependent H3K9me3 chromatin to specifically repress intact LINE elements in the ESC epigenome.

  8. Outdoor Field Experience with Autonomous Stations

    CERN Document Server

    Lopes, L; Blanco, A; Carolino, N; Cerda, M A; Conceicao, R; Cunha, O; Ferreira, M; Fonte, P; Luz, R; Mendes, L; Pereira, A; Pimenta, M; Sarmento, R; Tome, B

    2016-01-01

    In the last two decades Resistive Plate Chambers were employed in the Cosmic Ray Experiments COVER-PLASTEX and ARGO/YBJ. In both experiments the detectors were housed indoors, likely owing to gas distribution requirements and the need to control environment variables that directly affect RPCs operational stability. But in experiments where Extended Air Shower (EAS) sampling is necessary, large area arrays composed by dispersed stations are deployed, rendering this kind of approach impossible. In this situation, it would be mandatory to have detectors that could be deployed in small standalone stations, with very rare opportunities for maintenance, and with good resilience to environmental conditions. Aiming to meet these requirements, we started some years ago the development of RPCs for Autonomous Stations. The results from indoor tests and measurements were very promising, both concerning performance and stability under very low gas flow rate, which is the main requirement for Autonomous Stations. In this w...

  9. 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.

  10. Unmanned air vehicle: autonomous takeoff and landing

    Science.gov (United States)

    Lim, K. L.; Gitano-Briggs, Horizon Walker

    2010-03-01

    UAVs are increasing in popularity and sophistication due to the demonstrated performance which cannot be attained by manned aircraft1. These developments have been made possible by development of sensors, instrumentation, telemetry and controls during the last few decades. UAVs are now common in areas such as aerial observation and as communication relays3. Most UAVs, however, are still flown by a human pilot via remote control from a ground station. Even the existing autonomous UAVs often require a human pilot to handle the most difficult tasks of take off and landing2 (TOL). This is mainly because the navigation of the airplane requires observation, constant situational assessment and hours of experience from the pilot himself4. Therefore, an autonomous takeoff and landing system (TLS) for UAVs using a few practical design rules with various sensors, instrumentation, etc has been developed. This paper details the design and modeling of the UAV TLS. The model indicates that the UAV's TLS shows promising stability.

  11. Forced synchronization of autonomous dynamical Boolean networks.

    Science.gov (United States)

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

    2015-08-01

    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.

  12. Development of autonomous grasping and navigating robot

    Science.gov (United States)

    Kudoh, Hiroyuki; Fujimoto, Keisuke; Nakayama, Yasuichi

    2015-01-01

    The ability to find and grasp target items in an unknown environment is important for working robots. We developed an autonomous navigating and grasping robot. The operations are locating a requested item, moving to where the item is placed, finding the item on a shelf or table, and picking the item up from the shelf or the table. To achieve these operations, we designed the robot with three functions: an autonomous navigating function that generates a map and a route in an unknown environment, an item position recognizing function, and a grasping function. We tested this robot in an unknown environment. It achieved a series of operations: moving to a destination, recognizing the positions of items on a shelf, picking up an item, placing it on a cart with its hand, and returning to the starting location. The results of this experiment show the applicability of reducing the workforce with robots.

  13. Autonomous reinforcement learning with experience replay.

    Science.gov (United States)

    Wawrzyński, Paweł; Tanwani, Ajay Kumar

    2013-05-01

    This paper considers the issues of efficiency and autonomy that are required to make reinforcement learning suitable for real-life control tasks. A real-time reinforcement learning algorithm is presented that repeatedly adjusts the control policy with the use of previously collected samples, and autonomously estimates the appropriate step-sizes for the learning updates. The algorithm is based on the actor-critic with experience replay whose step-sizes are determined on-line by an enhanced fixed point algorithm for on-line neural network training. An experimental study with simulated octopus arm and half-cheetah demonstrates the feasibility of the proposed algorithm to solve difficult learning control problems in an autonomous way within reasonably short time.

  14. 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 ...

  15. Integrating Autonomous Load Controllers in Power Systems

    DEFF Research Database (Denmark)

    Douglass, Philip James

    violations of voltage constraints. This voltage-sensitive controller can also operate alone, without the frequency-sensitive controller, to provide voltage regulation service and increase load diversity in any distribution network where lower voltage level corresponds to higher load.The frequency......-sensitive and voltage-sensitive autonomous load are viable alternatives to conventional frequency and voltage control devices. When used in combination, they complement each other. In systems where the operator has centrally dispatchable resources to regulate frequency, these resources can be used to dispatch otherwise...... autonomous frequency-sensitive loads. Moreover, where centrally dispatchable frequency regulation resources can rapidly change operating points, such as in a micro-grid, the energy sources can be used as transmitters for a ultra-low-bandwidth uni-directional power line communication system....

  16. 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.

  17. Autonomous vehicle platforms from modular robotic components

    Science.gov (United States)

    Schonlau, William J.

    2004-09-01

    A brief survey of current autonomous vehicle (AV) projects is presented with intent to find common infrastructure or subsystems that can be configured from commercially available modular robotic components, thereby providing developers with greatly reduced timelines and costs and encouraging focus on the selected problem domain. The Modular Manipulator System (MMS) robotic system, based on single degree of freedom rotary and linear modules, is introduced and some approaches to autonomous vehicle configuration and deployment are examined. The modules may be configured to provide articulated suspensions for very rugged terrain and fall recovery, articulated sensors and tooling plus a limited capacity for self repair and self reconfiguration. The MMS on-board visually programmed control software (Model Manager) supports experimentation with novel physical configurations and behavior algorithms via real-time 3D graphics for operations simulation and provides useful subsystems for vision, learning and planning to host intelligent behavior.

  18. 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...

  19. Autonomous microexplosives subsurface tracing system final report.

    Energy Technology Data Exchange (ETDEWEB)

    Engler, Bruce Phillip; Nogan, John; Melof, Brian Matthew; Uhl, James Eugene; Dulleck, George R., Jr.; Ingram, Brian V.; Grubelich, Mark Charles; Rivas, Raul R.; Cooper, Paul W.; Warpinski, Norman Raymond; Kravitz, Stanley H.

    2004-04-01

    The objective of the autonomous micro-explosive subsurface tracing system is to image the location and geometry of hydraulically induced fractures in subsurface petroleum reservoirs. This system is based on the insertion of a swarm of autonomous micro-explosive packages during the fracturing process, with subsequent triggering of the energetic material to create an array of micro-seismic sources that can be detected and analyzed using existing seismic receiver arrays and analysis software. The project included investigations of energetic mixtures, triggering systems, package size and shape, and seismic output. Given the current absence of any technology capable of such high resolution mapping of subsurface structures, this technology has the potential for major impact on petroleum industry, which spends approximately $1 billion dollar per year on hydraulic fracturing operations in the United States alone.

  20. Autonomous Environment Recognition by Robotic Manipulators

    OpenAIRE

    Senda, Kei; Okano, Yuzo

    2001-01-01

    This paper discusses methods of autonomus environment recognition and action by a robotic manipulator working with dynamic interaction to the enviroment, e.g., assembling. A method automatically recognizes the contacting situation with the work site from the sensor outputs and the robotic manipulator motion. The autonomous recognition then discriminates the constraint conditions at manopulator hand using the self-organizing map that is a kind of unsupervisedlearning of neural networks. The di...

  1. Precise laser gyroscope for autonomous inertial navigation

    Energy Technology Data Exchange (ETDEWEB)

    Kuznetsov, A G; Molchanov, A V; Izmailov, E A [Joint Stock Company ' Moscow Institute of Electromechanics and Automatics' , Moscow (Russian Federation); Chirkin, M V [Ryazan State Radio Engineering University (Russian Federation)

    2015-01-31

    Requirements to gyroscopes of strapdown inertial navigation systems for aircraft application are formulated. The construction of a ring helium – neon laser designed for autonomous navigation is described. The processes that determine the laser service life and the relation between the random error of the angular velocity measurement and the surface relief features of the cavity mirrors are analysed. The results of modelling one of the promising approaches to processing the laser gyroscope signals are presented. (laser gyroscopes)

  2. Autonomous Rendezvous and Docking Conference, volume 1

    Science.gov (United States)

    1990-01-01

    This document consists of the presentation submitted at the Autonomous Rendezvous and Docking (ARD) Conference. It contains three volumes: ARD hardware technology; ARD software technology; and ARD operations. The purpose of this conference is to identify the technologies required for an on orbit demonstration of the ARD, assess the maturity of these technologies, and provide the necessary insight for a quality assessment of the programmatic management, technical, schedule, and cost risks.

  3. Autonomous Rendezvous and Docking Conference, volume 3

    Science.gov (United States)

    1990-01-01

    This document consists of the presentation submitted at the Autonomous Rendezvous and Docking (ARD) Conference. The document contains three volumes: ARD hardware technology; ARD software technology; and ARD operations. The purpose of this conference is to identify the technologies required for an on orbit demonstration of ARD, assess the maturity of these technologies, and provide the necessary insight for a quality assessment of programmatic management, technical, schedule, and cost risks.

  4. Autonomous Deicing System For Airplane Wing

    Science.gov (United States)

    Hickman, G. A.; Gerardi, J. J.

    1993-01-01

    Prototype autonomous deicing system for airplane includes network of electronic and electromechanical modules at various locations in wings and connected to central data-processing unit. Small, integrated solid-state device, using long coils installed under leading edge, exciting small vibrations to detect ice and larger vibrations to knock ice off. In extension of concept, outputs of vibration sensors and other sensors used to detect rivet-line fractures, fatigue cracks, and other potentially dangerous defects.

  5. 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.

  6. An architecture for an autonomous learning robot

    Science.gov (United States)

    Tillotson, Brian

    1988-01-01

    An autonomous learning device must solve the example bounding problem, i.e., it must divide the continuous universe into discrete examples from which to learn. We describe an architecture which incorporates an example bounder for learning. The architecture is implemented in the GPAL program. An example run with a real mobile robot shows that the program learns and uses new causal, qualitative, and quantitative relationships.

  7. Autonomous Underwater Vehicle Planning for Information Exploitation

    Science.gov (United States)

    2012-03-01

    Remotely Operated Vehicles (ROV’s) and Autonomous Underwater Vehicles (AUVs) are being used extensively in fields of underwater cartography , exploration...controls required to follow each candidate trajectory. What we are essentially doing is computing the time- histories of the states and controls along...numerically differentiate (3.24) in order to check a given constraint on Ψ such as |Ψ̇(t)| ≤ Ψ̇max. The net result is a time- history of the states and

  8. 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.

    2016-01-01

    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. PMID:27999307

  9. Autonomic neuropathy and diabetic foot ulceration.

    Science.gov (United States)

    Edmonds, M E; Nicolaides, K H; Watkins, P J

    1986-01-01

    Autonomic function was studied in three groups of insulin-dependent diabetic patients. Heart rate changes during deep breathing and on standing were significantly less in 28 patients with a recent history of foot ulceration compared with 40 patients with peripheral neuropathy but without ulceration (p less than 0.001) and 54 patients without neuropathy (p less than 0.001). Sympathetic function was assessed in 36 of these patients from peripheral arterial diastolic flow patterns obtained by Doppler ultrasound measurements and expressed as the pulsatility index (PI). Patients with a history of ulceration (n = 10) showed considerably increased diastolic flow (PI = 4.28 +/- 0.53, mean +/- S.E.M.) compared with 12 neuropathic patients with no history of ulceration (PI = 7.80 +/- 0.68, p less than 0.002) and 14 patients without neuropathy (PI = 9.55 +/- 0.89, p less than 0.002). Severely abnormal autonomic function occurs in association with neuropathic foot ulceration, but patients without ulcers have lesser degrees of autonomic neuropathy, thus a causal relationship has not been established.

  10. Autonomous system for cross-country navigation

    Science.gov (United States)

    Stentz, Anthony; Brumitt, Barry L.; Coulter, R. C.; Kelly, Alonzo

    1993-05-01

    Autonomous cross-country navigation is essential for outdoor robots moving about in unstructured environments. Most existing systems use range sensors to determine the shape of the terrain, plan a trajectory that avoids obstacles, and then drive the trajectory. Performance has been limited by the range and accuracy of sensors, insufficient vehicle-terrain interaction models, and the availability of high-speed computers. As these elements improve, higher- speed navigation on rougher terrain becomes possible. We have developed a software system for autonomous navigation that provides for greater capability. The perception system supports a large braking distance by fusing multiple range images to build a map of the terrain in front of the vehicle. The system identifies range shadows and interpolates undersamples regions to account for rough terrain effects. The motion planner reduces computational complexity by investigating a minimum number of trajectories. Speeds along the trajectory are set to provide for dynamic stability. The entire system was tested in simulation, and a subset of the capability was demonstrated on a real vehicle. Results to date include a continuous 5.1 kilometer run across moderate terrain with obstacles. This paper begins with the applications, prior work, limitations, and current paradigms for autonomous cross-country navigation, and then describes our contribution to the area.

  11. Review of Static Compensation of Autonomous Systems

    Directory of Open Access Journals (Sweden)

    Ambarnath Banerji

    2012-01-01

    Full Text Available Abstract Deregulation of the electric power energy market has thrown open opportunities for tapping the large number of small pockets of renewable energy sources with the asynchronous generators. Whether the power is supplied by asynchronous generator or by the grid at the remote location, its quality has become an important aspect for consumers of electricity. Efforts have been made to improve the power quality using passive filters, active filters and the new concept of Custom Power. Use of Custom power devices ensures that a load do not pollute the power supply of the other loads. One such custom power device is the DSTATCOM (Distribution Static Compensator which is connected in shunt at the load end. The heart of the DSTATCOM is an inverter. The focus on the autonomous generation has increased in the recent years. The paper presents a comprehensive review of the DSTATCOM used for autonomous generation. It is aimed at providing a broad perspective on the status of DSTATCOM, used with Asynchronous generators, vis-à-vis its working principle, topology, solid state switching devices and technology, supply system, control methodologies and approaches, technical and economic considerations, etc. to researchers and application engineers dealing with power quality aspects of Autonomous Systems. Classified manner in which the references are presented in this paper will serve them as quick and useful reference.

  12. 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.

  13. Multi-mission, autonomous, synthetic aperture radar

    Science.gov (United States)

    Walls, Thomas J.; Wilson, Michael L.; Madsen, David; Jensen, Mark; Sullivan, Stephanie; Addario, Michael; Hally, Iain

    2014-05-01

    Unmanned aerial systems (UASs) have become a critical asset in current battlespaces and continue to play an increasing role for intelligence, surveillance and reconnaissance (ISR) missions. With the development of medium-to-low altitude, rapidly deployable aircraft platforms, the ISR community has seen an increasing push to develop ISR sensors and systems with real-time mission support capabilities. This paper describes recent flight demonstrations and test results of the RASAR (Real-time, Autonomous, Synthetic Aperture Radar) sensor system. RASAR is a modular, multi-band (L and X) synthetic aperture radar (SAR) imaging sensor designed for self-contained, autonomous, real-time operation with mission flexibility to support a wide range of ISR needs within the size, weight and power constraints of Group III UASs. The sensor command and control and real-time image formation processing are designed to allow integration of RASAR into a larger, multi-intelligence system of systems. The multi-intelligence architecture and a demonstration of real-time autonomous cross-cueing of a separate optical sensor will be presented.

  14. SOLON: An autonomous vehicle mission planner

    Science.gov (United States)

    Dudziak, M. J.

    1987-01-01

    The State-Operator Logic Machine (SOLON) Planner provides an architecture for effective real-time planning and replanning for an autonomous vehicle. The highlights of the system, which distinguish it from other AI-based planners that have been designed previously, are its hybrid application of state-driven control architecture and the use of both schematic representations and logic programming for the management of its knowledge base. SOLON is designed to provide multiple levels of planning for a single autonomous vehicle which is supplied with a skeletal, partially-specified mission plan at the outset of the vehicle's operations. This mission plan consists of a set of objectives, each of which will be decomposable by the planner into tasks. These tasks are themselves comparatively complex sets of actions which are executable by a conventional real-time control system which does not perform planning but which is capable of making adjustments or modifications to the provided tasks according to constraints and tolerances provided by the Planner. The current implementation of the SOLON is in the form of a real-time simulation of the Planner module of an Intelligent Vehicle Controller (IVC) on-board an autonomous underwater vehicle (AUV). The simulation is embedded within a larger simulator environment known as ICDS (Intelligent Controller Development System) operating on a Symbolics 3645/75 computer.

  15. 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.

  16. Diagnosing faults in autonomous robot plan execution

    Science.gov (United States)

    Lam, Raymond K.; Doshi, Rajkumar S.; Atkinson, David J.; Lawson, Denise M.

    1988-01-01

    A major requirement for an autonomous robot is the capability to diagnose faults during plan execution in an uncertain environment. Many diagnostic researches concentrate only on hardware failures within an autonomous robot. Taking a different approach, the implementation of a Telerobot Diagnostic System that addresses, in addition to the hardware failures, failures caused by unexpected event changes in the environment or failures due to plan errors, is described. One feature of the system is the utilization of task-plan knowledge and context information to deduce fault symptoms. This forward deduction provides valuable information on past activities and the current expectations of a robotic event, both of which can guide the plan-execution inference process. The inference process adopts a model-based technique to recreate the plan-execution process and to confirm fault-source hypotheses. This technique allows the system to diagnose multiple faults due to either unexpected plan failures or hardware errors. This research initiates a major effort to investigate relationships between hardware faults and plan errors, relationships which were not addressed in the past. The results of this research will provide a clear understanding of how to generate a better task planner for an autonomous robot and how to recover the robot from faults in a critical environment.

  17. Hemicrania continua. Unquestionably a trigeminal autonomic cephalalgia.

    Science.gov (United States)

    Vincent, Maurice B

    2013-05-01

    Hemicrania continua (HC) is a well-known primary headache. The present version of the International Classification of Headache Disorders lists HC in the "other primary headaches" group. However, evidence has emerged demonstrating that HC is a phenotype that belongs to the trigeminal autonomic cephalalgias together with cluster headache, paroxysmal hemicrania (PH), and short-lasting, unilateral neuralgiform headache attacks with conjunctival injection and tearing. This is supported by a common general clinical picture - paroxysmal, fluctuating, unilateral, side-locked headaches located to the ocular, frontal, and/or temporal regions, accompanied by ipsilateral autonomic dysfunctions including for example, tearing and conjunctival injection. Apart from the remarkable clinical similarities, the absolute and incomparable effect of indomethacin in HC parallels the effect of this drug in PH, suggesting a shared core pathogenesis. Finally, neuroimage findings demonstrate a posterior hypothalamic activation in HC similarly to cluster headache, PH, and short-lasting, unilateral neuralgiform headache attacks with conjunctival injection and tearing. Taken together, data indicate that HC is certainly a type of trigeminal autonomic cephalalgia that should no longer be placed in a group of miscellaneous primary headache disorders.

  18. Autonomic function in manganese alloy workers.

    Science.gov (United States)

    Barrington, W W; Angle, C R; Willcockson, N K; Padula, M A; 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/m3 in 29% and 0.2 mg/m3 in 62%. Twenty-four-hour electrocardiographic (Holter) monitoring was used to determine the temporal variability of the heartrate (RR' interval) and the rates of change at low frequency (0.04-0.15 Hz) and high frequency (0.15-0.40 Hz). MMPI and MCMI personality assessment and short-term memory, figure copy, controlled oral word association, and symbol digit tests were used. The five frog shop workers had abnormal sympathovagal balance with decreased high frequency variability (increased ln LF/ln HF). Seven of the eight workers had symptoms of autonomic dysfunction and significantly decreased heart rate variability (rMSSD) but these did not distinguish the relative exposure. Mood or affect was disturbed in all with associated changes in short-term memory and attention in four of the subjects. There were no significant correlations with serum or urine manganese. Power spectrum analysis of 24-h ambulatory ECG indicating a decrease in parasympathetic high frequency activation of heart rate variability may provide a sensitive index of central autonomic dysfunction reflecting increased exposure to manganese, although the contribution of exposures to solvents and other metals cannot be excluded. Neurotoxicity due to the gouging

  19. The nature of the autonomic dysfunction in multiple system atrophy

    Science.gov (United States)

    Parikh, Samir M.; Diedrich, Andre; Biaggioni, Italo; Robertson, David

    2002-01-01

    The concept that multiple system atrophy (MSA, Shy-Drager syndrome) is a disorder of the autonomic nervous system is several decades old. While there has been renewed interest in the movement disorder associated with MSA, two recent consensus statements confirm the centrality of the autonomic disorder to the diagnosis. Here, we reexamine the autonomic pathophysiology in MSA. Whereas MSA is often thought of as "autonomic failure", new evidence indicates substantial persistence of functioning sympathetic and parasympathetic nerves even in clinically advanced disease. These findings help explain some of the previously poorly understood features of MSA. Recognition that MSA entails persistent, constitutive autonomic tone requires a significant revision of our concepts of its diagnosis and therapy. We will review recent evidence bearing on autonomic tone in MSA and discuss their therapeutic implications, particularly in terms of the possible development of a bionic baroreflex for better control of blood pressure.

  20. The 5′ Untranslated Region and Gag product of Idefix, a Long Terminal Repeat-Retrotransposon from Drosophila melanogaster, Act Together To Initiate a Switch between Translated and Untranslated States of the Genomic mRNA

    OpenAIRE

    Meignin, Carine; Bailly, Jean-Luc; Arnaud, Frédérick; Dastugue, Bernard; Vaury, Chantal

    2003-01-01

    Idefix is a long terminal repeat (LTR)-retrotransposon present in Drosophila melanogaster which shares similarities with vertebrates retroviruses both in its genomic arrangement and in the mechanism of transposition. Like in retroviruses, its two LTRs flank a long 5′ untranslated region (5′UTR) and three open reading frames referred to as the gag, pol, and env genes. Here we report that its 5′UTR, located upstream of the gag gene, can fold into highly structured domains that are known to be i...

  1. Cultivation of Autonomous Learning Ability of Students Learning College English

    Institute of Scientific and Technical Information of China (English)

    Yang Ruping; Qiu Shifeng

    2014-01-01

    As the mode of college English teaching is gradually transformed from the teacher-centered into the student-centered teaching mode, the cultivation of college English autonomous learning ability has become increasingly important. This paper, starting from the theory of autonomous learning, makes an analysis of current situation of college English teaching and points out the necessity of this ability-cultivation for English learning. In the end, it puts forward several strategies of cultivating the ability of college English autonomous learning.

  2. THE USE OF GENETIC ALGORITHM IN DIMENSIONING HYBRID AUTONOMOUS SYSTEMS

    Directory of Open Access Journals (Sweden)

    RUS T.

    2016-03-01

    Full Text Available In this paper is presented the working principle of genetic algorithms used to dimension autonomous hybrid systems. It is presented a study case in which is dimensioned and optimized an autonomous hybrid system for a residential house located in Cluj-Napoca. After the autonomous hybrid system optimization is performed, it is achieved a reduction of the total cost of system investment, a reduction of energy produced in excess and a reduction of CO2 emissions.

  3. Equipment Proposal for the Autonomous Vehicle Systems Laboratory at UIW

    Science.gov (United States)

    2015-04-29

    SECURITY CLASSIFICATION OF: This final technical report details the status of the Autonomous Vehicle Systems (AVS) Research and Education Laboratory...Approved for Public Release; Distribution Unlimited Final Report: Equipment Proposal for the Autonomous Vehicle Systems Laboratory at UIW The views...P.O. Box 12211 Research Triangle Park, NC 27709-2211 Final Report for UIW Autonomous Vehicle Systems Research and Education Laboratory REPORT

  4. Behavior-Based Power Management in Autonomous Mobile Robots

    Science.gov (United States)

    2008-03-27

    Behavior-Based Power Management In Autonomous Mobile Robots THESIS Charles A. Fetzek, First Lieutenant, USAF AFIT/GCE/ENG/08-05 DEPARTMENT OF THE AIR...of Defense, or the United States Government. AFIT/GCE/ENG/08-05 Behavior-Based Power Management In Autonomous Mobile Robots THESIS Presented to the...Management In Autonomous Mobile Robots Charles A. Fetzek, B.S.C.E. First Lieutenant, USAF Approved: /signed/ 4 Mar 2008 Dr. Gilbert L. Peterson (Chairman

  5. Experiences in Deploying Test Arenas for Autonomous Mobile Robots

    Science.gov (United States)

    2001-09-01

    Experiences in Deploying Test Arenas for Autonomous Mobile Robots Adam Jacoff, Elena Messina, John Evans Intelligent Systems Division National...test arenas for autonomous mobile robots . The first set of arenas was modeled after the Urban Search and Rescue (USAR) application and was designed to...00-00-2001 to 00-00-2001 4. TITLE AND SUBTITLE Experiences in Deploying Test Arenas for Autonomous Mobile Robots 5a. CONTRACT NUMBER 5b. GRANT

  6. Modelling of a PMSG Wind Turbine with Autonomous Control

    OpenAIRE

    Chia-Nan Wang; Wen-Chang Lin; Xuan-Khoa Le

    2014-01-01

    The aim of this research is to model an autonomous control wind turbine driven permanent magnetic synchronous generator (PMSG) which feeds alternating current (AC) power to the utility grid. Furthermore, this research also demonstrates the effects and the efficiency of PMSG wind turbine which is integrated by autonomous controllers. In order for well autonomous control, two voltage source inverters are used to control wind turbine connecting with the grid. The generator-side inverter is used ...

  7. Hereditary sensory autonomic neuropathy and anaesthesia - a case report

    Directory of Open Access Journals (Sweden)

    Nandini Dave

    2007-01-01

    Full Text Available The hereditary sensory and autonomic neuropathies are a rare group of disorders characterized by progressive loss of function that predominantly affects the peripheral sensory nerves. Autonomic dysfunction is present to a variable degree and can have several implications for anaesthesia. We report the case of a patient with Hereditary sensory and autonomic neuropathy who was posted for a below knee amputation and discuss the anaesthesia management.

  8. The influencing factors and Countermeasures of College Students' Autonomous Learning

    Institute of Scientific and Technical Information of China (English)

    安雨

    2016-01-01

    with the continuous development of society, people's life has become increasingly rich, but with the development of society, we are increasingly being tempted, the most obvious is our life in the University, the students focused on autonomous learning, but with the temptation is more and more big, the college students' autonomous learning learning ability to drop, a lot of people irresistible university life becomes boring temptation. What are the factors that affect college students' autonomous learning?

  9. Hjertefrekvensvariationer til vurdering af det autonome nervesystem. En oversigt

    DEFF Research Database (Denmark)

    Johansen, T L; Kambskar, G; Mehlsen, J

    1997-01-01

    activity in the different branches of the autonomic nervous system. In the diagnosis of autonomic neuropathy, short-term forced variations in heart rate are employed in order to describe the dynamic capacity of the parasympathetic nervous system. In the subsequent data-analysis several different principles......Analysis of heart rate variability is increasingly used for testing the function of the autonomic nervous system in cardiovascular disease and for the diagnosis of autonomic neuropathy. In cardiovascular disease, long-term data collection (several hours) is primarily used to describe the static...

  10. Adaptive Supervisory Engine for Autonomous Formation Flying GNC Project

    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...

  11. Intelligent Autonomous Aerial Vehicles in the National Airspace Project

    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...

  12. The Relationship between Vascular Function and the Autonomic Nervous System.

    Science.gov (United States)

    Amiya, Eisuke; Watanabe, Masafumi; Komuro, Issei

    2014-01-01

    Endothelial dysfunction and autonomic nervous system dysfunction are both risk factors for atherosclerosis. There is evidence demonstrating that there is a close interrelationship between these two systems. In hypertension, endothelial dysfunction affects the pathologic process through autonomic nervous pathways, and the pathophysiological process of autonomic neuropathy in diabetes mellitus is closely related with vascular function. However, detailed mechanisms of this interrelationship have not been clearly explained. In this review, we summarize findings concerning the interrelationship between vascular function and the autonomic nervous system from both experimental and clinical studies. The clarification of this interrelationship may provide more comprehensive risk stratification and a new effective therapeutic strategy against atherosclerosis.

  13. Security-Enhanced Autonomous Network Management for Space Networking Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Intelligent Automation Inc. (IAI) proposes an innovative Security-Enhanced Autonomous Network Management (SEANM) scheme for reliable communication in space...

  14. 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.

  15. A MusD retrotransposon insertion in the mouse Slc6a5 gene causes alterations in neuromuscular junction maturation and behavioral phenotypes.

    Directory of Open Access Journals (Sweden)

    Laurent P Bogdanik

    Full Text Available Glycine is the major inhibitory neurotransmitter in the spinal cord and some brain regions. The presynaptic glycine transporter, GlyT2, is required for sustained glycinergic transmission through presynaptic reuptake and recycling of glycine. Mutations in SLC6A5, encoding GlyT2, cause hereditary hyperekplexia in humans, and similar phenotypes in knock-out mice, and variants are associated with schizophrenia. We identified a spontaneous mutation in mouse Slc6a5, caused by a MusD retrotransposon insertion. The GlyT2 protein is undetectable in homozygous mutants, indicating a null allele. Homozygous mutant mice are normal at birth, but develop handling-induced spasms at five days of age, and only survive for two weeks, but allow the study of early activity-regulated developmental processes. At the neuromuscular junction, synapse elimination and the switch from embryonic to adult acetylcholine receptor subunits are hastened, consistent with a presumed increase in motor neuron activity, and transcription of acetylcholine receptors is elevated. Heterozygous mice, which show no reduction in lifespan but nonetheless have reduced levels of GlyT2, have a normal thermal sensitivity with the hot-plate test, but differences in repetitive grooming and decreased sleep time with home-cage monitoring. Open-field and elevated plus-maze tests did not detect anxiety-like behaviors; however, the latter showed a hyperactivity phenotype. Importantly, grooming and hyperactivity are observed in mouse schizophrenia models. Thus, mutations in Slc6a5 show changes in neuromuscular junction development as homozygotes, and behavioral phenotypes as heterozygotes, indicating their usefulness for studies related to glycinergic dysfunction.

  16. Polymorphic SVA retrotransposons at four loci and their association with classical HLA class I alleles in Japanese, Caucasians and African Americans.

    Science.gov (United States)

    Kulski, Jerzy K; Shigenari, Atsuko; Inoko, Hidetoshi

    2010-04-01

    Polymorphic insertion frequencies of the retrotransposons known as the "SVA" elements were investigated at four loci in the MHC class I genomic region to determine their allele and haplotype frequencies and associations with the HLA-A, -B or -C genes for 100 Japanese, 100 African Americans, 174 Australian Caucasians and 66 reference cell lines obtained from different ethnic groups. The SVA insertions representing different subfamily members varied in frequency between none for SVA-HF in Japanese and 65% for SVA-HB in Caucasians or African Americans with significant differences in frequencies between the three populations at least at three loci. The SVA loci were in Hardy-Weinberg equilibrium except for the SVA-HA locus which deviated significantly in African Americans and Caucasians possibly because of a genomic deletion of this locus in individuals with the HLA-A*24 allele. Strong linkage disequilibria and high percentage associations between the human leucocyte antigen (HLA) class I gene alleles and some of the SVA insertions were detected in all three populations in spite of significant frequency differences for the SVA and HLA class I alleles between the three populations. The highest percentage associations (>86%) were between SVA-HB and HLA-B*08, -B*27, -B*37 to -B*41, -B*52 and -B*53; SVA-HC and HLA-B*07; SVA-HA and HLA-A*03, -A*11 and -A*30; and SVA-HF and HLA-A*03 and HLA-B*47. From pairwise associations in the three populations and the homozygous cell line results, it was possible to deduce the SVA and HLA class I allelic combinations (haplotypes), population differences and the identity by descent of several common HLA-A allelic lineages.

  17. 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.

  18. 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.

  19. 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.

  20. The Ways of Fostering Student's Autonomous Learning

    Institute of Scientific and Technical Information of China (English)

    赖湲

    2016-01-01

    With the development of science and technology, knowledge is being replaced faster and faster. The students nowadays must be cultivated into lifelong learners to adjust themselves to the times of knowledge explosion. This study is to arouse students to be aware of the importance of autonomy in English learning and to enable them to have assistive attitude toward English learning. After gaining the knowledge of autonomy, this thesis give the whole society, including schools, parents, and students themselves some ways to foster and develop their autonomous learning.

  1. Microscale autonomous sensor and communications module

    Science.gov (United States)

    Okandan, Murat; Nielson, Gregory N

    2014-03-25

    Various technologies pertaining to a microscale autonomous sensor and communications module are described herein. Such a module includes a sensor that generates a sensor signal that is indicative of an environmental parameter. An integrated circuit receives the sensor signal and generates an output signal based at least in part upon the sensor signal. An optical emitter receives the output signal and generates an optical signal as a function of the output signal. An energy storage device is configured to provide power to at least the integrated circuit and the optical emitter, and wherein the module has a relatively small diameter and thickness.

  2. Polymers with autonomous life-cycle control

    Science.gov (United States)

    Patrick, Jason F.; Robb, Maxwell J.; Sottos, Nancy R.; Moore, Jeffrey S.; White, Scott R.

    2016-12-01

    The lifetime of man-made materials is controlled largely by the wear and tear of everyday use, environmental stress and unexpected damage, which ultimately lead to failure and disposal. Smart materials that mimic the ability of living systems to autonomously protect, report, heal and even regenerate in response to damage could increase the lifetime, safety and sustainability of many manufactured items. There are several approaches to achieving these functions using polymer-based materials, but making them work in highly variable, real-world situations is proving challenging.

  3. 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

  4. Autonomous Mission Operations for Sensor Webs

    Science.gov (United States)

    Underbrink, A.; Witt, K.; Stanley, J.; Mandl, D.

    2008-12-01

    We present interim results of a 2005 ROSES AIST project entitled, "Using Intelligent Agents to Form a Sensor Web for Autonomous Mission Operations", or SWAMO. The goal of the SWAMO project is to shift the control of spacecraft missions from a ground-based, centrally controlled architecture to a collaborative, distributed set of intelligent agents. The network of intelligent agents intends to reduce management requirements by utilizing model-based system prediction and autonomic model/agent collaboration. SWAMO agents are distributed throughout the Sensor Web environment, which may include multiple spacecraft, aircraft, ground systems, and ocean systems, as well as manned operations centers. The agents monitor and manage sensor platforms, Earth sensing systems, and Earth sensing models and processes. The SWAMO agents form a Sensor Web of agents via peer-to-peer coordination. Some of the intelligent agents are mobile and able to traverse between on-orbit and ground-based systems. Other agents in the network are responsible for encapsulating system models to perform prediction of future behavior of the modeled subsystems and components to which they are assigned. The software agents use semantic web technologies to enable improved information sharing among the operational entities of the Sensor Web. The semantics include ontological conceptualizations of the Sensor Web environment, plus conceptualizations of the SWAMO agents themselves. By conceptualizations of the agents, we mean knowledge of their state, operational capabilities, current operational capacities, Web Service search and discovery results, agent collaboration rules, etc. The need for ontological conceptualizations over the agents is to enable autonomous and autonomic operations of the Sensor Web. The SWAMO ontology enables automated decision making and responses to the dynamic Sensor Web environment and to end user science requests. The current ontology is compatible with Open Geospatial Consortium (OGC

  5. Autonomous Observations in Antarctica with AMICA

    CERN Document Server

    Di Rico, Gianluca; Dolci, Mauro; Straniero, Oscar; Valentini, Angelo; Valentini, Gaetano; Di Cianno, Amico; Giuliani, Croce; Magrin, Demetrio; Bonoli, Carlotta; Bortoletto, Favio; D'Alessandro, Maurizio; Corcione, Leonardo; Riva, Alberto

    2010-01-01

    The Antarctic Multiband Infrared Camera (AMICA) is a double channel camera operating in the 2-28 micron infrared domain (KLMNQ bands) that will allow to characterize and exploit the exceptional advantages for Astronomy, expected from Dome C in Antarctica. The development of the camera control system is at its final stage. After the investigation of appropriate solutions against the critical environment, a reliable instrumentation has been developed. It is currently being integrated and tested to ensure the correct execution of automatic operations. Once it will be mounted on the International Robotic Antarctic Infrared Telescope (IRAIT), AMICA and its equipment will contribute to the accomplishment of a fully autonomous observatory.

  6. 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.

  7. 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 producers...... and in shallow systems the macrophytes can completely dominate primary production. This was despite the fact that the plants in the studied system were light-saturated most of the light hours and occasionally carbon limited. It was also shown that the GPP and the total phytoplankton biomass in a nutrient...

  8. Fremdrift og energiforbruk for autonom landbruksrobot

    OpenAIRE

    Meltzer, Fredrik

    2014-01-01

    Denne oppgaven omhandler en prototype for en mobil elektrisk landbruksrobot, som utvikles og bygges ved Norges miljø- og biovitenskapelige universitet våren 2014. Målet med roboten er at den ved hjelp av en utskiftbar verktøysmodul, skal kunne utføre flere forskjellige arbeidsoppgaver. Den skal utstyres med en datamaskin og sensorer, slik at den kan kjøre og arbeide uten behov for menneskelig tilstedeværelse. Vårt prosjekt fokuserer på rammen og det som skal til for autonom kjøring. Robot...

  9. Autonomous Rendezvous and Docking Conference, volume 2

    Science.gov (United States)

    1990-01-01

    Autonomous Rendezvous and Docking (ARD) will be a requirement for future space programs. Clear examples include satellite servicing, repair, recovery, and reboost in the near term, and the longer range lunar and planetary exploration programs. ARD will permit more aggressive unmanned space activities, while providing a valuable operational capability for manned missions. The purpose of the conference is to identify the technologies required for an on-orbit demonstration of ARD, assess the maturity of those technologies, and provide the necessary insight for a quality assessment of programmatic management, technical, schedule, and cost risks.

  10. A polling model with an autonomous server

    OpenAIRE

    2007-01-01

    Polling models are used as an analytical performance tool in several application areas. In these models, the focus often is on controlling the operation of the server as to optimize some performance measure. For several applications, controlling the server is not an issue as the server moves independently in the system. We present the analysis for such a polling model with a so-called autonomous server. In this model, the server remains for an exogenous random time at a queue, which also impl...

  11. PRIMUS: autonomous driving robot for military applications

    Science.gov (United States)

    Schwartz, Ingo

    2000-07-01

    This article describes the government experimental program PRIMUS (PRogram of Intelligent Mobile Unmanned Systems) and the achieved results of phase C demonstrated in summer 1999 on a military prooving ground. In this program there shall be shown the autonomous driving on an unmanned robot in open terrain. The most possible degree of autonomy shall be reached with today's technology to get a platform for different missions. The goal is to release the soldier from high dangerous tasks, to increase the performance and to come to a reduction of personnel and costs with unmanned systems. In phase C of the program two small tracked vehicles (Digitized Wiesel 2, airtransportable by CH53) are used. One as a robot vehicle the other as a command & control system. The Wiesel 2 is configured as a drive by wire-system and therefore well suited for the adaption of control computers. The autonomous detection and avoidance of obstacles in unknown, not cooperative environment is the main task. For navigation and orientation a sensor package is integrated. To detect obstacles the scene in the driving corridor of the robot is scanned 4 times per second by a 3D- Range image camera (LADAR). The measured 3D-range image is converted into a 2D-obstacle map and used as input for calculation of an obstacle free path. The combination of local navigation (obstacle avoidance) and global navigation leads to a collission free driving in open terrain to a predefined goal point with a velocity of up to 25km/h. A contour tracker with a TV-camera as sensor is also implemented which allows to follow contours (e.g. edge of a meadow) or to drive on paved or unpaved roads with a velocity up to 50km/h. In addition to these autonomous driving modes the operator in the command & control station can drive the robot by remote control. All the functions were successfully demonstrated in the summer 1999 on a military prooving ground. During a mission example the robot vehicle covered a distance of several

  12. A relativistic and autonomous navigation satellite system

    CERN Document Server

    Delva, Pacôme; Kostić, Uros; Carloni, Sante

    2011-01-01

    A relativistic positioning system has been proposed by Bartolom\\'e Coll in 2002. Since then, several group developed this topic with different approaches. I will present a work done in collaboration with Ljubljana University and the ESA Advanced Concepts Team. We developed a concept, Autonomous Basis of Coordinates, in order to take advantage of the full autonomy of a satellite constellation for navigation and positioning, by means of satellite inter-links. I will present the advantages of this new paradigm and a number of potential application for reference systems, geophysics and relativistic gravitation.

  13. 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....

  14. Navigation and control of an autonomous vehicle

    Energy Technology Data Exchange (ETDEWEB)

    Simon, A.; Soehnitz, I.; Becker, J.C.; Schumacher, W. [Technical Univ. Braunschweig (Germany). Inst. of Control Engineering

    2000-07-01

    This paper describes the fusion of sensor data for the navigation of an autonomous vehicle as well as two lateral control concepts to track the vehicle along a desired path. The fusion of navigation data is based on information provided by multiple object-detecting sensors. The object data is fused to increase the accuracy and to obtain the vehicle's state from the relative movement w.r.t. the objects. The presented lateral control methods are an LQG/H{sub 2}-design and an input-output linearizing algorithm. These control schemes were both implemented on a test vehicle. (orig.)

  15. 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.

  16. Fault Diagnosis of Autonomous Underwater Vehicles

    Directory of Open Access Journals (Sweden)

    Xiao Liang

    2013-04-01

    Full Text Available In this study, we propose the least disturbance algorithm adding scale factor and shift factor. The dynamic learning ratio can be calculated to minimize the scale factor and shift factor of wavelet function and the variation of net weights and the algorithm improve the stability and the convergence of wavelet neural network. It was applied to build the dynamical model of autonomous underwater vehicles and the residuals are generated by comparing the outputs of the dynamical model with the real state values in the condition of thruster fault. Fault detection rules are distilled by residual analysis to execute thruster fault diagnosis. The results of simulation prove the effectiveness.

  17. AMID: autonomous modeler of intragenic duplication.

    Science.gov (United States)

    Kummerfeld, Sarah K; Weiss, Anthony S; Fekete, Alan; Jermiin, Lars S

    2003-01-01

    Intragenic duplication is an evolutionary process where segments of a gene become duplicated. While there has been much research into whole-gene or domain duplication, there have been very few studies of non-tandem intragenic duplication. The identification of intragenically replicated sequences may provide insight into the evolution of proteins, helping to link sequence data with structure and function. This paper describes a tool for autonomously modelling intragenic duplication. AMID provides: identification of modularly repetitive genes; an algorithm for identifying repeated modules; and a scoring system for evaluating the modules' similarity. An evaluation of the algorithms and use cases are presented.

  18. [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.

  19. Autonomous unmanned air vehicles (UAV) techniques

    Science.gov (United States)

    Hsu, Ming-Kai; Lee, Ting N.

    2007-04-01

    The UAVs (Unmanned Air Vehicles) have great potentials in different civilian applications, such as oil pipeline surveillance, precision farming, forest fire fighting (yearly), search and rescue, boarder patrol, etc. The related industries of UAVs can create billions of dollars for each year. However, the road block of adopting UAVs is that it is against FAA (Federal Aviation Administration) and ATC (Air Traffic Control) regulations. In this paper, we have reviewed the latest technologies and researches on UAV navigation and obstacle avoidance. We have purposed a system design of Jittering Mosaic Image Processing (JMIP) with stereo vision and optical flow to fulfill the functionalities of autonomous UAVs.

  20. 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.

  1. Diastolic and autonomic dysfunction in early cirrhosis

    DEFF Research Database (Denmark)

    Dahl, Emilie Kristine; Møller, Søren; Kjær, Andreas

    2014-01-01

    cirrhosis during maximal β-adrenergic drive. MATERIAL AND METHODS. Nineteen patients with Child A (n = 12) and Child B cirrhosis (n = 7) and seven matched controls were studied during cardiac stress induced by increasing dosages of dobutamine and atropine. RESULTS. Pharmacological responsiveness was similar...... indicate that patients with early stage cirrhosis exhibit early diastolic and autonomic dysfunction as well as elevated pro-ANP. However, the cardiac chronotropic and inotropic responses to dobutamine stress were normal. The dynamics of ventricular repolarization appears normal in patients with early stage...

  2. Quantifying Emergent Behavior of Autonomous Robots

    Directory of Open Access Journals (Sweden)

    Georg Martius

    2015-10-01

    Full Text Available Quantifying behaviors of robots which were generated autonomously from task-independent objective functions is an important prerequisite for objective comparisons of algorithms and movements of animals. The temporal sequence of such a behavior can be considered as a time series and hence complexity measures developed for time series are natural candidates for its quantification. The predictive information and the excess entropy are such complexity measures. They measure the amount of information the past contains about the future and thus quantify the nonrandom structure in the temporal sequence. However, when using these measures for systems with continuous states one has to deal with the fact that their values will depend on the resolution with which the systems states are observed. For deterministic systems both measures will diverge with increasing resolution. We therefore propose a new decomposition of the excess entropy in resolution dependent and resolution independent parts and discuss how they depend on the dimensionality of the dynamics, correlations and the noise level. For the practical estimation we propose to use estimates based on the correlation integral instead of the direct estimation of the mutual information based on next neighbor statistics because the latter allows less control of the scale dependencies. Using our algorithm we are able to show how autonomous learning generates behavior of increasing complexity with increasing learning duration.

  3. Unmanned vehicle mobility: Limits of autonomous navigation

    Science.gov (United States)

    McCormac, A. W.; Hanna, D. M.; McFee, J.

    Considerable research is being conducted on the development of unmanned vehicles for military and civilian applications, particularly for hostile environments. It is desirable to produce a vehicle which can select its own route, not requiring remote navigation, but then it would be required to sense its surroundings. Although imaging systems and modern computers make this possible, the extreme data processing demands usually make it impractical. It is suggested that an inverse relationship exists between vehicle mobility and the complexity of the autonomous navigation system required for an unmanned vehicle. An overview of vehicle navigation is presented which shows the degree to which navigation is affected by increasing inherent mobility. If the inherent mobility of a vehicle is greatly enhanced, the scene image processing requirements and navigational computations are greatly simplified. This means the vehicle path selection and speed and steering adjustments may be made more quickly, resulting in higher vehicle speeds whenever possible. Combined with reduced deviation from the intended path, this would greatly increase the speed of the vehicle from one given point to another, suggesting that high speed autonomous navigation may be feasible.

  4. 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.

  5. 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.

  6. File Transfer Algorithm for Autonomous Decentralized System

    Institute of Scientific and Technical Information of China (English)

    GUI Xun; TAN Yong-dong; Qian Qing-quan

    2008-01-01

    A file transfer algorithm based on ADP (autonomous decentralized protocol) was proposed to solve the problem that the ADS (autonomous decentralized system) middleware (NeXUS/Dlink) lacks of file transfer functions for Windows. The algorithm realizes the peer-to-peer file transfer, one-to-N inquiry/multi-response file transfer and one-to-N file distribution in the same data field based on communication patterns provided by the ADP. The peer-to-peer file transfer is implemented through a peer-to-peer communication path, one-to-N inquiry/multi-response file transfer and one-to-N file distribution are implemented through multicast commtmieation. In this algorithm, a file to be transferred is named with a GUID ( global unique identification), every data packet is marked with a sequence number, and file-receiving in parallel is implemented by caching DPOs (data processing objects) and multithread technologies. The algorithm is applied in a simulation system of the decentralized control platform, and the test results and long time stable mrming prove the feasibility of the algorithm.

  7. Autonomous exoskeleton reduces metabolic cost of walking.

    Science.gov (United States)

    Mooney, Luke M; Rouse, Elliott J; Herr, Hugh M

    2014-01-01

    We developed an autonomous powered leg exoskeleton capable of providing large amounts of positive mechanical power to the wearer during powered plantarflexion phase of walking. The autonomous exoskeleton consisted of a winch actuator fasted to the shin which pulled on fiberglass struts attached to a boot. The fiberglass struts formed a rigid extension of the foot when the proximal end of the strut was pulled in forward by the winch actuator. This lightweight, geometric transmission allowed the electric winch actuator to efficiently produce biological levels of power at the ankle joint. The exoskeleton was powered and controlled by lithium polymer batteries and motor controller worn around the waist. Preliminary testing on two subjects walking at 1.4 m/s resulted in the exoskeleton reducing the metabolic cost of walking by 6-11% as compared to not wearing the device. The exoskeleton provided a peak mechanical power of over 180 W at each ankle (mean standard ± deviation) and an average positive mechanical power of 27 ± 1 W total to both ankles, while electrically using 75-89 W of electricity. The batteries (800 g) used in this experiment are estimated to be capable of providing this level of assistance for up to 7 km of walking.

  8. Electrophysiology of autonomic neuromuscular transmission involving ATP.

    Science.gov (United States)

    Sneddon, P

    2000-07-01

    Electrophysiological investigations of autonomic neuromuscular transmission have provided great insights into the role of ATP as a neurotransmitter. Burnstock and Holman made the first recordings of excitatory junction potentials (e.j.p.s) produced by sympathetic nerves innervating the smooth muscle of the guinea-pig vas deferens. This led to the identification of ATP as the mediator of e.j.p.s in this tissue, where ATP acts as a cotransmitter with noradrenaline. The e.j.p.s are mediated solely by ATP acting on P2X(1) receptors leading to action potentials and a rapid phasic contraction, whilst noradrenaline mediates a slower, tonic contraction which is not dependent on membrane depolarisation. Subsequent electrophysiological studies of the autonomic innervation of smooth muscles of the urogenital, gastrointestinal and cardiovascular systems have revealed a similar pattern of response, where ATP mediates a fast electrical and mechanical response, whilst another transmitter such as noradrenaline, acetylcholine, nitric oxide or a peptide mediates a slower response. The modulation of junction potentials by a variety of pre-junctional receptors and the mechanism of inactivation of ATP as a neurotransmitter will also be described.

  9. Safety analysis of autonomous excavator functionality

    Energy Technology Data Exchange (ETDEWEB)

    Seward, D.; Pace, C.; Morrey, R.; Sommerville, I

    2000-10-01

    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.

  10. 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.

  11. Acceptance Criteria Framework for Autonomous Biological Detectors

    Energy Technology Data Exchange (ETDEWEB)

    Dzenitis, J M

    2006-12-12

    The purpose of this study was to examine a set of user acceptance criteria for autonomous biological detection systems for application in high-traffic, public facilities. The test case for the acceptance criteria was the Autonomous Pathogen Detection System (APDS) operating in high-traffic facilities in New York City (NYC). However, the acceptance criteria were designed to be generally applicable to other biological detection systems in other locations. For such detection systems, ''users'' will include local authorities (e.g., facility operators, public health officials, and law enforcement personnel) and national authorities [including personnel from the Department of Homeland Security (DHS), the BioWatch Program, the Centers for Disease Control and Prevention (CDC), and the Federal Bureau of Investigation (FBI)]. The panel members brought expertise from a broad range of backgrounds to complete this picture. The goals of this document are: (1) To serve as informal guidance for users in considering the benefits and costs of these systems. (2) To serve as informal guidance for developers in understanding the needs of users. In follow-up work, this framework will be used to systematically document the APDS for appropriateness and readiness for use in NYC.

  12. 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.

  13. Nutritional stimulation of the autonomic nervous system

    Institute of Scientific and Technical Information of China (English)

    Misha DP Luyer; Quirine Habes; Richard van Hak; Wim Buurman

    2011-01-01

    Disturbance of the inflammatory response in the gut is important in several clinical diseases ranging from inflammatory bowel disease to postoperative ileus. Several feedback mechanisms exist that control the inflammatory cascade and avoid collateral damage. In the gastrointestinal tract, it is of particular importance to control the immune response to maintain the balance that allows dietary uptake and utilization of nutrients on one hand, while preventing invasion of bacteria and toxins on the other hand. The process of digestion and absorption of nutrients requires a relative hyporesponsiveness of the immune cells in the gut to luminal contents which is not yet fully understood. Recently, the autonomic nervous system has been identified as an important pathway to control local and systemic inflammation and gut barrier integrity. Activation of the pathway is possible via electrical or via pharmacological interventions, but is also achieved in a physiological manner by ingestion of dietary lipids. Administration of dietary lipids has been shown to be very effective in reducing the inflammatory cascade and maintaining intestinal barrier integrity in several experimental studies. This beneficial effect of nutrition on the inflammatory inflammatory response and intestinal barrier integrity opens new therapeutic opportunities for treatment of certain gastrointestinal disorders. Furthermore, this neural feedback mechanism provides more insight in the relative hyporesponsiveness of the immune cells in the gut. Here, we will discuss the regulatory function of the autonomic nervous system on the inflammatory response and gut barrier function and the potential benefit in a clinical setting.

  14. 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.

  15. The 5' untranslated region and Gag product of Idefix, a long terminal repeat-retrotransposon from Drosophila melanogaster, act together to initiate a switch between translated and untranslated states of the genomic mRNA.

    Science.gov (United States)

    Meignin, Carine; Bailly, Jean-Luc; Arnaud, Frédérick; Dastugue, Bernard; Vaury, Chantal

    2003-11-01

    Idefix is a long terminal repeat (LTR)-retrotransposon present in Drosophila melanogaster which shares similarities with vertebrates retroviruses both in its genomic arrangement and in the mechanism of transposition. Like in retroviruses, its two LTRs flank a long 5' untranslated region (5'UTR) and three open reading frames referred to as the gag, pol, and env genes. Here we report that its 5'UTR, located upstream of the gag gene, can fold into highly structured domains that are known to be incompatible with efficient translation by ribosome scanning. Using dicistronic plasmids analyzed by both (i) in vitro transcription and translation in rabbit reticulocyte or wheat germ lysates and (ii) in vivo expression in transgenic flies, we show that the 5'UTR of Idefix exhibits an internal ribosome entry site (IRES) activity that is able to promote translation of a downstream cistron in a cap-independent manner. The functional state of this novel IRES depends on eukaryotic factors that are independent of their host origin. However, in vivo, its function can be down-regulated by trans-acting factors specific to tissues or developmental stages of its host. We identify one of these trans-acting factors as the Gag protein encoded by Idefix itself. Our data support a model in which nascent Gag is able to block translation initiated from the viral mRNA and thus its own translation. These data highlight the fact that LTR-retrotransposons may autoregulate their replication cycle through their Gag production.

  16. Autonomic dysfunction in childhood Guillain-Barré syndrome.

    Science.gov (United States)

    Dimario, Francis J; Edwards, Carrie

    2012-05-01

    This investigation correlated incidence and degree of autonomic dysfunction with the degree of motor impairment in children hospitalized with Guillain-Barré syndrome. Motor weakness varies, as does the effect on autonomic function including heart rate, vasomotor stability, sweating, continence, and blood pressure. After Institutional Review Board approval, hospitalized patients with Guillain-Barré syndrome syndrome.

  17. 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…

  18. Autonomic and surgical substrate modulation of atrial fibrillation

    NARCIS (Netherlands)

    Krul, S.P.J.

    2016-01-01

    This thesis focuses on the effects of fibrosis and the autonomic nervous system on conduction in patients with atrial fibrillation and the surgical ablation of the atria and autonomic nervous system as treatment of atrial fibrillation. Atrial fibrillation is the most common arrhythmia and results fr

  19. Autonomous Experimentation of Carbon Nanotube Using Response Surface Methods

    Science.gov (United States)

    2015-03-26

    on the unique challenges of creating autonomous research robots . v Table of Contents Page Abstract...direction could represent a small region where a local maximum exists. If outliers or other nuisance factors are continually problematic , experiment...materials research technology, detailed discussion is also provided on the unique challenges of creating autonomous research robots . 15. SUBJECT

  20. 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…

  1. Non-autonomous Degenerate KdV Systems

    OpenAIRE

    Turhan, Refik

    2002-01-01

    Non-autonomous degenerate KdV systems in (1+1) dimensions are considered for integrability classification. Integrability of the systems is associated with the existence of a recursion operator. Some new non-autonomous degenerate two-component KdV systems are found.

  2. On the equivalence classes of linear non-autonomous systems *

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    In this paper, the equivalence classification of the linear non-autonomous dynamic systems near singularities is given. Under some conditions their equivalence classes are the same as the autonomous ones. Using a series of linear and nonlinear transforms, the equivalence classification is proved.

  3. Valuation Model for Adding Energy Resource into Autonomous Energy Cluster

    NARCIS (Netherlands)

    De Kok, E.; Negeri, E.O.; Van Wijk, A.; Baken, N.

    2013-01-01

    With the availability of distributed generation (DG), clusters that can autonomously manage their energy profile are emerging in the power grid. These autonomous clusters manage their load profiles by orchestrating their energy resources, such as DG, storage, flexible energy consuming appliances, et

  4. ANTS: Exploring the Solar System with an Autonomous Nanotechnology Swarm

    Science.gov (United States)

    Clark, P. E.; Curtis, S.; Rilee, M.; Truszkowski, W.; Marr, G.

    2002-01-01

    ANTS (Autonomous Nano-Technology Swarm), a NASA advanced mission concept, calls for a large (1000 member) swarm of pico-class (1 kg) totally autonomous spacecraft to prospect the asteroid belt. Additional information is contained in the original extended abstract.

  5. 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.

  6. Cardiac Autonomic Control in Individuals With Down Syndrome

    Science.gov (United States)

    Goulopoulou, Styliani; Baynard, Tracy; Collier, Scott; Giannopoulou, Ifigenia; Figueroa, Arturo; Beets, Michael; Pitetti, Kenneth; Fernhall, Bo

    2006-01-01

    Our goal in this study was to compare cardiac autonomic control at rest between 50 individuals with Down syndrome and 24 control participants without disabilities. Resting autonomic function was assessed using analysis of heart rate variability. Participants with Down syndrome had reduced total heart rate variability, which indicates possible…

  7. 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 desig

  8. 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...

  9. Experimental and numerical study of an autonomous flap

    NARCIS (Netherlands)

    Bernhammer, L.O.; Navalkar, S.T.; Sodja, J.; De Breuker, R.; Karpel, M.

    2015-01-01

    This paper presents the experimental and numerical study of an autonomous load alleviation concept using trailing edge flaps. The flaps are autonomous units, which for instance can be used for gust load alleviation. The unit is self-powered and self-actuated through trailing edge tabs which are moun

  10. Properties of autonomous and injection locked flux flow oscillators

    DEFF Research Database (Denmark)

    Mygind, Jesper; Koshelets, V. P.; Shchukin, A. V.;

    1995-01-01

    performed both for two autonomous FFOs and with one of the FFOs injection-locked to a narrow-band external microwave source. By beating the two autonomous FFOs an integral spectral linewidth as low as 750 kHz is measured at 280 GHz. Mechanisms leading to a broadening of the FFO linewidth are discussed...

  11. Autonomic dysfunction in diabetes : a consequence of cardiovascular damage

    NARCIS (Netherlands)

    Lefrandt, J D; Smit, A J; Zeebregts, C J; Gans, R O B; Hoogenberg, K H

    2010-01-01

    In 1976, D.J. Ewing showed a clear survival disadvantage for diabetic patients that had 'diabetic autonomic neuropathy', as assessed by heart rate and blood pressure variations during a battery of bedside tests. However, these variations do not solely depend on autonomic nervous system function, but

  12. 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 ...

  13. Decreased myocardial perfusion reserve in diabetic autonomic neuropathy

    DEFF Research Database (Denmark)

    Taskiran, Mustafa; Fritz-Hansen, Thomas; Rasmussen, Verner

    2002-01-01

    The pathophysiological mechanisms responsible for increased cardiovascular mortality in diabetic autonomic neuropathy are unknown. To investigate the effect of autonomic neuropathy on myocardial function, we performed dynamic contrast-enhanced magnetic resonance perfusion imaging during baseline...... conditions and after Dipyridamole-induced vasodilatation in nine type 1 diabetic patients with autonomic neuropathy (AN+), defined by cardiovascular tests, as well as in 10 type 1 diabetic patients without autonomic neuropathy (AN-) and 10 healthy control subjects. Baseline myocardial perfusion index (K...... blood pressure response to Dipyridamole and myocardial perfusion reserve index. We conclude that type 1 diabetic patients with autonomic neuropathy have a decreased myocardial perfusion reserve capacity when challenged with a vasodilatator, a finding that may in part be the pathophysiological substrate...

  14. 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...

  15. Evolutionary active transposable elements in the genome of the coelacanth.

    Science.gov (United States)

    Chalopin, Domitille; Fan, Shaohua; Simakov, Oleg; Meyer, Axel; Schartl, Manfred; Volff, Jean-Nicolas

    2014-09-01

    The apparent morphological stasis in the lineage of the coelacanth, which has been called a "living fossil" by many, has been suggested to be causally related to a slow evolution of its genome, with strongly reduced activity of transposable elements (TEs). Analysis of the African coelacanth showed that at least 25% of its genome is constituted of transposable elements including retrotransposons, endogenous retroviruses and DNA transposons, with a strong predominance of non-Long Terminal Repeat (non-LTR) retrotransposons. The coelacanth genome has been shaped by four major general bursts of transposition during evolution, with major contributions of LINE1, LINE2, CR1, and Deu non-LTR retrotransposons. Many transposable elements are expressed in different tissues and might be active. The number of TE families in coelacanth, but also in lungfish, is lower than in teleost fish, but is higher than in chicken and human. This observation is in agreement with the hypothesis of a sequential elimination of many TE families in the sarcopterygian lineage during evolution. Taken together, our analysis indicates that the coelacanth contains more TE families than birds and mammals, and that these elements have been active during the evolution of the coelacanth lineage. Hence, at the level of transposable element activity, the coelacanth genome does not appear to evolve particularly slowly.

  16. Autonomous Rover for Polar GPR Surveys

    Science.gov (United States)

    Ray, L.; Lever, J. H.; Courville, Z.; Walker, B.; Arcone, S. A.

    2015-12-01

    We deployed Yeti, an 80-kg, 4WD battery-powered rover to conduct ground-penetrating radar (GPR) surveys over crevasse-ridden ice sheets in Antarctica and Greenland. The rover navigated using GPS waypoint following and had 3 - 4 hr endurance at 5 km/hr while towing 60 - 70 kg of GPR equipment. Yeti's low ground pressure allowed it to cross thinly bridged crevasses without interrupting a survey. In Feb - Mar 2014, Yeti executed 23 autonomous GPR surveys covering 94 km of terrain on the ice transition to the main ice sheet in northwest Greenland. This was the first robotic effort directly to support manual crevasse surveys to map a safe route for vehicle travel, in this case a resupply traverse to Summit Station. Yeti towed a radar controller, 400 MHz antenna, GPS receiver and battery pack. Radar scan rate was 16 scans/m and pulse timing allowed good spatial resolution to about 20-m depth. The resulting data allowed us to map hundreds of subsurface crevasses and provide the results nightly to the manual survey team to compliment its efforts. We met our objectives: (a) to enhance operational efficiency of the concurrent manual surveys, and (b) to create a geo-referenced database of crevasse signatures to validate aerial- and satellite-based crevasse-mapping platforms. In Oct - Nov 2014, we deployed Yeti in Antarctica to conduct systematic GPR surveys across a crevasse-ridden section of the shear margin between the Ross and McMurdo ice shelves and thereby gain insight into its state of fracture and long-term stability. Yeti flawlessly executed a total of 613 km of autonomous GPR surveys at temperatures as low as - 33ºC. The rover towed a a radar controlling a 400 MHz and a 200 MHz antenna, the latter added to profile 160 m through the ice sheet. The main survey grid covered 5.7 km x 5.0 km, with survey lines at 50-m spacing oriented west-east across the Shear Zone (575 km total length). Yeti's tracks normally deviated only 1 - 2 m from a straight line between the two

  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. 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

  19. High-efficiency Autonomous Laser Adaptive Optics

    CERN Document Server

    Baranec, Christoph; Law, Nicholas M; Ramaprakash, A N; Tendulkar, Shriharsh; Hogstrom, Kristina; Bui, Khanh; Burse, Mahesh; Chordia, Pravin; Das, Hillol; Dekany, Richard; Kulkarni, Shrinivas; Punnadi, Sujit

    2014-01-01

    As new large-scale astronomical surveys greatly increase the number of objects targeted and discoveries made, the requirement for efficient follow-up observations is crucial. Adaptive optics imaging, which compensates for the image-blurring effects of Earth's turbulent atmosphere, is essential for these surveys, but the scarcity, complexity and high demand of current systems limits their availability for following up large numbers of targets. To address this need, we have engineered and implemented Robo-AO, a fully autonomous laser adaptive optics and imaging system that routinely images over 200 objects per night with an acuity 10 times sharper at visible wavelengths than typically possible from the ground. By greatly improving the angular resolution, sensitivity, and efficiency of 1-3 m class telescopes, we have eliminated a major obstacle in the follow-up of the discoveries from current and future large astronomical surveys.

  20. Autonomous Formations of Multi-Agent Systems

    Science.gov (United States)

    Dhali, Sanjana; Joshi, Suresh M.

    2013-01-01

    Autonomous formation control of multi-agent dynamic systems has a number of applications that include ground-based and aerial robots and satellite formations. For air vehicles, formation flight ("flocking") has the potential to significantly increase airspace utilization as well as fuel efficiency. This presentation addresses two main problems in multi-agent formations: optimal role assignment to minimize the total cost (e.g., combined distance traveled by all agents); and maintaining formation geometry during flock motion. The Kuhn-Munkres ("Hungarian") algorithm is used for optimal assignment, and consensus-based leader-follower type control architecture is used to maintain formation shape despite the leader s independent movements. The methods are demonstrated by animated simulations.